Daily Papers

We focus on the problem of species distribution modeling using global-scale presence-only data. Most previous studies have mapped the range of a given species using geographical and environmental features alone. To capture a stronger implicit relationship between species, we encode the taxonomic hierarchy of species using a large language model. This enables range mapping for any taxonomic rank and unseen species without additional supervision. Further, we propose a novel proximity-aware evaluation metric that enables evaluating species distribution models using any pixel-level representation of ground-truth species range map. The proposed metric penalizes the predictions of a model based on its proximity to the ground truth. We describe the effectiveness of our model by systematically evaluating on the task of species range prediction, zero-shot prediction and geo-feature regression against the state-of-the-art. Results show our model outperforms the strong baselines when trained with a variety of multi-label learning losses.

The difficulty of monitoring biodiversity at fine scales and over large areas limits ecological knowledge and conservation efforts. To fill this gap, Species Distribution Models (SDMs) predict species across space from spatially explicit features. Yet, they face the challenge of integrating the rich but heterogeneous data made available over the past decade, notably millions of opportunistic species observations and standardized surveys, as well as multi-modal remote sensing data. In light of that, we have designed and developed a new European-scale dataset for SDMs at high spatial resolution (10-50 m), including more than 10k species (i.e., most of the European flora). The dataset comprises 5M heterogeneous Presence-Only records and 90k exhaustive Presence-Absence survey records, all accompanied by diverse environmental rasters (e.g., elevation, human footprint, and soil) that are traditionally used in SDMs. In addition, it provides Sentinel-2 RGB and NIR satellite images with 10 m resolution, a 20-year time-series of climatic variables, and satellite time-series from the Landsat program. In addition to the data, we provide an openly accessible SDM benchmark (hosted on Kaggle), which has already attracted an active community and a set of strong baselines for single predictor/modality and multimodal approaches. All resources, e.g., the dataset, pre-trained models, and baseline methods (in the form of notebooks), are available on Kaggle, allowing one to start with our dataset literally with two mouse clicks.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

We propose a metadata-aware self-supervised learning~(SSL)~framework useful for fine-grained classification and ecological mapping of bird species around the world. Our framework unifies two SSL strategies: Contrastive Learning~(CL) and Masked Image Modeling~(MIM), while also enriching the embedding space with metadata available with ground-level imagery of birds. We separately train uni-modal and cross-modal ViT on a novel cross-view global bird species dataset containing ground-level imagery, metadata (location, time), and corresponding satellite imagery. We demonstrate that our models learn fine-grained and geographically conditioned features of birds, by evaluating on two downstream tasks: fine-grained visual classification~(FGVC) and cross-modal retrieval. Pre-trained models learned using our framework achieve SotA performance on FGVC of iNAT-2021 birds and in transfer learning settings for CUB-200-2011 and NABirds datasets. Moreover, the impressive cross-modal retrieval performance of our model enables the creation of species distribution maps across any geographic region. The dataset and source code will be released at https://github.com/mvrl/BirdSAT}.

Model uncertainty and limited data are fundamental challenges to robust management of human intervention in a natural system. These challenges are acutely highlighted by concerns that many ecological systems may contain tipping points, such as Allee population sizes. Before a collapse, we do not know where the tipping points lie, if they exist at all. Hence, we know neither a complete model of the system dynamics nor do we have access to data in some large region of state-space where such a tipping point might exist. We illustrate how a Bayesian Non-Parametric (BNP) approach using a Gaussian Process (GP) prior provides a flexible representation of this inherent uncertainty. We embed GPs in a Stochastic Dynamic Programming (SDP) framework in order to make robust management predictions with both model uncertainty and limited data. We use simulations to evaluate this approach as compared with the standard approach of using model selection to choose from a set of candidate models. We find that model selection erroneously favors models without tipping points -- leading to harvest policies that guarantee extinction. The GPDP performs nearly as well as the true model and significantly outperforms standard approaches. We illustrate this using examples of simulated single-species dynamics, where the standard model selection approach should be most effective, and find that it still fails to account for uncertainty appropriately and leads to population crashes, while management based on the GPDP does not, since it does not underestimate the uncertainty outside of the observed data.

Phylogenetic comparative methods may fail to produce meaningful results when either the underlying model is inappropriate or the data contain insufficient information to inform the inference. The ability to measure the statistical power of these methods has become crucial to ensure that data quantity keeps pace with growing model complexity. Through simulations, we show that commonly applied model choice methods based on information criteria can have remarkably high error rates; this can be a problem because methods to estimate the uncertainty or power are not widely known or applied. Furthermore, the power of comparative methods can depend significantly on the structure of the data. We describe a Monte Carlo based method which addresses both of these challenges, and show how this approach both quantifies and substantially reduces errors relative to information criteria. The method also produces meaningful confidence intervals for model parameters. We illustrate how the power to distinguish different models, such as varying levels of selection, varies both with number of taxa and structure of the phylogeny. We provide an open-source implementation in the pmc ("Phylogenetic Monte Carlo") package for the R programming language. We hope such power analysis becomes a routine part of model comparison in comparative methods.

Global climate models typically operate at a grid resolution of hundreds of kilometers and fail to resolve atmospheric mesoscale processes, e.g., clouds, precipitation, and gravity waves (GWs). Model representation of these processes and their sources is essential to the global circulation and planetary energy budget, but subgrid scale contributions from these processes are often only approximately represented in models using parameterizations. These parameterizations are subject to approximations and idealizations, which limit their capability and accuracy. The most drastic of these approximations is the "single-column approximation" which completely neglects the horizontal evolution of these processes, resulting in key biases in current climate models. With a focus on atmospheric GWs, we present the first-ever global simulation of atmospheric GW fluxes using machine learning (ML) models trained on the WINDSET dataset to emulate global GW emulation in the atmosphere, as an alternative to traditional single-column parameterizations. Using an Attention U-Net-based architecture trained on globally resolved GW momentum fluxes, we illustrate the importance and effectiveness of global nonlocality, when simulating GWs using data-driven schemes.

Due to their high predictive performance and flexibility, machine learning models are an appropriate and efficient tool for ecologists. However, implementing a machine learning model is not yet a trivial task and may seem intimidating to ecologists with no previous experience in this area. Here we provide a series of tips to help ecologists in implementing machine learning models. We focus on classification problems as many ecological studies aim to assign data into predefined classes such as ecological states or biological entities. Each of the nine tips identifies a common error, trap or challenge in developing machine learning models and provides recommendations to facilitate their use in ecological studies.

Invasive species in water bodies pose a major threat to the environment and biodiversity globally. Due to increased transportation and trade, non-native species have been introduced to new environments, causing damage to ecosystems and leading to economic losses in agriculture, forestry, and fisheries. Therefore, there is a pressing need for risk assessment and management techniques to mitigate the impact of these invasions. This study aims to develop a new physics-inspired model to forecast maritime shipping traffic and thus inform risk assessment of invasive species spread through global transportation networks. Inspired by the gravity model for international trades, our model considers various factors that influence the likelihood and impact of vessel activities, such as shipping flux density, distance between ports, trade flow, and centrality measures of transportation hubs. Additionally, by analyzing the risk network of invasive species, we provide a comprehensive framework for assessing the invasion threat level given a pair of origin and destination. Accordingly, this paper introduces transformers to gravity models to rebuild the short- and long-term dependencies that make the risk analysis feasible. Thus, we introduce a physics-inspired framework that achieves an 89% segmentation accuracy for existing and non-existing trajectories and an 84.8% accuracy for the number of vessels flowing between key port areas, representing more than 10% improvement over the traditional deep-gravity model. Along these lines, this research contributes to a better understanding of invasive species risk assessment. It allows policymakers, conservationists, and stakeholders to prioritize management actions by identifying high-risk invasion pathways. Besides, our model is versatile and can include new data sources, making it suitable for assessing species invasion risks in a changing global landscape.

Generating diverse responses from large language models (LLMs) is crucial for applications such as planning/search and synthetic data generation, where diversity provides distinct answers across generations. Prior approaches rely on increasing temperature to increase diversity. However, contrary to popular belief, we show not only does this approach produce lower quality individual generations as temperature increases, but it depends on model's next-token probabilities being similar to the true distribution of answers. We propose , an alternative approach that uses the language model itself to partition the space into strata. At inference, a random stratum is selected and a sample drawn from within the strata. To measure diversity, we introduce CoverageQA, a dataset of underspecified questions with multiple equally plausible answers, and assess diversity by measuring KL Divergence between the output distribution and uniform distribution over valid ground truth answers. As computing probability per response/solution for proprietary models is infeasible, we measure recall on ground truth solutions. Our evaluation show using SimpleStrat achieves higher recall by 0.05 compared to GPT-4o and 0.36 average reduction in KL Divergence compared to Llama 3.

The rise of accurate machine learning methods for weather forecasting is creating radical new possibilities for modeling the atmosphere. In the time of climate change, having access to high-resolution forecasts from models like these is also becoming increasingly vital. While most existing Neural Weather Prediction (NeurWP) methods focus on global forecasting, an important question is how these techniques can be applied to limited area modeling. In this work we adapt the graph-based NeurWP approach to the limited area setting and propose a multi-scale hierarchical model extension. Our approach is validated by experiments with a local model for the Nordic region.

Global climate models (GCMs) are the main tools for understanding and predicting climate change. However, due to limited numerical resolutions, these models suffer from major structural uncertainties; e.g., they cannot resolve critical processes such as small-scale eddies in atmospheric and oceanic turbulence. Thus, such small-scale processes have to be represented as a function of the resolved scales via closures (parametrization). The accuracy of these closures is particularly important for capturing climate extremes. Traditionally, such closures are based on heuristics and simplifying assumptions about the unresolved physics. Recently, supervised-learned closures, trained offline on high-fidelity data, have been shown to outperform the classical physics-based closures. However, this approach requires a significant amount of high-fidelity training data and can also lead to instabilities. Reinforcement learning is emerging as a potent alternative for developing such closures as it requires only low-order statistics and leads to stable closures. In Scientific Multi-Agent Reinforcement Learning (SMARL) computational elements serve a dual role of discretization points and learning agents. We leverage SMARL and fundamentals of turbulence physics to learn closures for prototypes of atmospheric and oceanic turbulence. The policy is trained using only the enstrophy spectrum, which is nearly invariant and can be estimated from a few high-fidelity samples (these few samples are far from enough for supervised/offline learning). We show that these closures lead to stable low-resolution simulations that, at a fraction of the cost, can reproduce the high-fidelity simulations' statistics, including the tails of the probability density functions. The results demonstrate the high potential of SMARL for closure modeling for GCMs, especially in the regime of scarce data and indirect observations.

From crop mapping to flood detection, machine learning in remote sensing has a wide range of societally beneficial applications. The commonalities between remote sensing data in these applications present an opportunity for pretrained machine learning models tailored to remote sensing to reduce the labeled data and effort required to solve individual tasks. However, such models must be: (i) flexible enough to ingest input data of varying sensor modalities and shapes (i.e., of varying spatial and temporal dimensions), and (ii) able to model Earth surface phenomena of varying scales and types. To solve this gap, we present Galileo, a family of pretrained remote sensing models designed to flexibly process multimodal remote sensing data. We also introduce a novel and highly effective self-supervised learning approach to learn both large- and small-scale features, a challenge not addressed by previous models. Our Galileo models obtain state-of-the-art results across diverse remote sensing tasks.

Understanding the world and explaining it with scientific theories is a central aspiration of artificial intelligence research. Proposing theories, designing experiments to test them, and then revising them based on data are fundamental to scientific discovery. Despite the significant promise of LLM-based scientific agents, no benchmarks systematically test LLM's ability to propose scientific models, collect experimental data, and revise them in light of new data. We introduce BoxingGym, a benchmark with 10 environments for systematically evaluating both experimental design (e.g. collecting data to test a scientific theory) and model discovery (e.g. proposing and revising scientific theories). To enable tractable and quantitative evaluation, we implement each environment as a generative probabilistic model with which a scientific agent can run interactive experiments. These probabilistic models are drawn from various real-world scientific domains ranging from psychology to ecology. To quantitatively evaluate a scientific agent's ability to collect informative experimental data, we compute the expected information gain (EIG), an information-theoretic quantity which measures how much an experiment reduces uncertainty about the parameters of a generative model. A good scientific theory is a concise and predictive explanation. Therefore, to quantitatively evaluate model discovery, we ask a scientific agent to explain their model and then assess whether this explanation enables another scientific agent to make reliable predictions about this environment. In addition to this explanation-based evaluation, we compute standard model evaluation metrics such as prediction errors. We find that current LLMs, such as GPT-4o, struggle with both experimental design and model discovery. We find that augmenting the LLM-based agent with an explicit statistical model does not reliably improve these results.

Air pollution constitutes a global problem of paramount importance that affects not only human health, but also the environment. The existence of spatial and temporal data regarding the concentrations of pollutants is crucial for performing air pollution studies and monitor emissions. However, although observation data presents great temporal coverage, the number of stations is very limited and they are usually built in more populated areas. The main objective of this work is to create models capable of inferring pollutant concentrations in locations where no observation data exists. A machine learning model, more specifically the random forest model, was developed for predicting concentrations in the Iberian Peninsula in 2019 for five selected pollutants: NO_2, O_3 SO_2, PM10, and PM2.5. Model features include satellite measurements, meteorological variables, land use classification, temporal variables (month, day of year), and spatial variables (latitude, longitude, altitude). The models were evaluated using various methods, including station 10-fold cross-validation, in which in each fold observations from 10\% of the stations are used as testing data and the rest as training data. The R^2, RMSE and mean bias were determined for each model. The NO_2 and O_3 models presented good values of R^2, 0.5524 and 0.7462, respectively. However, the SO_2, PM10, and PM2.5 models performed very poorly in this regard, with R^2 values of -0.0231, 0.3722, and 0.3303, respectively. All models slightly overestimated the ground concentrations, except the O_3 model. All models presented acceptable cross-validation RMSE, except the O_3 and PM10 models where the mean value was a little higher (12.5934 mu g/m^3 and 10.4737 mu g/m^3, respectively).

Earth system models suffer from various structural and parametric errors in their representation of nonlinear, multi-scale processes, leading to uncertainties in their long-term projections. The effects of many of these errors (particularly those due to fast physics) can be quantified in short-term simulations, e.g., as differences between the predicted and observed states (analysis increments). With the increase in the availability of high-quality observations and simulations, learning nudging from these increments to correct model errors has become an active research area. However, most studies focus on using neural networks, which while powerful, are hard to interpret, are data-hungry, and poorly generalize out-of-distribution. Here, we show the capabilities of Model Error Discovery with Interpretability and Data Assimilation (MEDIDA), a general, data-efficient framework that uses sparsity-promoting equation-discovery techniques to learn model errors from analysis increments. Using two-layer quasi-geostrophic turbulence as the test case, MEDIDA is shown to successfully discover various linear and nonlinear structural/parametric errors when full observations are available. Discovery from spatially sparse observations is found to require highly accurate interpolation schemes. While NNs have shown success as interpolators in recent studies, here, they are found inadequate due to their inability to accurately represent small scales, a phenomenon known as spectral bias. We show that a general remedy, adding a random Fourier feature layer to the NN, resolves this issue enabling MEDIDA to successfully discover model errors from sparse observations. These promising results suggest that with further development, MEDIDA could be scaled up to models of the Earth system and real observations.

Motivation The genotype assignment problem consists of predicting, from the genotype of an individual, which of a known set of populations it originated from. The problem arises in a variety of contexts, including wildlife forensics, invasive species detection and biodiversity monitoring. Existing approaches perform well under ideal conditions but are sensitive to a variety of common violations of the assumptions they rely on. Results In this article, we introduce Mycorrhiza, a machine learning approach for the genotype assignment problem. Our algorithm makes use of phylogenetic networks to engineer features that encode the evolutionary relationships among samples. Those features are then used as input to a Random Forests classifier. The classification accuracy was assessed on multiple published empirical SNP, microsatellite or consensus sequence datasets with wide ranges of size, geographical distribution and population structure and on simulated datasets. It compared favorably against widely used assessment tests or mixture analysis methods such as STRUCTURE and Admixture, and against another machine-learning based approach using principal component analysis for dimensionality reduction. Mycorrhiza yields particularly significant gains on datasets with a large average fixation index (FST) or deviation from the Hardy-Weinberg equilibrium. Moreover, the phylogenetic network approach estimates mixture proportions with good accuracy.

The objective of this study is to evaluate the potential for History Matching (HM) to tune a climate system with multi-scale dynamics. By considering a toy climate model, namely, the two-scale Lorenz96 model and producing experiments in perfect-model setting, we explore in detail how several built-in choices need to be carefully tested. We also demonstrate the importance of introducing physical expertise in the range of parameters, a priori to running HM. Finally we revisit a classical procedure in climate model tuning, that consists of tuning the slow and fast components separately. By doing so in the Lorenz96 model, we illustrate the non-uniqueness of plausible parameters and highlight the specificity of metrics emerging from the coupling. This paper contributes also to bridging the communities of uncertainty quantification, machine learning and climate modeling, by making connections between the terms used by each community for the same concept and presenting promising collaboration avenues that would benefit climate modeling research.

