Daily Papers

The meaningful use of electronic health records (EHR) continues to progress in the digital era with clinical decision support systems augmented by artificial intelligence. A priority in improving provider experience is to overcome information overload and reduce the cognitive burden so fewer medical errors and cognitive biases are introduced during patient care. One major type of medical error is diagnostic error due to systematic or predictable errors in judgment that rely on heuristics. The potential for clinical natural language processing (cNLP) to model diagnostic reasoning in humans with forward reasoning from data to diagnosis and potentially reduce the cognitive burden and medical error has not been investigated. Existing tasks to advance the science in cNLP have largely focused on information extraction and named entity recognition through classification tasks. We introduce a novel suite of tasks coined as Diagnostic Reasoning Benchmarks, DR.BENCH, as a new benchmark for developing and evaluating cNLP models with clinical diagnostic reasoning ability. The suite includes six tasks from ten publicly available datasets addressing clinical text understanding, medical knowledge reasoning, and diagnosis generation. DR.BENCH is the first clinical suite of tasks designed to be a natural language generation framework to evaluate pre-trained language models. Experiments with state-of-the-art pre-trained generative language models using large general domain models and models that were continually trained on a medical corpus demonstrate opportunities for improvement when evaluated in DR. BENCH. We share DR. BENCH as a publicly available GitLab repository with a systematic approach to load and evaluate models for the cNLP community.

Accurate and efficient question-answering systems are essential for delivering high-quality patient care in the medical field. While Large Language Models (LLMs) have made remarkable strides across various domains, they continue to face significant challenges in medical question answering, particularly in understanding domain-specific terminologies and performing complex reasoning. These limitations undermine their effectiveness in critical medical applications. To address these issues, we propose a novel approach incorporating similar case generation within a multi-agent medical question-answering (MedQA) system. Specifically, we leverage the Llama3.1:70B model, a state-of-the-art LLM, in a multi-agent architecture to enhance performance on the MedQA dataset using zero-shot learning. Our method capitalizes on the model's inherent medical knowledge and reasoning capabilities, eliminating the need for additional training data. Experimental results show substantial performance gains over existing benchmark models, with improvements of 7% in both accuracy and F1-score across various medical QA tasks. Furthermore, we examine the model's interpretability and reliability in addressing complex medical queries. This research not only offers a robust solution for medical question answering but also establishes a foundation for broader applications of LLMs in the medical domain.

Large language models (LLMs) can potentially democratize access to medical knowledge. While many efforts have been made to harness and improve LLMs' medical knowledge and reasoning capacities, the resulting models are either closed-source (e.g., PaLM, GPT-4) or limited in scale (<= 13B parameters), which restricts their abilities. In this work, we improve access to large-scale medical LLMs by releasing MEDITRON: a suite of open-source LLMs with 7B and 70B parameters adapted to the medical domain. MEDITRON builds on Llama-2 (through our adaptation of Nvidia's Megatron-LM distributed trainer), and extends pretraining on a comprehensively curated medical corpus, including selected PubMed articles, abstracts, and internationally-recognized medical guidelines. Evaluations using four major medical benchmarks show significant performance gains over several state-of-the-art baselines before and after task-specific finetuning. Overall, MEDITRON achieves a 6% absolute performance gain over the best public baseline in its parameter class and 3% over the strongest baseline we finetuned from Llama-2. Compared to closed-source LLMs, MEDITRON-70B outperforms GPT-3.5 and Med-PaLM and is within 5% of GPT-4 and 10% of Med-PaLM-2. We release our code for curating the medical pretraining corpus and the MEDITRON model weights to drive open-source development of more capable medical LLMs.

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare seven public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting regime for medical question-answering (QA) tasks. For instance, across the tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 12.1% of cases, reach a (statistical) tie in 49.8% of cases, and are significantly worse than their base models in the remaining 38.2% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

Several recent works seek to develop foundation models specifically for medical applications, adapting general-purpose large language models (LLMs) and vision-language models (VLMs) via continued pretraining on publicly available biomedical corpora. These works typically claim that such domain-adaptive pretraining (DAPT) improves performance on downstream medical tasks, such as answering medical licensing exam questions. In this paper, we compare ten public "medical" LLMs and two VLMs against their corresponding base models, arriving at a different conclusion: all medical VLMs and nearly all medical LLMs fail to consistently improve over their base models in the zero-/few-shot prompting and supervised fine-tuning regimes for medical question-answering (QA). For instance, across all tasks and model pairs we consider in the 3-shot setting, medical LLMs only outperform their base models in 22.7% of cases, reach a (statistical) tie in 36.8% of cases, and are significantly worse than their base models in the remaining 40.5% of cases. Our conclusions are based on (i) comparing each medical model head-to-head, directly against the corresponding base model; (ii) optimizing the prompts for each model separately in zero-/few-shot prompting; and (iii) accounting for statistical uncertainty in comparisons. While these basic practices are not consistently adopted in the literature, our ablations show that they substantially impact conclusions. Meanwhile, we find that after fine-tuning on specific QA tasks, medical LLMs can show performance improvements, but the benefits do not carry over to tasks based on clinical notes. Our findings suggest that state-of-the-art general-domain models may already exhibit strong medical knowledge and reasoning capabilities, and offer recommendations to strengthen the conclusions of future studies.

This study presents a comprehensive analysis and comparison of two predominant fine-tuning methodologies - full-parameter fine-tuning and parameter-efficient tuning - within the context of medical Large Language Models (LLMs). We developed and refined a series of LLMs, based on the Llama-2 architecture, specifically designed to enhance medical knowledge retrieval, reasoning, and question-answering capabilities. Our experiments systematically evaluate the effectiveness of these tuning strategies across various well-known medical benchmarks. Notably, our medical LLM Med42 showed an accuracy level of 72% on the US Medical Licensing Examination (USMLE) datasets, setting a new standard in performance for openly available medical LLMs. Through this comparative analysis, we aim to identify the most effective and efficient method for fine-tuning LLMs in the medical domain, thereby contributing significantly to the advancement of AI-driven healthcare applications.

Several studies showed that Large Language Models (LLMs) can answer medical questions correctly, even outperforming the average human score in some medical exams. However, to our knowledge, no study has been conducted to assess the ability of language models to validate existing or generated medical text for correctness and consistency. In this paper, we introduce MEDEC (https://github.com/abachaa/MEDEC), the first publicly available benchmark for medical error detection and correction in clinical notes, covering five types of errors (Diagnosis, Management, Treatment, Pharmacotherapy, and Causal Organism). MEDEC consists of 3,848 clinical texts, including 488 clinical notes from three US hospital systems that were not previously seen by any LLM. The dataset has been used for the MEDIQA-CORR shared task to evaluate seventeen participating systems [Ben Abacha et al., 2024]. In this paper, we describe the data creation methods and we evaluate recent LLMs (e.g., o1-preview, GPT-4, Claude 3.5 Sonnet, and Gemini 2.0 Flash) for the tasks of detecting and correcting medical errors requiring both medical knowledge and reasoning capabilities. We also conducted a comparative study where two medical doctors performed the same task on the MEDEC test set. The results showed that MEDEC is a sufficiently challenging benchmark to assess the ability of models to validate existing or generated notes and to correct medical errors. We also found that although recent LLMs have a good performance in error detection and correction, they are still outperformed by medical doctors in these tasks. We discuss the potential factors behind this gap, the insights from our experiments, the limitations of current evaluation metrics, and share potential pointers for future research.

We introduce MedXpertQA, a highly challenging and comprehensive benchmark to evaluate expert-level medical knowledge and advanced reasoning. MedXpertQA includes 4,460 questions spanning 17 specialties and 11 body systems. It includes two subsets, Text for text evaluation and MM for multimodal evaluation. Notably, MM introduces expert-level exam questions with diverse images and rich clinical information, including patient records and examination results, setting it apart from traditional medical multimodal benchmarks with simple QA pairs generated from image captions. MedXpertQA applies rigorous filtering and augmentation to address the insufficient difficulty of existing benchmarks like MedQA, and incorporates specialty board questions to improve clinical relevance and comprehensiveness. We perform data synthesis to mitigate data leakage risk and conduct multiple rounds of expert reviews to ensure accuracy and reliability. We evaluate 16 leading models on MedXpertQA. Moreover, medicine is deeply connected to real-world decision-making, providing a rich and representative setting for assessing reasoning abilities beyond mathematics and code. To this end, we develop a reasoning-oriented subset to facilitate the assessment of o1-like models.

Recently, large language model (LLM) based artificial intelligence (AI) systems have demonstrated remarkable capabilities in natural language understanding and generation. However, these models face a significant challenge when it comes to sensitive applications, such as reasoning over medical knowledge and answering medical questions in a physician-like manner. Prior studies attempted to overcome this challenge by increasing the model size (>100B) to learn more general medical knowledge, while there is still room for improvement in LLMs with smaller-scale model sizes (<100B). In this work, we start from a pre-trained general LLM model (AntGLM-10B) and fine-tune it from a medical beginner towards a medical expert (called AntGLM-Med-10B), which leverages a 3-stage optimization procedure, i.e., general medical knowledge injection, medical domain instruction tuning, and specific medical task adaptation. Our contributions are threefold: (1) We specifically investigate how to adapt a pre-trained general LLM in medical domain, especially for a specific medical task. (2) We collect and construct large-scale medical datasets for each stage of the optimization process. These datasets encompass various data types and tasks, such as question-answering, medical reasoning, multi-choice questions, and medical conversations. (3) Specifically for multi-choice questions in the medical domain, we propose a novel Verification-of-Choice approach for prompting engineering, which significantly enhances the reasoning ability of LLMs. Remarkably, by combining the above approaches, our AntGLM-Med-10B model can outperform the most of LLMs on PubMedQA, including both general and medical LLMs, even when these LLMs have larger model size.

In recent advancements, multimodal large language models (MLLMs) have been fine-tuned on specific medical image datasets to address medical visual question answering (Med-VQA) tasks. However, this common approach of task-specific fine-tuning is costly and necessitates separate models for each downstream task, limiting the exploration of zero-shot capabilities. In this paper, we introduce MC-CoT, a modular cross-modal collaboration Chain-of-Thought (CoT) framework designed to enhance the zero-shot performance of MLLMs in Med-VQA by leveraging large language models (LLMs). MC-CoT improves reasoning and information extraction by integrating medical knowledge and task-specific guidance, where LLM provides various complex medical reasoning chains and MLLM provides various observations of medical images based on instructions of the LLM. Our experiments on datasets such as SLAKE, VQA-RAD, and PATH-VQA show that MC-CoT surpasses standalone MLLMs and various multimodality CoT frameworks in recall rate and accuracy. These findings highlight the importance of incorporating background information and detailed guidance in addressing complex zero-shot Med-VQA tasks.

Large language models (LLMs) have recently demonstrated their potential in clinical applications, providing valuable medical knowledge and advice. For example, a large dialog LLM like ChatGPT has successfully passed part of the US medical licensing exam. However, LLMs currently have difficulty processing images, making it challenging to interpret information from medical images, which are rich in information that supports clinical decisions. On the other hand, computer-aided diagnosis (CAD) networks for medical images have seen significant success in the medical field by using advanced deep-learning algorithms to support clinical decision-making. This paper presents a method for integrating LLMs into medical-image CAD networks. The proposed framework uses LLMs to enhance the output of multiple CAD networks, such as diagnosis networks, lesion segmentation networks, and report generation networks, by summarizing and reorganizing the information presented in natural language text format. The goal is to merge the strengths of LLMs' medical domain knowledge and logical reasoning with the vision understanding capability of existing medical-image CAD models to create a more user-friendly and understandable system for patients compared to conventional CAD systems. In the future, LLM's medical knowledge can be also used to improve the performance of vision-based medical-image CAD models.

Large Language Models (LLMs) have the potential of facilitating the development of Artificial Intelligence technology to assist medical experts for interactive decision support, which has been demonstrated by their competitive performances in Medical QA. However, while impressive, the required quality bar for medical applications remains far from being achieved. Currently, LLMs remain challenged by outdated knowledge and by their tendency to generate hallucinated content. Furthermore, most benchmarks to assess medical knowledge lack reference gold explanations which means that it is not possible to evaluate the reasoning of LLMs predictions. Finally, the situation is particularly grim if we consider benchmarking LLMs for languages other than English which remains, as far as we know, a totally neglected topic. In order to address these shortcomings, in this paper we present MedExpQA, the first multilingual benchmark based on medical exams to evaluate LLMs in Medical Question Answering. To the best of our knowledge, MedExpQA includes for the first time reference gold explanations written by medical doctors which can be leveraged to establish various gold-based upper-bounds for comparison with LLMs performance. Comprehensive multilingual experimentation using both the gold reference explanations and Retrieval Augmented Generation (RAG) approaches show that performance of LLMs still has large room for improvement, especially for languages other than English. Furthermore, and despite using state-of-the-art RAG methods, our results also demonstrate the difficulty of obtaining and integrating readily available medical knowledge that may positively impact results on downstream evaluations for Medical Question Answering. So far the benchmark is available in four languages, but we hope that this work may encourage further development to other languages.

Multimodal large language models (MLLMs) have made significant strides, yet they face challenges in the medical domain due to limited specialized knowledge. While recent medical MLLMs demonstrate strong performance in lab settings, they often struggle in real-world applications, highlighting a substantial gap between research and practice. In this paper, we seek to address this gap at various stages of the end-to-end learning pipeline, including data collection, model fine-tuning, and evaluation. At the data collection stage, we introduce SemiHVision, a dataset that combines human annotations with automated augmentation techniques to improve both medical knowledge representation and diagnostic reasoning. For model fine-tuning, we trained PMC-Cambrian-8B-AN over 2400 H100 GPU hours, resulting in performance that surpasses public medical models like HuatuoGPT-Vision-34B (79.0% vs. 66.7%) and private general models like Claude3-Opus (55.7%) on traditional benchmarks such as SLAKE and VQA-RAD. In the evaluation phase, we observed that traditional benchmarks cannot accurately reflect realistic clinical task capabilities. To overcome this limitation and provide more targeted guidance for model evaluation, we introduce the JAMA Clinical Challenge, a novel benchmark specifically designed to evaluate diagnostic reasoning. On this benchmark, PMC-Cambrian-AN achieves state-of-the-art performance with a GPT-4 score of 1.29, significantly outperforming HuatuoGPT-Vision-34B (1.13) and Claude3-Opus (1.17), demonstrating its superior diagnostic reasoning abilities.

Medical knowledge is context-dependent and requires consistent reasoning across various natural language expressions of semantically equivalent phrases. This is particularly crucial for drug names, where patients often use brand names like Advil or Tylenol instead of their generic equivalents. To study this, we create a new robustness dataset, RABBITS, to evaluate performance differences on medical benchmarks after swapping brand and generic drug names using physician expert annotations. We assess both open-source and API-based LLMs on MedQA and MedMCQA, revealing a consistent performance drop ranging from 1-10\%. Furthermore, we identify a potential source of this fragility as the contamination of test data in widely used pre-training datasets. All code is accessible at https://github.com/BittermanLab/RABBITS, and a HuggingFace leaderboard is available at https://huggingface.co/spaces/AIM-Harvard/rabbits-leaderboard.

Excellence in a wide variety of medical applications poses considerable challenges for AI, requiring advanced reasoning, access to up-to-date medical knowledge and understanding of complex multimodal data. Gemini models, with strong general capabilities in multimodal and long-context reasoning, offer exciting possibilities in medicine. Building on these core strengths of Gemini, we introduce Med-Gemini, a family of highly capable multimodal models that are specialized in medicine with the ability to seamlessly use web search, and that can be efficiently tailored to novel modalities using custom encoders. We evaluate Med-Gemini on 14 medical benchmarks, establishing new state-of-the-art (SoTA) performance on 10 of them, and surpass the GPT-4 model family on every benchmark where a direct comparison is viable, often by a wide margin. On the popular MedQA (USMLE) benchmark, our best-performing Med-Gemini model achieves SoTA performance of 91.1% accuracy, using a novel uncertainty-guided search strategy. On 7 multimodal benchmarks including NEJM Image Challenges and MMMU (health & medicine), Med-Gemini improves over GPT-4V by an average relative margin of 44.5%. We demonstrate the effectiveness of Med-Gemini's long-context capabilities through SoTA performance on a needle-in-a-haystack retrieval task from long de-identified health records and medical video question answering, surpassing prior bespoke methods using only in-context learning. Finally, Med-Gemini's performance suggests real-world utility by surpassing human experts on tasks such as medical text summarization, alongside demonstrations of promising potential for multimodal medical dialogue, medical research and education. Taken together, our results offer compelling evidence for Med-Gemini's potential, although further rigorous evaluation will be crucial before real-world deployment in this safety-critical domain.

As opposed to evaluating computation and logic-based reasoning, current benchmarks for evaluating large language models (LLMs) in medicine are primarily focused on question-answering involving domain knowledge and descriptive reasoning. While such qualitative capabilities are vital to medical diagnosis, in real-world scenarios, doctors frequently use clinical calculators that follow quantitative equations and rule-based reasoning paradigms for evidence-based decision support. To this end, we propose MedCalc-Bench, a first-of-its-kind dataset focused on evaluating the medical calculation capability of LLMs. MedCalc-Bench contains an evaluation set of over 1000 manually reviewed instances from 55 different medical calculation tasks. Each instance in MedCalc-Bench consists of a patient note, a question requesting to compute a specific medical value, a ground truth answer, and a step-by-step explanation showing how the answer is obtained. While our evaluation results show the potential of LLMs in this area, none of them are effective enough for clinical settings. Common issues include extracting the incorrect entities, not using the correct equation or rules for a calculation task, or incorrectly performing the arithmetic for the computation. We hope our study highlights the quantitative knowledge and reasoning gaps in LLMs within medical settings, encouraging future improvements of LLMs for various clinical calculation tasks.

The paper describes the open Russian medical language understanding benchmark covering several task types (classification, question answering, natural language inference, named entity recognition) on a number of novel text sets. Given the sensitive nature of the data in healthcare, such a benchmark partially closes the problem of Russian medical dataset absence. We prepare the unified format labeling, data split, and evaluation metrics for new tasks. The remaining tasks are from existing datasets with a few modifications. A single-number metric expresses a model's ability to cope with the benchmark. Moreover, we implement several baseline models, from simple ones to neural networks with transformer architecture, and release the code. Expectedly, the more advanced models yield better performance, but even a simple model is enough for a decent result in some tasks. Furthermore, for all tasks, we provide a human evaluation. Interestingly the models outperform humans in the large-scale classification tasks. However, the advantage of natural intelligence remains in the tasks requiring more knowledge and reasoning.

Large Language Models (LLMs) like ChatGPT demonstrate significant potential in the medical field, often evaluated using multiple-choice questions (MCQs) similar to those found on the USMLE. Despite their prevalence in medical education, MCQs have limitations that might be exacerbated when assessing LLMs. To evaluate the effectiveness of MCQs in assessing the performance of LLMs, we developed a fictional medical benchmark focused on a non-existent gland, the Glianorex. This approach allowed us to isolate the knowledge of the LLM from its test-taking abilities. We used GPT-4 to generate a comprehensive textbook on the Glianorex in both English and French and developed corresponding multiple-choice questions in both languages. We evaluated various open-source, proprietary, and domain-specific LLMs using these questions in a zero-shot setting. The models achieved average scores around 67%, with minor performance differences between larger and smaller models. Performance was slightly higher in English than in French. Fine-tuned medical models showed some improvement over their base versions in English but not in French. The uniformly high performance across models suggests that traditional MCQ-based benchmarks may not accurately measure LLMs' clinical knowledge and reasoning abilities, instead highlighting their pattern recognition skills. This study underscores the need for more robust evaluation methods to better assess the true capabilities of LLMs in medical contexts.

In real world applications, knowledge graphs (KG) are widely used in various domains (e.g. medical applications and dialogue agents). However, for fact verification, KGs have not been adequately utilized as a knowledge source. KGs can be a valuable knowledge source in fact verification due to their reliability and broad applicability. A KG consists of nodes and edges which makes it clear how concepts are linked together, allowing machines to reason over chains of topics. However, there are many challenges in understanding how these machine-readable concepts map to information in text. To enable the community to better use KGs, we introduce a new dataset, FactKG: Fact Verification via Reasoning on Knowledge Graphs. It consists of 108k natural language claims with five types of reasoning: One-hop, Conjunction, Existence, Multi-hop, and Negation. Furthermore, FactKG contains various linguistic patterns, including colloquial style claims as well as written style claims to increase practicality. Lastly, we develop a baseline approach and analyze FactKG over these reasoning types. We believe FactKG can advance both reliability and practicality in KG-based fact verification.