This paper introduces ClimateGPT, a model family of domain-specific large language models that synthesize interdisciplinary research on climate change. We trained two 7B models from scratch on a science-oriented dataset of 300B tokens. For the first model, the 4.2B domain-specific tokens were included during pre-training and the second was adapted to the climate domain after pre-training. Additionally, ClimateGPT-7B, 13B and 70B are continuously pre-trained from Llama~2 on a domain-specific dataset of 4.2B tokens. Each model is instruction fine-tuned on a high-quality and human-generated domain-specific dataset that has been created in close cooperation with climate scientists. To reduce the number of hallucinations, we optimize the model for retrieval augmentation and propose a hierarchical retrieval strategy. To increase the accessibility of our model to non-English speakers, we propose to make use of cascaded machine translation and show that this approach can perform comparably to natively multilingual models while being easier to scale to a large number of languages. Further, to address the intrinsic interdisciplinary aspect of climate change we consider different research perspectives. Therefore, the model can produce in-depth answers focusing on different perspectives in addition to an overall answer. We propose a suite of automatic climate-specific benchmarks to evaluate LLMs. On these benchmarks, ClimateGPT-7B performs on par with the ten times larger Llama-2-70B Chat model while not degrading results on general domain benchmarks. Our human evaluation confirms the trends we saw in our benchmarks. All models were trained and evaluated using renewable energy and are released publicly.

A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of large-scale image repositories in biology and recent advances in generative modeling, there is an opportunity to accelerate the discovery of evolutionary traits automatically from images. Toward this goal, we introduce Phylo-Diffusion, a novel framework for conditioning diffusion models with phylogenetic knowledge represented in the form of HIERarchical Embeddings (HIER-Embeds). We also propose two new experiments for perturbing the embedding space of Phylo-Diffusion: trait masking and trait swapping, inspired by counterpart experiments of gene knockout and gene editing/swapping. Our work represents a novel methodological advance in generative modeling to structure the embedding space of diffusion models using tree-based knowledge. Our work also opens a new chapter of research in evolutionary biology by using generative models to visualize evolutionary changes directly from images. We empirically demonstrate the usefulness of Phylo-Diffusion in capturing meaningful trait variations for fishes and birds, revealing novel insights about the biological mechanisms of their evolution.

Figuring out which Pre-Trained Model (PTM) from a model zoo fits the target task is essential to take advantage of plentiful model resources. With the availability of numerous heterogeneous PTMs from diverse fields, efficiently selecting the most suitable PTM is challenging due to the time-consuming costs of carrying out forward or backward passes over all PTMs. In this paper, we propose Model Spider, which tokenizes both PTMs and tasks by summarizing their characteristics into vectors to enable efficient PTM selection. By leveraging the approximated performance of PTMs on a separate set of training tasks, Model Spider learns to construct tokens and measure the fitness score between a model-task pair via their tokens. The ability to rank relevant PTMs higher than others generalizes to new tasks. With the top-ranked PTM candidates, we further learn to enrich task tokens with their PTM-specific semantics to re-rank the PTMs for better selection. Model Spider balances efficiency and selection ability, making PTM selection like a spider preying on a web. Model Spider demonstrates promising performance in various configurations of model zoos.

Full-complexity Earth system models (ESMs) are computationally very expensive, limiting their use in exploring the climate outcomes of multiple emission pathways. More efficient emulators that approximate ESMs can directly map emissions onto climate outcomes, and benchmarks are being used to evaluate their accuracy on standardized tasks and datasets. We investigate a popular benchmark in data-driven climate emulation, ClimateBench, on which deep learning-based emulators are currently achieving the best performance. We implement a linear regression-based emulator, akin to pattern scaling, and find that it outperforms the incumbent 100M-parameter deep learning foundation model, ClimaX, on 3 out of 4 regionally-resolved surface-level climate variables. While emulating surface temperature is expected to be predominantly linear, this result is surprising for emulating precipitation. We identify that this outcome is a result of high levels of internal variability in the benchmark targets. To address internal variability, we update the benchmark targets with ensemble averages from the MPI-ESM1.2-LR model that contain 50 instead of 3 climate simulations per emission pathway. Using the new targets, we show that linear pattern scaling continues to be more accurate on temperature, but can be outperformed by a deep learning-based model for emulating precipitation. We publish our code, data, and an interactive tutorial at github.com/blutjens/climate-emulator.

This paper introduces PhyloLM, a method adapting phylogenetic algorithms to Large Language Models (LLMs) to explore whether and how they relate to each other and to predict their performance characteristics. Our method calculates a phylogenetic distance metrics based on the similarity of LLMs' output. The resulting metric is then used to construct dendrograms, which satisfactorily capture known relationships across a set of 111 open-source and 45 closed models. Furthermore, our phylogenetic distance predicts performance in standard benchmarks, thus demonstrating its functional validity and paving the way for a time and cost-effective estimation of LLM capabilities. To sum up, by translating population genetic concepts to machine learning, we propose and validate a tool to evaluate LLM development, relationships and capabilities, even in the absence of transparent training information.

A data-driven model (DDM) suitable for regional weather forecasting applications is presented. The model extends the Artificial Intelligence Forecasting System by introducing a stretched-grid architecture that dedicates higher resolution over a regional area of interest and maintains a lower resolution elsewhere on the globe. The model is based on graph neural networks, which naturally affords arbitrary multi-resolution grid configurations. The model is applied to short-range weather prediction for the Nordics, producing forecasts at 2.5 km spatial and 6 h temporal resolution. The model is pre-trained on 43 years of global ERA5 data at 31 km resolution and is further refined using 3.3 years of 2.5 km resolution operational analyses from the MetCoOp Ensemble Prediction System (MEPS). The performance of the model is evaluated using surface observations from measurement stations across Norway and is compared to short-range weather forecasts from MEPS. The DDM outperforms both the control run and the ensemble mean of MEPS for 2 m temperature. The model also produces competitive precipitation and wind speed forecasts, but is shown to underestimate extreme events.

Agent-based modeling (ABM) seeks to understand the behavior of complex systems by simulating a collection of agents that act and interact within an environment. Their practical utility requires capturing realistic environment dynamics and adaptive agent behavior while efficiently simulating million-size populations. Recent advancements in large language models (LLMs) present an opportunity to enhance ABMs by using LLMs as agents with further potential to capture adaptive behavior. However, the computational infeasibility of using LLMs for large populations has hindered their widespread adoption. In this paper, we introduce AgentTorch -- a framework that scales ABMs to millions of agents while capturing high-resolution agent behavior using LLMs. We benchmark the utility of LLMs as ABM agents, exploring the trade-off between simulation scale and individual agency. Using the COVID-19 pandemic as a case study, we demonstrate how AgentTorch can simulate 8.4 million agents representing New York City, capturing the impact of isolation and employment behavior on health and economic outcomes. We compare the performance of different agent architectures based on heuristic and LLM agents in predicting disease waves and unemployment rates. Furthermore, we showcase AgentTorch's capabilities for retrospective, counterfactual, and prospective analyses, highlighting how adaptive agent behavior can help overcome the limitations of historical data in policy design. AgentTorch is an open-source project actively being used for policy-making and scientific discovery around the world. The framework is available here: github.com/AgentTorch/AgentTorch.

Climate models have been key for assessing the impact of climate change and simulating future climate scenarios. The machine learning (ML) community has taken an increased interest in supporting climate scientists' efforts on various tasks such as climate model emulation, downscaling, and prediction tasks. Many of those tasks have been addressed on datasets created with single climate models. However, both the climate science and ML communities have suggested that to address those tasks at scale, we need large, consistent, and ML-ready climate model datasets. Here, we introduce ClimateSet, a dataset containing the inputs and outputs of 36 climate models from the Input4MIPs and CMIP6 archives. In addition, we provide a modular dataset pipeline for retrieving and preprocessing additional climate models and scenarios. We showcase the potential of our dataset by using it as a benchmark for ML-based climate model emulation. We gain new insights about the performance and generalization capabilities of the different ML models by analyzing their performance across different climate models. Furthermore, the dataset can be used to train an ML emulator on several climate models instead of just one. Such a "super emulator" can quickly project new climate change scenarios, complementing existing scenarios already provided to policymakers. We believe ClimateSet will create the basis needed for the ML community to tackle climate-related tasks at scale.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Diffusion models have emerged as a powerful new family of deep generative models with record-breaking performance in many applications, including image synthesis, video generation, and molecule design. In this survey, we provide an overview of the rapidly expanding body of work on diffusion models, categorizing the research into three key areas: efficient sampling, improved likelihood estimation, and handling data with special structures. We also discuss the potential for combining diffusion models with other generative models for enhanced results. We further review the wide-ranging applications of diffusion models in fields spanning from computer vision, natural language generation, temporal data modeling, to interdisciplinary applications in other scientific disciplines. This survey aims to provide a contextualized, in-depth look at the state of diffusion models, identifying the key areas of focus and pointing to potential areas for further exploration. Github: https://github.com/YangLing0818/Diffusion-Models-Papers-Survey-Taxonomy.

As Artificial Intelligence (AI) has developed rapidly over the past few decades, the new generation of AI, Large Language Models (LLMs) trained on massive datasets, has achieved ground-breaking performance in many applications. Further progress has been made in multimodal LLMs, with many datasets created to evaluate LLMs with vision abilities. However, none of those datasets focuses solely on marine mammals, which are indispensable for ecological equilibrium. In this work, we build a benchmark dataset with 1,423 images of 65 kinds of marine mammals, where each animal is uniquely classified into different levels of class, ranging from species-level to medium-level to group-level. Moreover, we evaluate several approaches for classifying these marine mammals: (1) machine learning (ML) algorithms using embeddings provided by neural networks, (2) influential pre-trained neural networks, (3) zero-shot models: CLIP and LLMs, and (4) a novel LLM-based multi-agent system (MAS). The results demonstrate the strengths of traditional models and LLMs in different aspects, and the MAS can further improve the classification performance. The dataset is available on GitHub: https://github.com/yeyimilk/LLM-Vision-Marine-Animals.git.

We introduce Arboretum, the largest publicly accessible dataset designed to advance AI for biodiversity applications. This dataset, curated from the iNaturalist community science platform and vetted by domain experts to ensure accuracy, includes 134.6 million images, surpassing existing datasets in scale by an order of magnitude. The dataset encompasses image-language paired data for a diverse set of species from birds (Aves), spiders/ticks/mites (Arachnida), insects (Insecta), plants (Plantae), fungus/mushrooms (Fungi), snails (Mollusca), and snakes/lizards (Reptilia), making it a valuable resource for multimodal vision-language AI models for biodiversity assessment and agriculture research. Each image is annotated with scientific names, taxonomic details, and common names, enhancing the robustness of AI model training. We showcase the value of Arboretum by releasing a suite of CLIP models trained using a subset of 40 million captioned images. We introduce several new benchmarks for rigorous assessment, report accuracy for zero-shot learning, and evaluations across life stages, rare species, confounding species, and various levels of the taxonomic hierarchy. We anticipate that Arboretum will spur the development of AI models that can enable a variety of digital tools ranging from pest control strategies, crop monitoring, and worldwide biodiversity assessment and environmental conservation. These advancements are critical for ensuring food security, preserving ecosystems, and mitigating the impacts of climate change. Arboretum is publicly available, easily accessible, and ready for immediate use. Please see the https://baskargroup.github.io/Arboretum/{project website} for links to our data, models, and code.

With the success of machine learning (ML) applied to climate reaching further every day, emulators have begun to show promise not only for weather but for multi-year time scales in the atmosphere. Similar work for the ocean remains nascent, with state-of-the-art limited to models running for shorter time scales or only for regions of the globe. In this work, we demonstrate high-skill global emulation for surface ocean fields over 5-8 years of model rollout, accurately representing modes of variability for two different ML architectures (ConvNext and Transformers). In addition, we address the outstanding question of generalization, an essential consideration if the end-use of emulation is to model warming scenarios outside of the model training data. We show that 1) generalization is not an intrinsic feature of a data-driven emulator, 2) fine-tuning the emulator on only small amounts of additional data from a distribution similar to the test set can enable the emulator to perform well in a warmed climate, and 3) the forced emulators are robust to noise in the forcing.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

Data-driven deep learning models are transforming global weather forecasting. It is an open question if this success can extend to climate modeling, where the complexity of the data and long inference rollouts pose significant challenges. Here, we present the first conditional generative model that produces accurate and physically consistent global climate ensemble simulations by emulating a coarse version of the United States' primary operational global forecast model, FV3GFS. Our model integrates the dynamics-informed diffusion framework (DYffusion) with the Spherical Fourier Neural Operator (SFNO) architecture, enabling stable 100-year simulations at 6-hourly timesteps while maintaining low computational overhead compared to single-step deterministic baselines. The model achieves near gold-standard performance for climate model emulation, outperforming existing approaches and demonstrating promising ensemble skill. This work represents a significant advance towards efficient, data-driven climate simulations that can enhance our understanding of the climate system and inform adaptation strategies.

Triggered by the realization that AI emulators can rival the performance of traditional numerical weather prediction models running on HPC systems, there is now an increasing number of large AI models that address use cases such as forecasting, downscaling, or nowcasting. While the parallel developments in the AI literature focus on foundation models -- models that can be effectively tuned to address multiple, different use cases -- the developments on the weather and climate side largely focus on single-use cases with particular emphasis on mid-range forecasting. We close this gap by introducing Prithvi WxC, a 2.3 billion parameter foundation model developed using 160 variables from the Modern-Era Retrospective Analysis for Research and Applications, Version 2 (MERRA-2). Prithvi WxC employs an encoder-decoder-based architecture, incorporating concepts from various recent transformer models to effectively capture both regional and global dependencies in the input data. The model has been designed to accommodate large token counts to model weather phenomena in different topologies at fine resolutions. Furthermore, it is trained with a mixed objective that combines the paradigms of masked reconstruction with forecasting. We test the model on a set of challenging downstream tasks namely: Autoregressive rollout forecasting, Downscaling, Gravity wave flux parameterization, and Extreme events estimation. The pretrained model with 2.3 billion parameters, along with the associated fine-tuning workflows, has been publicly released as an open-source contribution via Hugging Face.

Many social and environmental phenomena are associated with macroscopic changes in the built environment, captured by satellite imagery on a global scale and with daily temporal resolution. While widely used for prediction, these images and especially image sequences remain underutilized for causal inference, especially in the context of randomized controlled trials (RCTs), where causal identification is established by design. In this paper, we develop and compare a set of general tools for analyzing Conditional Average Treatment Effects (CATEs) from temporal satellite data that can be applied to any RCT where geographical identifiers are available. Through a simulation study, we analyze different modeling strategies for estimating CATE in sequences of satellite images. We find that image sequence representation models with more parameters generally yield a greater ability to detect heterogeneity. To explore the role of model and data choice in practice, we apply the approaches to two influential RCTs -- Banerjee et al. (2015), a poverty study in Cusco, Peru, and Bolsen et al. (2014), a water conservation experiment in Georgia, USA. We benchmark our image sequence models against image-only, tabular-only, and combined image-tabular data sources, summarizing practical implications for investigators in a multivariate analysis. Land cover classifications over satellite images facilitate interpretation of what image features drive heterogeneity. We also show robustness to data and model choice of satellite-based generalization of the RCT results to larger geographical areas outside the original. Overall, this paper shows how satellite sequence data can be incorporated into the analysis of RCTs, and provides evidence about the implications of data, model, and evaluation metric choice for causal analysis.

Climate change poses an urgent global threat, needing the rapid identification and deployment of innovative solutions. We hypothesise that many of these solutions already exist within scientific literature but remain underutilised. To address this gap, this study employs a curated dataset sourced from OpenAlex, a comprehensive repository of scientific papers. Utilising Large Language Models (LLMs), such as GPT4-o from OpenAI, we evaluate title-abstract pairs from scientific papers on seven dimensions, covering climate change mitigation potential, stage of technological development, and readiness for deployment. The outputs of the language models are then compared with human evaluations to assess their effectiveness in identifying promising yet overlooked climate innovations. Our findings suggest that these LLM-based models can effectively augment human expertise, uncovering climate solutions that are potentially impactful but with far greater speed, throughput and consistency. Here, we focused on UK-based solutions, but the workflow is region-agnostic. This work contributes to the discovery of neglected innovations in scientific literature and demonstrates the potential of AI in enhancing climate action strategies.

Modeling weather and climate is an essential endeavor to understand the near- and long-term impacts of climate change, as well as inform technology and policymaking for adaptation and mitigation efforts. In recent years, there has been a surging interest in applying data-driven methods based on machine learning for solving core problems such as weather forecasting and climate downscaling. Despite promising results, much of this progress has been impaired due to the lack of large-scale, open-source efforts for reproducibility, resulting in the use of inconsistent or underspecified datasets, training setups, and evaluations by both domain scientists and artificial intelligence researchers. We introduce ClimateLearn, an open-source PyTorch library that vastly simplifies the training and evaluation of machine learning models for data-driven climate science. ClimateLearn consists of holistic pipelines for dataset processing (e.g., ERA5, CMIP6, PRISM), implementation of state-of-the-art deep learning models (e.g., Transformers, ResNets), and quantitative and qualitative evaluation for standard weather and climate modeling tasks. We supplement these functionalities with extensive documentation, contribution guides, and quickstart tutorials to expand access and promote community growth. We have also performed comprehensive forecasting and downscaling experiments to showcase the capabilities and key features of our library. To our knowledge, ClimateLearn is the first large-scale, open-source effort for bridging research in weather and climate modeling with modern machine learning systems. Our library is available publicly at https://github.com/aditya-grover/climate-learn.

Score-based generative models (SGMs) are a powerful class of generative models that exhibit remarkable empirical performance. Score-based generative modelling (SGM) consists of a ``noising'' stage, whereby a diffusion is used to gradually add Gaussian noise to data, and a generative model, which entails a ``denoising'' process defined by approximating the time-reversal of the diffusion. Existing SGMs assume that data is supported on a Euclidean space, i.e. a manifold with flat geometry. In many domains such as robotics, geoscience or protein modelling, data is often naturally described by distributions living on Riemannian manifolds and current SGM techniques are not appropriate. We introduce here Riemannian Score-based Generative Models (RSGMs), a class of generative models extending SGMs to Riemannian manifolds. We demonstrate our approach on a variety of manifolds, and in particular with earth and climate science spherical data.

Diffusion models are a class of probabilistic generative models that have been widely used as a prior for image processing tasks like text conditional generation and inpainting. We demonstrate that these models can be adapted to make predictions and provide uncertainty quantification for chaotic dynamical systems. In these applications, diffusion models can implicitly represent knowledge about outliers and extreme events; however, querying that knowledge through conditional sampling or measuring probabilities is surprisingly difficult. Existing methods for conditional sampling at inference time seek mainly to enforce the constraints, which is insufficient to match the statistics of the distribution or compute the probability of the chosen events. To achieve these ends, optimally one would use the conditional score function, but its computation is typically intractable. In this work, we develop a probabilistic approximation scheme for the conditional score function which provably converges to the true distribution as the noise level decreases. With this scheme we are able to sample conditionally on nonlinear userdefined events at inference time, and matches data statistics even when sampling from the tails of the distribution.

Ocean scientists have been collecting visual data to study marine organisms for decades. These images and videos are extremely valuable both for basic science and environmental monitoring tasks. There are tools for automatically processing these data, but none that are capable of handling the extreme variability in sample populations, image quality, and habitat characteristics that are common in visual sampling of the ocean. Such distribution shifts can occur over very short physical distances and in narrow time windows. Creating models that are able to recognize when an image or video sequence contains a new organism, an unusual collection of animals, or is otherwise out-of-sample is critical to fully leverage visual data in the ocean. The FathomNet2023 competition dataset presents a realistic scenario where the set of animals in the target data differs from the training data. The challenge is both to identify the organisms in a target image and assess whether it is out-of-sample.

Temperature scaling is a popular technique for tuning the sharpness of a model distribution. It is used extensively for sampling likely generations and calibrating model uncertainty, and even features as a controllable parameter to many large language models in deployment. However, autoregressive models rely on myopic temperature scaling that greedily optimizes the next token. To address this, we propose Long Horizon Temperature Scaling (LHTS), a novel approach for sampling from temperature-scaled joint distributions. LHTS is compatible with all likelihood-based models, and optimizes for the long-horizon likelihood of samples. We derive a temperature-dependent LHTS objective, and show that fine-tuning a model on a range of temperatures produces a single model capable of generation with a controllable long-horizon temperature parameter. We experiment with LHTS on image diffusion models and character/language autoregressive models, demonstrating advantages over myopic temperature scaling in likelihood and sample quality, and showing improvements in accuracy on a multiple choice analogy task by 10%.

Language models (LMs) are increasingly used as simulacra for people, yet their ability to match the distribution of views of a specific demographic group and be distributionally aligned remains uncertain. This notion of distributional alignment is complex, as there is significant variation in the types of attributes that are simulated. Prior works have underexplored the role of three critical variables -- the question domain, steering method, and distribution expression method -- which motivates our contribution of a benchmark explicitly addressing these dimensions. We construct a dataset expanding beyond political values, create human baselines for this task, and evaluate the extent to which an LM can align with a particular group's opinion distribution to inform design choices of such simulation systems. Our analysis reveals open problems regarding if, and how, LMs can be used to simulate humans, and that LLMs can more accurately describe the opinion distribution than simulate such distributions.

This study explores strategies for efficiently classifying scientific full texts using both small, BERT-based models and local large language models like Llama-3.1 8B. We focus on developing methods for selecting subsets of input sentences to reduce input size while simultaneously enhancing classification performance. To this end, we compile a novel dataset consisting of full-text scientific papers from the field of invasion biology, specifically addressing the impacts of invasive species. These papers are aligned with publicly available impact assessments created by researchers for the International Union for Conservation of Nature (IUCN). Through extensive experimentation, we demonstrate that various sources like human evidence annotations, LLM-generated annotations or explainability scores can be used to train sentence selection models that improve the performance of both encoder- and decoder-based language models while optimizing efficiency through the reduction in input length, leading to improved results even if compared to models like ModernBERT that are able to handle the complete text as input. Additionally, we find that repeated sampling of shorter inputs proves to be a very effective strategy that, at a slightly increased cost, can further improve classification performance.

Global solar photospheric magnetic maps play a critical role in solar and heliospheric physics research. Routine magnetograph measurements of the field occur only along the Sun-Earth line, leaving the far-side of the Sun unobserved. Surface Flux Transport (SFT) models attempt to mitigate this by modeling the surface evolution of the field. While such models have long been established in the community (with several releasing public full-Sun maps), none are open source. The Open Source Flux Transport (OFT) model seeks to fill this gap by providing an open and user-extensible SFT model that also builds on the knowledge of previous models with updated numerical and data acquisition/assimilation methods along with additional user-defined features. In this first of a series of papers on OFT, we introduce its computational core: the High-performance Flux Transport (HipFT) code (github.com/predsci/hipft). HipFT implements advection, diffusion, and data assimilation in a modular design that supports a variety of flow models and options. It can compute multiple realizations in a single run across model parameters to create ensembles of maps for uncertainty quantification and is high-performance through the use of multi-CPU and multi-GPU parallelism. HipFT is designed to enable users to easily write extensions, enhancing its flexibility and adaptability. We describe HipFT's model features, validations of its numerical methods, performance of its parallel and GPU-accelerated code implementation, analysis/post-processing options, and example use cases.

The advancement of Large Language Models (LLMs) for domain applications in fields such as materials science and engineering depends on the development of fine-tuning strategies that adapt models for specialized, technical capabilities. In this work, we explore the effects of Continued Pretraining (CPT), Supervised Fine-Tuning (SFT), and various preference-based optimization approaches, including Direct Preference Optimization (DPO) and Odds Ratio Preference Optimization (ORPO), on fine-tuned LLM performance. Our analysis shows how these strategies influence model outcomes and reveals that the merging of multiple fine-tuned models can lead to the emergence of capabilities that surpass the individual contributions of the parent models. We find that model merging leads to new functionalities that neither parent model could achieve alone, leading to improved performance in domain-specific assessments. Experiments with different model architectures are presented, including Llama 3.1 8B and Mistral 7B models, where similar behaviors are observed. Exploring whether the results hold also for much smaller models, we use a tiny LLM with 1.7 billion parameters and show that very small LLMs do not necessarily feature emergent capabilities under model merging, suggesting that model scaling may be a key component. In open-ended yet consistent chat conversations between a human and AI models, our assessment reveals detailed insights into how different model variants perform and show that the smallest model achieves a high intelligence score across key criteria including reasoning depth, creativity, clarity, and quantitative precision. Other experiments include the development of image generation prompts based on disparate biological material design concepts, to create new microstructures, architectural concepts, and urban design based on biological materials-inspired construction principles.

Recent work has highlighted the complex influence training hyperparameters, e.g., the number of training epochs, can have on the prunability of machine learning models. Perhaps surprisingly, a systematic approach to predict precisely how adjusting a specific hyperparameter will affect prunability remains elusive. To address this gap, we introduce a phenomenological model grounded in the statistical mechanics of learning. Our approach uses temperature-like and load-like parameters to model the impact of neural network (NN) training hyperparameters on pruning performance. A key empirical result we identify is a sharp transition phenomenon: depending on the value of a load-like parameter in the pruned model, increasing the value of a temperature-like parameter in the pre-pruned model may either enhance or impair subsequent pruning performance. Based on this transition, we build a three-regime model by taxonomizing the global structure of the pruned NN loss landscape. Our model reveals that the dichotomous effect of high temperature is associated with transitions between distinct types of global structures in the post-pruned model. Based on our results, we present three case-studies: 1) determining whether to increase or decrease a hyperparameter for improved pruning; 2) selecting the best model to prune from a family of models; and 3) tuning the hyperparameter of the Sharpness Aware Minimization method for better pruning performance.

Natural language processing (NLP) practitioners are leveraging large language models (LLM) to create structured datasets from semi-structured and unstructured data sources such as patents, papers, and theses, without having domain-specific knowledge. At the same time, ecological experts are searching for a variety of means to preserve biodiversity. To contribute to these efforts, we focused on endangered species and through in-context learning, we distilled knowledge from GPT-4. In effect, we created datasets for both named entity recognition (NER) and relation extraction (RE) via a two-stage process: 1) we generated synthetic data from GPT-4 of four classes of endangered species, 2) humans verified the factual accuracy of the synthetic data, resulting in gold data. Eventually, our novel dataset contains a total of 3.6K sentences, evenly divided between 1.8K NER and 1.8K RE sentences. The constructed dataset was then used to fine-tune both general BERT and domain-specific BERT variants, completing the knowledge distillation process from GPT-4 to BERT, because GPT-4 is resource intensive. Experiments show that our knowledge transfer approach is effective at creating a NER model suitable for detecting endangered species from texts.

Most state-of-the-art approaches for weather and climate modeling are based on physics-informed numerical models of the atmosphere. These approaches aim to model the non-linear dynamics and complex interactions between multiple variables, which are challenging to approximate. Additionally, many such numerical models are computationally intensive, especially when modeling the atmospheric phenomenon at a fine-grained spatial and temporal resolution. Recent data-driven approaches based on machine learning instead aim to directly solve a downstream forecasting or projection task by learning a data-driven functional mapping using deep neural networks. However, these networks are trained using curated and homogeneous climate datasets for specific spatiotemporal tasks, and thus lack the generality of numerical models. We develop and demonstrate ClimaX, a flexible and generalizable deep learning model for weather and climate science that can be trained using heterogeneous datasets spanning different variables, spatio-temporal coverage, and physical groundings. ClimaX extends the Transformer architecture with novel encoding and aggregation blocks that allow effective use of available compute while maintaining general utility. ClimaX is pre-trained with a self-supervised learning objective on climate datasets derived from CMIP6. The pre-trained ClimaX can then be fine-tuned to address a breadth of climate and weather tasks, including those that involve atmospheric variables and spatio-temporal scales unseen during pretraining. Compared to existing data-driven baselines, we show that this generality in ClimaX results in superior performance on benchmarks for weather forecasting and climate projections, even when pretrained at lower resolutions and compute budgets.

Diffusion models have shown promising ability in generating high-quality time series (TS) data. Despite the initial success, existing works mostly focus on the authenticity of data at the individual level, but pay less attention to preserving the population-level properties on the entire dataset. Such population-level properties include value distributions for each dimension and distributions of certain functional dependencies (e.g., cross-correlation, CC) between different dimensions. For instance, when generating house energy consumption TS data, the value distributions of the outside temperature and the kitchen temperature should be preserved, as well as the distribution of CC between them. Preserving such TS population-level properties is critical in maintaining the statistical insights of the datasets, mitigating model bias, and augmenting downstream tasks like TS prediction. Yet, it is often overlooked by existing models. Hence, data generated by existing models often bear distribution shifts from the original data. We propose Population-aware Diffusion for Time Series (PaD-TS), a new TS generation model that better preserves the population-level properties. The key novelties of PaD-TS include 1) a new training method explicitly incorporating TS population-level property preservation, and 2) a new dual-channel encoder model architecture that better captures the TS data structure. Empirical results in major benchmark datasets show that PaD-TS can improve the average CC distribution shift score between real and synthetic data by 5.9x while maintaining a performance comparable to state-of-the-art models on individual-level authenticity.

Early warning signals have been proposed to forecast the possibility of a critical transition, such as the eutrophication of a lake, the collapse of a coral reef, or the end of a glacial period. Because such transitions often unfold on temporal and spatial scales that can be difficult to approach by experimental manipulation, research has often relied on historical observations as a source of natural experiments. Here we examine a critical difference between selecting systems for study based on the fact that we have observed a critical transition and those systems for which we wish to forecast the approach of a transition. This difference arises by conditionally selecting systems known to experience a transition of some sort and failing to account for the bias this introduces -- a statistical error often known as the Prosecutor's Fallacy. By analysing simulated systems that have experienced transitions purely by chance, we reveal an elevated rate of false positives in common warning signal statistics. We further demonstrate a model-based approach that is less subject to this bias than these more commonly used summary statistics. We note that experimental studies with replicates avoid this pitfall entirely.

We consider a biological population whose environment varies periodically in time, exhibiting two very different "seasons" : one is favorable and the other one is unfavorable. For monotone differential models with concave nonlinearities, we address the following question: the system's period being fixed, under what conditions does there exist a critical duration for the unfavorable season? By "critical duration" we mean that above some threshold, the population cannot sustain and extincts, while below this threshold, the system converges to a unique periodic and positive solution. We term this a "sharp seasonal threshold property" (SSTP, for short). Building upon a previous result, we obtain sufficient conditions for SSTP in any dimension and apply our criterion to a two-dimensional model featuring juvenile and adult populations of insects.

The emergence and impact of tipping points have garnered significant interest in both the social and natural sciences. Despite widespread recognition of the importance of feedbacks between human and natural systems, it is often assumed that the observed nonlinear dynamics in these coupled systems rests within either underlying human or natural processes, rather than the rates at which they interact. Using adoption of agricultural diversification practices as a case study, we show how two stable management paradigms (one dominated by conventional, homogeneous practices, the other by diversified practices) can emerge purely from temporal feedbacks between human decisions and ecological responses. We explore how this temporal mechanism of tipping points provides insight into designing more effective interventions that promote farmers transitions towards sustainable agriculture. Moreover, our flexible modeling framework could be applied to other cases to provide insight into numerous questions in social-ecological systems research and environmental policy.

How areas of land are allocated for different uses, such as forests, urban areas, and agriculture, has a large effect on the terrestrial carbon balance, and therefore climate change. Based on available historical data on land-use changes and a simulation of the associated carbon emissions and removals, a surrogate model can be learned that makes it possible to evaluate the different options available to decision-makers efficiently. An evolutionary search process can then be used to discover effective land-use policies for specific locations. Such a system was built on the Project Resilience platform and evaluated with the Land-Use Harmonization dataset LUH2 and the bookkeeping model BLUE. It generates Pareto fronts that trade off carbon impact and amount of land-use change customized to different locations, thus providing a potentially useful tool for land-use planning.

We introduce Lagrangian Flow Networks (LFlows) for modeling fluid densities and velocities continuously in space and time. By construction, the proposed LFlows satisfy the continuity equation, a PDE describing mass conservation in its differentiable form. Our model is based on the insight that solutions to the continuity equation can be expressed as time-dependent density transformations via differentiable and invertible maps. This follows from classical theory of the existence and uniqueness of Lagrangian flows for smooth vector fields. Hence, we model fluid densities by transforming a base density with parameterized diffeomorphisms conditioned on time. The key benefit compared to methods relying on numerical ODE solvers or PINNs is that the analytic expression of the velocity is always consistent with changes in density. Furthermore, we require neither expensive numerical solvers, nor additional penalties to enforce the PDE. LFlows show higher predictive accuracy in density modeling tasks compared to competing models in 2D and 3D, while being computationally efficient. As a real-world application, we model bird migration based on sparse weather radar measurements.