Medical vision-and-language pre-training (Med-VLP) has received considerable attention owing to its applicability to extracting generic vision-and-language representations from medical images and texts. Most existing methods mainly contain three elements: uni-modal encoders (i.e., a vision encoder and a language encoder), a multi-modal fusion module, and pretext tasks, with few studies considering the importance of medical domain expert knowledge and explicitly exploiting such knowledge to facilitate Med-VLP. Although there exist knowledge-enhanced vision-and-language pre-training (VLP) methods in the general domain, most require off-the-shelf toolkits (e.g., object detectors and scene graph parsers), which are unavailable in the medical domain. In this paper, we propose a systematic and effective approach to enhance Med-VLP by structured medical knowledge from three perspectives. First, considering knowledge can be regarded as the intermediate medium between vision and language, we align the representations of the vision encoder and the language encoder through knowledge. Second, we inject knowledge into the multi-modal fusion model to enable the model to perform reasoning using knowledge as the supplementation of the input image and text. Third, we guide the model to put emphasis on the most critical information in images and texts by designing knowledge-induced pretext tasks. To perform a comprehensive evaluation and facilitate further research, we construct a medical vision-and-language benchmark including three tasks. Experimental results illustrate the effectiveness of our approach, where state-of-the-art performance is achieved on all downstream tasks. Further analyses explore the effects of different components of our approach and various settings of pre-training.

Medical multiple-choice question answering (MCQA) is particularly difficult. Questions may describe patient symptoms and ask for the correct diagnosis, which requires domain knowledge and complex reasoning. Standard language modeling pretraining alone is not sufficient to achieve the best results. jin2020disease showed that focusing masked language modeling on disease name prediction when using medical encyclopedic paragraphs as input leads to considerable MCQA accuracy improvement. In this work, we show that (1) fine-tuning on generated MCQA dataset outperforms the masked language modeling based objective and (2) correctly masking the cues to the answers is critical for good performance. We release new pretraining datasets and achieve state-of-the-art results on 4 MCQA datasets, notably +5.7\% with base-size model on MedQA-USMLE.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Reinforcement learning from verifiable rewards (RLVR) has recently gained attention for its ability to elicit self-evolved reasoning capabilitie from base language models without explicit reasoning supervisions, as demonstrated by DeepSeek-R1. While prior work on RLVR has primarily focused on mathematical and coding domains, its applicability to other tasks and domains remains unexplored. In this work, we investigate whether medical reasoning can emerge from RLVR. We introduce Med-RLVR as an initial study of RLVR in the medical domain leveraging medical multiple-choice question answering (MCQA) data as verifiable labels. Our results demonstrate that RLVR is not only effective for math and coding but also extends successfully to medical question answering. Notably, Med-RLVR achieves performance comparable to traditional supervised fine-tuning (SFT) on in-distribution tasks while significantly improving out-of-distribution generalization, with an 8-point accuracy gain. Further analysis of training dynamics reveals that, with no explicit reasoning supervision, reasoning emerges from the 3B-parameter base model. These findings underscore the potential of RLVR in domains beyond math and coding, opening new avenues for its application in knowledge-intensive fields such as medicine.

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate PaLM (a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM, on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. To resolve this we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

Biomedical knowledge is uniquely complex and structured, requiring distinct reasoning strategies compared to other scientific disciplines like physics or chemistry. Biomedical scientists do not rely on a single approach to reasoning; instead, they use various strategies, including rule-based, prototype-based, and case-based reasoning. This diversity calls for flexible approaches that accommodate multiple reasoning strategies while leveraging in-domain knowledge. We introduce KGARevion, a knowledge graph (KG) based agent designed to address the complexity of knowledge-intensive medical queries. Upon receiving a query, KGARevion generates relevant triplets by using the knowledge base of the LLM. These triplets are then verified against a grounded KG to filter out erroneous information and ensure that only accurate, relevant data contribute to the final answer. Unlike RAG-based models, this multi-step process ensures robustness in reasoning while adapting to different models of medical reasoning. Evaluations on four gold-standard medical QA datasets show that KGARevion improves accuracy by over 5.2%, outperforming 15 models in handling complex medical questions. To test its capabilities, we curated three new medical QA datasets with varying levels of semantic complexity, where KGARevion achieved a 10.4% improvement in accuracy.

Answering complex questions about textual narratives requires reasoning over both stated context and the world knowledge that underlies it. However, pretrained language models (LM), the foundation of most modern QA systems, do not robustly represent latent relationships between concepts, which is necessary for reasoning. While knowledge graphs (KG) are often used to augment LMs with structured representations of world knowledge, it remains an open question how to effectively fuse and reason over the KG representations and the language context, which provides situational constraints and nuances. In this work, we propose GreaseLM, a new model that fuses encoded representations from pretrained LMs and graph neural networks over multiple layers of modality interaction operations. Information from both modalities propagates to the other, allowing language context representations to be grounded by structured world knowledge, and allowing linguistic nuances (e.g., negation, hedging) in the context to inform the graph representations of knowledge. Our results on three benchmarks in the commonsense reasoning (i.e., CommonsenseQA, OpenbookQA) and medical question answering (i.e., MedQA-USMLE) domains demonstrate that GreaseLM can more reliably answer questions that require reasoning over both situational constraints and structured knowledge, even outperforming models 8x larger.

This work introduces RARE (Retrieval-Augmented Reasoning Enhancement), a versatile extension to the mutual reasoning framework (rStar), aimed at enhancing reasoning accuracy and factual integrity across large language models (LLMs) for complex, knowledge-intensive tasks such as commonsense and medical reasoning. RARE incorporates two innovative actions within the Monte Carlo Tree Search (MCTS) framework: A6, which generates search queries based on the initial problem statement, performs information retrieval using those queries, and augments reasoning with the retrieved data to formulate the final answer; and A7, which leverages information retrieval specifically for generated sub-questions and re-answers these sub-questions with the relevant contextual information. Additionally, a Retrieval-Augmented Factuality Scorer is proposed to replace the original discriminator, prioritizing reasoning paths that meet high standards of factuality. Experimental results with LLaMA 3.1 show that RARE enables open-source LLMs to achieve competitive performance with top open-source models like GPT-4 and GPT-4o. This research establishes RARE as a scalable solution for improving LLMs in domains where logical coherence and factual integrity are critical.

We introduce RJUA-QA, a novel medical dataset for question answering (QA) and reasoning with clinical evidence, contributing to bridge the gap between general large language models (LLMs) and medical-specific LLM applications. RJUA-QA is derived from realistic clinical scenarios and aims to facilitate LLMs in generating reliable diagnostic and advice. The dataset contains 2,132 curated Question-Context-Answer pairs, corresponding about 25,000 diagnostic records and clinical cases. The dataset covers 67 common urological disease categories, where the disease coverage exceeds 97.6\% of the population seeking medical services in urology. Each data instance in RJUA-QA comprises: (1) a question mirroring real patient to inquiry about clinical symptoms and medical conditions, (2) a context including comprehensive expert knowledge, serving as a reference for medical examination and diagnosis, (3) a doctor response offering the diagnostic conclusion and suggested examination guidance, (4) a diagnosed clinical disease as the recommended diagnostic outcome, and (5) clinical advice providing recommendations for medical examination. RJUA-QA is the first medical QA dataset for clinical reasoning over the patient inquiries, where expert-level knowledge and experience are required for yielding diagnostic conclusions and medical examination advice. A comprehensive evaluation is conducted to evaluate the performance of both medical-specific and general LLMs on the RJUA-QA dataset.

Large language models (LLMs) have shown remarkable progress in encoding clinical knowledge and responding to complex medical queries with appropriate clinical reasoning. However, their applicability in subspecialist or complex medical settings remains underexplored. In this work, we probe the performance of AMIE, a research conversational diagnostic AI system, in the subspecialist domain of breast oncology care without specific fine-tuning to this challenging domain. To perform this evaluation, we curated a set of 50 synthetic breast cancer vignettes representing a range of treatment-naive and treatment-refractory cases and mirroring the key information available to a multidisciplinary tumor board for decision-making (openly released with this work). We developed a detailed clinical rubric for evaluating management plans, including axes such as the quality of case summarization, safety of the proposed care plan, and recommendations for chemotherapy, radiotherapy, surgery and hormonal therapy. To improve performance, we enhanced AMIE with the inference-time ability to perform web search retrieval to gather relevant and up-to-date clinical knowledge and refine its responses with a multi-stage self-critique pipeline. We compare response quality of AMIE with internal medicine trainees, oncology fellows, and general oncology attendings under both automated and specialist clinician evaluations. In our evaluations, AMIE outperformed trainees and fellows demonstrating the potential of the system in this challenging and important domain. We further demonstrate through qualitative examples, how systems such as AMIE might facilitate conversational interactions to assist clinicians in their decision making. However, AMIE's performance was overall inferior to attending oncologists suggesting that further research is needed prior to consideration of prospective uses.

Vision-Language Models (VLM) can support clinicians by analyzing medical images and engaging in natural language interactions to assist in diagnostic and treatment tasks. However, VLMs often exhibit "hallucinogenic" behavior, generating textual outputs not grounded in contextual multimodal information. This challenge is particularly pronounced in the medical domain, where we do not only require VLM outputs to be accurate in single interactions but also to be consistent with clinical reasoning and diagnostic pathways throughout multi-turn conversations. For this purpose, we propose a new alignment algorithm that uses symbolic representations of clinical reasoning to ground VLMs in medical knowledge. These representations are utilized to (i) generate GPT-4-guided visual instruction tuning data at scale, simulating clinician-VLM conversations with demonstrations of clinical reasoning, and (ii) create an automatic reward function that evaluates the clinical validity of VLM generations throughout clinician-VLM interactions. Our algorithm eliminates the need for human involvement in training data generation or reward model construction, reducing costs compared to standard reinforcement learning with human feedback (RLHF). We apply our alignment algorithm to develop Dr-LLaVA, a conversational VLM finetuned for analyzing bone marrow pathology slides, demonstrating strong performance in multi-turn medical conversations.

Large Language Models (LLMs), despite their remarkable progress across various general domains, encounter significant barriers in medicine and healthcare. This field faces unique challenges such as domain-specific terminologies and the reasoning over specialized knowledge. To address these obstinate issues, we propose a novel Multi-disciplinary Collaboration (MC) framework for the medical domain that leverages role-playing LLM-based agents who participate in a collaborative multi-round discussion, thereby enhancing LLM proficiency and reasoning capabilities. This training-free and interpretable framework encompasses five critical steps: gathering domain experts, proposing individual analyses, summarising these analyses into a report, iterating over discussions until a consensus is reached, and ultimately making a decision. Our work particularly focuses on the zero-shot scenario, our results on nine data sets (MedQA, MedMCQA, PubMedQA, and six subtasks from MMLU) establish that our proposed MC framework excels at mining and harnessing the medical expertise in LLMs, as well as extending its reasoning abilities. Based on these outcomes, we further conduct a human evaluation to pinpoint and categorize common errors within our method, as well as ablation studies aimed at understanding the impact of various factors on overall performance. Our code can be found at https://github.com/gersteinlab/MedAgents.

Although large language models (LLMs) often produce impressive outputs, it remains unclear how they perform in real-world scenarios requiring strong reasoning skills and expert domain knowledge. We set out to investigate whether close- and open-source models (GPT-3.5, LLama-2, etc.) can be applied to answer and reason about difficult real-world-based questions. We focus on three popular medical benchmarks (MedQA-USMLE, MedMCQA, and PubMedQA) and multiple prompting scenarios: Chain-of-Thought (CoT, think step-by-step), few-shot and retrieval augmentation. Based on an expert annotation of the generated CoTs, we found that InstructGPT can often read, reason and recall expert knowledge. Last, by leveraging advances in prompt engineering (few-shot and ensemble methods), we demonstrated that GPT-3.5 not only yields calibrated predictive distributions, but also reaches the passing score on three datasets: MedQA-USMLE 60.2%, MedMCQA 62.7% and PubMedQA 78.2%. Open-source models are closing the gap: Llama-2 70B also passed the MedQA-USMLE with 62.5% accuracy.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Recent advancements in large language models (LLMs) have shown promise in medical applications such as disease diagnosis and treatment planning. However, most existing medical LLMs struggle with the advanced reasoning required for complex clinical scenarios, such as differential diagnosis or personalized treatment suggestions. We proposed FineMedLM-o1, which leverages high-quality synthetic medical data and long-form reasoning data for Supervised Fine-Tuning (SFT) and Direct Preference Optimization (DPO), enabling advanced dialogue and deep reasoning capabilities. Additionally, we introduced Test-Time Training (TTT) in the medical domain for the first time, facilitating domain adaptation and ensuring reliable, accurate reasoning. Experimental results demonstrate that FineMedLM-o1 achieves a 23% average performance improvement over prior models on key medical benchmarks. Furthermore, the introduction of TTT provides an additional 14% performance boost, highlighting its effectiveness in enhancing medical reasoning capabilities. To support this process, we also proposed a novel method for synthesizing medical dialogue. Compared to other open-source datasets, our dataset stands out as superior in both quality and complexity. The project and data will be released on GitHub.

The breakthrough of OpenAI o1 highlights the potential of enhancing reasoning to improve LLM. Yet, most research in reasoning has focused on mathematical tasks, leaving domains like medicine underexplored. The medical domain, though distinct from mathematics, also demands robust reasoning to provide reliable answers, given the high standards of healthcare. However, verifying medical reasoning is challenging, unlike those in mathematics. To address this, we propose verifiable medical problems with a medical verifier to check the correctness of model outputs. This verifiable nature enables advancements in medical reasoning through a two-stage approach: (1) using the verifier to guide the search for a complex reasoning trajectory for fine-tuning LLMs, (2) applying reinforcement learning (RL) with verifier-based rewards to enhance complex reasoning further. Finally, we introduce HuatuoGPT-o1, a medical LLM capable of complex reasoning, which outperforms general and medical-specific baselines using only 40K verifiable problems. Experiments show complex reasoning improves medical problem-solving and benefits more from RL. We hope our approach inspires advancements in reasoning across medical and other specialized domains.

Large language models (LLMs), particularly those with reasoning capabilities, have rapidly advanced in recent years, demonstrating significant potential across a wide range of applications. However, their deployment in healthcare, especially in disease reasoning tasks, is hindered by the challenge of acquiring expert-level cognitive data. In this paper, we introduce Citrus, a medical language model that bridges the gap between clinical expertise and AI reasoning by emulating the cognitive processes of medical experts. The model is trained on a large corpus of simulated expert disease reasoning data, synthesized using a novel approach that accurately captures the decision-making pathways of clinicians. This approach enables Citrus to better simulate the complex reasoning processes involved in diagnosing and treating medical conditions.To further address the lack of publicly available datasets for medical reasoning tasks, we release the last-stage training data, including a custom-built medical diagnostic dialogue dataset. This open-source contribution aims to support further research and development in the field. Evaluations using authoritative benchmarks such as MedQA, covering tasks in medical reasoning and language understanding, show that Citrus achieves superior performance compared to other models of similar size. These results highlight Citrus potential to significantly enhance medical decision support systems, providing a more accurate and efficient tool for clinical decision-making.

Explaining Artificial Intelligence (AI) decisions is a major challenge nowadays in AI, in particular when applied to sensitive scenarios like medicine and law. However, the need to explain the rationale behind decisions is a main issue also for human-based deliberation as it is important to justify why a certain decision has been taken. Resident medical doctors for instance are required not only to provide a (possibly correct) diagnosis, but also to explain how they reached a certain conclusion. Developing new tools to aid residents to train their explanation skills is therefore a central objective of AI in education. In this paper, we follow this direction, and we present, to the best of our knowledge, the first multilingual dataset for Medical Question Answering where correct and incorrect diagnoses for a clinical case are enriched with a natural language explanation written by doctors. These explanations have been manually annotated with argument components (i.e., premise, claim) and argument relations (i.e., attack, support), resulting in the Multilingual CasiMedicos-Arg dataset which consists of 558 clinical cases in four languages (English, Spanish, French, Italian) with explanations, where we annotated 5021 claims, 2313 premises, 2431 support relations, and 1106 attack relations. We conclude by showing how competitive baselines perform over this challenging dataset for the argument mining task.

Large language models (LLMs) have exhibited remarkable capabilities across various domains and tasks, pushing the boundaries of our knowledge in learning and cognition. The latest model, OpenAI's o1, stands out as the first LLM with an internalized chain-of-thought technique using reinforcement learning strategies. While it has demonstrated surprisingly strong capabilities on various general language tasks, its performance in specialized fields such as medicine remains unknown. To this end, this report provides a comprehensive exploration of o1 on different medical scenarios, examining 3 key aspects: understanding, reasoning, and multilinguality. Specifically, our evaluation encompasses 6 tasks using data from 37 medical datasets, including two newly constructed and more challenging question-answering (QA) tasks based on professional medical quizzes from the New England Journal of Medicine (NEJM) and The Lancet. These datasets offer greater clinical relevance compared to standard medical QA benchmarks such as MedQA, translating more effectively into real-world clinical utility. Our analysis of o1 suggests that the enhanced reasoning ability of LLMs may (significantly) benefit their capability to understand various medical instructions and reason through complex clinical scenarios. Notably, o1 surpasses the previous GPT-4 in accuracy by an average of 6.2% and 6.6% across 19 datasets and two newly created complex QA scenarios. But meanwhile, we identify several weaknesses in both the model capability and the existing evaluation protocols, including hallucination, inconsistent multilingual ability, and discrepant metrics for evaluation. We release our raw data and model outputs at https://ucsc-vlaa.github.io/o1_medicine/ for future research.

Reasoning is a critical frontier for advancing medical image analysis, where transparency and trustworthiness play a central role in both clinician trust and regulatory approval. Although Medical Visual Language Models (VLMs) show promise for radiological tasks, most existing VLMs merely produce final answers without revealing the underlying reasoning. To address this gap, we introduce MedVLM-R1, a medical VLM that explicitly generates natural language reasoning to enhance transparency and trustworthiness. Instead of relying on supervised fine-tuning (SFT), which often suffers from overfitting to training distributions and fails to foster genuine reasoning, MedVLM-R1 employs a reinforcement learning framework that incentivizes the model to discover human-interpretable reasoning paths without using any reasoning references. Despite limited training data (600 visual question answering samples) and model parameters (2B), MedVLM-R1 boosts accuracy from 55.11% to 78.22% across MRI, CT, and X-ray benchmarks, outperforming larger models trained on over a million samples. It also demonstrates robust domain generalization under out-of-distribution tasks. By unifying medical image analysis with explicit reasoning, MedVLM-R1 marks a pivotal step toward trustworthy and interpretable AI in clinical practice.

Large Language Models (LLMs) have attained human-level accuracy on medical question-answer (QA) benchmarks. However, their limitations in navigating open-ended clinical scenarios have recently been shown, raising concerns about the robustness and generalizability of LLM reasoning across diverse, real-world medical tasks. To probe potential LLM failure modes in clinical problem-solving, we present the medical abstraction and reasoning corpus (M-ARC). M-ARC assesses clinical reasoning through scenarios designed to exploit the Einstellung effect -- the fixation of thought arising from prior experience, targeting LLM inductive biases toward inflexible pattern matching from their training data rather than engaging in flexible reasoning. We find that LLMs, including current state-of-the-art o1 and Gemini models, perform poorly compared to physicians on M-ARC, often demonstrating lack of commonsense medical reasoning and a propensity to hallucinate. In addition, uncertainty estimation analyses indicate that LLMs exhibit overconfidence in their answers, despite their limited accuracy. The failure modes revealed by M-ARC in LLM medical reasoning underscore the need to exercise caution when deploying these models in clinical settings.

Medical Dialogue Generation serves a critical role in telemedicine by facilitating the dissemination of medical expertise to patients. Existing studies focus on incorporating textual representations, which have limited their ability to represent the semantics of text, such as ignoring important medical entities. To enhance the model's understanding of the textual semantics and the medical knowledge including entities and relations, we introduce the use of Abstract Meaning Representations (AMR) to construct graphical representations that delineate the roles of language constituents and medical entities within the dialogues. In this paper, We propose a novel framework that models dialogues between patients and healthcare professionals using AMR graphs, where the neural networks incorporate textual and graphical knowledge with a dual attention mechanism. Experimental results show that our framework outperforms strong baseline models in medical dialogue generation, demonstrating the effectiveness of AMR graphs in enhancing the representations of medical knowledge and logical relationships. Furthermore, to support future research in this domain, we provide the corresponding source code at https://github.com/Bernard-Yang/MedDiaAMR.

In recent years, the application of Large Language Models (LLMs) in healthcare has shown significant promise in improving the accessibility and dissemination of medical knowledge. This paper presents a detailed study of various LLMs trained on the MedQuAD medical question-answering dataset, with a focus on identifying the most effective model for providing accurate medical information. Among the models tested, the Sentence-t5 combined with Mistral 7B demonstrated superior performance, achieving a precision score of 0.762. This model's enhanced capabilities are attributed to its advanced pretraining techniques, robust architecture, and effective prompt construction methodologies. By leveraging these strengths, the Sentence-t5 + Mistral 7B model excels in understanding and generating precise medical answers. Our findings highlight the potential of integrating sophisticated LLMs in medical contexts to facilitate efficient and accurate medical knowledge retrieval, thus significantly enhancing patient education and support.

Building upon our previous investigations of O1 replication (Part 1: Journey Learning [Qin et al., 2024] and Part 2: Distillation [Huang et al., 2024]), this work explores the potential of inference-time scaling in large language models (LLMs) for medical reasoning tasks, ranging from diagnostic decision-making to treatment planning. Through extensive experiments on medical benchmarks of varying complexity (MedQA, Medbullets, and JAMA Clinical Challenges), our investigation reveals several key insights: (1) Increasing inference time does lead to improved performance. With a modest training set of 500 samples, our model yields substantial performance improvements of 6%-11%. (2) Task complexity directly correlates with the required length of reasoning chains, confirming the necessity of extended thought processes for challenging problems. (3) The differential diagnoses generated by our model adhere to the principles of the hypothetico-deductive method, producing a list of potential conditions that may explain a patient's symptoms and systematically narrowing these possibilities by evaluating the evidence. These findings demonstrate the promising synergy between inference-time scaling and journey learning in advancing LLMs' real-world clinical reasoning capabilities.

Reasoning, as an essential ability for complex problem-solving, can provide back-end support for various real-world applications, such as medical diagnosis, negotiation, etc. This paper provides a comprehensive survey of cutting-edge research on reasoning with language model prompting. We introduce research works with comparisons and summaries and provide systematic resources to help beginners. We also discuss the potential reasons for emerging such reasoning abilities and highlight future research directions. Resources are available at https://github.com/zjunlp/Prompt4ReasoningPapers (updated periodically).

Recent artificial intelligence (AI) systems have reached milestones in "grand challenges" ranging from Go to protein-folding. The capability to retrieve medical knowledge, reason over it, and answer medical questions comparably to physicians has long been viewed as one such grand challenge. Large language models (LLMs) have catalyzed significant progress in medical question answering; Med-PaLM was the first model to exceed a "passing" score in US Medical Licensing Examination (USMLE) style questions with a score of 67.2% on the MedQA dataset. However, this and other prior work suggested significant room for improvement, especially when models' answers were compared to clinicians' answers. Here we present Med-PaLM 2, which bridges these gaps by leveraging a combination of base LLM improvements (PaLM 2), medical domain finetuning, and prompting strategies including a novel ensemble refinement approach. Med-PaLM 2 scored up to 86.5% on the MedQA dataset, improving upon Med-PaLM by over 19% and setting a new state-of-the-art. We also observed performance approaching or exceeding state-of-the-art across MedMCQA, PubMedQA, and MMLU clinical topics datasets. We performed detailed human evaluations on long-form questions along multiple axes relevant to clinical applications. In pairwise comparative ranking of 1066 consumer medical questions, physicians preferred Med-PaLM 2 answers to those produced by physicians on eight of nine axes pertaining to clinical utility (p < 0.001). We also observed significant improvements compared to Med-PaLM on every evaluation axis (p < 0.001) on newly introduced datasets of 240 long-form "adversarial" questions to probe LLM limitations. While further studies are necessary to validate the efficacy of these models in real-world settings, these results highlight rapid progress towards physician-level performance in medical question answering.

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to enhance various aspects of healthcare, ranging from medical education to clinical decision support. However, medicine involves multifaceted data modalities and nuanced reasoning skills, presenting challenges for integrating LLMs. This paper provides a comprehensive review on the applications and implications of LLMs in medicine. It begins by examining the fundamental applications of general-purpose and specialized LLMs, demonstrating their utilities in knowledge retrieval, research support, clinical workflow automation, and diagnostic assistance. Recognizing the inherent multimodality of medicine, the review then focuses on multimodal LLMs, investigating their ability to process diverse data types like medical imaging and EHRs to augment diagnostic accuracy. To address LLMs' limitations regarding personalization and complex clinical reasoning, the paper explores the emerging development of LLM-powered autonomous agents for healthcare. Furthermore, it summarizes the evaluation methodologies for assessing LLMs' reliability and safety in medical contexts. Overall, this review offers an extensive analysis on the transformative potential of LLMs in modern medicine. It also highlights the pivotal need for continuous optimizations and ethical oversight before these models can be effectively integrated into clinical practice. Visit https://github.com/mingze-yuan/Awesome-LLM-Healthcare for an accompanying GitHub repository containing latest papers.

Developing the required technology to assist medical experts in their everyday activities is currently a hot topic in the Artificial Intelligence research field. Thus, a number of large language models (LLMs) and automated benchmarks have recently been proposed with the aim of facilitating information extraction in Evidence-Based Medicine (EBM) using natural language as a tool for mediating in human-AI interaction. The most representative benchmarks are limited to either multiple-choice or long-form answers and are available only in English. In order to address these shortcomings, in this paper we present a new dataset which, unlike previous work: (i) includes not only explanatory arguments for the correct answer, but also arguments to reason why the incorrect answers are not correct; (ii) the explanations are written originally by medical doctors to answer questions from the Spanish Residency Medical Exams. Furthermore, this new benchmark allows us to setup a novel extractive task which consists of identifying the explanation of the correct answer written by medical doctors. An additional benefit of our setting is that we can leverage the extractive QA paradigm to automatically evaluate performance of LLMs without resorting to costly manual evaluation by medical experts. Comprehensive experimentation with language models for Spanish shows that sometimes multilingual models fare better than monolingual ones, even outperforming models which have been adapted to the medical domain. Furthermore, results across the monolingual models are mixed, with supposedly smaller and inferior models performing competitively. In any case, the obtained results show that our novel dataset and approach can be an effective technique to help medical practitioners in identifying relevant evidence-based explanations for medical questions.

Current medical question answering systems have difficulty processing long, detailed and informally worded questions submitted by patients, called Consumer Health Questions (CHQs). To address this issue, we introduce a medical question understanding and answering system with knowledge grounding and semantic self-supervision. Our system is a pipeline that first summarizes a long, medical, user-written question, using a supervised summarization loss. Then, our system performs a two-step retrieval to return answers. The system first matches the summarized user question with an FAQ from a trusted medical knowledge base, and then retrieves a fixed number of relevant sentences from the corresponding answer document. In the absence of labels for question matching or answer relevance, we design 3 novel, self-supervised and semantically-guided losses. We evaluate our model against two strong retrieval-based question answering baselines. Evaluators ask their own questions and rate the answers retrieved by our baselines and own system according to their relevance. They find that our system retrieves more relevant answers, while achieving speeds 20 times faster. Our self-supervised losses also help the summarizer achieve higher scores in ROUGE, as well as in human evaluation metrics. We release our code to encourage further research.

The exponential surge in online health information, coupled with its increasing use by non-experts, highlights the pressing need for advanced Health Information Retrieval models that consider not only topical relevance but also the factual accuracy of the retrieved information, given the potential risks associated with health misinformation. To this aim, this paper introduces a solution driven by Retrieval-Augmented Generation (RAG), which leverages the capabilities of generative Large Language Models (LLMs) to enhance the retrieval of health-related documents grounded in scientific evidence. In particular, we propose a three-stage model: in the first stage, the user's query is employed to retrieve topically relevant passages with associated references from a knowledge base constituted by scientific literature. In the second stage, these passages, alongside the initial query, are processed by LLMs to generate a contextually relevant rich text (GenText). In the last stage, the documents to be retrieved are evaluated and ranked both from the point of view of topical relevance and factual accuracy by means of their comparison with GenText, either through stance detection or semantic similarity. In addition to calculating factual accuracy, GenText can offer a layer of explainability for it, aiding users in understanding the reasoning behind the retrieval. Experimental evaluation of our model on benchmark datasets and against baseline models demonstrates its effectiveness in enhancing the retrieval of both topically relevant and factually accurate health information, thus presenting a significant step forward in the health misinformation mitigation problem.

We present a new dataset for machine comprehension in the medical domain. Our dataset uses clinical case reports with around 100,000 gap-filling queries about these cases. We apply several baselines and state-of-the-art neural readers to the dataset, and observe a considerable gap in performance (20% F1) between the best human and machine readers. We analyze the skills required for successful answering and show how reader performance varies depending on the applicable skills. We find that inferences using domain knowledge and object tracking are the most frequently required skills, and that recognizing omitted information and spatio-temporal reasoning are the most difficult for the machines.

In the expanding field of language model applications, medical knowledge representation remains a significant challenge due to the specialized nature of the domain. Large language models, such as GPT-4, obtain reasonable scores on medical question answering tasks, but smaller models are far behind. In this work, we introduce a method to improve the proficiency of a small language model in the medical domain by employing a two-fold approach. We first fine-tune the model on a corpus of medical textbooks. Then, we use GPT-4 to generate questions similar to the downstream task, prompted with textbook knowledge, and use them to fine-tune the model. Additionally, we introduce ECN-QA, a novel medical question answering dataset containing ``progressive questions'' composed of related sequential questions. We show the benefits of our training strategy on this dataset. The study's findings highlight the potential of small language models in the medical domain when appropriately fine-tuned. The code and weights are available at https://github.com/raidium-med/MQG.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Reasoning is a fundamental aspect of human intelligence that plays a crucial role in activities such as problem solving, decision making, and critical thinking. In recent years, large language models (LLMs) have made significant progress in natural language processing, and there is observation that these models may exhibit reasoning abilities when they are sufficiently large. However, it is not yet clear to what extent LLMs are capable of reasoning. This paper provides a comprehensive overview of the current state of knowledge on reasoning in LLMs, including techniques for improving and eliciting reasoning in these models, methods and benchmarks for evaluating reasoning abilities, findings and implications of previous research in this field, and suggestions on future directions. Our aim is to provide a detailed and up-to-date review of this topic and stimulate meaningful discussion and future work.

The emergent abilities of large language models (LLMs) have demonstrated great potential in solving medical questions. They can possess considerable medical knowledge, but may still hallucinate and are inflexible in the knowledge updates. While Retrieval-Augmented Generation (RAG) has been proposed to enhance the medical question-answering capabilities of LLMs with external knowledge bases, it may still fail in complex cases where multiple rounds of information-seeking are required. To address such an issue, we propose iterative RAG for medicine (i-MedRAG), where LLMs can iteratively ask follow-up queries based on previous information-seeking attempts. In each iteration of i-MedRAG, the follow-up queries will be answered by a vanilla RAG system and they will be further used to guide the query generation in the next iteration. Our experiments show the improved performance of various LLMs brought by i-MedRAG compared with vanilla RAG on complex questions from clinical vignettes in the United States Medical Licensing Examination (USMLE), as well as various knowledge tests in the Massive Multitask Language Understanding (MMLU) dataset. Notably, our zero-shot i-MedRAG outperforms all existing prompt engineering and fine-tuning methods on GPT-3.5, achieving an accuracy of 69.68\% on the MedQA dataset. In addition, we characterize the scaling properties of i-MedRAG with different iterations of follow-up queries and different numbers of queries per iteration. Our case studies show that i-MedRAG can flexibly ask follow-up queries to form reasoning chains, providing an in-depth analysis of medical questions. To the best of our knowledge, this is the first-of-its-kind study on incorporating follow-up queries into medical RAG.

Large language models (LLMs) have demonstrated impressive reasoning abilities in complex tasks. However, they lack up-to-date knowledge and experience hallucinations during reasoning, which can lead to incorrect reasoning processes and diminish their performance and trustworthiness. Knowledge graphs (KGs), which capture vast amounts of facts in a structured format, offer a reliable source of knowledge for reasoning. Nevertheless, existing KG-based LLM reasoning methods only treat KGs as factual knowledge bases and overlook the importance of their structural information for reasoning. In this paper, we propose a novel method called reasoning on graphs (RoG) that synergizes LLMs with KGs to enable faithful and interpretable reasoning. Specifically, we present a planning-retrieval-reasoning framework, where RoG first generates relation paths grounded by KGs as faithful plans. These plans are then used to retrieve valid reasoning paths from the KGs for LLMs to conduct faithful reasoning. Furthermore, RoG not only distills knowledge from KGs to improve the reasoning ability of LLMs through training but also allows seamless integration with any arbitrary LLMs during inference. Extensive experiments on two benchmark KGQA datasets demonstrate that RoG achieves state-of-the-art performance on KG reasoning tasks and generates faithful and interpretable reasoning results.

Large Language Models (LLMs) have exhibited impressive proficiency in various natural language processing (NLP) tasks, which involve increasingly complex reasoning. Knowledge reasoning, a primary type of reasoning, aims at deriving new knowledge from existing one.While it has been widely studied in the context of knowledge graphs (KGs), knowledge reasoning in LLMs remains underexplored. In this paper, we introduce Chain-of-Knowledge, a comprehensive framework for knowledge reasoning, including methodologies for both dataset construction and model learning. For dataset construction, we create KnowReason via rule mining on KGs. For model learning, we observe rule overfitting induced by naive training. Hence, we enhance CoK with a trial-and-error mechanism that simulates the human process of internal knowledge exploration. We conduct extensive experiments with KnowReason. Our results show the effectiveness of CoK in refining LLMs in not only knowledge reasoning, but also general reasoning benchmarkms.

While recent advancements in commercial large language models (LM) have shown promising results in medical tasks, their closed-source nature poses significant privacy and security concerns, hindering their widespread use in the medical field. Despite efforts to create open-source models, their limited parameters often result in insufficient multi-step reasoning capabilities required for solving complex medical problems. To address this, we introduce Meerkat-7B, a novel medical AI system with 7 billion parameters. Meerkat-7B was trained using our new synthetic dataset consisting of high-quality chain-of-thought reasoning paths sourced from 18 medical textbooks, along with diverse instruction-following datasets. Our system achieved remarkable accuracy across seven medical benchmarks, surpassing GPT-3.5 by 13.1%, as well as outperforming the previous best 7B models such as MediTron-7B and BioMistral-7B by 13.4% and 9.8%, respectively. Notably, it surpassed the passing threshold of the United States Medical Licensing Examination (USMLE) for the first time for a 7B-parameter model. Additionally, our system offered more detailed free-form responses to clinical queries compared to existing 7B and 13B models, approaching the performance level of GPT-3.5. This significantly narrows the performance gap with large LMs, showcasing its effectiveness in addressing complex medical challenges.

Retrieval-augmented generation (RAG) has emerged as a promising approach to enhance the performance of large language models (LLMs) in knowledge-intensive tasks such as those from medical domain. However, the sensitive nature of the medical domain necessitates a completely accurate and trustworthy system. While existing RAG benchmarks primarily focus on the standard retrieve-answer setting, they overlook many practical scenarios that measure crucial aspects of a reliable medical system. This paper addresses this gap by providing a comprehensive evaluation framework for medical question-answering (QA) systems in a RAG setting for these situations, including sufficiency, integration, and robustness. We introduce Medical Retrieval-Augmented Generation Benchmark (MedRGB) that provides various supplementary elements to four medical QA datasets for testing LLMs' ability to handle these specific scenarios. Utilizing MedRGB, we conduct extensive evaluations of both state-of-the-art commercial LLMs and open-source models across multiple retrieval conditions. Our experimental results reveals current models' limited ability to handle noise and misinformation in the retrieved documents. We further analyze the LLMs' reasoning processes to provides valuable insights and future directions for developing RAG systems in this critical medical domain.

Large Language Models (LLMs) have demonstrated remarkable success in diverse natural language processing (NLP) tasks in general domains. However, LLMs sometimes generate responses with the hallucination about medical facts due to limited domain knowledge. Such shortcomings pose potential risks in the utilization of LLMs within medical contexts. To address this challenge, we propose knowledge-tuning, which leverages structured medical knowledge bases for the LLMs to grasp domain knowledge efficiently and facilitate reliable response generation. We also release cMedKnowQA, a Chinese medical knowledge question-answering dataset constructed from medical knowledge bases to assess the medical knowledge proficiency of LLMs. Experimental results show that the LLMs which are knowledge-tuned with cMedKnowQA, can exhibit higher levels of accuracy in response generation compared with vanilla instruction-tuning and offer a new reliable way for the domain adaptation of LLMs.

Large language models (LLMs) have demonstrated remarkable capabilities in natural language understanding and generation across various domains, including medicine. We present a comprehensive evaluation of GPT-4, a state-of-the-art LLM, on medical competency examinations and benchmark datasets. GPT-4 is a general-purpose model that is not specialized for medical problems through training or engineered to solve clinical tasks. Our analysis covers two sets of official practice materials for the USMLE, a three-step examination program used to assess clinical competency and grant licensure in the United States. We also evaluate performance on the MultiMedQA suite of benchmark datasets. Beyond measuring model performance, experiments were conducted to investigate the influence of test questions containing both text and images on model performance, probe for memorization of content during training, and study probability calibration, which is of critical importance in high-stakes applications like medicine. Our results show that GPT-4, without any specialized prompt crafting, exceeds the passing score on USMLE by over 20 points and outperforms earlier general-purpose models (GPT-3.5) as well as models specifically fine-tuned on medical knowledge (Med-PaLM, a prompt-tuned version of Flan-PaLM 540B). In addition, GPT-4 is significantly better calibrated than GPT-3.5, demonstrating a much-improved ability to predict the likelihood that its answers are correct. We also explore the behavior of the model qualitatively through a case study that shows the ability of GPT-4 to explain medical reasoning, personalize explanations to students, and interactively craft new counterfactual scenarios around a medical case. Implications of the findings are discussed for potential uses of GPT-4 in medical education, assessment, and clinical practice, with appropriate attention to challenges of accuracy and safety.

Large language models have exhibited exceptional performance on various Natural Language Processing (NLP) tasks, leveraging techniques such as the pre-training, and instruction fine-tuning. Despite these advances, their effectiveness in medical applications is limited, due to challenges such as factual inaccuracies, reasoning abilities, and lack grounding in real-world experience. In this study, we present ClinicalGPT, a language model explicitly designed and optimized for clinical scenarios. By incorporating extensive and diverse real-world data, such as medical records, domain-specific knowledge, and multi-round dialogue consultations in the training process, ClinicalGPT is better prepared to handle multiple clinical task. Furthermore, we introduce a comprehensive evaluation framework that includes medical knowledge question-answering, medical exams, patient consultations, and diagnostic analysis of medical records. Our results demonstrate that ClinicalGPT significantly outperforms other models in these tasks, highlighting the effectiveness of our approach in adapting large language models to the critical domain of healthcare.

Large Language Models (LLMs) have shown impressive performance on existing medical question-answering benchmarks. This high performance makes it increasingly difficult to meaningfully evaluate and differentiate advanced methods. We present MedAgentsBench, a benchmark that focuses on challenging medical questions requiring multi-step clinical reasoning, diagnosis formulation, and treatment planning-scenarios where current models still struggle despite their strong performance on standard tests. Drawing from seven established medical datasets, our benchmark addresses three key limitations in existing evaluations: (1) the prevalence of straightforward questions where even base models achieve high performance, (2) inconsistent sampling and evaluation protocols across studies, and (3) lack of systematic analysis of the interplay between performance, cost, and inference time. Through experiments with various base models and reasoning methods, we demonstrate that the latest thinking models, DeepSeek R1 and OpenAI o3, exhibit exceptional performance in complex medical reasoning tasks. Additionally, advanced search-based agent methods offer promising performance-to-cost ratios compared to traditional approaches. Our analysis reveals substantial performance gaps between model families on complex questions and identifies optimal model selections for different computational constraints. Our benchmark and evaluation framework are publicly available at https://github.com/gersteinlab/medagents-benchmark.