Nematode worms are one of most abundant metazoan groups on the earth, occupying diverse ecological niches. Accurate recognition or identification of nematodes are of great importance for pest control, soil ecology, bio-geography, habitat conservation and against climate changes. Computer vision and image processing have witnessed a few successes in species recognition of nematodes; however, it is still in great demand. In this paper, we identify two main bottlenecks: (1) the lack of a publicly available imaging dataset for diverse species of nematodes (especially the species only found in natural environment) which requires considerable human resources in field work and experts in taxonomy, and (2) the lack of a standard benchmark of state-of-the-art deep learning techniques on this dataset which demands the discipline background in computer science. With these in mind, we propose an image dataset consisting of diverse nematodes (both laboratory cultured and naturally isolated), which, to our knowledge, is the first time in the community. We further set up a species recognition benchmark by employing state-of-the-art deep learning networks on this dataset. We discuss the experimental results, compare the recognition accuracy of different networks, and show the challenges of our dataset. We make our dataset publicly available at: https://github.com/xuequanlu/I-Nema

Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains challenging: the high complexity of tree space poses a significant obstacle for the current combinatorial and probabilistic techniques. In this paper, we adopt the framework of generative flow networks (GFlowNets) to tackle two core problems in phylogenetics: parsimony-based and Bayesian phylogenetic inference. Because GFlowNets are well-suited for sampling complex combinatorial structures, they are a natural choice for exploring and sampling from the multimodal posterior distribution over tree topologies and evolutionary distances. We demonstrate that our amortized posterior sampler, PhyloGFN, produces diverse and high-quality evolutionary hypotheses on real benchmark datasets. PhyloGFN is competitive with prior works in marginal likelihood estimation and achieves a closer fit to the target distribution than state-of-the-art variational inference methods. Our code is available at https://github.com/zmy1116/phylogfn.

Biodiversity plays a crucial role in maintaining the balance of the ecosystem. However, poaching and unintentional human activities contribute to the decline in the population of many species. Hence, active monitoring is required to preserve these endangered species. Current human-led monitoring techniques are prone to errors and are labor-intensive. Therefore, we study the application of deep learning methods like Convolutional Neural Networks (CNNs) and transfer learning, which can aid in automating the process of monitoring endangered species. For this, we create our custom dataset utilizing trustworthy online databases like iNaturalist and ZooChat. To choose the best model for our use case, we compare the performance of different architectures like DenseNet, ResNet, VGGNet, and YOLOv8 on the custom wildlife dataset. Transfer learning reduces training time by freezing the pre-trained weights and replacing only the output layer with custom, fully connected layers designed for our dataset. Our results indicate that YOLOv8 performs better, achieving a training accuracy of 97.39 % and an F1 score of 96.50 %, surpassing other models. Our findings suggest that integrating YOLOv8 into conservation efforts could revolutionize wildlife monitoring with its high accuracy and efficiency, potentially transforming how endangered species are monitored and protected worldwide.

Language models have been effective in a wide range of applications, yet the most sophisticated models are often proprietary. For example, GPT-4 by OpenAI and various models by Anthropic are expensive and consume substantial energy. In contrast, the open-source community has produced competitive models, like Llama3. Furthermore, niche-specific smaller language models, such as those tailored for legal, medical or financial tasks, have outperformed their proprietary counterparts. This paper introduces a novel approach that employs functional tokens to integrate multiple open-source models, each optimized for particular tasks. Our newly developed Octopus v4 model leverages functional tokens to intelligently direct user queries to the most appropriate vertical model and reformat the query to achieve the best performance. Octopus v4, an evolution of the Octopus v1, v2, and v3 models, excels in selection and parameter understanding and reformatting. Additionally, we explore the use of graph as a versatile data structure that effectively coordinates multiple open-source models by harnessing the capabilities of the Octopus model and functional tokens. Use our open-sourced GitHub (https://www.nexa4ai.com/) to try Octopus v4 models (https://huggingface.co/NexaAIDev/Octopus-v4), and contrite to a larger graph of language models. By activating models less than 10B parameters, we achieved SOTA MMLU score of 74.8 among the same level models.

Understanding how machine learning models respond to distributional shifts is a key research challenge. Mazes serve as an excellent testbed due to varied generation algorithms offering a nuanced platform to simulate both subtle and pronounced distributional shifts. To enable systematic investigations of model behavior on out-of-distribution data, we present maze-dataset, a comprehensive library for generating, processing, and visualizing datasets consisting of maze-solving tasks. With this library, researchers can easily create datasets, having extensive control over the generation algorithm used, the parameters fed to the algorithm of choice, and the filters that generated mazes must satisfy. Furthermore, it supports multiple output formats, including rasterized and text-based, catering to convolutional neural networks and autoregressive transformer models. These formats, along with tools for visualizing and converting between them, ensure versatility and adaptability in research applications.

The ubiquity of large-scale Pre-Trained Models (PTMs) is on the rise, sparking interest in model hubs, and dedicated platforms for hosting PTMs. Despite this trend, a comprehensive exploration of the challenges that users encounter and how the community leverages PTMs remains lacking. To address this gap, we conducted an extensive mixed-methods empirical study by focusing on discussion forums and the model hub of HuggingFace, the largest public model hub. Based on our qualitative analysis, we present a taxonomy of the challenges and benefits associated with PTM reuse within this community. We then conduct a quantitative study to track model-type trends and model documentation evolution over time. Our findings highlight prevalent challenges such as limited guidance for beginner users, struggles with model output comprehensibility in training or inference, and a lack of model understanding. We also identified interesting trends among models where some models maintain high upload rates despite a decline in topics related to them. Additionally, we found that despite the introduction of model documentation tools, its quantity has not increased over time, leading to difficulties in model comprehension and selection among users. Our study sheds light on new challenges in reusing PTMs that were not reported before and we provide recommendations for various stakeholders involved in PTM reuse.

The application of machine learning (ML) in a range of geospatial tasks is increasingly common but often relies on globally available covariates such as satellite imagery that can either be expensive or lack predictive power. Here we explore the question of whether the vast amounts of knowledge found in Internet language corpora, now compressed within large language models (LLMs), can be leveraged for geospatial prediction tasks. We first demonstrate that LLMs embed remarkable spatial information about locations, but naively querying LLMs using geographic coordinates alone is ineffective in predicting key indicators like population density. We then present GeoLLM, a novel method that can effectively extract geospatial knowledge from LLMs with auxiliary map data from OpenStreetMap. We demonstrate the utility of our approach across multiple tasks of central interest to the international community, including the measurement of population density and economic livelihoods. Across these tasks, our method demonstrates a 70% improvement in performance (measured using Pearson's r^2) relative to baselines that use nearest neighbors or use information directly from the prompt, and performance equal to or exceeding satellite-based benchmarks in the literature. With GeoLLM, we observe that GPT-3.5 outperforms Llama 2 and RoBERTa by 19% and 51% respectively, suggesting that the performance of our method scales well with the size of the model and its pretraining dataset. Our experiments reveal that LLMs are remarkably sample-efficient, rich in geospatial information, and robust across the globe. Crucially, GeoLLM shows promise in mitigating the limitations of existing geospatial covariates and complementing them well. Code is available on the project website: https://rohinmanvi.github.io/GeoLLM

We study the class of location-scale or heteroscedastic noise models (LSNMs), in which the effect Y can be written as a function of the cause X and a noise source N independent of X, which may be scaled by a positive function g over the cause, i.e., Y = f(X) + g(X)N. Despite the generality of the model class, we show the causal direction is identifiable up to some pathological cases. To empirically validate these theoretical findings, we propose two estimators for LSNMs: an estimator based on (non-linear) feature maps, and one based on neural networks. Both model the conditional distribution of Y given X as a Gaussian parameterized by its natural parameters. When the feature maps are correctly specified, we prove that our estimator is jointly concave, and a consistent estimator for the cause-effect identification task. Although the the neural network does not inherit those guarantees, it can fit functions of arbitrary complexity, and reaches state-of-the-art performance across benchmarks.

Large language models (LLMs) mark a key shift in natural language processing (NLP), having advanced text generation, translation, and domain-specific reasoning. Closed-source models like GPT-4, powered by proprietary datasets and extensive computational resources, lead with state-of-the-art performance today. However, they face criticism for their "black box" nature and for limiting accessibility in a manner that hinders reproducibility and equitable AI development. By contrast, open-source initiatives like LLaMA and BLOOM prioritize democratization through community-driven development and computational efficiency. These models have significantly reduced performance gaps, particularly in linguistic diversity and domain-specific applications, while providing accessible tools for global researchers and developers. Notably, both paradigms rely on foundational architectural innovations, such as the Transformer framework by Vaswani et al. (2017). Closed-source models excel by scaling effectively, while open-source models adapt to real-world applications in underrepresented languages and domains. Techniques like Low-Rank Adaptation (LoRA) and instruction-tuning datasets enable open-source models to achieve competitive results despite limited resources. To be sure, the tension between closed-source and open-source approaches underscores a broader debate on transparency versus proprietary control in AI. Ethical considerations further highlight this divide. Closed-source systems restrict external scrutiny, while open-source models promote reproducibility and collaboration but lack standardized auditing documentation frameworks to mitigate biases. Hybrid approaches that leverage the strengths of both paradigms are likely to shape the future of LLM innovation, ensuring accessibility, competitive technical performance, and ethical deployment.

The increasing demand for commodities is leading to changes in land use worldwide. In the tropics, deforestation, which causes high carbon emissions and threatens biodiversity, is often linked to agricultural expansion. While the need for deforestation-free global supply chains is widely recognized, making progress in practice remains a challenge. Here, we propose an automated approach that aims to support conservation and sustainable land use planning decisions by mapping tropical landscapes at large scale and high spatial resolution following the High Carbon Stock (HCS) approach. A deep learning approach is developed that estimates canopy height for each 10 m Sentinel-2 pixel by learning from sparse GEDI LIDAR reference data, achieving an overall RMSE of 6.3 m. We show that these wall-to-wall maps of canopy top height are predictive for classifying HCS forests and degraded areas with an overall accuracy of 86 % and produce a first high carbon stock map for Indonesia, Malaysia, and the Philippines.

A model involving Gaussian processes (GPs) is introduced to simultaneously handle multi-task learning, clustering, and prediction for multiple functional data. This procedure acts as a model-based clustering method for functional data as well as a learning step for subsequent predictions for new tasks. The model is instantiated as a mixture of multi-task GPs with common mean processes. A variational EM algorithm is derived for dealing with the optimisation of the hyper-parameters along with the hyper-posteriors' estimation of latent variables and processes. We establish explicit formulas for integrating the mean processes and the latent clustering variables within a predictive distribution, accounting for uncertainty on both aspects. This distribution is defined as a mixture of cluster-specific GP predictions, which enhances the performances when dealing with group-structured data. The model handles irregular grid of observations and offers different hypotheses on the covariance structure for sharing additional information across tasks. The performances on both clustering and prediction tasks are assessed through various simulated scenarios and real datasets. The overall algorithm, called MagmaClust, is publicly available as an R package.

Measuring biodiversity is crucial for understanding ecosystem health. While prior works have developed machine learning models for taxonomic classification of photographic images and DNA separately, in this work, we introduce a multimodal approach combining both, using CLIP-style contrastive learning to align images, barcode DNA, and text-based representations of taxonomic labels in a unified embedding space. This allows for accurate classification of both known and unknown insect species without task-specific fine-tuning, leveraging contrastive learning for the first time to fuse DNA and image data. Our method surpasses previous single-modality approaches in accuracy by over 8% on zero-shot learning tasks, showcasing its effectiveness in biodiversity studies.

Machine learning systems deployed in the wild are often trained on a source distribution but deployed on a different target distribution. Unlabeled data can be a powerful point of leverage for mitigating these distribution shifts, as it is frequently much more available than labeled data and can often be obtained from distributions beyond the source distribution as well. However, existing distribution shift benchmarks with unlabeled data do not reflect the breadth of scenarios that arise in real-world applications. In this work, we present the WILDS 2.0 update, which extends 8 of the 10 datasets in the WILDS benchmark of distribution shifts to include curated unlabeled data that would be realistically obtainable in deployment. These datasets span a wide range of applications (from histology to wildlife conservation), tasks (classification, regression, and detection), and modalities (photos, satellite images, microscope slides, text, molecular graphs). The update maintains consistency with the original WILDS benchmark by using identical labeled training, validation, and test sets, as well as the evaluation metrics. On these datasets, we systematically benchmark state-of-the-art methods that leverage unlabeled data, including domain-invariant, self-training, and self-supervised methods, and show that their success on WILDS is limited. To facilitate method development and evaluation, we provide an open-source package that automates data loading and contains all of the model architectures and methods used in this paper. Code and leaderboards are available at https://wilds.stanford.edu.

Catastrophic regime shifts in complex natural systems may be averted through advanced detection. Recent work has provided a proof-of-principle that many systems approaching a catastrophic transition may be identified through the lens of early warning indicators such as rising variance or increased return times. Despite widespread appreciation of the difficulties and uncertainty involved in such forecasts, proposed methods hardly ever characterize their expected error rates. Without the benefits of replicates, controls, or hindsight, applications of these approaches must quantify how reliable different indicators are in avoiding false alarms, and how sensitive they are to missing subtle warning signs. We propose a model based approach in order to quantify this trade-off between reliability and sensitivity and allow comparisons between different indicators. We show these error rates can be quite severe for common indicators even under favorable assumptions, and also illustrate how a model-based indicator can improve this performance. We demonstrate how the performance of an early warning indicator varies in different data sets, and suggest that uncertainty quantification become a more central part of early warning predictions.

Maintaining genetic diversity as a means to avoid premature convergence is critical in Genetic Programming. Several approaches have been proposed to achieve this, with some focusing on the mating phase from coupling dissimilar solutions to some form of self-adaptive selection mechanism. In nature, genetic diversity can be the consequence of many different factors, but when considering reproduction Sexual Selection can have an impact on promoting variety within a species. Specifically, Mate Choice often results in different selective pressures between sexes, which in turn may trigger evolutionary differences among them. Although some mechanisms of Sexual Selection have been applied to Genetic Programming in the past, the literature is scarce when it comes to mate choice. Recently, a way of modelling mating preferences by ideal mate representations was proposed, achieving good results when compared to a standard approach. These mating preferences evolve freely in a self-adaptive fashion, creating an evolutionary driving force of its own alongside fitness pressure. The inner mechanisms of this approach operate from personal choice, as each individual has its own representation of a perfect mate which affects the mate to be selected. In this paper, we compare this method against a random mate choice to assess whether there are advantages in evolving personal preferences. We conducted experiments using three symbolic regression problems and different mutation rates. The results show that self-adaptive mating preferences are able to create a more diverse set of solutions when compared to the traditional approach and a random mate approach (with statistically significant differences) and have a higher success rate in three of the six instances tested.

Large language models have gained immense importance in recent years and have demonstrated outstanding results in solving various tasks. However, despite these achievements, many questions remain unanswered in the context of large language models. Besides the optimal use of the models for inference and the alignment of the results to the desired specifications, the transfer of models to other languages is still an underdeveloped area of research. The recent publication of models such as Llama-2 and Zephyr has provided new insights into architectural improvements and the use of human feedback. However, insights into adapting these techniques to other languages remain scarce. In this paper, we build on latest improvements and apply the Direct Preference Optimization(DPO) approach to the German language. The model is available at https://huggingface.co/DRXD1000/Phoenix.

Building generalist agents that can handle diverse tasks and evolve themselves across different environments is a long-term goal in the AI community. Large language models (LLMs) are considered a promising foundation to build such agents due to their generalized capabilities. Current approaches either have LLM-based agents imitate expert-provided trajectories step-by-step, requiring human supervision, which is hard to scale and limits environmental exploration; or they let agents explore and learn in isolated environments, resulting in specialist agents with limited generalization. In this paper, we take the first step towards building generally-capable LLM-based agents with self-evolution ability. We identify a trinity of ingredients: 1) diverse environments for agent exploration and learning, 2) a trajectory set to equip agents with basic capabilities and prior knowledge, and 3) an effective and scalable evolution method. We propose AgentGym, a new framework featuring a variety of environments and tasks for broad, real-time, uni-format, and concurrent agent exploration. AgentGym also includes a database with expanded instructions, a benchmark suite, and high-quality trajectories across environments. Next, we propose a novel method, AgentEvol, to investigate the potential of agent self-evolution beyond previously seen data across tasks and environments. Experimental results show that the evolved agents can achieve results comparable to SOTA models. We release the AgentGym suite, including the platform, dataset, benchmark, checkpoints, and algorithm implementations. The AgentGym suite is available on https://github.com/WooooDyy/AgentGym.

Diffusion models are a class of generative models that learn to synthesize samples by inverting a diffusion process that gradually maps data into noise. While these models have enjoyed great success recently, a full theoretical understanding of their observed properties is still lacking, in particular, their weak sensitivity to the choice of noise family and the role of adequate scheduling of noise levels for good synthesis. By identifying a correspondence between diffusion models and a well-known paradigm in cognitive science known as serial reproduction, whereby human agents iteratively observe and reproduce stimuli from memory, we show how the aforementioned properties of diffusion models can be explained as a natural consequence of this correspondence. We then complement our theoretical analysis with simulations that exhibit these key features. Our work highlights how classic paradigms in cognitive science can shed light on state-of-the-art machine learning problems.