LLMs have demonstrated impressive performance in answering medical questions, such as passing scores on medical licensing examinations. However, medical board exam questions or general clinical questions do not capture the complexity of realistic clinical cases. Moreover, the lack of reference explanations means we cannot easily evaluate the reasoning of model decisions, a crucial component of supporting doctors in making complex medical decisions. To address these challenges, we construct two new datasets: JAMA Clinical Challenge and Medbullets. JAMA Clinical Challenge consists of questions based on challenging clinical cases, while Medbullets comprises USMLE Step 2&3 style clinical questions. Both datasets are structured as multiple-choice question-answering tasks, where each question is accompanied by an expert-written explanation. We evaluate four LLMs on the two datasets using various prompts. Experiments demonstrate that our datasets are harder than previous benchmarks. The inconsistency between automatic and human evaluations of model-generated explanations highlights the need to develop new metrics to support future research on explainable medical QA.

The recent emergence of Medical Large Vision Language Models (Med-LVLMs) has enhanced medical diagnosis. However, current Med-LVLMs frequently encounter factual issues, often generating responses that do not align with established medical facts. Retrieval-Augmented Generation (RAG), which utilizes external knowledge, can improve the factual accuracy of these models but introduces two major challenges. First, limited retrieved contexts might not cover all necessary information, while excessive retrieval can introduce irrelevant and inaccurate references, interfering with the model's generation. Second, in cases where the model originally responds correctly, applying RAG can lead to an over-reliance on retrieved contexts, resulting in incorrect answers. To address these issues, we propose RULE, which consists of two components. First, we introduce a provably effective strategy for controlling factuality risk through the calibrated selection of the number of retrieved contexts. Second, based on samples where over-reliance on retrieved contexts led to errors, we curate a preference dataset to fine-tune the model, balancing its dependence on inherent knowledge and retrieved contexts for generation. We demonstrate the effectiveness of RULE on three medical VQA datasets, achieving an average improvement of 20.8% in factual accuracy. We publicly release our benchmark and code in https://github.com/richard-peng-xia/RULE.

There are two main barriers to using large language models (LLMs) in clinical reasoning. Firstly, while LLMs exhibit significant promise in Natural Language Processing (NLP) tasks, their performance in complex reasoning and planning falls short of expectations. Secondly, LLMs use uninterpretable methods to make clinical decisions that are fundamentally different from the clinician's cognitive processes. This leads to user distrust. In this paper, we present a multi-agent framework called ArgMed-Agents, which aims to enable LLM-based agents to make explainable clinical decision reasoning through interaction. ArgMed-Agents performs self-argumentation iterations via Argumentation Scheme for Clinical Discussion (a reasoning mechanism for modeling cognitive processes in clinical reasoning), and then constructs the argumentation process as a directed graph representing conflicting relationships. Ultimately, use symbolic solver to identify a series of rational and coherent arguments to support decision. We construct a formal model of ArgMed-Agents and present conjectures for theoretical guarantees. ArgMed-Agents enables LLMs to mimic the process of clinical argumentative reasoning by generating explanations of reasoning in a self-directed manner. The setup experiments show that ArgMed-Agents not only improves accuracy in complex clinical decision reasoning problems compared to other prompt methods, but more importantly, it provides users with decision explanations that increase their confidence.

Reasoning is an essential component of human intelligence as it plays a fundamental role in our ability to think critically, support responsible decisions, and solve challenging problems. Traditionally, AI has addressed reasoning in the context of logic-based representations of knowledge. However, the recent leap forward in natural language processing, with the emergence of language models based on transformers, is hinting at the possibility that these models exhibit reasoning abilities, particularly as they grow in size and are trained on more data. Despite ongoing discussions about what reasoning is in language models, it is still not easy to pin down to what extent these models are actually capable of reasoning. The goal of this workshop is to create a platform for researchers from different disciplines and/or AI perspectives, to explore approaches and techniques with the aim to reconcile reasoning between language models using transformers and using logic-based representations. The specific objectives include analyzing the reasoning abilities of language models measured alongside KR methods, injecting KR-style reasoning abilities into language models (including by neuro-symbolic means), and formalizing the kind of reasoning language models carry out. This exploration aims to uncover how language models can effectively integrate and leverage knowledge and reasoning with it, thus improving their application and utility in areas where precision and reliability are a key requirement.

Recent research on large language models (LLMs) has primarily focused on their adaptation and application in specialized domains. The application of LLMs in the medical field is mainly concentrated on tasks such as the automation of medical report generation, summarization, diagnostic reasoning, and question-and-answer interactions between doctors and patients. The challenge of becoming a good teacher is more formidable than that of becoming a good student, and this study pioneers the application of LLMs in the field of medical education. In this work, we investigate the extent to which LLMs can generate medical qualification exam questions and corresponding answers based on few-shot prompts. Utilizing a real-world Chinese dataset of elderly chronic diseases, we tasked the LLMs with generating open-ended questions and answers based on a subset of sampled admission reports across eight widely used LLMs, including ERNIE 4, ChatGLM 4, Doubao, Hunyuan, Spark 4, Qwen, Llama 3, and Mistral. Furthermore, we engaged medical experts to manually evaluate these open-ended questions and answers across multiple dimensions. The study found that LLMs, after using few-shot prompts, can effectively mimic real-world medical qualification exam questions, whereas there is room for improvement in the correctness, evidence-based statements, and professionalism of the generated answers. Moreover, LLMs also demonstrate a decent level of ability to correct and rectify reference answers. Given the immense potential of artificial intelligence in the medical field, the task of generating questions and answers for medical qualification exams aimed at medical students, interns and residents can be a significant focus of future research.

We present MedConceptsQA, a dedicated open source benchmark for medical concepts question answering. The benchmark comprises of questions of various medical concepts across different vocabularies: diagnoses, procedures, and drugs. The questions are categorized into three levels of difficulty: easy, medium, and hard. We conducted evaluations of the benchmark using various Large Language Models. Our findings show that pre-trained clinical Large Language Models achieved accuracy levels close to random guessing on this benchmark, despite being pre-trained on medical data. However, GPT-4 achieves an absolute average improvement of nearly 27%-37% (27% for zero-shot learning and 37% for few-shot learning) when compared to clinical Large Language Models. Our benchmark serves as a valuable resource for evaluating the understanding and reasoning of medical concepts by Large Language Models. Our benchmark is available at https://huggingface.co/datasets/ofir408/MedConceptsQA

Medical open-domain question answering demands substantial access to specialized knowledge. Recent efforts have sought to decouple knowledge from model parameters, counteracting architectural scaling and allowing for training on common low-resource hardware. The retrieve-then-read paradigm has become ubiquitous, with model predictions grounded on relevant knowledge pieces from external repositories such as PubMed, textbooks, and UMLS. An alternative path, still under-explored but made possible by the advent of domain-specific large language models, entails constructing artificial contexts through prompting. As a result, "to generate or to retrieve" is the modern equivalent of Hamlet's dilemma. This paper presents MedGENIE, the first generate-then-read framework for multiple-choice question answering in medicine. We conduct extensive experiments on MedQA-USMLE, MedMCQA, and MMLU, incorporating a practical perspective by assuming a maximum of 24GB VRAM. MedGENIE sets a new state-of-the-art (SOTA) in the open-book setting of each testbed, even allowing a small-scale reader to outcompete zero-shot closed-book 175B baselines while using up to 706times fewer parameters. Overall, our findings reveal that generated passages are more effective than retrieved counterparts in attaining higher accuracy.

This paper introduces MedExQA, a novel benchmark in medical question-answering, to evaluate large language models' (LLMs) understanding of medical knowledge through explanations. By constructing datasets across five distinct medical specialties that are underrepresented in current datasets and further incorporating multiple explanations for each question-answer pair, we address a major gap in current medical QA benchmarks which is the absence of comprehensive assessments of LLMs' ability to generate nuanced medical explanations. Our work highlights the importance of explainability in medical LLMs, proposes an effective methodology for evaluating models beyond classification accuracy, and sheds light on one specific domain, speech language pathology, where current LLMs including GPT4 lack good understanding. Our results show generation evaluation with multiple explanations aligns better with human assessment, highlighting an opportunity for a more robust automated comprehension assessment for LLMs. To diversify open-source medical LLMs (currently mostly based on Llama2), this work also proposes a new medical model, MedPhi-2, based on Phi-2 (2.7B). The model outperformed medical LLMs based on Llama2-70B in generating explanations, showing its effectiveness in the resource-constrained medical domain. We will share our benchmark datasets and the trained model.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

Despite their success at many natural language processing (NLP) tasks, large language models (LLMs) still struggle to effectively leverage knowledge for knowledge-intensive tasks, manifesting limitations such as generating incomplete, non-factual, or illogical answers. These limitations stem from inadequate knowledge awareness of LLMs during vanilla fine-tuning. To address these problems, we propose a knowledge-aware fine-tuning (KnowTuning) method to explicitly and implicitly improve the knowledge awareness of LLMs. We devise an explicit knowledge-aware generation stage to train LLMs to explicitly identify knowledge triples in answers. We also propose an implicit knowledge-aware comparison stage to train LLMs to implicitly distinguish between reliable and unreliable knowledge, in three aspects: completeness, factuality, and logicality. Extensive experiments on both generic and medical question answering (QA) datasets confirm the effectiveness of KnowTuning, through automatic and human evaluations, across various sizes of LLMs. Finally, we demonstrate that the improvements of KnowTuning generalize to unseen QA datasets.

This paper introduces MedMCQA, a new large-scale, Multiple-Choice Question Answering (MCQA) dataset designed to address real-world medical entrance exam questions. More than 194k high-quality AIIMS \& NEET PG entrance exam MCQs covering 2.4k healthcare topics and 21 medical subjects are collected with an average token length of 12.77 and high topical diversity. Each sample contains a question, correct answer(s), and other options which requires a deeper language understanding as it tests the 10+ reasoning abilities of a model across a wide range of medical subjects \& topics. A detailed explanation of the solution, along with the above information, is provided in this study.

Large-scale language models (LLMs) have achieved remarkable success across various language tasks but suffer from hallucinations and temporal misalignment. To mitigate these shortcomings, Retrieval-augmented generation (RAG) has been utilized to provide external knowledge to facilitate the answer generation. However, applying such models to the medical domain faces several challenges due to the lack of domain-specific knowledge and the intricacy of real-world scenarios. In this study, we explore LLMs with RAG framework for knowledge-intensive tasks in the medical field. To evaluate the capabilities of LLMs, we introduce MedicineQA, a multi-round dialogue benchmark that simulates the real-world medication consultation scenario and requires LLMs to answer with retrieved evidence from the medicine database. MedicineQA contains 300 multi-round question-answering pairs, each embedded within a detailed dialogue history, highlighting the challenge posed by this knowledge-intensive task to current LLMs. We further propose a new Distill-Retrieve-Read framework instead of the previous Retrieve-then-Read. Specifically, the distillation and retrieval process utilizes a tool calling mechanism to formulate search queries that emulate the keyword-based inquiries used by search engines. With experimental results, we show that our framework brings notable performance improvements and surpasses the previous counterparts in the evidence retrieval process in terms of evidence retrieval accuracy. This advancement sheds light on applying RAG to the medical domain.

Large Language Models (LLMs) have shown remarkable capabilities in general domains but often struggle with tasks requiring specialized knowledge. Conventional Retrieval-Augmented Generation (RAG) techniques typically retrieve external information from static knowledge bases, which can be outdated or incomplete, missing fine-grained clinical details essential for accurate medical question answering. In this work, we propose SearchRAG, a novel framework that overcomes these limitations by leveraging real-time search engines. Our method employs synthetic query generation to convert complex medical questions into search-engine-friendly queries and utilizes uncertainty-based knowledge selection to filter and incorporate the most relevant and informative medical knowledge into the LLM's input. Experimental results demonstrate that our method significantly improves response accuracy in medical question answering tasks, particularly for complex questions requiring detailed and up-to-date knowledge.

Seeking health-related advice on the internet has become a common practice in the digital era. Determining the trustworthiness of medical claims found online and finding appropriate evidence for this information is increasingly challenging. Fact-checking has emerged as an approach to assess the veracity of factual claims using evidence from credible knowledge sources. To help advance the automation of this task, in this paper, we introduce a novel dataset of 750 health-related claims, labeled for veracity by medical experts and backed with evidence from appropriate clinical studies. We provide an analysis of the dataset, highlighting its characteristics and challenges. The dataset can be used for Machine Learning tasks related to automated fact-checking such as evidence retrieval, veracity prediction, and explanation generation. For this purpose, we provide baseline models based on different approaches, examine their performance, and discuss the findings.

Logical reasoning is fundamental for humans yet presents a substantial challenge in the domain of Artificial Intelligence. Initially, researchers used Knowledge Representation and Reasoning (KR) systems that did not scale and required non trivial manual effort. Recently, the emergence of large language models (LLMs) has demonstrated the ability to overcome various limitations of formal Knowledge Representation (KR) systems. Consequently, there is a growing interest in using LLMs for logical reasoning via natural language. This work strives to understand the proficiency of LLMs in logical reasoning by offering a brief review of the latest progress in this area; with a focus on the logical reasoning datasets, tasks, and the methods adopted to utilize LLMs for reasoning. To offer a thorough analysis, we have compiled a benchmark titled LogiGLUE. This includes 24 varied datasets encompassing deductive, abductive, and inductive reasoning. We have standardized these datasets into Seq2Seq tasks to facilitate straightforward training and evaluation for future research. Utilizing LogiGLUE as a foundation, we have trained an instruction fine tuned language model, resulting in LogiT5. We study single task training, multi task training, and a chain of thought knowledge distillation fine tuning technique to assess the performance of model across the different logical reasoning categories. By this comprehensive process, we aim to shed light on the capabilities and potential pathways for enhancing logical reasoning proficiency in LLMs, paving the way for more advanced and nuanced developments in this critical field.

Recently, Large Language Models (LLMs) have showcased remarkable capabilities in natural language understanding. While demonstrating proficiency in everyday conversations and question-answering situations, these models frequently struggle in domains that require precision, such as medical applications, due to their lack of domain-specific knowledge. In this paper, we describe the procedure for building a powerful, open-source language model specifically designed for medicine applications, termed as PMC-LLaMA. Our contributions are threefold: (i) we systematically investigate the process of adapting a general-purpose foundation language model towards medical domain, this involves data-centric knowledge injection through the integration of 4.8M biomedical academic papers and 30K medical textbooks, as well as comprehensive fine-tuning for alignment with domain-specific instructions; (ii) we contribute a large-scale, comprehensive dataset for instruction tuning. This dataset encompasses medical question-answering (QA), rationale for reasoning, and conversational dialogues, comprising a total of 202M tokens; (iii) we conduct thorough ablation studies to demonstrate the effectiveness of each proposed component. While evaluating on various public medical question-answering benchmarks, our lightweight PMCLLaMA, which consists of only 13 billion parameters, exhibits superior performance, even surpassing ChatGPT. All models, codes, datasets can be found in https://github.com/chaoyi-wu/PMC-LLaMA.

In recent years, there have been significant breakthroughs in the field of natural language processing, particularly with the development of large language models (LLMs). These LLMs have showcased remarkable capabilities on various benchmarks. In the healthcare field, the exact role LLMs and other future AI models will play remains unclear. There is a potential for these models in the future to be used as part of adaptive physician training, medical co-pilot applications, and digital patient interaction scenarios. The ability of AI models to participate in medical training and patient care will depend in part on their mastery of the knowledge content of specific medical fields. This study investigated the medical knowledge capability of LLMs, specifically in the context of internal medicine subspecialty multiple-choice test-taking ability. We compared the performance of several open-source LLMs (Koala 7B, Falcon 7B, Stable-Vicuna 13B, and Orca Mini 13B), to GPT-4 and Claude 2 on multiple-choice questions in the field of Nephrology. Nephrology was chosen as an example of a particularly conceptually complex subspecialty field within internal medicine. The study was conducted to evaluate the ability of LLM models to provide correct answers to nephSAP (Nephrology Self-Assessment Program) multiple-choice questions. The overall success of open-sourced LLMs in answering the 858 nephSAP multiple-choice questions correctly was 17.1% - 25.5%. In contrast, Claude 2 answered 54.4% of the questions correctly, whereas GPT-4 achieved a score of 73.3%. We show that current widely used open-sourced LLMs do poorly in their ability for zero-shot reasoning when compared to GPT-4 and Claude 2. The findings of this study potentially have significant implications for the future of subspecialty medical training and patient care.

LLMs usually exhibit limitations in their ability to incorporate new knowledge, the generation of hallucinations, and the transparency of their decision-making process. In this paper, we explore how to prompt LLMs with knowledge graphs (KG), working as a remedy to engage LLMs with up-to-date knowledge and elicit the reasoning pathways from LLMs. Specifically, we build a prompting pipeline that endows LLMs with the capability of comprehending KG inputs and inferring with a combined implicit knowledge and the retrieved external knowledge. In addition, we investigate eliciting the mind map on which LLMs perform the reasoning and generate the answers. It is identified that the produced mind map exhibits the reasoning pathways of LLMs grounded on the ontology of knowledge, hence bringing the prospects of probing and gauging LLM inference in production. The experiments on three question & answering datasets also show that MindMap prompting leads to a striking empirical gain. For instance, prompting a GPT-3.5 with MindMap yields an overwhelming performance over GPT-4 consistently. We also demonstrate that with structured facts retrieved from KG, MindMap can outperform a series of prompting-with-document-retrieval methods, benefiting from more accurate, concise, and comprehensive knowledge from KGs. To reproduce our results and extend the framework further, we make our codebase available at https://github.com/wyl.willing/MindMap.

Analytical reasoning is an essential and challenging task that requires a system to analyze a scenario involving a set of particular circumstances and perform reasoning over it to make conclusions. In this paper, we study the challenge of analytical reasoning of text and introduce a new dataset consisting of questions from the Law School Admission Test from 1991 to 2016. We analyze what knowledge understanding and reasoning abilities are required to do well on this task. Furthermore, to address this reasoning challenge, we design two different baselines: (1) a Transformer-based method which leverages the state-of-the-art pre-trained language models and (2) Analytical Reasoning Machine (ARM), a logical-level reasoning framework extracting symbolic knowledge (e.g, participants, facts, logical functions) to deduce legitimate solutions. In our experiments, we find that the Transformer-based models struggle to solve this task as their performance is close to random guess and ARM achieves better performance by leveraging symbolic knowledge and interpretable reasoning steps. Results show that both methods still lag far behind human performance, which leave further space for future research.

Knowledge bases (KBs) and text often contain complementary knowledge: KBs store structured knowledge that can support long range reasoning, while text stores more comprehensive and timely knowledge in an unstructured way. Separately embedding the individual knowledge sources into vector spaces has demonstrated tremendous successes in encoding the respective knowledge, but how to jointly embed and reason with both knowledge sources to fully leverage the complementary information is still largely an open problem. We conduct a large-scale, systematic investigation of aligning KB and text embeddings for joint reasoning. We set up a novel evaluation framework with two evaluation tasks, few-shot link prediction and analogical reasoning, and evaluate an array of KB-text embedding alignment methods. We also demonstrate how such alignment can infuse textual information into KB embeddings for more accurate link prediction on emerging entities and events, using COVID-19 as a case study.

Background: Large language models (LLMs) are trained to follow directions, but this introduces a vulnerability to blindly comply with user requests even if they generate wrong information. In medicine, this could accelerate the generation of misinformation that impacts human well-being. Objectives/Methods: We analyzed compliance to requests to generate misleading content about medications in settings where models know the request is illogical. We investigated whether in-context directions and instruction-tuning of LLMs to prioritize logical reasoning over compliance reduced misinformation risk. Results: While all frontier LLMs complied with misinformation requests, both prompt-based and parameter-based approaches can improve the detection of logic flaws in requests and prevent the dissemination of medical misinformation. Conclusion: Shifting LLMs to prioritize logic over compliance could reduce risks of exploitation for medical misinformation.

Exploiting large language models (LLMs) to tackle deductive reasoning has garnered growing attention. It still remains highly challenging to achieve satisfactory results in complex deductive problems, characterized by plenty of premises (i.e., facts or rules) entailing intricate relationships among entities and requiring multi-hop reasoning. One intuitive solution is to decompose the original task into smaller sub-tasks, and then chain the multiple casual reasoning steps together in a forward (e.g., Selection-Inference) or backward (e.g., LAMBADA) direction. However, these techniques inevitably necessitate a large number of overall stages, leading to computationally expensive operations and a higher possibility of making misleading steps. In addition to stage-by-stage decomposition, we draw inspiration from another aspect of human problem-solving. Humans tend to distill the most relevant information and organize their thoughts systematically (e.g., creating mind maps), which assists them in answering questions or drawing conclusions precisely and quickly. In light of this, we propose a novel reasoning approach named Concise and Organized Perception (COP). COP carefully analyzes the given statements to efficiently identify the most pertinent information while eliminating redundancy. It then prompts the LLMs in a more organized form that adapts to the model's inference process. By perceiving concise and organized proofs, the deductive reasoning abilities of LLMs can be better elicited, and the risk of acquiring errors caused by excessive reasoning stages is mitigated. Furthermore, our approach can be combined with the aforementioned ones to further boost their performance. Extensive experimental results on three popular deductive benchmarks (i.e., ProofWriter, PrOntoQA and PrOntoQA-OOD) show that COP significantly outperforms previous state-of-the-art methods.

Medical language models (MLMs) have become pivotal in advancing medical natural language processing. However, prior models that rely on pre-training or supervised fine-tuning often exhibit low data efficiency and limited practicality in real-world clinical applications. While OpenAIs O1 highlights test-time scaling in mathematics, attempts to replicate this approach in medicine typically distill responses from GPT-series models to open-source models, focusing primarily on multiple-choice tasks. This strategy, though straightforward, neglects critical concerns like data privacy and realistic deployment in clinical settings. In this work, we present a deployable, small-scale medical language model, \mone, designed for long-chain reasoning in clinical tasks using a self-evolution paradigm. Starting with a seed dataset of around 8,000 instances spanning five domains and 16 datasets, we prompt a base policy model to perform Monte Carlo Tree Search (MCTS) to construct verifiable reasoning chains. Each reasoning step is assigned an evolution rollout value, allowing verified trajectories to train the policy model and the reward model. During inference, the policy model generates multiple responses, and the reward model selects the one with the highest reward score. Experiments on eleven evaluation datasets demonstrate that \mone outperforms prior open-source models by 2 points, with the addition of the reward model further boosting performance (sim13 points), surpassing GPT-4o-mini. Code and data are available at https://github.com/pixas/MedSSS.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

Recent advancements in the field of large language models, particularly through the Chain of Thought (CoT) approach, have demonstrated significant improvements in solving complex problems. However, existing models either tend to sacrifice detailed reasoning for brevity due to user preferences, or require extensive and expensive training data to learn complicated reasoning ability, limiting their potential in solving complex tasks. To bridge this gap, following the concept of scaling test-time, we propose a simple method by encouraging models to adopt a more patient reasoning style without the need of introducing new knowledge or skills. To employ a preference optimization approach, we generate detailed reasoning processes as positive examples and simple answers as negative examples, thereby training the model to favor thoroughness in its responses. Our results demonstrate a performance increase of up to 6.7% on GSM8k with training just on a lightweight dataset.

Large Language Models (LLMs) have succeeded remarkably in various natural language processing (NLP) tasks, yet their reasoning capabilities remain a fundamental challenge. While LLMs exhibit impressive fluency and factual recall, their ability to perform complex reasoning-spanning logical deduction, mathematical problem-solving, commonsense inference, and multi-step reasoning-often falls short of human expectations. This survey provides a comprehensive review of emerging techniques enhancing reasoning in LLMs. We categorize existing methods into key approaches, including prompting strategies (e.g., Chain-of-Thought reasoning, Self-Consistency, and Tree-of-Thought reasoning), architectural innovations (e.g., retrieval-augmented models, modular reasoning networks, and neuro-symbolic integration), and learning paradigms (e.g., fine-tuning with reasoning-specific datasets, reinforcement learning, and self-supervised reasoning objectives). Additionally, we explore evaluation frameworks used to assess reasoning in LLMs and highlight open challenges, such as hallucinations, robustness, and reasoning generalization across diverse tasks. By synthesizing recent advancements, this survey aims to provide insights into promising directions for future research and practical applications of reasoning-augmented LLMs.

Recently, slow-thinking reasoning systems, such as o1, have demonstrated remarkable capabilities in solving complex reasoning tasks. These systems typically engage in an extended thinking process before responding to a query, allowing them to generate more thorough, accurate, and well-reasoned solutions. These systems are primarily developed and maintained by industry, with their core techniques not publicly disclosed. In response, an increasing number of studies from the research community aim to explore the technical foundations underlying these powerful reasoning systems. Building on these prior efforts, this paper presents a reproduction report on implementing o1-like reasoning systems. We introduce an "imitate, explore, and self-improve" framework as our primary technical approach to train the reasoning model. In the initial phase, we use distilled long-form thought data to fine-tune the reasoning model, enabling it to invoke a slow-thinking mode. The model is then encouraged to explore challenging problems by generating multiple rollouts, which can result in increasingly more high-quality trajectories that lead to correct answers. Furthermore, the model undergoes self-improvement by iteratively refining its training dataset. To verify the effectiveness of this approach, we conduct extensive experiments on three challenging benchmarks. The experimental results demonstrate that our approach achieves competitive performance compared to industry-level reasoning systems on these benchmarks.

Large reasoning models (LRMs) like OpenAI-o1 have demonstrated impressive long stepwise reasoning capabilities through large-scale reinforcement learning. However, their extended reasoning processes often suffer from knowledge insufficiency, leading to frequent uncertainties and potential errors. To address this limitation, we introduce Search-o1, a framework that enhances LRMs with an agentic retrieval-augmented generation (RAG) mechanism and a Reason-in-Documents module for refining retrieved documents. Search-o1 integrates an agentic search workflow into the reasoning process, enabling dynamic retrieval of external knowledge when LRMs encounter uncertain knowledge points. Additionally, due to the verbose nature of retrieved documents, we design a separate Reason-in-Documents module to deeply analyze the retrieved information before injecting it into the reasoning chain, minimizing noise and preserving coherent reasoning flow. Extensive experiments on complex reasoning tasks in science, mathematics, and coding, as well as six open-domain QA benchmarks, demonstrate the strong performance of Search-o1. This approach enhances the trustworthiness and applicability of LRMs in complex reasoning tasks, paving the way for more reliable and versatile intelligent systems. The code is available at https://github.com/sunnynexus/Search-o1.

Large language models (LLMs) are capable of answering knowledge-intensive complex questions with chain-of-thought (CoT) reasoning. However, they tend to generate factually incorrect reasoning steps when the required knowledge is not available or up-to-date in models' parameters. Recent works turn to retrieving external knowledge to augment CoT reasoning. Despite being promising, these chain-based methods suffer from: 1) Negative retrieval. Unnecessary or incorrect retrieval may mislead the reasoning; 2) Limited sight. Lacking the ability to look backward or forward, a local error in one step will propagate along the chain. In this paper, we propose a novel approach: Probabilistic Tree-of-thought Reasoning (ProbTree). First, LLMs translate a complex question into a query tree, in which each non-root node denotes a sub-question of its parent node. Then, probabilistic reasoning is conducted over the tree, by solving questions from leaf to root considering the confidence of both question decomposing and answering. During reasoning, for leaf nodes, LLMs choose a more confident answer from Closed-book QA that employs parametric knowledge and Open-book QA that employs retrieved external knowledge, thus eliminating the negative retrieval problem. For non-leaf nodes, with the hierarchical structure, LLMs have broader sights and are able to globally reason with the information from child nodes, thus recovering from local errors. The experiments on three Complex QA datasets under the open-domain setting show that our approach outperforms SOTA methods significantly, demonstrating the effect of probabilistic tree-of-thought reasoning.

Generating Natural Language Explanations (NLEs) for model predictions on medical images, particularly those depicting thoracic pathologies, remains a critical and challenging task. Existing methodologies often struggle due to general models' insufficient domain-specific medical knowledge and privacy concerns associated with retrieval-based augmentation techniques. To address these issues, we propose a novel Vision-Language framework augmented with a Knowledge Graph (KG)-based datastore, which enhances the model's understanding by incorporating additional domain-specific medical knowledge essential for generating accurate and informative NLEs. Our framework employs a KG-based retrieval mechanism that not only improves the precision of the generated explanations but also preserves data privacy by avoiding direct data retrieval. The KG datastore is designed as a plug-and-play module, allowing for seamless integration with various model architectures. We introduce and evaluate three distinct frameworks within this paradigm: KG-LLaVA, which integrates the pre-trained LLaVA model with KG-RAG; Med-XPT, a custom framework combining MedCLIP, a transformer-based projector, and GPT-2; and Bio-LLaVA, which adapts LLaVA by incorporating the Bio-ViT-L vision model. These frameworks are validated on the MIMIC-NLE dataset, where they achieve state-of-the-art results, underscoring the effectiveness of KG augmentation in generating high-quality NLEs for thoracic pathologies.

Large-scale language models (LLMs), such as ChatGPT, are capable of generating human-like responses for various downstream tasks, such as task-oriented dialogues and question answering. However, applying LLMs to medical domains remains challenging due to their inability to leverage domain-specific knowledge. In this study, we present the Large-scale Language Models Augmented with Medical Textbooks (LLM-AMT), which integrates authoritative medical textbooks as the cornerstone of its design, enhancing its proficiency in the specialized domain through plug-and-play modules, comprised of a Hybrid Textbook Retriever, supplemented by the Query Augmenter and the LLM Reader. Experimental evaluation on three open-domain medical question-answering tasks reveals a substantial enhancement in both the professionalism and accuracy of the LLM responses when utilizing LLM-AMT, exhibiting an improvement ranging from 11.4% to 13.2%. Despite being 100 times smaller, we found that medical textbooks as the retrieval corpus serves as a more valuable external knowledge source than Wikipedia in the medical domain. Our experiments show that textbook augmentation results in a performance improvement ranging from 9.7% to 12.2% over Wikipedia augmentation.

To combat COVID-19, both clinicians and scientists need to digest vast amounts of relevant biomedical knowledge in scientific literature to understand the disease mechanism and related biological functions. We have developed a novel and comprehensive knowledge discovery framework, COVID-KG to extract fine-grained multimedia knowledge elements (entities and their visual chemical structures, relations, and events) from scientific literature. We then exploit the constructed multimedia knowledge graphs (KGs) for question answering and report generation, using drug repurposing as a case study. Our framework also provides detailed contextual sentences, subfigures, and knowledge subgraphs as evidence.

Although large language models (LLMs) have been assessed for general medical knowledge using medical licensing exams, their ability to effectively support clinical decision-making tasks, such as selecting and using medical calculators, remains uncertain. Here, we evaluate the capability of both medical trainees and LLMs to recommend medical calculators in response to various multiple-choice clinical scenarios such as risk stratification, prognosis, and disease diagnosis. We assessed eight LLMs, including open-source, proprietary, and domain-specific models, with 1,009 question-answer pairs across 35 clinical calculators and measured human performance on a subset of 100 questions. While the highest-performing LLM, GPT-4o, provided an answer accuracy of 74.3% (CI: 71.5-76.9%), human annotators, on average, outperformed LLMs with an accuracy of 79.5% (CI: 73.5-85.0%). With error analysis showing that the highest-performing LLMs continue to make mistakes in comprehension (56.6%) and calculator knowledge (8.1%), our findings emphasize that humans continue to surpass LLMs on complex clinical tasks such as calculator recommendation.

The capabilities and limitations of Large Language Models have been sketched out in great detail in recent years, providing an intriguing yet conflicting picture. On the one hand, LLMs demonstrate a general ability to solve problems. On the other hand, they show surprising reasoning gaps when compared to humans, casting doubt on the robustness of their generalisation strategies. The sheer volume of data used in the design of LLMs has precluded us from applying the method traditionally used to measure generalisation: train-test set separation. To overcome this, we study what kind of generalisation strategies LLMs employ when performing reasoning tasks by investigating the pretraining data they rely on. For two models of different sizes (7B and 35B) and 2.5B of their pretraining tokens, we identify what documents influence the model outputs for three simple mathematical reasoning tasks and contrast this to the data that are influential for answering factual questions. We find that, while the models rely on mostly distinct sets of data for each factual question, a document often has a similar influence across different reasoning questions within the same task, indicating the presence of procedural knowledge. We further find that the answers to factual questions often show up in the most influential data. However, for reasoning questions the answers usually do not show up as highly influential, nor do the answers to the intermediate reasoning steps. When we characterise the top ranked documents for the reasoning questions qualitatively, we confirm that the influential documents often contain procedural knowledge, like demonstrating how to obtain a solution using formulae or code. Our findings indicate that the approach to reasoning the models use is unlike retrieval, and more like a generalisable strategy that synthesises procedural knowledge from documents doing a similar form of reasoning.

Large Language Models (LLMs) have shown promising performance in knowledge-intensive reasoning tasks that require a compound understanding of knowledge. However, deployment of the LLMs in real-world applications can be challenging due to their high computational requirements and concerns on data privacy. Previous studies have focused on building task-specific small language models (LMs) by fine-tuning them with labeled data or distilling LLMs. However, these approaches are ill-suited for knowledge-intensive reasoning tasks due to the limited capacity of small LMs in memorizing the knowledge required. Motivated by our theoretical analysis on memorization, we propose Knowledge-Augmented Reasoning Distillation (KARD), a novel method that fine-tunes small LMs to generate rationales with augmented knowledge retrieved from an external knowledge base. Moreover, we further propose a neural reranker to obtain documents relevant to rationale generation. We empirically show that KARD significantly improves the performance of small T5 and Flan-T5 models on the challenging knowledge-intensive reasoning datasets, namely MedQA-USMLE and StrategyQA. Notably, our method makes the 250M models achieve superior performance against the fine-tuned 3B models, having 12 times larger parameters, on both MedQA-USMLE and StrategyQA benchmarks.

In response to the pressing need for advanced clinical problem-solving tools in healthcare, we introduce BooksMed, a novel framework based on a Large Language Model (LLM). BooksMed uniquely emulates human cognitive processes to deliver evidence-based and reliable responses, utilizing the GRADE (Grading of Recommendations, Assessment, Development, and Evaluations) framework to effectively quantify evidence strength. For clinical decision-making to be appropriately assessed, an evaluation metric that is clinically aligned and validated is required. As a solution, we present ExpertMedQA, a multispecialty clinical benchmark comprised of open-ended, expert-level clinical questions, and validated by a diverse group of medical professionals. By demanding an in-depth understanding and critical appraisal of up-to-date clinical literature, ExpertMedQA rigorously evaluates LLM performance. BooksMed outperforms existing state-of-the-art models Med-PaLM 2, Almanac, and ChatGPT in a variety of medical scenarios. Therefore, a framework that mimics human cognitive stages could be a useful tool for providing reliable and evidence-based responses to clinical inquiries.

Logical reasoning consistently plays a fundamental and significant role in the domains of knowledge engineering and artificial intelligence. Recently, Large Language Models (LLMs) have emerged as a noteworthy innovation in natural language processing (NLP), exhibiting impressive achievements across various classic NLP tasks. However, the question of whether LLMs can effectively address the task of logical reasoning, which requires gradual cognitive inference similar to human intelligence, remains unanswered. To this end, we aim to bridge this gap and provide comprehensive evaluations in this paper. Firstly, to offer systematic evaluations, we select fifteen typical logical reasoning datasets and organize them into deductive, inductive, abductive and mixed-form reasoning settings. Considering the comprehensiveness of evaluations, we include three representative LLMs (i.e., text-davinci-003, ChatGPT and BARD) and evaluate them on all selected datasets under zero-shot, one-shot and three-shot settings. Secondly, different from previous evaluations relying only on simple metrics (e.g., accuracy), we propose fine-level evaluations from objective and subjective manners, covering both answers and explanations. Additionally, to uncover the logical flaws of LLMs, problematic cases will be attributed to five error types from two dimensions, i.e., evidence selection process and reasoning process. Thirdly, to avoid the influences of knowledge bias and purely focus on benchmarking the logical reasoning capability of LLMs, we propose a new dataset with neutral content. It contains 3,000 samples and covers deductive, inductive and abductive settings. Based on the in-depth evaluations, this paper finally forms a general evaluation scheme of logical reasoning capability from six dimensions. It reflects the pros and cons of LLMs and gives guiding directions for future works.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

Medical visual question answering (Med-VQA) has tremendous potential in healthcare. However, the development of this technology is hindered by the lacking of publicly-available and high-quality labeled datasets for training and evaluation. In this paper, we present a large bilingual dataset, SLAKE, with comprehensive semantic labels annotated by experienced physicians and a new structural medical knowledge base for Med-VQA. Besides, SLAKE includes richer modalities and covers more human body parts than the currently available dataset. We show that SLAKE can be used to facilitate the development and evaluation of Med-VQA systems. The dataset can be downloaded from http://www.med-vqa.com/slake.

The recent success of Large Language Models (LLMs) has had a significant impact on the healthcare field, providing patients with medical advice, diagnostic information, and more. However, due to a lack of professional medical knowledge, patients are easily misled by generated erroneous information from LLMs, which may result in serious medical problems. To address this issue, we focus on tuning the LLMs to be medical assistants who collaborate with more experienced doctors. We first conduct a two-stage survey by inspiration-feedback to gain a broad understanding of the real needs of doctors for medical assistants. Based on this, we construct a Chinese medical dataset called DoctorFLAN to support the entire workflow of doctors, which includes 92K Q\&A samples from 22 tasks and 27 specialists. Moreover, we evaluate LLMs in doctor-oriented scenarios by constructing the DoctorFLAN-test containing 550 single-turn Q\&A and DotaBench containing 74 multi-turn conversations. The evaluation results indicate that being a medical assistant still poses challenges for existing open-source models, but DoctorFLAN can help them significantly. It demonstrates that the doctor-oriented dataset and benchmarks we construct can complement existing patient-oriented work and better promote medical LLMs research.

Procedural text describes dynamic state changes during a step-by-step natural process (e.g., photosynthesis). In this work, we focus on the task of procedural text understanding, which aims to comprehend such documents and track entities' states and locations during a process. Although recent approaches have achieved substantial progress, their results are far behind human performance. Two challenges, the difficulty of commonsense reasoning and data insufficiency, still remain unsolved, which require the incorporation of external knowledge bases. Previous works on external knowledge injection usually rely on noisy web mining tools and heuristic rules with limited applicable scenarios. In this paper, we propose a novel KnOwledge-Aware proceduraL text understAnding (KOALA) model, which effectively leverages multiple forms of external knowledge in this task. Specifically, we retrieve informative knowledge triples from ConceptNet and perform knowledge-aware reasoning while tracking the entities. Besides, we employ a multi-stage training schema which fine-tunes the BERT model over unlabeled data collected from Wikipedia before further fine-tuning it on the final model. Experimental results on two procedural text datasets, ProPara and Recipes, verify the effectiveness of the proposed methods, in which our model achieves state-of-the-art performance in comparison to various baselines.

Equipped with Chain-of-Thought (CoT), Large language models (LLMs) have shown impressive reasoning ability in various downstream tasks. Even so, suffering from hallucinations and the inability to access external knowledge, LLMs often come with incorrect or unfaithful intermediate reasoning steps, especially in the context of answering knowledge-intensive tasks such as KBQA. To alleviate this issue, we propose a framework called Knowledge-Driven Chain-of-Thought (KD-CoT) to verify and modify reasoning traces in CoT via interaction with external knowledge, and thus overcome the hallucinations and error propagation. Concretely, we formulate the CoT rationale process of LLMs into a structured multi-round QA format. In each round, LLMs interact with a QA system that retrieves external knowledge and produce faithful reasoning traces based on retrieved precise answers. The structured CoT reasoning of LLMs is facilitated by our developed KBQA CoT collection, which serves as in-context learning demonstrations and can also be utilized as feedback augmentation to train a robust retriever. Extensive experiments on WebQSP and ComplexWebQuestion datasets demonstrate the effectiveness of proposed KD-CoT in task-solving reasoning generation, which outperforms the vanilla CoT ICL with an absolute success rate of 8.0% and 5.1%. Furthermore, our proposed feedback-augmented retriever outperforms the state-of-the-art baselines for retrieving knowledge, achieving significant improvement in Hit performance.