As infamous invaders to the North American ecosystem, the Asian giant hornet (Vespa mandarinia) is devastating not only to native bee colonies, but also to local apiculture. One of the most effective way to combat the harmful species is to locate and destroy their nests. By mobilizing the public to actively report possible sightings of the Asian giant hornet, the governmentcould timely send inspectors to confirm and possibly destroy the nests. However, such confirmation requires lab expertise, where manually checking the reports one by one is extremely consuming of human resources. Further given the limited knowledge of the public about the Asian giant hornet and the randomness of report submission, only few of the numerous reports proved positive, i.e. existing nests. How to classify or prioritize the reports efficiently and automatically, so as to determine the dispatch of personnel, is of great significance to the control of the Asian giant hornet. In this paper, we propose a method to predict the priority of sighting reports based on machine learning. We model the problem of optimal prioritization of sighting reports as a problem of classification and prediction. We extracted a variety of rich features in the report: location, time, image(s), and textual description. Based on these characteristics, we propose a classification model based on logistic regression to predict the credibility of a certain report. Furthermore, our model quantifies the impact between reports to get the priority ranking of the reports. Extensive experiments on the public dataset from the WSDA (the Washington State Department of Agriculture) have proved the effectiveness of our method.

In hematology, computational models offer significant potential to improve diagnostic accuracy, streamline workflows, and reduce the tedious work of analyzing single cells in peripheral blood or bone marrow smears. However, clinical adoption of computational models has been hampered by the lack of generalization due to large batch effects, small dataset sizes, and poor performance in transfer learning from natural images. To address these challenges, we introduce DinoBloom, the first foundation model for single cell images in hematology, utilizing a tailored DINOv2 pipeline. Our model is built upon an extensive collection of 13 diverse, publicly available datasets of peripheral blood and bone marrow smears, the most substantial open-source cohort in hematology so far, comprising over 380,000 white blood cell images. To assess its generalization capability, we evaluate it on an external dataset with a challenging domain shift. We show that our model outperforms existing medical and non-medical vision models in (i) linear probing and k-nearest neighbor evaluations for cell-type classification on blood and bone marrow smears and (ii) weakly supervised multiple instance learning for acute myeloid leukemia subtyping by a large margin. A family of four DinoBloom models (small, base, large, and giant) can be adapted for a wide range of downstream applications, be a strong baseline for classification problems, and facilitate the assessment of batch effects in new datasets. All models are available at github.com/marrlab/DinoBloom.

Accurate estimates of Above Ground Biomass (AGB) are essential in addressing two of humanity's biggest challenges, climate change and biodiversity loss. Existing datasets for AGB estimation from satellite imagery are limited. Either they focus on specific, local regions at high resolution, or they offer global coverage at low resolution. There is a need for a machine learning-ready, globally representative, high-resolution benchmark. Our findings indicate significant variability in biomass estimates across different vegetation types, emphasizing the necessity for a dataset that accurately captures global diversity. To address these gaps, we introduce a comprehensive new dataset that is globally distributed, covers a range of vegetation types, and spans several years. This dataset combines AGB reference data from the GEDI mission with data from Sentinel-2 and PALSAR-2 imagery. Additionally, it includes pre-processed high-level features such as a dense canopy height map, an elevation map, and a land-cover classification map. We also produce a dense, high-resolution (10m) map of AGB predictions for the entire area covered by the dataset. Rigorously tested, our dataset is accompanied by several benchmark models and is publicly available. It can be easily accessed using a single line of code, offering a solid basis for efforts towards global AGB estimation. The GitHub repository github.com/ghjuliasialelli/AGBD serves as a one-stop shop for all code and data.

The proliferation of pretrained models, as a result of advancements in pretraining techniques, has led to the emergence of a vast zoo of publicly available models. Effectively utilizing these resources to obtain models with robust out-of-distribution generalization capabilities for downstream tasks has become a crucial area of research. Previous research has primarily focused on identifying the most powerful models within the model zoo, neglecting to fully leverage the diverse inductive biases contained within. This paper argues that the knowledge contained in weaker models is valuable and presents a method for leveraging the diversity within the model zoo to improve out-of-distribution generalization capabilities. Specifically, we investigate the behaviors of various pretrained models across different domains of downstream tasks by characterizing the variations in their encoded representations in terms of two dimensions: diversity shift and correlation shift. This characterization enables us to propose a new algorithm for integrating diverse pretrained models, not limited to the strongest models, in order to achieve enhanced out-of-distribution generalization performance. Our proposed method demonstrates state-of-the-art empirical results on a variety of datasets, thus validating the benefits of utilizing diverse knowledge.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

The topic of Climate Change (CC) has received limited attention in NLP despite its real world urgency. Activists and policy-makers need NLP tools in order to effectively process the vast and rapidly growing textual data produced on CC. Their utility, however, primarily depends on whether the current state-of-the-art models can generalize across various tasks in the CC domain. In order to address this gap, we introduce Climate Change Benchmark (ClimaBench), a benchmark collection of existing disparate datasets for evaluating model performance across a diverse set of CC NLU tasks systematically. Further, we enhance the benchmark by releasing two large-scale labelled text classification and question-answering datasets curated from publicly available environmental disclosures. Lastly, we provide an analysis of several generic and CC-oriented models answering whether fine-tuning on domain text offers any improvements across these tasks. We hope this work provides a standard assessment tool for research on CC text data.

The introduction of the transformer architecture and the self-attention mechanism has led to an explosive production of language models trained on specific downstream tasks and data domains. With over 200, 000 models in the Hugging Face ecosystem, users grapple with selecting and optimizing models to suit multifaceted workflows and data domains while addressing computational, security, and recency concerns. There is an urgent need for machine learning frameworks that can eliminate the burden of model selection and customization and unleash the incredible power of the vast emerging model library for end users. Here, we propose a context-aware routing system, Tryage, that leverages a language model router for optimal selection of expert models from a model library based on analysis of individual input prompts. Inspired by the thalamic router in the brain, Tryage employs a perceptive router to predict down-stream model performance on prompts and, then, makes a routing decision using an objective function that integrates performance predictions with user goals and constraints that are incorporated through flags (e.g., model size, model recency). Tryage allows users to explore a Pareto front and automatically trade-off between task accuracy and secondary goals including minimization of model size, recency, security, verbosity, and readability. Across heterogeneous data sets that include code, text, clinical data, and patents, the Tryage framework surpasses Gorilla and GPT3.5 turbo in dynamic model selection identifying the optimal model with an accuracy of 50.9% , compared to 23.6% by GPT 3.5 Turbo and 10.8% by Gorilla. Conceptually, Tryage demonstrates how routing models can be applied to program and control the behavior of multi-model LLM systems to maximize efficient use of the expanding and evolving language model ecosystem.

Large Language Models (LLMs) are trained on corpora disproportionally weighted in favor of Standard American English. As a result, speakers of other dialects experience significantly more failures when interacting with these technologies. In practice, these speakers often accommodate their speech to be better understood. Our work shares the belief that language technologies should be designed to accommodate the diversity in English dialects and not the other way around. However, prior works on dialect struggle with generalizing to evolving and emerging dialects in a scalable manner. To fill this gap, our method, HyperLoRA, leverages expert linguistic knowledge to enable resource-efficient adaptation via hypernetworks. By disentangling dialect-specific and cross-dialectal information, HyperLoRA improves generalization to unseen dialects in a task-agnostic fashion. Not only is HyperLoRA more scalable in the number of parameters, but it also achieves the best or most competitive performance across 5 dialects in a zero-shot setting. In this way, our approach facilitates access to language technology for billions of English dialect speakers who are traditionally underrepresented.

The current biodiversity loss crisis makes animal monitoring a relevant field of study. In light of this, data collected through monitoring can provide essential insights, and information for decision-making aimed at preserving global biodiversity. Despite the importance of such data, there is a notable scarcity of datasets featuring videos of birds, and none of the existing datasets offer detailed annotations of bird behaviors in video format. In response to this gap, our study introduces the first fine-grained video dataset specifically designed for bird behavior detection and species classification. This dataset addresses the need for comprehensive bird video datasets and provides detailed data on bird actions, facilitating the development of deep learning models to recognize these, similar to the advancements made in human action recognition. The proposed dataset comprises 178 videos recorded in Spanish wetlands, capturing 13 different bird species performing 7 distinct behavior classes. In addition, we also present baseline results using state of the art models on two tasks: bird behavior recognition and species classification.

This Perspective explores the transformative potential of Multi-Agent Systems (MAS) powered by Large Language Models (LLMs) in the geosciences. Users of geoscientific data repositories face challenges due to the complexity and diversity of data formats, inconsistent metadata practices, and a considerable number of unprocessed datasets. MAS possesses transformative potential for improving scientists' interaction with geoscientific data by enabling intelligent data processing, natural language interfaces, and collaborative problem-solving capabilities. We illustrate this approach with "PANGAEA GPT", a specialized MAS pipeline integrated with the diverse PANGAEA database for Earth and Environmental Science, demonstrating how MAS-driven workflows can effectively manage complex datasets and accelerate scientific discovery. We discuss how MAS can address current data challenges in geosciences, highlight advancements in other scientific fields, and propose future directions for integrating MAS into geoscientific data processing pipelines. In this Perspective, we show how MAS can fundamentally improve data accessibility, promote cross-disciplinary collaboration, and accelerate geoscientific discoveries.

Generative tasks about molecules, including but not limited to molecule generation, are crucial for drug discovery and material design, and have consistently attracted significant attention. In recent years, diffusion models have emerged as an impressive class of deep generative models, sparking extensive research and leading to numerous studies on their application to molecular generative tasks. Despite the proliferation of related work, there remains a notable lack of up-to-date and systematic surveys in this area. Particularly, due to the diversity of diffusion model formulations, molecular data modalities, and generative task types, the research landscape is challenging to navigate, hindering understanding and limiting the area's growth. To address this, this paper conducts a comprehensive survey of diffusion model-based molecular generative methods. We systematically review the research from the perspectives of methodological formulations, data modalities, and task types, offering a novel taxonomy. This survey aims to facilitate understanding and further flourishing development in this area. The relevant papers are summarized at: https://github.com/AzureLeon1/awesome-molecular-diffusion-models.

Distribution shifts -- where the training distribution differs from the test distribution -- can substantially degrade the accuracy of machine learning (ML) systems deployed in the wild. Despite their ubiquity in the real-world deployments, these distribution shifts are under-represented in the datasets widely used in the ML community today. To address this gap, we present WILDS, a curated benchmark of 10 datasets reflecting a diverse range of distribution shifts that naturally arise in real-world applications, such as shifts across hospitals for tumor identification; across camera traps for wildlife monitoring; and across time and location in satellite imaging and poverty mapping. On each dataset, we show that standard training yields substantially lower out-of-distribution than in-distribution performance. This gap remains even with models trained by existing methods for tackling distribution shifts, underscoring the need for new methods for training models that are more robust to the types of distribution shifts that arise in practice. To facilitate method development, we provide an open-source package that automates dataset loading, contains default model architectures and hyperparameters, and standardizes evaluations. Code and leaderboards are available at https://wilds.stanford.edu.

We present a new dataset, Functional Map of the World (fMoW), which aims to inspire the development of machine learning models capable of predicting the functional purpose of buildings and land use from temporal sequences of satellite images and a rich set of metadata features. The metadata provided with each image enables reasoning about location, time, sun angles, physical sizes, and other features when making predictions about objects in the image. Our dataset consists of over 1 million images from over 200 countries. For each image, we provide at least one bounding box annotation containing one of 63 categories, including a "false detection" category. We present an analysis of the dataset along with baseline approaches that reason about metadata and temporal views. Our data, code, and pretrained models have been made publicly available.

We introduce Diffusion World Model (DWM), a conditional diffusion model capable of predicting multistep future states and rewards concurrently. As opposed to traditional one-step dynamics models, DWM offers long-horizon predictions in a single forward pass, eliminating the need for recursive quires. We integrate DWM into model-based value estimation, where the short-term return is simulated by future trajectories sampled from DWM. In the context of offline reinforcement learning, DWM can be viewed as a conservative value regularization through generative modeling. Alternatively, it can be seen as a data source that enables offline Q-learning with synthetic data. Our experiments on the D4RL dataset confirm the robustness of DWM to long-horizon simulation. In terms of absolute performance, DWM significantly surpasses one-step dynamics models with a 44% performance gain, and achieves state-of-the-art performance.

World models constitute a promising approach for training reinforcement learning agents in a safe and sample-efficient manner. Recent world models predominantly operate on sequences of discrete latent variables to model environment dynamics. However, this compression into a compact discrete representation may ignore visual details that are important for reinforcement learning. Concurrently, diffusion models have become a dominant approach for image generation, challenging well-established methods modeling discrete latents. Motivated by this paradigm shift, we introduce DIAMOND (DIffusion As a Model Of eNvironment Dreams), a reinforcement learning agent trained in a diffusion world model. We analyze the key design choices that are required to make diffusion suitable for world modeling, and demonstrate how improved visual details can lead to improved agent performance. DIAMOND achieves a mean human normalized score of 1.46 on the competitive Atari 100k benchmark; a new best for agents trained entirely within a world model. To foster future research on diffusion for world modeling, we release our code, agents and playable world models at https://github.com/eloialonso/diamond.

The distribution of subpopulations is an important property hidden within a dataset. Uncovering and analyzing the subpopulation distribution within datasets provides a comprehensive understanding of the datasets, standing as a powerful tool beneficial to various downstream tasks, including Dataset Subpopulation Organization, Subpopulation Shift, and Slice Discovery. Despite its importance, there has been no work that systematically explores the subpopulation distribution of datasets to our knowledge. To address the limitation and solve all the mentioned tasks in a unified way, we introduce a novel concept of subpopulation structures to represent, analyze, and utilize subpopulation distributions within datasets. To characterize the structures in an interpretable manner, we propose the Subpopulation Structure Discovery with Large Language Models (SSD-LLM) framework, which employs world knowledge and instruction-following capabilities of Large Language Models (LLMs) to linguistically analyze informative image captions and summarize the structures. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery. Furthermore, we propose complete workflows to address downstream tasks, named Task-specific Tuning, showcasing the application of the discovered structure to a spectrum of subpopulation-related tasks, including dataset subpopulation organization, subpopulation shift, and slice discovery.

Many cellular processes involve information processing and decision making. We can probe these processes at increasing molecular detail. The analysis of heterogeneous data remains a challenge that requires new ways of thinking about cells in quantitative, predictive, and mechanistic ways. We discuss the role of mathematical models in the context of cell-fate decision making systems across the tree of life. Complex multi-cellular organisms have been a particular focus, but single celled organisms also have to sense and respond to their environment. We center our discussion around the idea of design principles which we can learn from observations and modeling, and exploit in order to (re)-design or guide cellular behavior.

Popular approaches for quantifying predictive uncertainty in deep neural networks often involve distributions over weights or multiple models, for instance via Markov Chain sampling, ensembling, or Monte Carlo dropout. These techniques usually incur overhead by having to train multiple model instances or do not produce very diverse predictions. This comprehensive and extensive survey aims to familiarize the reader with an alternative class of models based on the concept of Evidential Deep Learning: For unfamiliar data, they aim to admit "what they don't know", and fall back onto a prior belief. Furthermore, they allow uncertainty estimation in a single model and forward pass by parameterizing distributions over distributions. This survey recapitulates existing works, focusing on the implementation in a classification setting, before surveying the application of the same paradigm to regression. We also reflect on the strengths and weaknesses compared to other existing methods and provide the most fundamental derivations using a unified notation to aid future research.

Large language models (LLMs) are useful in many NLP tasks and become more capable with size, with the best open-source models having over 50 billion parameters. However, using these 50B+ models requires high-end hardware, making them inaccessible to most researchers. In this work, we investigate methods for cost-efficient inference and fine-tuning of LLMs, comparing local and distributed strategies. We observe that a large enough model (50B+) can run efficiently even on geodistributed devices in a consumer-grade network. This could allow running LLM efficiently by pooling together idle compute resources of multiple research groups and volunteers. We address two open problems: (1) how to perform inference and fine-tuning reliably if any device can disconnect abruptly and (2) how to partition LLMs between devices with uneven hardware, joining and leaving at will. In order to do that, we develop special fault-tolerant inference algorithms and load-balancing protocols that automatically assign devices to maximize the total system throughput. We showcase these algorithms in Petals - a decentralized system that runs Llama 2 (70B) and BLOOM (176B) over the Internet up to 10x faster than offloading for interactive generation. We evaluate the performance of our system in simulated conditions and a real-world setup spanning two continents.

We introduce marginalization models (MaMs), a new family of generative models for high-dimensional discrete data. They offer scalable and flexible generative modeling with tractable likelihoods by explicitly modeling all induced marginal distributions. Marginalization models enable fast evaluation of arbitrary marginal probabilities with a single forward pass of the neural network, which overcomes a major limitation of methods with exact marginal inference, such as autoregressive models (ARMs). We propose scalable methods for learning the marginals, grounded in the concept of "marginalization self-consistency". Unlike previous methods, MaMs support scalable training of any-order generative models for high-dimensional problems under the setting of energy-based training, where the goal is to match the learned distribution to a given desired probability (specified by an unnormalized (log) probability function such as energy function or reward function). We demonstrate the effectiveness of the proposed model on a variety of discrete data distributions, including binary images, language, physical systems, and molecules, for maximum likelihood and energy-based training settings. MaMs achieve orders of magnitude speedup in evaluating the marginal probabilities on both settings. For energy-based training tasks, MaMs enable any-order generative modeling of high-dimensional problems beyond the capability of previous methods. Code is at https://github.com/PrincetonLIPS/MaM.