Composing knowledge from multiple pieces of texts is a key challenge in multi-hop question answering. We present a multi-hop reasoning dataset, Question Answering via Sentence Composition(QASC), that requires retrieving facts from a large corpus and composing them to answer a multiple-choice question. QASC is the first dataset to offer two desirable properties: (a) the facts to be composed are annotated in a large corpus, and (b) the decomposition into these facts is not evident from the question itself. The latter makes retrieval challenging as the system must introduce new concepts or relations in order to discover potential decompositions. Further, the reasoning model must then learn to identify valid compositions of these retrieved facts using common-sense reasoning. To help address these challenges, we provide annotation for supporting facts as well as their composition. Guided by these annotations, we present a two-step approach to mitigate the retrieval challenges. We use other multiple-choice datasets as additional training data to strengthen the reasoning model. Our proposed approach improves over current state-of-the-art language models by 11% (absolute). The reasoning and retrieval problems, however, remain unsolved as this model still lags by 20% behind human performance.

Large language models (LLMs) often fail to ask effective questions under uncertainty, making them unreliable in domains where proactive information-gathering is essential for decisionmaking. We present ALFA, a framework that improves LLM question-asking by (i) decomposing the notion of a "good" question into a set of theory-grounded attributes (e.g., clarity, relevance), (ii) controllably synthesizing attribute-specific question variations, and (iii) aligning models via preference-based optimization to explicitly learn to ask better questions along these fine-grained attributes. Focusing on clinical reasoning as a case study, we introduce the MediQ-AskDocs dataset, composed of 17k real-world clinical interactions augmented with 80k attribute-specific preference pairs of follow-up questions, as well as a novel expert-annotated interactive healthcare QA task to evaluate question-asking abilities. Models aligned with ALFA reduce diagnostic errors by 56.6% on MediQ-AskDocs compared to SOTA instruction-tuned LLMs, with a question-level win-rate of 64.4% and strong generalizability. Our findings suggest that explicitly guiding question-asking with structured, fine-grained attributes offers a scalable path to improve LLMs, especially in expert application domains.

The deployment of large language models (LLMs) within the healthcare sector has sparked both enthusiasm and apprehension. These models exhibit the remarkable capability to provide proficient responses to free-text queries, demonstrating a nuanced understanding of professional medical knowledge. This comprehensive survey delves into the functionalities of existing LLMs designed for healthcare applications, elucidating the trajectory of their development, starting from traditional Pretrained Language Models (PLMs) to the present state of LLMs in healthcare sector. First, we explore the potential of LLMs to amplify the efficiency and effectiveness of diverse healthcare applications, particularly focusing on clinical language understanding tasks. These tasks encompass a wide spectrum, ranging from named entity recognition and relation extraction to natural language inference, multi-modal medical applications, document classification, and question-answering. Additionally, we conduct an extensive comparison of the most recent state-of-the-art LLMs in the healthcare domain, while also assessing the utilization of various open-source LLMs and highlighting their significance in healthcare applications. Furthermore, we present the essential performance metrics employed to evaluate LLMs in the biomedical domain, shedding light on their effectiveness and limitations. Finally, we summarize the prominent challenges and constraints faced by large language models in the healthcare sector, offering a holistic perspective on their potential benefits and shortcomings. This review provides a comprehensive exploration of the current landscape of LLMs in healthcare, addressing their role in transforming medical applications and the areas that warrant further research and development.

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

This study focuses on improving the performance of lightweight Large Language Models (LLMs) in mathematical reasoning tasks. We introduce a novel method for measuring mathematical logic similarity and design an automatic screening mechanism to construct a set of reference problems that integrate both semantic and logical similarity. By employing carefully crafted positive and negative example prompts, we guide the model towards adopting sound reasoning logic. To the best of our knowledge, this is the first attempt to utilize retrieval-enhanced generation for mathematical problem-solving. Experimental results demonstrate that our method achieves a 15.8% improvement over the Chain of Thought approach on the SVAMP dataset and a 21.5 % improvement on the GSM8K dataset. Further application of this method to a large-scale model with 175 billion parameters yields performance comparable to the best results on both aforementioned datasets. Finally, we conduct an analysis of errors during the reasoning process, providing valuable insights and directions for future research on reasoning tasks using large language models.

Visual mathematical reasoning, as a fundamental visual reasoning ability, has received widespread attention from the Large Multimodal Models (LMMs) community. Existing benchmarks, such as MathVista and MathVerse, focus more on the result-oriented performance but neglect the underlying principles in knowledge acquisition and generalization. Inspired by human-like mathematical reasoning, we introduce WE-MATH, the first benchmark specifically designed to explore the problem-solving principles beyond end-to-end performance. We meticulously collect and categorize 6.5K visual math problems, spanning 67 hierarchical knowledge concepts and five layers of knowledge granularity. We decompose composite problems into sub-problems according to the required knowledge concepts and introduce a novel four-dimensional metric, namely Insufficient Knowledge (IK), Inadequate Generalization (IG), Complete Mastery (CM), and Rote Memorization (RM), to hierarchically assess inherent issues in LMMs' reasoning process. With WE-MATH, we conduct a thorough evaluation of existing LMMs in visual mathematical reasoning and reveal a negative correlation between solving steps and problem-specific performance. We confirm the IK issue of LMMs can be effectively improved via knowledge augmentation strategies. More notably, the primary challenge of GPT-4o has significantly transitioned from IK to IG, establishing it as the first LMM advancing towards the knowledge generalization stage. In contrast, other LMMs exhibit a marked inclination towards Rote Memorization - they correctly solve composite problems involving multiple knowledge concepts yet fail to answer sub-problems. We anticipate that WE-MATH will open new pathways for advancements in visual mathematical reasoning for LMMs. The WE-MATH data and evaluation code are available at https://github.com/We-Math/We-Math.

Despite the success of large language models (LLMs) in various natural language processing (NLP) tasks, the stored knowledge in these models may inevitably be incomplete, out-of-date, or incorrect. This motivates the need to utilize external knowledge to assist LLMs. Unfortunately, current methods for incorporating external knowledge often require additional training or fine-tuning, which can be costly and may not be feasible for LLMs. To address this issue, we propose a novel post-processing approach, rethinking with retrieval (RR), which retrieves relevant external knowledge based on the decomposed reasoning steps obtained from the chain-of-thought (CoT) prompting. This lightweight approach does not require additional training or fine-tuning and is not limited by the input length of LLMs. We evaluate the effectiveness of RR through extensive experiments with GPT-3 on three complex reasoning tasks: commonsense reasoning, temporal reasoning, and tabular reasoning. Our results show that RR can produce more faithful explanations and improve the performance of LLMs.

In this paper, we propose to leverage the unique characteristics of dialogues sharing commonsense knowledge across participants, to resolve the difficulties in summarizing them. We present SICK, a framework that uses commonsense inferences as additional context. Compared to previous work that solely relies on the input dialogue, SICK uses an external knowledge model to generate a rich set of commonsense inferences and selects the most probable one with a similarity-based selection method. Built upon SICK, SICK++ utilizes commonsense as supervision, where the task of generating commonsense inferences is added upon summarizing the dialogue in a multi-task learning setting. Experimental results show that with injected commonsense knowledge, our framework generates more informative and consistent summaries than existing methods.

Artificial intelligence has advanced in Medical Visual Question Answering (Med-VQA), but prevalent research tends to focus on the accuracy of the answers, often overlooking the reasoning paths and interpretability, which are crucial in clinical settings. Besides, current Med-VQA algorithms, typically reliant on singular models, lack the robustness needed for real-world medical diagnostics which usually require collaborative expert evaluation. To address these shortcomings, this paper presents MedCoT, a novel hierarchical expert verification reasoning chain method designed to enhance interpretability and accuracy in biomedical imaging inquiries. MedCoT is predicated on two principles: The necessity for explicit reasoning paths in Med-VQA and the requirement for multi-expert review to formulate accurate conclusions. The methodology involves an Initial Specialist proposing diagnostic rationales, followed by a Follow-up Specialist who validates these rationales, and finally, a consensus is reached through a vote among a sparse Mixture of Experts within the locally deployed Diagnostic Specialist, which then provides the definitive diagnosis. Experimental evaluations on four standard Med-VQA datasets demonstrate that MedCoT surpasses existing state-of-the-art approaches, providing significant improvements in performance and interpretability.

Large Language Models (LLMs) have shown outstanding performance across wide range of downstream tasks. This competency is attributed to their substantial parameter size and pre-training on extensive corpus. Moreover, LLMs have exhibited enhanced reasoning capabilities in tackling complex reasoning tasks, owing to the utilization of a method named ``Chain-of-Thought (CoT) prompting''. This method is designed to generate intermediate reasoning steps that guide the inference of the final answer. However, it is essential to highlight that these advanced reasoning abilities appear to emerge in models with a minimum of 10 billion parameters, thereby limiting its efficacy in situations where computational resources are constrained. In this paper, we investigate the possibility of transferring the reasoning capabilities of LLMs to smaller models via knowledge distillation. Specifically, we propose Sci-CoT, a two-stage framework that separates the processes of generating rationales and inferring answers. This method enables a more efficient use of rationales during the answer inference stage, leading to improved performance on scientific question-answering tasks. Utilizing Sci-CoT, our 80-million parameter model is able to exceed the performance of BLOOM-176B in the ARC-Easy dataset under the few shot setting.

Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the usage of KGs in many AI applications, such as question answering, recommendation systems, and etc. According to the graph types, existing KGR models can be roughly divided into three categories, i.e., static models, temporal models, and multi-modal models. Early works in this domain mainly focus on static KGR, and recent works try to leverage the temporal and multi-modal information, which are more practical and closer to real-world. However, no survey papers and open-source repositories comprehensively summarize and discuss models in this important direction. To fill the gap, we conduct a first survey for knowledge graph reasoning tracing from static to temporal and then to multi-modal KGs. Concretely, the models are reviewed based on bi-level taxonomy, i.e., top-level (graph types) and base-level (techniques and scenarios). Besides, the performances, as well as datasets, are summarized and presented. Moreover, we point out the challenges and potential opportunities to enlighten the readers. The corresponding open-source repository is shared on GitHub https://github.com/LIANGKE23/Awesome-Knowledge-Graph-Reasoning.

Large Language Models (LLMs) demonstrate remarkable capabilities, yet struggle with hallucination and outdated knowledge when tasked with complex knowledge reasoning, resulting in factually incorrect outputs. Previous studies have attempted to mitigate it by retrieving factual knowledge from large-scale knowledge graphs (KGs) to assist LLMs in logical reasoning and prediction of answers. However, this kind of approach often introduces noise and irrelevant data, especially in situations with extensive context from multiple knowledge aspects. In this way, LLM attention can be potentially mislead from question and relevant information. In our study, we introduce an Adaptive Multi-Aspect Retrieval-augmented over KGs (Amar) framework. This method retrieves knowledge including entities, relations, and subgraphs, and converts each piece of retrieved text into prompt embeddings. The Amar framework comprises two key sub-components: 1) a self-alignment module that aligns commonalities among entities, relations, and subgraphs to enhance retrieved text, thereby reducing noise interference; 2) a relevance gating module that employs a soft gate to learn the relevance score between question and multi-aspect retrieved data, to determine which information should be used to enhance LLMs' output, or even filtered altogether. Our method has achieved state-of-the-art performance on two common datasets, WebQSP and CWQ, showing a 1.9\% improvement in accuracy over its best competitor and a 6.6\% improvement in logical form generation over a method that directly uses retrieved text as context prompts. These results demonstrate the effectiveness of Amar in improving the reasoning of LLMs.

Large Language Models (LLMs), although powerful in general domains, often perform poorly on domain-specific tasks like medical question answering (QA). Moreover, they tend to function as "black-boxes," making it challenging to modify their behavior. Addressing this, our study delves into model editing utilizing in-context learning, aiming to improve LLM responses without the need for fine-tuning or retraining. Specifically, we propose a comprehensive retrieval strategy to extract medical facts from an external knowledge base, and then we incorporate them into the query prompt for the LLM. Focusing on medical QA using the MedQA-SMILE dataset, we evaluate the impact of different retrieval models and the number of facts provided to the LLM. Notably, our edited Vicuna model exhibited an accuracy improvement from 44.46% to 48.54%. This work underscores the potential of model editing to enhance LLM performance, offering a practical approach to mitigate the challenges of black-box LLMs.

To achieve faithful reasoning that aligns with human expectations, large language models (LLMs) need to ground their reasoning to real-world knowledge (e.g., web facts, math and physical rules). Tools help LLMs access this external knowledge, but there remains challenges for fine-tuning LLM agents (e.g., Toolformer) to invoke tools in multi-step reasoning problems, where inter-connected tool calls require holistic and efficient tool usage planning. In this work, we propose a new method for LLMs to better leverage tools in multi-step reasoning. Our method, Chain-of-Abstraction (CoA), trains LLMs to first decode reasoning chains with abstract placeholders, and then call domain tools to reify each reasoning chain by filling in specific knowledge. This planning with abstract chains enables LLMs to learn more general reasoning strategies, which are robust to shifts of domain knowledge (e.g., math results) relevant to different reasoning questions. It also allows LLMs to perform decoding and calling of external tools in parallel, which avoids the inference delay caused by waiting for tool responses. In mathematical reasoning and Wiki QA domains, we show that our method consistently outperforms previous chain-of-thought and tool-augmented baselines on both in-distribution and out-of-distribution test sets, with an average ~6% absolute QA accuracy improvement. LLM agents trained with our method also show more efficient tool use, with inference speed being on average ~1.4x faster than baseline tool-augmented LLMs.

Recent advancements in large language models (LLMs) have transformed the field of question answering (QA). However, evaluating LLMs in the medical field is challenging due to the lack of standardized and comprehensive datasets. To address this gap, we introduce CMExam, sourced from the Chinese National Medical Licensing Examination. CMExam consists of 60K+ multiple-choice questions for standardized and objective evaluations, as well as solution explanations for model reasoning evaluation in an open-ended manner. For in-depth analyses of LLMs, we invited medical professionals to label five additional question-wise annotations, including disease groups, clinical departments, medical disciplines, areas of competency, and question difficulty levels. Alongside the dataset, we further conducted thorough experiments with representative LLMs and QA algorithms on CMExam. The results show that GPT-4 had the best accuracy of 61.6% and a weighted F1 score of 0.617. These results highlight a great disparity when compared to human accuracy, which stood at 71.6%. For explanation tasks, while LLMs could generate relevant reasoning and demonstrate improved performance after finetuning, they fall short of a desired standard, indicating ample room for improvement. To the best of our knowledge, CMExam is the first Chinese medical exam dataset to provide comprehensive medical annotations. The experiments and findings of LLM evaluation also provide valuable insights into the challenges and potential solutions in developing Chinese medical QA systems and LLM evaluation pipelines. The dataset and relevant code are available at https://github.com/williamliujl/CMExam.

Medical Visual Question Answering (MedVQA), which offers language responses to image-based medical inquiries, represents a challenging task and significant advancement in healthcare. It assists medical experts to swiftly interpret medical images, thereby enabling faster and more accurate diagnoses. However, the model interpretability and transparency of existing MedVQA solutions are often limited, posing challenges in understanding their decision-making processes. To address this issue, we devise a semi-automated annotation process to streamline data preparation and build new benchmark MedVQA datasets R-RAD, R-SLAKE and R-Path. These datasets provide intermediate medical decision-making rationales generated by multimodal large language models and human annotations for question-answering pairs in existing MedVQA datasets, i.e., VQA-RAD, SLAKE and PathVQA. Moreover, we design a novel framework, MedThink, which finetunes lightweight pretrained generative models by incorporating medical decision-making rationales. MedThink includes three distinct strategies to generate decision outcomes and corresponding rationales, thereby clearly showcasing the medical decision-making process during reasoning. Our comprehensive experiments show that our method achieves an accuracy of 83.5% on R-RAD, 86.3% on R-SLAKE and 87.2% on R-Path. These results significantly exceed those of existing state-of-the-art models with comparable parameters. Datasets and code will be released.

Large language models (LLMs) have demonstrated impressive reasoning abilities, but they still struggle with faithful reasoning due to knowledge gaps and hallucinations. To address these issues, knowledge graphs (KGs) have been utilized to enhance LLM reasoning through their structured knowledge. However, existing KG-enhanced methods, either retrieval-based or agent-based, encounter difficulties in accurately retrieving knowledge and efficiently traversing KGs at scale. In this work, we introduce graph-constrained reasoning (GCR), a novel framework that bridges structured knowledge in KGs with unstructured reasoning in LLMs. To eliminate hallucinations, GCR ensures faithful KG-grounded reasoning by integrating KG structure into the LLM decoding process through KG-Trie, a trie-based index that encodes KG reasoning paths. KG-Trie constrains the decoding process, allowing LLMs to directly reason on graphs and generate faithful reasoning paths grounded in KGs. Additionally, GCR leverages a lightweight KG-specialized LLM for graph-constrained reasoning alongside a powerful general LLM for inductive reasoning over multiple reasoning paths, resulting in accurate reasoning with zero reasoning hallucination. Extensive experiments on several KGQA benchmarks demonstrate that GCR achieves state-of-the-art performance and exhibits strong zero-shot generalizability to unseen KGs without additional training.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Reasoning over knowledge graphs (KGs) is a challenging task that requires a deep understanding of the complex relationships between entities and the underlying logic of their relations. Current approaches rely on learning geometries to embed entities in vector space for logical query operations, but they suffer from subpar performance on complex queries and dataset-specific representations. In this paper, we propose a novel decoupled approach, Language-guided Abstract Reasoning over Knowledge graphs (LARK), that formulates complex KG reasoning as a combination of contextual KG search and logical query reasoning, to leverage the strengths of graph extraction algorithms and large language models (LLM), respectively. Our experiments demonstrate that the proposed approach outperforms state-of-the-art KG reasoning methods on standard benchmark datasets across several logical query constructs, with significant performance gain for queries of higher complexity. Furthermore, we show that the performance of our approach improves proportionally to the increase in size of the underlying LLM, enabling the integration of the latest advancements in LLMs for logical reasoning over KGs. Our work presents a new direction for addressing the challenges of complex KG reasoning and paves the way for future research in this area.

Emergent chain-of-thought (CoT) reasoning capabilities promise to improve performance and explainability of large language models (LLMs). However, uncertainties remain about how reasoning strategies formulated for previous model generations generalize to new model generations and different datasets. In this small-scale study, we compare different reasoning strategies induced by zero-shot prompting across six recently released LLMs (davinci-002, davinci-003, GPT-3.5-turbo, GPT-4, Flan-T5-xxl and Cohere command-xlarge) on a mixture of six question-answering datasets, including datasets from scientific and medical domains. Our findings demonstrate that while some variations in effectiveness occur, gains from CoT reasoning strategies remain robust across different models and datasets. GPT-4 has the most benefit from current state-of-the-art reasoning strategies and exhibits the best performance by applying a prompt previously discovered through automated discovery.

Beginning with McCarthy's Advice Taker (1959), AI has pursued the goal of providing a system with explicit, general knowledge and having the system reason over that knowledge. However, expressing the knowledge in a formal (logical or probabilistic) representation has been a major obstacle to this research. This paper investigates a modern approach to this problem where the facts and rules are provided as natural language sentences, thus bypassing a formal representation. We train transformers to reason (or emulate reasoning) over these sentences using synthetically generated data. Our models, that we call RuleTakers, provide the first empirical demonstration that this kind of soft reasoning over language is learnable, can achieve high (99%) accuracy, and generalizes to test data requiring substantially deeper chaining than seen during training (95%+ scores). We also demonstrate that the models transfer well to two hand-authored rulebases, and to rulebases paraphrased into more natural language. These findings are significant as it suggests a new role for transformers, namely as limited "soft theorem provers" operating over explicit theories in language. This in turn suggests new possibilities for explainability, correctability, and counterfactual reasoning in question-answering.

Large language models (LLMs), such as ChatGPT, have received substantial attention due to their impressive human language understanding and generation capabilities. Therefore, the application of LLMs in medicine to assist physicians and patient care emerges as a promising research direction in both artificial intelligence and clinical medicine. To reflect this trend, this survey provides a comprehensive overview of the principles, applications, and challenges faced by LLMs in medicine. Specifically, we aim to address the following questions: 1) How can medical LLMs be built? 2) What are the downstream performances of medical LLMs? 3) How can medical LLMs be utilized in real-world clinical practice? 4) What challenges arise from the use of medical LLMs? and 5) How can we better construct and utilize medical LLMs? As a result, this survey aims to provide insights into the opportunities and challenges of LLMs in medicine and serve as a valuable resource for constructing practical and effective medical LLMs. A regularly updated list of practical guides on medical LLMs can be found at https://github.com/AI-in-Health/MedLLMsPracticalGuide.

We present a corpus of 5,000 richly annotated abstracts of medical articles describing clinical randomized controlled trials. Annotations include demarcations of text spans that describe the Patient population enrolled, the Interventions studied and to what they were Compared, and the Outcomes measured (the `PICO' elements). These spans are further annotated at a more granular level, e.g., individual interventions within them are marked and mapped onto a structured medical vocabulary. We acquired annotations from a diverse set of workers with varying levels of expertise and cost. We describe our data collection process and the corpus itself in detail. We then outline a set of challenging NLP tasks that would aid searching of the medical literature and the practice of evidence-based medicine.

Despite the recent successes of deep learning, such models are still far from some human abilities like learning from few examples, reasoning and explaining decisions. In this paper, we focus on organ annotation in medical images and we introduce a reasoning framework that is based on learning fuzzy relations on a small dataset for generating explanations. Given a catalogue of relations, it efficiently induces the most relevant relations and combines them for building constraints in order to both solve the organ annotation task and generate explanations. We test our approach on a publicly available dataset of medical images where several organs are already segmented. A demonstration of our model is proposed with an example of explained annotations. It was trained on a small training set containing as few as a couple of examples.

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation; considering assumptions about the familiarity of the explanation beneficiary with the AI task under consideration; referring to specific elements that have contributed to the decision; making use of additional knowledge (e.g. expert evidence) which might not be part of the prediction process; and providing evidence supporting negative hypothesis. Finally, the system needs to formulate the explanation in a clearly interpretable, and possibly convincing, way. Given these considerations, ANTIDOTE fosters an integrated vision of explainable AI, where low-level characteristics of the deep learning process are combined with higher level schemes proper of the human argumentation capacity. ANTIDOTE will exploit cross-disciplinary competences in deep learning and argumentation to support a broader and innovative view of explainable AI, where the need for high-quality explanations for clinical cases deliberation is critical. As a first result of the project, we publish the Antidote CasiMedicos dataset to facilitate research on explainable AI in general, and argumentation in the medical domain in particular.

Large Language Models (LLMs) constitute a breakthrough state-of-the-art Artificial Intelligence (AI) technology which is rapidly evolving and promises to aid in medical diagnosis either by assisting doctors or by simulating a doctor's workflow in more advanced and complex implementations. In this technical paper, we outline Cognitive Network Evaluation Toolkit for Medical Domains (COGNET-MD), which constitutes a novel benchmark for LLM evaluation in the medical domain. Specifically, we propose a scoring-framework with increased difficulty to assess the ability of LLMs in interpreting medical text. The proposed framework is accompanied with a database of Multiple Choice Quizzes (MCQs). To ensure alignment with current medical trends and enhance safety, usefulness, and applicability, these MCQs have been constructed in collaboration with several associated medical experts in various medical domains and are characterized by varying degrees of difficulty. The current (first) version of the database includes the medical domains of Psychiatry, Dentistry, Pulmonology, Dermatology and Endocrinology, but it will be continuously extended and expanded to include additional medical domains.

Large language models (LLMs), such as ChatGPT and GPT-4, are versatile and can solve different tasks due to their emergent ability and generalizability. However, LLMs sometimes lack domain-specific knowledge to perform tasks, which would also cause hallucination during inference. In some previous works, additional modules like graph neural networks (GNNs) are trained on retrieved knowledge from external knowledge bases, aiming to mitigate the problem of lacking domain-specific knowledge. However, incorporating additional modules: 1) would need retraining additional modules when encountering novel domains; 2) would become a bottleneck since LLMs' strong abilities are not fully utilized for retrieval. In this paper, we propose a paradigm, termed Knowledge Solver (KSL), to teach LLMs to search for essential knowledge from external knowledge bases by harnessing their own strong generalizability. Specifically, we design a simple yet effective prompt to transform retrieval into a multi-hop decision sequence, which empowers LLMs with searching knowledge ability in zero-shot manner. Additionally, KSL is able to provide complete retrieval paths and therefore increase explainability of LLMs' reasoning processes. We conduct experiments on three datasets: CommonsenseQA, OpenbookQA, and MedQA-USMLE, and found that our approach improves LLM baseline performance by a relatively large margin.

Large language models (LLMs) have significantly advanced the field of natural language processing, with GPT models at the forefront. While their remarkable performance spans a range of tasks, adapting LLMs for real-world business scenarios still poses challenges warranting further investigation. This paper presents an empirical analysis aimed at bridging the gap in adapting LLMs to practical use cases. To do that, we select the question answering (QA) task of insurance as a case study due to its challenge of reasoning. Based on the task we design a new model relied on LLMs which are empowered by additional knowledge extracted from insurance policy rulebooks and DBpedia. The additional knowledge helps LLMs to understand new concepts of insurance for domain adaptation. Preliminary results on two QA datasets show that knowledge enhancement significantly improves the reasoning ability of GPT-3.5 (55.80% and 57.83% in terms of accuracy). The analysis also indicates that existing public knowledge bases, e.g., DBPedia is beneficial for knowledge enhancement. Our findings reveal that the inherent complexity of business scenarios often necessitates the incorporation of domain-specific knowledge and external resources for effective problem-solving.

People increasingly search online for answers to their medical questions but the rate at which medical questions are asked online significantly exceeds the capacity of qualified people to answer them. This leaves many questions unanswered or inadequately answered. Many of these questions are not unique, and reliable identification of similar questions would enable more efficient and effective question answering schema. COVID-19 has only exacerbated this problem. Almost every government agency and healthcare organization has tried to meet the informational need of users by building online FAQs, but there is no way for people to ask their question and know if it is answered on one of these pages. While many research efforts have focused on the problem of general question similarity, these approaches do not generalize well to domains that require expert knowledge to determine semantic similarity, such as the medical domain. In this paper, we show how a double fine-tuning approach of pretraining a neural network on medical question-answer pairs followed by fine-tuning on medical question-question pairs is a particularly useful intermediate task for the ultimate goal of determining medical question similarity. While other pretraining tasks yield an accuracy below 78.7% on this task, our model achieves an accuracy of 82.6% with the same number of training examples, an accuracy of 80.0% with a much smaller training set, and an accuracy of 84.5% when the full corpus of medical question-answer data is used. We also describe a currently live system that uses the trained model to match user questions to COVID-related FAQs.

Reasoning is central to a wide range of intellectual activities, and while the capabilities of large language models (LLMs) continue to advance, their performance in reasoning tasks remains limited. The processes and mechanisms underlying reasoning are not yet fully understood, but key elements include path exploration, selection of relevant knowledge, and multi-step inference. Problems are solved through the synthesis of these components. In this paper, we propose a benchmark that focuses on a specific aspect of reasoning ability: the direct evaluation of multi-step inference. To this end, we design a special reasoning task where multi-step inference is specifically focused by largely eliminating path exploration and implicit knowledge utilization. Our dataset comprises pairs of explicit instructions and corresponding questions, where the procedures necessary for solving the questions are entirely detailed within the instructions. This setup allows models to solve problems solely by following the provided directives. By constructing problems that require varying numbers of steps to solve and evaluating responses at each step, we enable a thorough assessment of state-of-the-art LLMs' ability to follow instructions. To ensure the robustness of our evaluation, we include multiple distinct tasks. Furthermore, by comparing accuracy across tasks, utilizing step-aware metrics, and applying separately defined measures of complexity, we conduct experiments that offer insights into the capabilities and limitations of LLMs in reasoning tasks. Our findings have significant implications for the development of LLMs and highlight areas for future research in advancing their reasoning abilities. Our dataset is available at https://huggingface.co/datasets/ifujisawa/procbench and code at https://github.com/ifujisawa/proc-bench.

Although Large Language Models (LLMs) achieve remarkable performance across various tasks, they often struggle with complex reasoning tasks, such as answering mathematical questions. Recent efforts to address this issue have primarily focused on leveraging mathematical datasets through supervised fine-tuning or self-improvement techniques. However, these methods often depend on high-quality datasets that are difficult to prepare, or they require substantial computational resources for fine-tuning. Inspired by findings that LLMs know how to produce the right answer but struggle to select the correct reasoning path, we propose a purely inference-based searching method -- MindStar (M*). This method formulates reasoning tasks as searching problems and proposes two search ideas to identify the optimal reasoning paths. We evaluate the M* framework on both the GSM8K and MATH datasets, comparing its performance with existing open and closed-source LLMs. Our results demonstrate that M* significantly enhances the reasoning abilities of open-source models, such as Llama-2-13B and Mistral-7B, and achieves comparable performance to GPT-3.5 and Grok-1, but with substantially reduced model size and computational costs.

With the emergence of advanced reasoning models like OpenAI o3 and DeepSeek-R1, large language models (LLMs) have demonstrated remarkable reasoning capabilities. However, their ability to perform rigorous logical reasoning remains an open question. This survey synthesizes recent advancements in logical reasoning within LLMs, a critical area of AI research. It outlines the scope of logical reasoning in LLMs, its theoretical foundations, and the benchmarks used to evaluate reasoning proficiency. We analyze existing capabilities across different reasoning paradigms - deductive, inductive, abductive, and analogical - and assess strategies to enhance reasoning performance, including data-centric tuning, reinforcement learning, decoding strategies, and neuro-symbolic approaches. The review concludes with future directions, emphasizing the need for further exploration to strengthen logical reasoning in AI systems.

AI-driven medical history-taking is an important component in symptom checking, automated patient intake, triage, and other AI virtual care applications. As history-taking is extremely varied, machine learning models require a significant amount of data to train. To overcome this challenge, existing systems are developed using indirect data or expert knowledge. This leads to a training-inference gap as models are trained on different kinds of data than what they observe at inference time. In this work, we present a two-stage re-ranking approach that helps close the training-inference gap by re-ranking the first-stage question candidates using a dialogue-contextualized model. For this, we propose a new model, global re-ranker, which cross-encodes the dialogue with all questions simultaneously, and compare it with several existing neural baselines. We test both transformer and S4-based language model backbones. We find that relative to the expert system, the best performance is achieved by our proposed global re-ranker with a transformer backbone, resulting in a 30% higher normalized discount cumulative gain (nDCG) and a 77% higher mean average precision (mAP).

Recent advances in Large Language Models (LLMs) have achieved remarkable breakthroughs in understanding and responding to user intents. However, their performance lag behind general use cases in some expertise domains, such as Chinese medicine. Existing efforts to incorporate Chinese medicine into LLMs rely on Supervised Fine-Tuning (SFT) with single-turn and distilled dialogue data. These models lack the ability for doctor-like proactive inquiry and multi-turn comprehension and cannot align responses with experts' intentions. In this work, we introduce Zhongjing, the first Chinese medical LLaMA-based LLM that implements an entire training pipeline from continuous pre-training, SFT, to Reinforcement Learning from Human Feedback (RLHF). Additionally, we construct a Chinese multi-turn medical dialogue dataset of 70,000 authentic doctor-patient dialogues, CMtMedQA, which significantly enhances the model's capability for complex dialogue and proactive inquiry initiation. We also define a refined annotation rule and evaluation criteria given the unique characteristics of the biomedical domain. Extensive experimental results show that Zhongjing outperforms baselines in various capacities and matches the performance of ChatGPT in some abilities, despite the 100x parameters. Ablation studies also demonstrate the contributions of each component: pre-training enhances medical knowledge, and RLHF further improves instruction-following ability and safety. Our code, datasets, and models are available at https://github.com/SupritYoung/Zhongjing.

Large Language Models (LLMs) have demonstrated impressive performance in natural language processing tasks by leveraging chain of thought (CoT) that enables step-by-step thinking. Extending LLMs with multimodal capabilities is the recent interest, but incurs computational cost and requires substantial hardware resources. To address these challenges, we propose KAM-CoT a framework that integrates CoT reasoning, Knowledge Graphs (KGs), and multiple modalities for a comprehensive understanding of multimodal tasks. KAM-CoT adopts a two-stage training process with KG grounding to generate effective rationales and answers. By incorporating external knowledge from KGs during reasoning, the model gains a deeper contextual understanding reducing hallucinations and enhancing the quality of answers. This knowledge-augmented CoT reasoning empowers the model to handle questions requiring external context, providing more informed answers. Experimental findings show KAM-CoT outperforms the state-of-the-art methods. On the ScienceQA dataset, we achieve an average accuracy of 93.87%, surpassing GPT-3.5 (75.17%) by 18% and GPT-4 (83.99%) by 10%. Remarkably, KAM-CoT achieves these results with only 280M trainable parameters at a time, demonstrating its cost-efficiency and effectiveness.

The rapid development of Large Language Models (LLMs) for healthcare applications has spurred calls for holistic evaluation beyond frequently-cited benchmarks like USMLE, to better reflect real-world performance. While real-world assessments are valuable indicators of utility, they often lag behind the pace of LLM evolution, likely rendering findings obsolete upon deployment. This temporal disconnect necessitates a comprehensive upfront evaluation that can guide model selection for specific clinical applications. We introduce MEDIC, a framework assessing LLMs across five critical dimensions of clinical competence: medical reasoning, ethics and bias, data and language understanding, in-context learning, and clinical safety. MEDIC features a novel cross-examination framework quantifying LLM performance across areas like coverage and hallucination detection, without requiring reference outputs. We apply MEDIC to evaluate LLMs on medical question-answering, safety, summarization, note generation, and other tasks. Our results show performance disparities across model sizes, baseline vs medically finetuned models, and have implications on model selection for applications requiring specific model strengths, such as low hallucination or lower cost of inference. MEDIC's multifaceted evaluation reveals these performance trade-offs, bridging the gap between theoretical capabilities and practical implementation in healthcare settings, ensuring that the most promising models are identified and adapted for diverse healthcare applications.

We present Eir Thai Medical LLM, a large language model with 8 billion parameters, specifically designed to enhance the accuracy of handling medical tasks in the Thai language. This model focuses on providing clear and easy-to-understand answers for both healthcare professionals and patients, thereby improving the efficiency of diagnosis and treatment processes. Human evaluation was conducted to ensure that the model adheres to care standards and provides unbiased answers. To prioritize data security, the model is deployed within the hospital's internal network, ensuring both high security and faster processing speeds. The internal API connection is secured with encryption and strict authentication measures to prevent data leaks and unauthorized access. We evaluated several open-source large language models with 8 billion parameters on four medical benchmarks: MedQA, MedMCQA, PubMedQA, and the medical subset of MMLU. The best-performing baselines were used to develop Eir Thai Medical LLM. Our evaluation employed multiple questioning strategies, including zero-shot, few-shot, chain-of-thought reasoning, and ensemble/self-consistency voting methods. Our model outperformed commercially available Thai-language large language models by more than 10%. In addition, we developed enhanced model testing tailored for clinical use in Thai across 18 clinical tasks, where our model exceeded GPT-4o performance by more than 11%

Knowledge graph embedding involves learning representations of entities -- the vertices of the graph -- and relations -- the edges of the graph -- such that the resulting representations encode the known factual information represented by the knowledge graph and can be used in the inference of new relations. We show that knowledge graph embedding is naturally expressed in the topological and categorical language of cellular sheaves: a knowledge graph embedding can be described as an approximate global section of an appropriate knowledge sheaf over the graph, with consistency constraints induced by the knowledge graph's schema. This approach provides a generalized framework for reasoning about knowledge graph embedding models and allows for the expression of a wide range of prior constraints on embeddings. Further, the resulting embeddings can be easily adapted for reasoning over composite relations without special training. We implement these ideas to highlight the benefits of the extensions inspired by this new perspective.

Medical information retrieval (MIR) is essential for retrieving relevant medical knowledge from diverse sources, including electronic health records, scientific literature, and medical databases. However, achieving effective zero-shot dense retrieval in the medical domain poses substantial challenges due to the lack of relevance-labeled data. In this paper, we introduce a novel approach called Self-Learning Hypothetical Document Embeddings (SL-HyDE) to tackle this issue. SL-HyDE leverages large language models (LLMs) as generators to generate hypothetical documents based on a given query. These generated documents encapsulate key medical context, guiding a dense retriever in identifying the most relevant documents. The self-learning framework progressively refines both pseudo-document generation and retrieval, utilizing unlabeled medical corpora without requiring any relevance-labeled data. Additionally, we present the Chinese Medical Information Retrieval Benchmark (CMIRB), a comprehensive evaluation framework grounded in real-world medical scenarios, encompassing five tasks and ten datasets. By benchmarking ten models on CMIRB, we establish a rigorous standard for evaluating medical information retrieval systems. Experimental results demonstrate that SL-HyDE significantly surpasses existing methods in retrieval accuracy while showcasing strong generalization and scalability across various LLM and retriever configurations. CMIRB data and evaluation code are publicly available at: https://github.com/CMIRB-benchmark/CMIRB.

In this paper, we introduce Knowledge-Orthogonal Reasoning (KOR), which minimizes the impact of domain-specific knowledge for a more accurate evaluation of models' reasoning abilities in out-of-distribution scenarios. Based on this concept, we propose the Knowledge-Orthogonal Reasoning Benchmark (KOR-Bench), encompassing five task categories: Operation, Logic, Cipher, Puzzle, and Counterfactual. KOR-Bench emphasizes the effectiveness of models in applying new rule descriptions to solve novel rule-driven questions, revealing that top-performing models like Claude-3.5-Sonnet and GPT-4o only achieve 58.96% and 58.00% accuracy, respectively. We conduct thorough analyses to identify bottlenecks in the Cipher task using Stepwise Prompting, discovering that two rounds of Self-Correction yield optimal results. Complex Task Processing evaluates model performance across three integrated tasks, while we also explore the impact of Tricks on the Puzzle task and visualize rule-focused attention to enhance our understanding of model behavior. We aim for KOR-Bench to be a valuable resource for enhancing models' reasoning capabilities and fostering further research in this field.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

Recently, the increasing demand for superior medical services has highlighted the discrepancies in the medical infrastructure. With big data, especially texts, forming the foundation of medical services, there is an exigent need for effective natural language processing (NLP) solutions tailored to the healthcare domain. Conventional approaches leveraging pre-trained models present promising results in this domain and current large language models (LLMs) offer advanced foundation for medical text processing. However, most medical LLMs are trained only with supervised fine-tuning (SFT), even though it efficiently empowers LLMs to understand and respond to medical instructions but is ineffective in learning domain knowledge and aligning with human preference. Another engineering barrier that prevents current medical LLM from better text processing ability is their restricted context length (e.g., 2,048 tokens), making it hard for the LLMs to process long context, which is frequently required in the medical domain. In this work, we propose ChiMed-GPT, a new benchmark LLM designed explicitly for Chinese medical domain, with enlarged context length to 4,096 tokens and undergoes a comprehensive training regime with pre-training, SFT, and RLHF. Evaluations on real-world tasks including information extraction, question answering, and dialogue generation demonstrate ChiMed-GPT's superior performance over general domain LLMs. Furthermore, we analyze possible biases through prompting ChiMed-GPT to perform attitude scales regarding discrimination of patients, so as to contribute to further responsible development of LLMs in the medical domain. The code and model are released at https://github.com/synlp/ChiMed-GPT.

With the increasing availability of structured and unstructured data and the swift progress of analytical techniques, Artificial Intelligence (AI) is bringing a revolution to the healthcare industry. With the increasingly indispensable role of AI in healthcare, there are growing concerns over the lack of transparency and explainability in addition to potential bias encountered by predictions of the model. This is where Explainable Artificial Intelligence (XAI) comes into the picture. XAI increases the trust placed in an AI system by medical practitioners as well as AI researchers, and thus, eventually, leads to an increasingly widespread deployment of AI in healthcare. In this paper, we present different interpretability techniques. The aim is to enlighten practitioners on the understandability and interpretability of explainable AI systems using a variety of techniques available which can be very advantageous in the health-care domain. Medical diagnosis model is responsible for human life and we need to be confident enough to treat a patient as instructed by a black-box model. Our paper contains examples based on the heart disease dataset and elucidates on how the explainability techniques should be preferred to create trustworthiness while using AI systems in healthcare.