As AI model size grows, neural scaling laws have become a crucial tool to predict the improvements of large models when increasing capacity and the size of original (human or natural) training data. Yet, the widespread use of popular models means that the ecosystem of online data and text will co-evolve to progressively contain increased amounts of synthesized data. In this paper we ask: How will the scaling laws change in the inevitable regime where synthetic data makes its way into the training corpus? Will future models, still improve, or be doomed to degenerate up to total (model) collapse? We develop a theoretical framework of model collapse through the lens of scaling laws. We discover a wide range of decay phenomena, analyzing loss of scaling, shifted scaling with number of generations, the ''un-learning" of skills, and grokking when mixing human and synthesized data. Our theory is validated by large-scale experiments with a transformer on an arithmetic task and text generation using the large language model Llama2.

Current LLM alignment techniques use pairwise human preferences at a sample level, and as such, they do not imply an alignment on the distributional level. We propose in this paper Alignment via Optimal Transport (AOT), a novel method for distributional preference alignment of LLMs. AOT aligns LLMs on unpaired preference data by making the reward distribution of the positive samples stochastically dominant in the first order on the distribution of negative samples. We introduce a convex relaxation of this first-order stochastic dominance and cast it as an optimal transport problem with a smooth and convex cost. Thanks to the one-dimensional nature of the resulting optimal transport problem and the convexity of the cost, it has a closed-form solution via sorting on empirical measures. We fine-tune LLMs with this AOT objective, which enables alignment by penalizing the violation of the stochastic dominance of the reward distribution of the positive samples on the reward distribution of the negative samples. We analyze the sample complexity of AOT by considering the dual of the OT problem and show that it converges at the parametric rate. Empirically, we show on a diverse set of alignment datasets and LLMs that AOT leads to state-of-the-art models in the 7B family of models when evaluated with Open LLM Benchmarks and AlpacaEval.

Climate change is increasing the intensity and frequency of many extreme weather events, including heatwaves, which results in increased thermal discomfort and mortality rates. While global mitigation action is undoubtedly necessary, so is climate adaptation, e.g., through climate-sensitive urban planning. Among the most promising strategies is harnessing the benefits of urban trees in shading and cooling pedestrian-level environments. Our work investigates the challenge of optimal placement of such trees. Physical simulations can estimate the radiative and thermal impact of trees on human thermal comfort but induce high computational costs. This rules out optimization of tree placements over large areas and considering effects over longer time scales. Hence, we employ neural networks to simulate the point-wise mean radiant temperatures--a driving factor of outdoor human thermal comfort--across various time scales, spanning from daily variations to extended time scales of heatwave events and even decades. To optimize tree placements, we harness the innate local effect of trees within the iterated local search framework with tailored adaptations. We show the efficacy of our approach across a wide spectrum of study areas and time scales. We believe that our approach is a step towards empowering decision-makers, urban designers and planners to proactively and effectively assess the potential of urban trees to mitigate heat stress.

The availability of reliable, high-resolution climate and weather data is important to inform long-term decisions on climate adaptation and mitigation and to guide rapid responses to extreme events. Forecasting models are limited by computational costs and, therefore, often generate coarse-resolution predictions. Statistical downscaling, including super-resolution methods from deep learning, can provide an efficient method of upsampling low-resolution data. However, despite achieving visually compelling results in some cases, such models frequently violate conservation laws when predicting physical variables. In order to conserve physical quantities, here we introduce methods that guarantee statistical constraints are satisfied by a deep learning downscaling model, while also improving their performance according to traditional metrics. We compare different constraining approaches and demonstrate their applicability across different neural architectures as well as a variety of climate and weather data sets. Besides enabling faster and more accurate climate predictions through downscaling, we also show that our novel methodologies can improve super-resolution for satellite data and natural images data sets.

Despite the rapid expansion of types of large language models, there remains a notable gap in models specifically designed for the Dutch language. This gap is not only a shortage in terms of pretrained Dutch models but also in terms of data, and benchmarks and leaderboards. This work provides a small step to improve the situation. First, we introduce two fine-tuned variants of the Llama 2 13B model. We first fine-tuned Llama 2 using Dutch-specific web-crawled data and subsequently refined this model further on multiple synthetic instruction and chat datasets. These datasets as well as the model weights are made available. In addition, we provide a leaderboard to keep track of the performance of (Dutch) models on a number of generation tasks, and we include results of a number of state-of-the-art models, including our own. Finally we provide a critical conclusion on what we believe is needed to push forward Dutch language models and the whole eco-system around the models.

Artificial Intelligence (AI) weather prediction (AIWP) models are powerful tools for medium-range forecasts but often lack physical consistency, leading to outputs that violate conservation laws. This study introduces a set of novel physics-based schemes designed to enforce the conservation of global dry air mass, moisture budget, and total atmospheric energy in AIWP models. The schemes are highly modular, allowing for seamless integration into a wide range of AI model architectures. Forecast experiments are conducted to demonstrate the benefit of conservation schemes using FuXi, an example AIWP model, modified and adapted for 1.0-degree grid spacing. Verification results show that the conservation schemes can guide the model in producing forecasts that obey conservation laws. The forecast skills of upper-air and surface variables are also improved, with longer forecast lead times receiving larger benefits. Notably, large performance gains are found in the total precipitation forecasts, owing to the reduction of drizzle bias. The proposed conservation schemes establish a foundation for implementing other physics-based schemes in the future. They also provide a new way to integrate atmospheric domain knowledge into the design and refinement of AIWP models.

Deep learning foundation models are revolutionizing many facets of science by leveraging vast amounts of data to learn general-purpose representations that can be adapted to tackle diverse downstream tasks. Foundation models hold the promise to also transform our ability to model our planet and its subsystems by exploiting the vast expanse of Earth system data. Here we introduce Aurora, a large-scale foundation model of the atmosphere trained on over a million hours of diverse weather and climate data. Aurora leverages the strengths of the foundation modelling approach to produce operational forecasts for a wide variety of atmospheric prediction problems, including those with limited training data, heterogeneous variables, and extreme events. In under a minute, Aurora produces 5-day global air pollution predictions and 10-day high-resolution weather forecasts that outperform state-of-the-art classical simulation tools and the best specialized deep learning models. Taken together, these results indicate that foundation models can transform environmental forecasting.

As Large Language Models (LLMs) excel across tasks and specialized domains, scaling LLMs based on existing models has garnered significant attention, which faces the challenge of decreasing performance when combining disparate models. Various techniques have been proposed for the aggregation of pre-trained LLMs, including model merging, Mixture-of-Experts, and stacking. Despite their merits, a comprehensive comparison and synergistic application of them to a diverse model zoo is yet to be adequately addressed. In light of this research gap, this paper introduces Model-GLUE, a holistic LLM scaling guideline. First, our work starts with a benchmarking of existing LLM scaling techniques, especially selective merging, and variants of mixture. Utilizing the insights from the benchmark results, we formulate an strategy for the selection and aggregation of a heterogeneous model zoo characterizing different architectures and initialization. Our methodology involves the clustering of mergeable models and optimal merging strategy selection, and the integration of clusters through a model mixture. Finally, evidenced by our experiments on a diverse Llama-2-based model zoo, Model-GLUE shows an average performance enhancement of 5.61%, achieved without additional training. Codes are available at: https://github.com/Model-GLUE/Model-GLUE.

The crystallization of modeling methods around the Transformer architecture has been a boon for practitioners. Simple, well-motivated architectural variations can transfer across tasks and scale, increasing the impact of modeling research. However, with the emergence of state-of-the-art 100B+ parameters models, large language models are increasingly expensive to accurately design and train. Notably, it can be difficult to evaluate how modeling decisions may impact emergent capabilities, given that these capabilities arise mainly from sheer scale alone. In the process of building BLOOM--the Big Science Large Open-science Open-access Multilingual language model--our goal is to identify an architecture and training setup that makes the best use of our 1,000,000 A100-GPU-hours budget. Specifically, we perform an ablation study at the billion-parameter scale comparing different modeling practices and their impact on zero-shot generalization. In addition, we study the impact of various popular pre-training corpora on zero-shot generalization. We also study the performance of a multilingual model and how it compares to the English-only one. Finally, we consider the scaling behaviour of Transformers to choose the target model size, shape, and training setup. All our models and code are open-sourced at https://huggingface.co/bigscience .

The capabilities of large language models (LLMs) have sparked debate over whether such systems just learn an enormous collection of superficial statistics or a coherent model of the data generating process -- a world model. We find evidence for the latter by analyzing the learned representations of three spatial datasets (world, US, NYC places) and three temporal datasets (historical figures, artworks, news headlines) in the Llama-2 family of models. We discover that LLMs learn linear representations of space and time across multiple scales. These representations are robust to prompting variations and unified across different entity types (e.g. cities and landmarks). In addition, we identify individual ``space neurons'' and ``time neurons'' that reliably encode spatial and temporal coordinates. Our analysis demonstrates that modern LLMs acquire structured knowledge about fundamental dimensions such as space and time, supporting the view that they learn not merely superficial statistics, but literal world models.

This paper introduces RiskCards, a framework for structured assessment and documentation of risks associated with an application of language models. As with all language, text generated by language models can be harmful, or used to bring about harm. Automating language generation adds both an element of scale and also more subtle or emergent undesirable tendencies to the generated text. Prior work establishes a wide variety of language model harms to many different actors: existing taxonomies identify categories of harms posed by language models; benchmarks establish automated tests of these harms; and documentation standards for models, tasks and datasets encourage transparent reporting. However, there is no risk-centric framework for documenting the complexity of a landscape in which some risks are shared across models and contexts, while others are specific, and where certain conditions may be required for risks to manifest as harms. RiskCards address this methodological gap by providing a generic framework for assessing the use of a given language model in a given scenario. Each RiskCard makes clear the routes for the risk to manifest harm, their placement in harm taxonomies, and example prompt-output pairs. While RiskCards are designed to be open-source, dynamic and participatory, we present a "starter set" of RiskCards taken from a broad literature survey, each of which details a concrete risk presentation. Language model RiskCards initiate a community knowledge base which permits the mapping of risks and harms to a specific model or its application scenario, ultimately contributing to a better, safer and shared understanding of the risk landscape.

The deployment of ever-larger machine learning models reflects a growing consensus that the more expressive the modelx2013and the more data one has access tox2013the more one can improve performance. As models get deployed in a variety of real world scenarios, they inevitably face strategic environments. In this work, we consider the natural question of how the interplay of models and strategic interactions affects scaling laws. We find that strategic interactions can break the conventional view of scaling lawsx2013meaning that performance does not necessarily monotonically improve as models get larger and/ or more expressive (even with infinite data). We show the implications of this phenomenon in several contexts including strategic regression, strategic classification, and multi-agent reinforcement learning through examples of strategic environments in whichx2013by simply restricting the expressivity of one's model or policy classx2013one can achieve strictly better equilibrium outcomes. Motivated by these examples, we then propose a new paradigm for model-selection in games wherein an agent seeks to choose amongst different model classes to use as their action set in a game.

Predicting wildfire spread is critical for land management and disaster preparedness. To this end, we present `Next Day Wildfire Spread,' a curated, large-scale, multivariate data set of historical wildfires aggregating nearly a decade of remote-sensing data across the United States. In contrast to existing fire data sets based on Earth observation satellites, our data set combines 2D fire data with multiple explanatory variables (e.g., topography, vegetation, weather, drought index, population density) aligned over 2D regions, providing a feature-rich data set for machine learning. To demonstrate the usefulness of this data set, we implement a neural network that takes advantage of the spatial information of this data to predict wildfire spread. We compare the performance of the neural network with other machine learning models: logistic regression and random forest. This data set can be used as a benchmark for developing wildfire propagation models based on remote sensing data for a lead time of one day.

In the field of environmental science, it is crucial to have robust evaluation metrics for large language models to ensure their efficacy and accuracy. We propose EnviroExam, a comprehensive evaluation method designed to assess the knowledge of large language models in the field of environmental science. EnviroExam is based on the curricula of top international universities, covering undergraduate, master's, and doctoral courses, and includes 936 questions across 42 core courses. By conducting 0-shot and 5-shot tests on 31 open-source large language models, EnviroExam reveals the performance differences among these models in the domain of environmental science and provides detailed evaluation standards. The results show that 61.3% of the models passed the 5-shot tests, while 48.39% passed the 0-shot tests. By introducing the coefficient of variation as an indicator, we evaluate the performance of mainstream open-source large language models in environmental science from multiple perspectives, providing effective criteria for selecting and fine-tuning language models in this field. Future research will involve constructing more domain-specific test sets using specialized environmental science textbooks to further enhance the accuracy and specificity of the evaluation.

Insect-pests significantly impact global agricultural productivity and quality. Effective management involves identifying the full insect community, including beneficial insects and harmful pests, to develop and implement integrated pest management strategies. Automated identification of insects under real-world conditions presents several challenges, including differentiating similar-looking species, intra-species dissimilarity and inter-species similarity, several life cycle stages, camouflage, diverse imaging conditions, and variability in insect orientation. A deep-learning model, InsectNet, is proposed to address these challenges. InsectNet is endowed with five key features: (a) utilization of a large dataset of insect images collected through citizen science; (b) label-free self-supervised learning for large models; (c) improving prediction accuracy for species with a small sample size; (d) enhancing model trustworthiness; and (e) democratizing access through streamlined MLOps. This approach allows accurate identification (>96% accuracy) of over 2500 insect species, including pollinator (e.g., butterflies, bees), parasitoid (e.g., some wasps and flies), predator species (e.g., lady beetles, mantises, dragonflies) and harmful pest species (e.g., armyworms, cutworms, grasshoppers, stink bugs). InsectNet can identify invasive species, provide fine-grained insect species identification, and work effectively in challenging backgrounds. It also can abstain from making predictions when uncertain, facilitating seamless human intervention and making it a practical and trustworthy tool. InsectNet can guide citizen science data collection, especially for invasive species where early detection is crucial. Similar approaches may transform other agricultural challenges like disease detection and underscore the importance of data collection, particularly through citizen science efforts..

The quantitative prediction of the intensity of rainfall events (light or heavy) has remained a challenge in Numerical Weather Prediction (NWP) models. For the first time the mean coefficient of diffusional growth rates are calculated using an Eulerian-Lagrangian particle-based small-scale model on in situ airborne measurement data of Cloud Aerosol Interaction and Precipitation Enhancement Experiment (CAIPEEX) during monsoon over Indian sub-continent. The results show that diffusional growth rates varies in the range of 0.00025 - 0.0015(cm/s). The generic problem of the overestimation of light rain in NWP models might be related with the choice of cm in the model. It is also shown from DNS experiment using Eulerian-Lagrangian particle-based small-scale model that the relative dispersion is constrained with average values in the range of ~ 0.2 - 0.37 (~ 0.1- 0.26) in less humid (more humid) conditions. This is in agreement with in situ airborne observation (dispersion ~ 0.36) and previous study over Indian sub-continent. The linear relationship between relative dispersion and cloud droplet number concentration (NC) is obtained from this study using CAIPEEX observation over Indian subcontinent. The dispersion based autoconversion-scheme for Indian region must be useful for the Indian summer monsoon precipitation calculation in the general circulation model. The present study also provide valuable guidance for the parameterization of effective radius, important for radiation scheme.

The presence of linear paths in parameter space between two different network solutions in certain cases, i.e., linear mode connectivity (LMC), has garnered interest from both theoretical and practical fronts. There has been significant research that either practically designs algorithms catered for connecting networks by adjusting for the permutation symmetries as well as some others that more theoretically construct paths through which networks can be connected. Yet, the core reasons for the occurrence of LMC, when in fact it does occur, in the highly non-convex loss landscapes of neural networks are far from clear. In this work, we take a step towards understanding it by providing a model of how the loss landscape needs to behave topographically for LMC (or the lack thereof) to manifest. Concretely, we present a `mountainside and ridge' perspective that helps to neatly tie together different geometric features that can be spotted in the loss landscape along the training runs. We also complement this perspective by providing a theoretical analysis of the barrier height, for which we provide empirical support, and which additionally extends as a faithful predictor of layer-wise LMC. We close with a toy example that provides further intuition on how barriers arise in the first place, all in all, showcasing the larger aim of the work -- to provide a working model of the landscape and its topography for the occurrence of LMC.

Multimodal large language models (MLLMs) have shown remarkable capabilities across a broad range of tasks but their knowledge and abilities in the geographic and geospatial domains are yet to be explored, despite potential wide-ranging benefits to navigation, environmental research, urban development, and disaster response. We conduct a series of experiments exploring various vision capabilities of MLLMs within these domains, particularly focusing on the frontier model GPT-4V, and benchmark its performance against open-source counterparts. Our methodology involves challenging these models with a small-scale geographic benchmark consisting of a suite of visual tasks, testing their abilities across a spectrum of complexity. The analysis uncovers not only where such models excel, including instances where they outperform humans, but also where they falter, providing a balanced view of their capabilities in the geographic domain. To enable the comparison and evaluation of future models, our benchmark will be publicly released.

Large language models (LLMs) have shown remarkable performance across a wide range of applications, often outperforming human experts. However, deploying these parameter-heavy models efficiently for diverse inference use cases requires carefully designed hardware platforms with ample computing, memory, and network resources. With LLM deployment scenarios and models evolving at breakneck speed, the hardware requirements to meet SLOs remains an open research question. In this work, we present an analytical tool, GenZ, to study the relationship between LLM inference performance and various platform design parameters. Our analysis provides insights into configuring platforms for different LLM workloads and use cases. We quantify the platform requirements to support SOTA LLMs models like LLaMA and GPT-4 under diverse serving settings. Furthermore, we project the hardware capabilities needed to enable future LLMs potentially exceeding hundreds of trillions of parameters. The trends and insights derived from GenZ can guide AI engineers deploying LLMs as well as computer architects designing next-generation hardware accelerators and platforms. Ultimately, this work sheds light on the platform design considerations for unlocking the full potential of large language models across a spectrum of applications. The source code is available at https://github.com/abhibambhaniya/GenZ-LLM-Analyzer .

Quantile regression is a fundamental problem in statistical learning motivated by a need to quantify uncertainty in predictions, or to model a diverse population without being overly reductive. For instance, epidemiological forecasts, cost estimates, and revenue predictions all benefit from being able to quantify the range of possible values accurately. As such, many models have been developed for this problem over many years of research in statistics, machine learning, and related fields. Rather than proposing yet another (new) algorithm for quantile regression we adopt a meta viewpoint: we investigate methods for aggregating any number of conditional quantile models, in order to improve accuracy and robustness. We consider weighted ensembles where weights may vary over not only individual models, but also over quantile levels, and feature values. All of the models we consider in this paper can be fit using modern deep learning toolkits, and hence are widely accessible (from an implementation point of view) and scalable. To improve the accuracy of the predicted quantiles (or equivalently, prediction intervals), we develop tools for ensuring that quantiles remain monotonically ordered, and apply conformal calibration methods. These can be used without any modification of the original library of base models. We also review some basic theory surrounding quantile aggregation and related scoring rules, and contribute a few new results to this literature (for example, the fact that post sorting or post isotonic regression can only improve the weighted interval score). Finally, we provide an extensive suite of empirical comparisons across 34 data sets from two different benchmark repositories.

Domain adaptation aims to mitigate distribution shifts among different domains. However, traditional formulations are mostly limited to categorical domains, greatly simplifying nuanced domain relationships in the real world. In this work, we tackle a generalization with taxonomy-structured domains, which formalizes domains with nested, hierarchical similarity structures such as animal species and product catalogs. We build on the classic adversarial framework and introduce a novel taxonomist, which competes with the adversarial discriminator to preserve the taxonomy information. The equilibrium recovers the classic adversarial domain adaptation's solution if given a non-informative domain taxonomy (e.g., a flat taxonomy where all leaf nodes connect to the root node) while yielding non-trivial results with other taxonomies. Empirically, our method achieves state-of-the-art performance on both synthetic and real-world datasets with successful adaptation. Code is available at https://github.com/Wang-ML-Lab/TSDA.

Irregularly sampled time series data arise naturally in many application domains including biology, ecology, climate science, astronomy, and health. Such data represent fundamental challenges to many classical models from machine learning and statistics due to the presence of non-uniform intervals between observations. However, there has been significant progress within the machine learning community over the last decade on developing specialized models and architectures for learning from irregularly sampled univariate and multivariate time series data. In this survey, we first describe several axes along which approaches to learning from irregularly sampled time series differ including what data representations they are based on, what modeling primitives they leverage to deal with the fundamental problem of irregular sampling, and what inference tasks they are designed to perform. We then survey the recent literature organized primarily along the axis of modeling primitives. We describe approaches based on temporal discretization, interpolation, recurrence, attention and structural invariance. We discuss similarities and differences between approaches and highlight primary strengths and weaknesses.

General world models represent a crucial pathway toward achieving Artificial General Intelligence (AGI), serving as the cornerstone for various applications ranging from virtual environments to decision-making systems. Recently, the emergence of the Sora model has attained significant attention due to its remarkable simulation capabilities, which exhibits an incipient comprehension of physical laws. In this survey, we embark on a comprehensive exploration of the latest advancements in world models. Our analysis navigates through the forefront of generative methodologies in video generation, where world models stand as pivotal constructs facilitating the synthesis of highly realistic visual content. Additionally, we scrutinize the burgeoning field of autonomous-driving world models, meticulously delineating their indispensable role in reshaping transportation and urban mobility. Furthermore, we delve into the intricacies inherent in world models deployed within autonomous agents, shedding light on their profound significance in enabling intelligent interactions within dynamic environmental contexts. At last, we examine challenges and limitations of world models, and discuss their potential future directions. We hope this survey can serve as a foundational reference for the research community and inspire continued innovation. This survey will be regularly updated at: https://github.com/GigaAI-research/General-World-Models-Survey.

Model merging has become one of the key technologies for enhancing the capabilities and efficiency of Large Language Models (LLMs). However, our understanding of the expected performance gains and principles when merging any two models remains limited. In this work, we introduce model kinship, the degree of similarity or relatedness between LLMs, analogous to biological evolution. With comprehensive empirical analysis, we find that there is a certain relationship between model kinship and the performance gains after model merging, which can help guide our selection of candidate models. Inspired by this, we propose a new model merging strategy: Top-k Greedy Merging with Model Kinship, which can yield better performance on benchmark datasets. Specifically, we discover that using model kinship as a criterion can assist us in continuously performing model merging, alleviating the degradation (local optima) in model evolution, whereas model kinship can serve as a guide to escape these traps. Code is available at https://github.com/zjunlp/ModelKinship.

We present a comprehensive evaluation of proprietary and open-weights large language models using the first astronomy-specific benchmarking dataset. This dataset comprises 4,425 multiple-choice questions curated from the Annual Review of Astronomy and Astrophysics, covering a broad range of astrophysical topics. Our analysis examines model performance across various astronomical subfields and assesses response calibration, crucial for potential deployment in research environments. Claude-3.5-Sonnet outperforms competitors by up to 4.6 percentage points, achieving 85.0% accuracy. For proprietary models, we observed a universal reduction in cost every 3-to-12 months to achieve similar score in this particular astronomy benchmark. Open-source models have rapidly improved, with LLaMA-3-70b (80.6%) and Qwen-2-72b (77.7%) now competing with some of the best proprietary models. We identify performance variations across topics, with non-English-focused models generally struggling more in exoplanet-related fields, stellar astrophysics, and instrumentation related questions. These challenges likely stem from less abundant training data, limited historical context, and rapid recent developments in these areas. This pattern is observed across both open-weights and proprietary models, with regional dependencies evident, highlighting the impact of training data diversity on model performance in specialized scientific domains. Top-performing models demonstrate well-calibrated confidence, with correlations above 0.9 between confidence and correctness, though they tend to be slightly underconfident. The development for fast, low-cost inference of open-weights models presents new opportunities for affordable deployment in astronomy. The rapid progress observed suggests that LLM-driven research in astronomy may become feasible in the near future.

Large Language Models (LLMs) excel in stand-alone code tasks like HumanEval and MBPP, but struggle with handling entire code repositories. This challenge has prompted research on enhancing LLM-codebase interaction at a repository scale. Current solutions rely on similarity-based retrieval or manual tools and APIs, each with notable drawbacks. Similarity-based retrieval often has low recall in complex tasks, while manual tools and APIs are typically task-specific and require expert knowledge, reducing their generalizability across diverse code tasks and real-world applications. To mitigate these limitations, we introduce \framework, a system that integrates LLM agents with graph database interfaces extracted from code repositories. By leveraging the structural properties of graph databases and the flexibility of the graph query language, \framework enables the LLM agent to construct and execute queries, allowing for precise, code structure-aware context retrieval and code navigation. We assess \framework using three benchmarks: CrossCodeEval, SWE-bench, and EvoCodeBench. Additionally, we develop five real-world coding applications. With a unified graph database schema, \framework demonstrates competitive performance and potential in both academic and real-world environments, showcasing its versatility and efficacy in software engineering. Our application demo: https://github.com/modelscope/modelscope-agent/tree/master/apps/codexgraph_agent.

We present Mantis Shrimp, a multi-survey deep learning model for photometric redshift estimation that fuses ultra-violet (GALEX), optical (PanSTARRS), and infrared (UnWISE) imagery. Machine learning is now an established approach for photometric redshift estimation, with generally acknowledged higher performance in areas with a high density of spectroscopically identified galaxies over template-based methods. Multiple works have shown that image-based convolutional neural networks can outperform tabular-based color/magnitude models. In comparison to tabular models, image models have additional design complexities: it is largely unknown how to fuse inputs from different instruments which have different resolutions or noise properties. The Mantis Shrimp model estimates the conditional density estimate of redshift using cutout images. The density estimates are well calibrated and the point estimates perform well in the distribution of available spectroscopically confirmed galaxies with (bias = 1e-2), scatter (NMAD = 2.44e-2) and catastrophic outlier rate (eta=17.53%). We find that early fusion approaches (e.g., resampling and stacking images from different instruments) match the performance of late fusion approaches (e.g., concatenating latent space representations), so that the design choice ultimately is left to the user. Finally, we study how the models learn to use information across bands, finding evidence that our models successfully incorporates information from all surveys. The applicability of our model to the analysis of large populations of galaxies is limited by the speed of downloading cutouts from external servers; however, our model could be useful in smaller studies such as generating priors over redshift for stellar population synthesis.

Deep learning (DL) models have emerged as a powerful tool in avian bioacoustics to diagnose environmental health and biodiversity. However, inconsistencies in research pose notable challenges hindering progress in this domain. Reliable DL models need to analyze bird calls flexibly across various species and environments to fully harness the potential of bioacoustics in a cost-effective passive acoustic monitoring scenario. Data fragmentation and opacity across studies complicate a comprehensive evaluation of general model performance. To overcome these challenges, we present the BirdSet benchmark, a unified framework consolidating research efforts with a holistic approach for classifying bird vocalizations in avian bioacoustics. BirdSet harmonizes open-source bird recordings into a curated dataset collection. This unified approach provides an in-depth understanding of model performance and identifies potential shortcomings across different tasks. By establishing baseline results of current models, BirdSet aims to facilitate comparability, guide subsequent data collection, and increase accessibility for newcomers to avian bioacoustics.

This technical report presents Prithvi-EO-2.0, a new geospatial foundation model that offers significant improvements over its predecessor, Prithvi-EO-1.0. Trained on 4.2M global time series samples from NASA's Harmonized Landsat and Sentinel-2 data archive at 30m resolution, the new 300M and 600M parameter models incorporate temporal and location embeddings for enhanced performance across various geospatial tasks. Through extensive benchmarking with GEO-Bench, the 600M version outperforms the previous Prithvi-EO model by 8\% across a range of tasks. It also outperforms six other geospatial foundation models when benchmarked on remote sensing tasks from different domains and resolutions (i.e. from 0.1m to 15m). The results demonstrate the versatility of the model in both classical earth observation and high-resolution applications. Early involvement of end-users and subject matter experts (SMEs) are among the key factors that contributed to the project's success. In particular, SME involvement allowed for constant feedback on model and dataset design, as well as successful customization for diverse SME-led applications in disaster response, land use and crop mapping, and ecosystem dynamics monitoring. Prithvi-EO-2.0 is available on Hugging Face and IBM terratorch, with additional resources on GitHub. The project exemplifies the Trusted Open Science approach embraced by all involved organizations.

Diffusion models, a powerful and universal generative AI technology, have achieved tremendous success in computer vision, audio, reinforcement learning, and computational biology. In these applications, diffusion models provide flexible high-dimensional data modeling, and act as a sampler for generating new samples under active guidance towards task-desired properties. Despite the significant empirical success, theory of diffusion models is very limited, potentially slowing down principled methodological innovations for further harnessing and improving diffusion models. In this paper, we review emerging applications of diffusion models, understanding their sample generation under various controls. Next, we overview the existing theories of diffusion models, covering their statistical properties and sampling capabilities. We adopt a progressive routine, beginning with unconditional diffusion models and connecting to conditional counterparts. Further, we review a new avenue in high-dimensional structured optimization through conditional diffusion models, where searching for solutions is reformulated as a conditional sampling problem and solved by diffusion models. Lastly, we discuss future directions about diffusion models. The purpose of this paper is to provide a well-rounded theoretical exposure for stimulating forward-looking theories and methods of diffusion models.

Diffusion models are generative models that have recently demonstrated impressive performances in terms of sampling quality and density estimation in high dimensions. They rely on a forward continuous diffusion process and a backward continuous denoising process, which can be described by a time-dependent vector field and is used as a generative model. In the original formulation of the diffusion model, this vector field is assumed to be the score function (i.e. it is the gradient of the log-probability at a given time in the diffusion process). Curiously, on the practical side, most studies on diffusion models implement this vector field as a neural network function and do not constrain it be the gradient of some energy function (that is, most studies do not constrain the vector field to be conservative). Even though some studies investigated empirically whether such a constraint will lead to a performance gain, they lead to contradicting results and failed to provide analytical results. Here, we provide three analytical results regarding the extent of the modeling freedom of this vector field. {Firstly, we propose a novel decomposition of vector fields into a conservative component and an orthogonal component which satisfies a given (gauge) freedom. Secondly, from this orthogonal decomposition, we show that exact density estimation and exact sampling is achieved when the conservative component is exactly equals to the true score and therefore conservativity is neither necessary nor sufficient to obtain exact density estimation and exact sampling. Finally, we show that when it comes to inferring local information of the data manifold, constraining the vector field to be conservative is desirable.

Score-based diffusion models are a class of generative models whose dynamics is described by stochastic differential equations that map noise into data. While recent works have started to lay down a theoretical foundation for these models, an analytical understanding of the role of the diffusion time T is still lacking. Current best practice advocates for a large T to ensure that the forward dynamics brings the diffusion sufficiently close to a known and simple noise distribution; however, a smaller value of T should be preferred for a better approximation of the score-matching objective and higher computational efficiency. Starting from a variational interpretation of diffusion models, in this work we quantify this trade-off, and suggest a new method to improve quality and efficiency of both training and sampling, by adopting smaller diffusion times. Indeed, we show how an auxiliary model can be used to bridge the gap between the ideal and the simulated forward dynamics, followed by a standard reverse diffusion process. Empirical results support our analysis; for image data, our method is competitive w.r.t. the state-of-the-art, according to standard sample quality metrics and log-likelihood.

MATSim (Multi-Agent Transport Simulation Toolkit) is an open source large-scale agent-based transportation planning project applied to various areas like road transport, public transport, freight transport, regional evacuation, etc. BEAM (Behavior, Energy, Autonomy, and Mobility) framework extends MATSim to enable powerful and scalable analysis of urban transportation systems. The agents from the BEAM simulation exhibit 'mode choice' behavior based on multinomial logit model. In our study, we consider eight mode choices viz. bike, car, walk, ride hail, driving to transit, walking to transit, ride hail to transit, and ride hail pooling. The 'alternative specific constants' for each mode choice are critical hyperparameters in a configuration file related to a particular scenario under experimentation. We use the 'Urbansim-10k' BEAM scenario (with 10,000 population size) for all our experiments. Since these hyperparameters affect the simulation in complex ways, manual calibration methods are time consuming. We present a parallel Bayesian optimization method with early stopping rule to achieve fast convergence for the given multi-in-multi-out problem to its optimal configurations. Our model is based on an open source HpBandSter package. This approach combines hierarchy of several 1D Kernel Density Estimators (KDE) with a cheap evaluator (Hyperband, a single multidimensional KDE). Our model has also incorporated extrapolation based early stopping rule. With our model, we could achieve a 25% L1 norm for a large-scale BEAM simulation in fully autonomous manner. To the best of our knowledge, our work is the first of its kind applied to large-scale multi-agent transportation simulations. This work can be useful for surrogate modeling of scenarios with very large populations.

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

As the open-weight AI landscape continues to proliferate-with model development, significant investment, and user interest-it becomes increasingly important to predict which models will ultimately drive innovation and shape AI ecosystems. Building on parallels with citation dynamics in scientific literature, we propose a framework to quantify how an open-weight model's influence evolves. Specifically, we adapt the model introduced by Wang et al. for scientific citations, using three key parameters-immediacy, longevity, and relative fitness-to track the cumulative number of fine-tuned models of an open-weight model. Our findings reveal that this citation-style approach can effectively capture the diverse trajectories of open-weight model adoption, with most models fitting well and outliers indicating unique patterns or abrupt jumps in usage.