Online medical consultation (OMC) restricts doctors to gathering patient information solely through inquiries, making the already complex sequential decision-making process of diagnosis even more challenging. Recently, the rapid advancement of large language models has demonstrated a significant potential to transform OMC. However, most studies have primarily focused on improving diagnostic accuracy under conditions of relatively sufficient information, while paying limited attention to the "inquiry" phase of the consultation process. This lack of focus has left the relationship between "inquiry" and "diagnosis" insufficiently explored. In this paper, we first extract real patient interaction strategies from authentic doctor-patient conversations and use these strategies to guide the training of a patient simulator that closely mirrors real-world behavior. By inputting medical records into our patient simulator to simulate patient responses, we conduct extensive experiments to explore the relationship between "inquiry" and "diagnosis" in the consultation process. Experimental results demonstrate that inquiry and diagnosis adhere to the Liebig's law: poor inquiry quality limits the effectiveness of diagnosis, regardless of diagnostic capability, and vice versa. Furthermore, the experiments reveal significant differences in the inquiry performance of various models. To investigate this phenomenon, we categorize the inquiry process into four types: (1) chief complaint inquiry; (2) specification of known symptoms; (3) inquiry about accompanying symptoms; and (4) gathering family or medical history. We analyze the distribution of inquiries across the four types for different models to explore the reasons behind their significant performance differences. We plan to open-source the weights and related code of our patient simulator at https://github.com/LIO-H-ZEN/PatientSimulator.

Studies have underscored how, regardless of the recent breakthrough and swift advances in AI research, even state-of-the-art Large Language models (LLMs) continue to struggle when performing logical and mathematical reasoning. The results seem to suggest that LLMs still work as (highly advanced) data pattern identifiers, scoring poorly when attempting to generalise and solve reasoning problems the models have never previously seen or that are not close to samples presented in their training data. To address this compelling concern, this paper makes use of the notion of critical questions from the literature on argumentation theory, focusing in particular on Toulmin's model of argumentation. We show that employing these critical questions can improve the reasoning capabilities of LLMs. By probing the rationale behind the models' reasoning process, the LLM can assess whether some logical mistake is occurring and correct it before providing the final reply to the user prompt. The underlying idea is drawn from the gold standard of any valid argumentative procedure: the conclusion is valid if it is entailed by accepted premises. Or, to paraphrase such Aristotelian principle in a real-world approximation, characterised by incomplete information and presumptive logic, the conclusion is valid if not proved otherwise. This approach successfully steers the models' output through a reasoning pipeline, resulting in better performance against the baseline and its Chain-of-Thought (CoT) implementation. To this end, an extensive evaluation of the proposed approach on the MT-Bench Reasoning and Math tasks across a range of LLMs is provided.

Large language models (LLMs) have shown increasing capability in problem-solving and decision-making, largely based on the step-by-step chain-of-thought reasoning processes. However, it has been increasingly challenging to evaluate the reasoning capability of LLMs. Concretely, existing outcome-based benchmarks begin to saturate and become less sufficient to monitor the progress. To this end, we present a process-based benchmark MR-BEN that demands a meta reasoning skill, where LMs are asked to locate and analyse potential errors in automatically generated reasoning steps. MR-BEN is a comprehensive benchmark comprising 5,975 questions collected from human experts, covering various subjects such as physics, chemistry, logic, coding, and more. Through our designed metrics for assessing meta-reasoning on this benchmark, we identify interesting limitations and weaknesses of current LLMs (open-source and closed-source models). For example, open-source models are seemingly comparable to GPT-4 on outcome-based benchmarks, but they lag far behind on our benchmark, revealing the underlying reasoning capability gap between them. Our dataset and codes are available on https://randolph-zeng.github.io/Mr-Ben.github.io/.

The ability to recognize analogies is fundamental to human cognition. Existing benchmarks to test word analogy do not reveal the underneath process of analogical reasoning of neural models. Holding the belief that models capable of reasoning should be right for the right reasons, we propose a first-of-its-kind Explainable Knowledge-intensive Analogical Reasoning benchmark (E-KAR). Our benchmark consists of 1,655 (in Chinese) and 1,251 (in English) problems sourced from the Civil Service Exams, which require intensive background knowledge to solve. More importantly, we design a free-text explanation scheme to explain whether an analogy should be drawn, and manually annotate them for each and every question and candidate answer. Empirical results suggest that this benchmark is very challenging for some state-of-the-art models for both explanation generation and analogical question answering tasks, which invites further research in this area.

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

The emergence of multimodal large models (MLMs) has significantly advanced the field of visual understanding, offering remarkable capabilities in the realm of visual question answering (VQA). Yet, the true challenge lies in the domain of knowledge-intensive VQA tasks, which necessitate not just recognition of visual elements, but also a deep comprehension of the visual information in conjunction with a vast repository of learned knowledge. To uncover such capabilities of MLMs, particularly the newly introduced GPT-4V and Gemini, we provide an in-depth evaluation from three perspectives: 1) Commonsense Knowledge, which assesses how well models can understand visual cues and connect to general knowledge; 2) Fine-grained World Knowledge, which tests the model's skill in reasoning out specific knowledge from images, showcasing their proficiency across various specialized fields; 3) Comprehensive Knowledge with Decision-making Rationales, which examines model's capability to provide logical explanations for its inference, facilitating a deeper analysis from the interpretability perspective. Additionally, we utilize a visual knowledge-enhanced training strategy and multimodal retrieval-augmented generation approach to enhance MLMs, highlighting the future need for advancements in this research direction. Extensive experiments indicate that: a) GPT-4V demonstrates enhanced explanation generation when using composite images as few-shots; b) GPT-4V and other MLMs produce severe hallucinations when dealing with world knowledge; c) Visual knowledge enhanced training and prompting technicals present potential to improve performance. Codes: https://github.com/HITsz-TMG/Cognitive-Visual-Language-Mapper

Language models can store vast amounts of factual knowledge, but their ability to use this knowledge for logical reasoning remains questionable. This paper explores a language model's ability to manipulate its stored knowledge during inference. We focus on four manipulation types: retrieval (e.g., "What is person A's attribute X"), classification (e.g., "Is A's attribute X even or odd?"), comparison (e.g., "Is A greater than B in attribute X?") and inverse search (e.g., "Which person's attribute X equals T?") We observe that pre-trained language models like GPT2/3/4 excel in knowledge retrieval but struggle with simple classification or comparison tasks unless Chain of Thoughts (CoTs) are employed during both training and inference. They also perform poorly in inverse knowledge search, irrespective of the prompts. Our primary contribution is a synthetic dataset for a controlled experiment that confirms these inherent weaknesses: a language model cannot efficiently manipulate knowledge from pre-training data, even when such knowledge is perfectly stored and fully extractable in the models, and despite adequate instruct fine-tuning.

The integration of Large Language Models (LLMs) into healthcare promises to transform medical diagnostics, research, and patient care. Yet, the progression of medical LLMs faces obstacles such as complex training requirements, rigorous evaluation demands, and the dominance of proprietary models that restrict academic exploration. Transparent, comprehensive access to LLM resources is essential for advancing the field, fostering reproducibility, and encouraging innovation in healthcare AI. We present Hippocrates, an open-source LLM framework specifically developed for the medical domain. In stark contrast to previous efforts, it offers unrestricted access to its training datasets, codebase, checkpoints, and evaluation protocols. This open approach is designed to stimulate collaborative research, allowing the community to build upon, refine, and rigorously evaluate medical LLMs within a transparent ecosystem. Also, we introduce Hippo, a family of 7B models tailored for the medical domain, fine-tuned from Mistral and LLaMA2 through continual pre-training, instruction tuning, and reinforcement learning from human and AI feedback. Our models outperform existing open medical LLMs models by a large-margin, even surpassing models with 70B parameters. Through Hippocrates, we aspire to unlock the full potential of LLMs not just to advance medical knowledge and patient care but also to democratize the benefits of AI research in healthcare, making them available across the globe.

Multi-hop logical reasoning is an established problem in the field of representation learning on knowledge graphs (KGs). It subsumes both one-hop link prediction as well as other more complex types of logical queries. Existing algorithms operate only on classical, triple-based graphs, whereas modern KGs often employ a hyper-relational modeling paradigm. In this paradigm, typed edges may have several key-value pairs known as qualifiers that provide fine-grained context for facts. In queries, this context modifies the meaning of relations, and usually reduces the answer set. Hyper-relational queries are often observed in real-world KG applications, and existing approaches for approximate query answering cannot make use of qualifier pairs. In this work, we bridge this gap and extend the multi-hop reasoning problem to hyper-relational KGs allowing to tackle this new type of complex queries. Building upon recent advancements in Graph Neural Networks and query embedding techniques, we study how to embed and answer hyper-relational conjunctive queries. Besides that, we propose a method to answer such queries and demonstrate in our experiments that qualifiers improve query answering on a diverse set of query patterns.

Recent developments, particularly OpenAI's O1 model, have demonstrated the remarkable potential of Large Language Models (LLMs) for complex reasoning tasks. Through analysis of O1's outputs and provided sample Chain-of-Thought (CoT) demonstrations, we observe that it approaches problem-solving in a distinctly human-like manner, systematically brainstorming ideas, testing hypotheses, verifying results, and planning comprehensive solutions. These sophisticated reasoning capabilities remain notably absent in other state-of-the-art language models. In this paper, we hypothesize that this performance gap stems from the limited availability of high-quality reasoning process data in current training sets. We demonstrate that by constructing a specialized dataset focused on explicit problem-solving workflows ("worked solutions"), we can elicit substantially improved planning capabilities from existing models. Additionally, we propose the Reasoning Enhancement Loop (REL), a method for generating synthetic worked solutions.

Large Language Models (LLMs) have demonstrated impressive real-world utility, exemplifying artificial useful intelligence (AUI). However, their ability to reason adaptively and robustly -- the hallmarks of artificial general intelligence (AGI) -- remains fragile. While LLMs seemingly succeed in commonsense reasoning, programming, and mathematics, they struggle to generalize algorithmic understanding across novel contexts. Our experiments with algorithmic tasks in esoteric programming languages reveal that LLM's reasoning overfits to the training data and is limited in its transferability. We hypothesize that the core issue underlying such limited transferability is the coupling of reasoning and knowledge in LLMs. To transition from AUI to AGI, we propose disentangling knowledge and reasoning through three key directions: (1) pretaining to reason using RL from scratch as an alternative to the widely used next-token prediction pretraining, (2) using a curriculum of synthetic tasks to ease the learning of a reasoning prior for RL that can then be transferred to natural language tasks, and (3) learning more generalizable reasoning functions using a small context window to reduce exploiting spurious correlations between tokens. Such a reasoning system coupled with a trained retrieval system and a large external memory bank as a knowledge store can overcome several limitations of existing architectures at learning to reason in novel scenarios.

Analogical reasoning is fundamental to human cognition and holds an important place in various fields. However, previous studies mainly focus on single-modal analogical reasoning and ignore taking advantage of structure knowledge. Notably, the research in cognitive psychology has demonstrated that information from multimodal sources always brings more powerful cognitive transfer than single modality sources. To this end, we introduce the new task of multimodal analogical reasoning over knowledge graphs, which requires multimodal reasoning ability with the help of background knowledge. Specifically, we construct a Multimodal Analogical Reasoning dataSet (MARS) and a multimodal knowledge graph MarKG. We evaluate with multimodal knowledge graph embedding and pre-trained Transformer baselines, illustrating the potential challenges of the proposed task. We further propose a novel model-agnostic Multimodal analogical reasoning framework with Transformer (MarT) motivated by the structure mapping theory, which can obtain better performance. Code and datasets are available in https://github.com/zjunlp/MKG_Analogy.

Mathematical reasoning---a core ability within human intelligence---presents some unique challenges as a domain: we do not come to understand and solve mathematical problems primarily on the back of experience and evidence, but on the basis of inferring, learning, and exploiting laws, axioms, and symbol manipulation rules. In this paper, we present a new challenge for the evaluation (and eventually the design) of neural architectures and similar system, developing a task suite of mathematics problems involving sequential questions and answers in a free-form textual input/output format. The structured nature of the mathematics domain, covering arithmetic, algebra, probability and calculus, enables the construction of training and test splits designed to clearly illuminate the capabilities and failure-modes of different architectures, as well as evaluate their ability to compose and relate knowledge and learned processes. Having described the data generation process and its potential future expansions, we conduct a comprehensive analysis of models from two broad classes of the most powerful sequence-to-sequence architectures and find notable differences in their ability to resolve mathematical problems and generalize their knowledge.

Recently, Chain-of-Thought (CoT) prompting has delivered success on complex reasoning tasks, which aims at designing a simple prompt like ``Let's think step by step'' or multiple in-context exemplars with well-designed rationales to elicit Large Language Models (LLMs) to generate intermediate reasoning steps. However, the generated rationales often come with mistakes, making unfactual and unfaithful reasoning chains. To mitigate this brittleness, we propose a novel Chain-of-Knowledge (CoK) prompting, where we aim at eliciting LLMs to generate explicit pieces of knowledge evidence in the form of structure triple. This is inspired by our human behaviors, i.e., we can draw a mind map or knowledge map as the reasoning evidence in the brain before answering a complex question. Benefiting from CoK, we additionally introduce a F^2-Verification method to estimate the reliability of the reasoning chains in terms of factuality and faithfulness. For the unreliable response, the wrong evidence can be indicated to prompt the LLM to rethink. Extensive experiments demonstrate that our method can further improve the performance of commonsense, factual, symbolic, and arithmetic reasoning tasks.

Large language models (LLMs) have demonstrated remarkable proficiency in understanding and generating responses to complex queries through large-scale pre-training. However, the efficacy of these models in memorizing and reasoning among large-scale structured knowledge, especially world knowledge that explicitly covers abundant factual information remains questionable. Addressing this gap, our research investigates whether LLMs can effectively store, recall, and reason with knowledge on a large scale comparable to latest knowledge bases (KBs) such as Wikidata. Specifically, we focus on three crucial aspects to study the viability: (1) the efficiency of LLMs with different sizes in memorizing the exact knowledge in the large-scale KB; (2) the flexibility of recalling the memorized knowledge in response to natural language queries; (3) the capability to infer new knowledge through reasoning. Our findings indicate that while LLMs hold promise as large-scale KBs capable of retrieving and responding with flexibility, enhancements in their reasoning capabilities are necessary to fully realize their potential.

This paper introduces Typhoon T1, an open effort to develop an open Thai reasoning model. A reasoning model is a relatively new type of generative model built on top of large language models (LLMs). A reasoning model generates a long chain of thought before arriving at a final answer, an approach found to improve performance on complex tasks. However, details on developing such a model are limited, especially for reasoning models that can generate traces in a low-resource language. Typhoon T1 presents an open effort that dives into the details of developing a reasoning model in a more cost-effective way by leveraging supervised fine-tuning using open datasets, instead of reinforcement learning. This paper shares the details about synthetic data generation and training, as well as our dataset and model weights. Additionally, we provide insights gained from developing a reasoning model that generalizes across domains and is capable of generating reasoning traces in a low-resource language, using Thai as an example. We hope this open effort provides a foundation for further research in this field.

Large language models (LLMs) have shown substantial progress in natural language understanding and generation, proving valuable especially in the medical field. Despite advancements, challenges persist due to the complexity and diversity inherent in medical tasks, which can be categorized as knowledge-intensive tasks and alignment-required tasks. Previous approaches either ignore the latter task or focus on a minority of tasks and hence lose generalization. To address these drawbacks, we propose a progressive fine-tuning pipeline. This pipeline employs a Knowledge Aggregator and a Noise aggregator to encode diverse knowledge in the first stage and filter out detrimental information. In the second stage, we drop the Noise Aggregator to avoid the interference of suboptimal representation and leverage an additional alignment module optimized towards an orthogonal direction to the knowledge space to mitigate knowledge forgetting. Based on this two-stage paradigm, we proposed a Medical LLM through decoupling Clinical Alignment and Knowledge Aggregation (MedCare), which is designed to achieve state-of-the-art (SOTA) performance on over 20 medical tasks, as well as SOTA results on specific medical alignment tasks. Various model sizes of MedCare (1.8B, 7B, 14B) all demonstrate significant improvements over existing models with similar model sizes.

Whilst there has been growing progress in Entity Linking (EL) for general language, existing datasets fail to address the complex nature of health terminology in layman's language. Meanwhile, there is a growing need for applications that can understand the public's voice in the health domain. To address this we introduce a new corpus called COMETA, consisting of 20k English biomedical entity mentions from Reddit expert-annotated with links to SNOMED CT, a widely-used medical knowledge graph. Our corpus satisfies a combination of desirable properties, from scale and coverage to diversity and quality, that to the best of our knowledge has not been met by any of the existing resources in the field. Through benchmark experiments on 20 EL baselines from string- to neural-based models we shed light on the ability of these systems to perform complex inference on entities and concepts under 2 challenging evaluation scenarios. Our experimental results on COMETA illustrate that no golden bullet exists and even the best mainstream techniques still have a significant performance gap to fill, while the best solution relies on combining different views of data.

Although contemporary large language models (LMs) demonstrate impressive question-answering capabilities, their answers are typically the product of a single call to the model. This entails an unwelcome degree of opacity and compromises performance, especially on problems that are inherently multi-step. To address these limitations, we show how LMs can be made to perform faithful multi-step reasoning via a process whose causal structure mirrors the underlying logical structure of the problem. Our approach works by chaining together reasoning steps, where each step results from calls to two fine-tuned LMs, one for selection and one for inference, to produce a valid reasoning trace. Our method carries out a beam search through the space of reasoning traces to improve reasoning quality. We demonstrate the effectiveness of our model on multi-step logical deduction and scientific question-answering, showing that it outperforms baselines on final answer accuracy, and generates humanly interpretable reasoning traces whose validity can be checked by the user.

Medical visual question answering (VQA) aims to answer clinically relevant questions regarding input medical images. This technique has the potential to improve the efficiency of medical professionals while relieving the burden on the public health system, particularly in resource-poor countries. Existing medical VQA methods tend to encode medical images and learn the correspondence between visual features and questions without exploiting the spatial, semantic, or medical knowledge behind them. This is partially because of the small size of the current medical VQA dataset, which often includes simple questions. Therefore, we first collected a comprehensive and large-scale medical VQA dataset, focusing on chest X-ray images. The questions involved detailed relationships, such as disease names, locations, levels, and types in our dataset. Based on this dataset, we also propose a novel baseline method by constructing three different relationship graphs: spatial relationship, semantic relationship, and implicit relationship graphs on the image regions, questions, and semantic labels. The answer and graph reasoning paths are learned for different questions.

Medicine is inherently multimodal, with rich data modalities spanning text, imaging, genomics, and more. Generalist biomedical artificial intelligence (AI) systems that flexibly encode, integrate, and interpret this data at scale can potentially enable impactful applications ranging from scientific discovery to care delivery. To enable the development of these models, we first curate MultiMedBench, a new multimodal biomedical benchmark. MultiMedBench encompasses 14 diverse tasks such as medical question answering, mammography and dermatology image interpretation, radiology report generation and summarization, and genomic variant calling. We then introduce Med-PaLM Multimodal (Med-PaLM M), our proof of concept for a generalist biomedical AI system. Med-PaLM M is a large multimodal generative model that flexibly encodes and interprets biomedical data including clinical language, imaging, and genomics with the same set of model weights. Med-PaLM M reaches performance competitive with or exceeding the state of the art on all MultiMedBench tasks, often surpassing specialist models by a wide margin. We also report examples of zero-shot generalization to novel medical concepts and tasks, positive transfer learning across tasks, and emergent zero-shot medical reasoning. To further probe the capabilities and limitations of Med-PaLM M, we conduct a radiologist evaluation of model-generated (and human) chest X-ray reports and observe encouraging performance across model scales. In a side-by-side ranking on 246 retrospective chest X-rays, clinicians express a pairwise preference for Med-PaLM M reports over those produced by radiologists in up to 40.50% of cases, suggesting potential clinical utility. While considerable work is needed to validate these models in real-world use cases, our results represent a milestone towards the development of generalist biomedical AI systems.