Language models now constitute essential tools for improving efficiency for many professional tasks such as writing, coding, or learning. For this reason, it is imperative to identify inherent biases. In the field of Natural Language Processing, five sources of bias are well-identified: data, annotation, representation, models, and research design. This study focuses on biases related to geographical knowledge. We explore the connection between geography and language models by highlighting their tendency to misrepresent spatial information, thus leading to distortions in the representation of geographical distances. This study introduces four indicators to assess these distortions, by comparing geographical and semantic distances. Experiments are conducted from these four indicators with ten widely used language models. Results underscore the critical necessity of inspecting and rectifying spatial biases in language models to ensure accurate and equitable representations.

As part of an ongoing worldwide effort to comprehend and monitor insect biodiversity, this paper presents the BIOSCAN-5M Insect dataset to the machine learning community and establish several benchmark tasks. BIOSCAN-5M is a comprehensive dataset containing multi-modal information for over 5 million insect specimens, and it significantly expands existing image-based biological datasets by including taxonomic labels, raw nucleotide barcode sequences, assigned barcode index numbers, and geographical information. We propose three benchmark experiments to demonstrate the impact of the multi-modal data types on the classification and clustering accuracy. First, we pretrain a masked language model on the DNA barcode sequences of the BIOSCAN-5M dataset, and demonstrate the impact of using this large reference library on species- and genus-level classification performance. Second, we propose a zero-shot transfer learning task applied to images and DNA barcodes to cluster feature embeddings obtained from self-supervised learning, to investigate whether meaningful clusters can be derived from these representation embeddings. Third, we benchmark multi-modality by performing contrastive learning on DNA barcodes, image data, and taxonomic information. This yields a general shared embedding space enabling taxonomic classification using multiple types of information and modalities. The code repository of the BIOSCAN-5M Insect dataset is available at {https://github.com/zahrag/BIOSCAN-5M}

Generalization is arguably the most important goal of statistical language modeling research. Publicly available benchmarks and papers published with an open-source code have been critical to advancing the field. However, it is often very difficult, and sometimes even impossible, to reproduce the results fully as reported in publications. In this paper, we propose a simple framework that should help advance the state of the art in language modeling in terms of generalization. We propose to publish not just the code, but also probabilities on dev and test sets with future publications so that one can easily add the new model into an ensemble. This has crucial advantages: it is much easier to determine whether a newly proposed model is actually complementary to the current baseline. Therefore, instead of inventing new names for the old tricks, the scientific community can advance faster. Finally, this approach promotes diversity of ideas: one does not need to create an individual model that is the new state of the art to attract attention; it will be sufficient to develop a new model that learns patterns which other models do not. Thus, even a suboptimal model can be found to have value. Remarkably, our approach has yielded new state-of-the-art results across various language modeling benchmarks up to 10%.

We introduce Biomaker CA: a Biome Maker project using Cellular Automata (CA). In Biomaker CA, morphogenesis is a first class citizen and small seeds need to grow into plant-like organisms to survive in a nutrient starved environment and eventually reproduce with variation so that a biome survives for long timelines. We simulate complex biomes by means of CA rules in 2D grids and parallelize all of its computation on GPUs through the Python JAX framework. We show how this project allows for several different kinds of environments and laws of 'physics', alongside different model architectures and mutation strategies. We further analyze some configurations to show how plant agents can grow, survive, reproduce, and evolve, forming stable and unstable biomes. We then demonstrate how one can meta-evolve models to survive in a harsh environment either through end-to-end meta-evolution or by a more surgical and efficient approach, called Petri dish meta-evolution. Finally, we show how to perform interactive evolution, where the user decides how to evolve a plant model interactively and then deploys it in a larger environment. We open source Biomaker CA at: https://tinyurl.com/2x8yu34s .

As the capabilities of Large Language Models (LLMs) in healthcare and medicine continue to advance, there is a growing need for competitive open-source models that can safeguard public interest. With the increasing availability of highly competitive open base models, the impact of continued pre-training is increasingly uncertain. In this work, we explore the role of instruct tuning, model merging, alignment, red teaming and advanced inference schemes, as means to improve current open models. To that end, we introduce the Aloe family, a set of open medical LLMs highly competitive within its scale range. Aloe models are trained on the current best base models (Mistral, LLaMA 3), using a new custom dataset which combines public data sources improved with synthetic Chain of Thought (CoT). Aloe models undergo an alignment phase, becoming one of the first few policy-aligned open healthcare LLM using Direct Preference Optimization, setting a new standard for ethical performance in healthcare LLMs. Model evaluation expands to include various bias and toxicity datasets, a dedicated red teaming effort, and a much-needed risk assessment for healthcare LLMs. Finally, to explore the limits of current LLMs in inference, we study several advanced prompt engineering strategies to boost performance across benchmarks, yielding state-of-the-art results for open healthcare 7B LLMs, unprecedented at this scale.

Large language models (LLM) have demonstrated emergent abilities in text generation, question answering, and reasoning, facilitating various tasks and domains. Despite their proficiency in various tasks, LLMs like LaPM 540B and Llama-3.1 405B face limitations due to large parameter sizes and computational demands, often requiring cloud API use which raises privacy concerns, limits real-time applications on edge devices, and increases fine-tuning costs. Additionally, LLMs often underperform in specialized domains such as healthcare and law due to insufficient domain-specific knowledge, necessitating specialized models. Therefore, Small Language Models (SLMs) are increasingly favored for their low inference latency, cost-effectiveness, efficient development, and easy customization and adaptability. These models are particularly well-suited for resource-limited environments and domain knowledge acquisition, addressing LLMs' challenges and proving ideal for applications that require localized data handling for privacy, minimal inference latency for efficiency, and domain knowledge acquisition through lightweight fine-tuning. The rising demand for SLMs has spurred extensive research and development. However, a comprehensive survey investigating issues related to the definition, acquisition, application, enhancement, and reliability of SLM remains lacking, prompting us to conduct a detailed survey on these topics. The definition of SLMs varies widely, thus to standardize, we propose defining SLMs by their capability to perform specialized tasks and suitability for resource-constrained settings, setting boundaries based on the minimal size for emergent abilities and the maximum size sustainable under resource constraints. For other aspects, we provide a taxonomy of relevant models/methods and develop general frameworks for each category to enhance and utilize SLMs effectively.

Deep Neural Networks (DNNs) are being adopted as components in software systems. Creating and specializing DNNs from scratch has grown increasingly difficult as state-of-the-art architectures grow more complex. Following the path of traditional software engineering, machine learning engineers have begun to reuse large-scale pre-trained models (PTMs) and fine-tune these models for downstream tasks. Prior works have studied reuse practices for traditional software packages to guide software engineers towards better package maintenance and dependency management. We lack a similar foundation of knowledge to guide behaviors in pre-trained model ecosystems. In this work, we present the first empirical investigation of PTM reuse. We interviewed 12 practitioners from the most popular PTM ecosystem, Hugging Face, to learn the practices and challenges of PTM reuse. From this data, we model the decision-making process for PTM reuse. Based on the identified practices, we describe useful attributes for model reuse, including provenance, reproducibility, and portability. Three challenges for PTM reuse are missing attributes, discrepancies between claimed and actual performance, and model risks. We substantiate these identified challenges with systematic measurements in the Hugging Face ecosystem. Our work informs future directions on optimizing deep learning ecosystems by automated measuring useful attributes and potential attacks, and envision future research on infrastructure and standardization for model registries.

Existing ML-based atmospheric models are not suitable for climate prediction, which requires long-term stability and physical consistency. We present ACE (AI2 Climate Emulator), a 200M-parameter, autoregressive machine learning emulator of an existing comprehensive 100-km resolution global atmospheric model. The formulation of ACE allows evaluation of physical laws such as the conservation of mass and moisture. The emulator is stable for 100 years, nearly conserves column moisture without explicit constraints and faithfully reproduces the reference model's climate, outperforming a challenging baseline on over 90% of tracked variables. ACE requires nearly 100x less wall clock time and is 100x more energy efficient than the reference model using typically available resources. Without fine-tuning, ACE can stably generalize to a previously unseen historical sea surface temperature dataset.

Recent work in scientific machine learning (SciML) has focused on incorporating partial differential equation (PDE) information into the learning process. Much of this work has focused on relatively ``easy'' PDE operators (e.g., elliptic and parabolic), with less emphasis on relatively ``hard'' PDE operators (e.g., hyperbolic). Within numerical PDEs, the latter problem class requires control of a type of volume element or conservation constraint, which is known to be challenging. Delivering on the promise of SciML requires seamlessly incorporating both types of problems into the learning process. To address this issue, we propose ProbConserv, a framework for incorporating conservation constraints into a generic SciML architecture. To do so, ProbConserv combines the integral form of a conservation law with a Bayesian update. We provide a detailed analysis of ProbConserv on learning with the Generalized Porous Medium Equation (GPME), a widely-applicable parameterized family of PDEs that illustrates the qualitative properties of both easier and harder PDEs. ProbConserv is effective for easy GPME variants, performing well with state-of-the-art competitors; and for harder GPME variants it outperforms other approaches that do not guarantee volume conservation. ProbConserv seamlessly enforces physical conservation constraints, maintains probabilistic uncertainty quantification (UQ), and deals well with shocks and heteroscedasticities. In each case, it achieves superior predictive performance on downstream tasks.

With the proliferation of domain-specific models, model merging has emerged as a set of techniques that combine the capabilities of multiple models into one that can multitask without the cost of additional training. In this paper, we propose a new model merging technique, Drop and rEscaLe via sampLing with mAgnitude (DELLA-Merging), that employs a novel pruning technique, MAGPRUNE, which shows significant advantages over DARE and TIES. MAGPRUNE first ranks the parameters in order of their magnitude and assigns higher dropout probabilities (p) to parameters with lower ranks corresponding to lower magnitudes. To approximate the original embeddings, MAGPRUNE employs a rescaling operation on the parameters that survive the random dropping by 1/(1 - p). On three different expert models considered for merging (LM, Math, Code) and corresponding benchmark datasets (AlpacaEval, GSM8K, MBPP), DELLA shows an average improvement of 2.4 points over baseline methods employing delta parameter pruning (an improvement of 3.6 points over TIES, 1.2 points over DARE), and 11.1 points over the no-pruning baseline (TA). We release the source code at: https://github.com/declare-lab/della.

Real-time detection and prediction of extreme weather protect human lives and infrastructure. Traditional methods rely on numerical threshold setting and manual interpretation of weather heatmaps with Geographic Information Systems (GIS), which can be slow and error-prone. Our research redefines Extreme Weather Events Detection (EWED) by framing it as a Visual Question Answering (VQA) problem, thereby introducing a more precise and automated solution. Leveraging Vision-Language Models (VLM) to simultaneously process visual and textual data, we offer an effective aid to enhance the analysis process of weather heatmaps. Our initial assessment of general-purpose VLMs (e.g., GPT-4-Vision) on EWED revealed poor performance, characterized by low accuracy and frequent hallucinations due to inadequate color differentiation and insufficient meteorological knowledge. To address these challenges, we introduce ClimateIQA, the first meteorological VQA dataset, which includes 8,760 wind gust heatmaps and 254,040 question-answer pairs covering four question types, both generated from the latest climate reanalysis data. We also propose Sparse Position and Outline Tracking (SPOT), an innovative technique that leverages OpenCV and K-Means clustering to capture and depict color contours in heatmaps, providing ClimateIQA with more accurate color spatial location information. Finally, we present Climate-Zoo, the first meteorological VLM collection, which adapts VLMs to meteorological applications using the ClimateIQA dataset. Experiment results demonstrate that models from Climate-Zoo substantially outperform state-of-the-art general VLMs, achieving an accuracy increase from 0% to over 90% in EWED verification. The datasets and models in this study are publicly available for future climate science research: https://github.com/AlexJJJChen/Climate-Zoo.

Many empirical studies of labor market questions rely on estimating relatively simple predictive models using small, carefully constructed longitudinal survey datasets based on hand-engineered features. Large Language Models (LLMs), trained on massive datasets, encode vast quantities of world knowledge and can be used for the next job prediction problem. However, while an off-the-shelf LLM produces plausible career trajectories when prompted, the probability with which an LLM predicts a particular job transition conditional on career history will not, in general, align with the true conditional probability in a given population. Recently, Vafa et al. (2024) introduced a transformer-based "foundation model", CAREER, trained using a large, unrepresentative resume dataset, that predicts transitions between jobs; it further demonstrated how transfer learning techniques can be used to leverage the foundation model to build better predictive models of both transitions and wages that reflect conditional transition probabilities found in nationally representative survey datasets. This paper considers an alternative where the fine-tuning of the CAREER foundation model is replaced by fine-tuning LLMs. For the task of next job prediction, we demonstrate that models trained with our approach outperform several alternatives in terms of predictive performance on the survey data, including traditional econometric models, CAREER, and LLMs with in-context learning, even though the LLM can in principle predict job titles that are not allowed in the survey data. Further, we show that our fine-tuned LLM-based models' predictions are more representative of the career trajectories of various workforce subpopulations than off-the-shelf LLM models and CAREER. We conduct experiments and analyses that highlight the sources of the gains in the performance of our models for representative predictions.

Accurate prediction of climate in the subseasonal-to-seasonal scale is crucial for disaster readiness, reduced economic risk, and improved policy-making amidst climate change. Yet, S2S prediction remains challenging due to the chaotic nature of the system. At present, existing benchmarks for weather and climate applications, tend to (1) have shorter forecasting range of up-to 14 days, (2) do not include a wide range of operational baseline forecasts, and (3) lack physics-based constraints for explainability. Thus, we propose ChaosBench, a large-scale, multi-channel, physics-based benchmark for S2S prediction. ChaosBench has over 460K frames of real-world observations and simulations, each with 60 variable-channels and spanning for up-to 45 years. We also propose several physics-based, in addition to vision-based metrics, that enables for a more physically-consistent model. Furthermore, we include a diverse set of physics-based forecasts from 4 national weather agencies as baselines to our data-driven counterpart. We establish two tasks that vary in complexity: full and sparse dynamics prediction. Our benchmark is one of the first to perform large-scale evaluation on existing models including PanguWeather, FourCastNetV2, GraphCast, and ClimaX, and finds methods originally developed for weather-scale applications fails on S2S task. We release our benchmark code and datasets at https://leap-stc.github.io/ChaosBench.

In domains ranging from computer vision to natural language processing, machine learning models have been shown to exhibit stark disparities, often performing worse for members of traditionally underserved groups. One factor contributing to these performance gaps is a lack of representation in the data the models are trained on. It is often unclear, however, how to operationalize representativeness in specific applications. Here we formalize the problem of creating equitable training datasets, and propose a statistical framework for addressing this problem. We consider a setting where a model builder must decide how to allocate a fixed data collection budget to gather training data from different subgroups. We then frame dataset creation as a constrained optimization problem, in which one maximizes a function of group-specific performance metrics based on (estimated) group-specific learning rates and costs per sample. This flexible approach incorporates preferences of model-builders and other stakeholders, as well as the statistical properties of the learning task. When data collection decisions are made sequentially, we show that under certain conditions this optimization problem can be efficiently solved even without prior knowledge of the learning rates. To illustrate our approach, we conduct a simulation study of polygenic risk scores on synthetic genomic data -- an application domain that often suffers from non-representative data collection. We find that our adaptive sampling strategy outperforms several common data collection heuristics, including equal and proportional sampling, demonstrating the value of strategic dataset design for building equitable models.

Supervised learning datasets may contain multiple cues that explain the training set equally well, i.e., learning any of them would lead to the correct predictions on the training data. However, many of them can be spurious, i.e., lose their predictive power under a distribution shift and consequently fail to generalize to out-of-distribution (OOD) data. Recently developed "diversification" methods (Lee et al., 2023; Pagliardini et al., 2023) approach this problem by finding multiple diverse hypotheses that rely on different features. This paper aims to study this class of methods and identify the key components contributing to their OOD generalization abilities. We show that (1) diversification methods are highly sensitive to the distribution of the unlabeled data used for diversification and can underperform significantly when away from a method-specific sweet spot. (2) Diversification alone is insufficient for OOD generalization. The choice of the used learning algorithm, e.g., the model's architecture and pretraining, is crucial. In standard experiments (classification on Waterbirds and Office-Home datasets), using the second-best choice leads to an up to 20\% absolute drop in accuracy. (3) The optimal choice of learning algorithm depends on the unlabeled data and vice versa i.e. they are co-dependent. (4) Finally, we show that, in practice, the above pitfalls cannot be alleviated by increasing the number of diverse hypotheses, the major feature of diversification methods. These findings provide a clearer understanding of the critical design factors influencing the OOD generalization abilities of diversification methods. They can guide practitioners in how to use the existing methods best and guide researchers in developing new, better ones.