Daily Papers

In this paper, we propose LSRNA, a novel framework for higher-resolution (exceeding 1K) image generation using diffusion models by leveraging super-resolution directly in the latent space. Existing diffusion models struggle with scaling beyond their training resolutions, often leading to structural distortions or content repetition. Reference-based methods address the issues by upsampling a low-resolution reference to guide higher-resolution generation. However, they face significant challenges: upsampling in latent space often causes manifold deviation, which degrades output quality. On the other hand, upsampling in RGB space tends to produce overly smoothed outputs. To overcome these limitations, LSRNA combines Latent space Super-Resolution (LSR) for manifold alignment and Region-wise Noise Addition (RNA) to enhance high-frequency details. Our extensive experiments demonstrate that integrating LSRNA outperforms state-of-the-art reference-based methods across various resolutions and metrics, while showing the critical role of latent space upsampling in preserving detail and sharpness. The code is available at https://github.com/3587jjh/LSRNA.

Denoising diffusion probabilistic models (DDPMs) employ a sequence of white Gaussian noise samples to generate an image. In analogy with GANs, those noise maps could be considered as the latent code associated with the generated image. However, this native noise space does not possess a convenient structure, and is thus challenging to work with in editing tasks. Here, we propose an alternative latent noise space for DDPM that enables a wide range of editing operations via simple means, and present an inversion method for extracting these edit-friendly noise maps for any given image (real or synthetically generated). As opposed to the native DDPM noise space, the edit-friendly noise maps do not have a standard normal distribution and are not statistically independent across timesteps. However, they allow perfect reconstruction of any desired image, and simple transformations on them translate into meaningful manipulations of the output image (e.g., shifting, color edits). Moreover, in text-conditional models, fixing those noise maps while changing the text prompt, modifies semantics while retaining structure. We illustrate how this property enables text-based editing of real images via the diverse DDPM sampling scheme (in contrast to the popular non-diverse DDIM inversion). We also show how it can be used within existing diffusion-based editing methods to improve their quality and diversity.

RNA plays a pivotal role in translating genetic instructions into functional outcomes, underscoring its importance in biological processes and disease mechanisms. Despite the emergence of numerous deep learning approaches for RNA, particularly universal RNA language models, there remains a significant lack of standardized benchmarks to assess the effectiveness of these methods. In this study, we introduce the first comprehensive RNA benchmark BEACON (BEnchmArk for COmprehensive RNA Task and Language Models). First, BEACON comprises 13 distinct tasks derived from extensive previous work covering structural analysis, functional studies, and engineering applications, enabling a comprehensive assessment of the performance of methods on various RNA understanding tasks. Second, we examine a range of models, including traditional approaches like CNNs, as well as advanced RNA foundation models based on language models, offering valuable insights into the task-specific performances of these models. Third, we investigate the vital RNA language model components from the tokenizer and positional encoding aspects. Notably, our findings emphasize the superiority of single nucleotide tokenization and the effectiveness of Attention with Linear Biases (ALiBi) over traditional positional encoding methods. Based on these insights, a simple yet strong baseline called BEACON-B is proposed, which can achieve outstanding performance with limited data and computational resources. The datasets and source code of our benchmark are available at https://github.com/terry-r123/RNABenchmark.

Ribonucleic acid (RNA) plays a variety of crucial roles in fundamental biological processes. Recently, RNA has become an interesting drug target, emphasizing the need to improve our understanding of its structures and functions. Over the years, sequencing technologies have produced an enormous amount of unlabeled RNA data, which hides important knowledge and potential. Motivated by the successes of protein language models, we introduce RiboNucleic Acid Language Model (RiNALMo) to help unveil the hidden code of RNA. RiNALMo is the largest RNA language model to date with 650 million parameters pre-trained on 36 million non-coding RNA sequences from several available databases. RiNALMo is able to extract hidden knowledge and capture the underlying structure information implicitly embedded within the RNA sequences. RiNALMo achieves state-of-the-art results on several downstream tasks. Notably, we show that its generalization capabilities can overcome the inability of other deep learning methods for secondary structure prediction to generalize on unseen RNA families. The code has been made publicly available on https://github.com/lbcb-sci/RiNALMo.

During both pretraining and fine-tuning, Large Language Models (LLMs) are trained on trillions of tokens of text of widely varying quality. Both phases of training typically involve heuristically filtering out ``low-quality'' or noisy training samples, yet little is known quantitatively about how the type or intensity of noise affects downstream performance. In this work, we study how noise in chain of thought (CoT) impacts task performance in the highly-controlled setting of algorithmically solvable tasks. First, we develop the Traced Integer (TInt) framework to generate highly customizable noised execution traces for any arithmetic function on lists of integers. We then define two types of noise: static noise, a local form of noise which is applied after the CoT trace is computed, and dynamic noise, a global form of noise which propagates errors in the trace as it is computed. We then evaluate the test performance of pretrained models both prompted and fine-tuned on noised datasets with varying levels of dataset contamination and intensity. We find fine-tuned models are extremely robust to high levels of static noise but struggle significantly more with lower levels of dynamic noise. In contrast, few-shot prompted models appear more sensitive to even static noise. We conclude with a discussion of how our findings impact noise filtering best-practices, in particular emphasizing the importance of removing samples containing destructive dynamic noise with global errors.

Diffusion models have opened the path to a wide range of text-based image editing frameworks. However, these typically build on the multi-step nature of the diffusion backwards process, and adapting them to distilled, fast-sampling methods has proven surprisingly challenging. Here, we focus on a popular line of text-based editing frameworks - the ``edit-friendly'' DDPM-noise inversion approach. We analyze its application to fast sampling methods and categorize its failures into two classes: the appearance of visual artifacts, and insufficient editing strength. We trace the artifacts to mismatched noise statistics between inverted noises and the expected noise schedule, and suggest a shifted noise schedule which corrects for this offset. To increase editing strength, we propose a pseudo-guidance approach that efficiently increases the magnitude of edits without introducing new artifacts. All in all, our method enables text-based image editing with as few as three diffusion steps, while providing novel insights into the mechanisms behind popular text-based editing approaches.

Non-coding RNA structure and function are essential to understanding various biological processes, such as cell signaling, gene expression, and post-transcriptional regulations. These are all among the core problems in the RNA field. With the rapid growth of sequencing technology, we have accumulated a massive amount of unannotated RNA sequences. On the other hand, expensive experimental observatory results in only limited numbers of annotated data and 3D structures. Hence, it is still challenging to design computational methods for predicting their structures and functions. The lack of annotated data and systematic study causes inferior performance. To resolve the issue, we propose a novel RNA foundation model (RNA-FM) to take advantage of all the 23 million non-coding RNA sequences through self-supervised learning. Within this approach, we discover that the pre-trained RNA-FM could infer sequential and evolutionary information of non-coding RNAs without using any labels. Furthermore, we demonstrate RNA-FM's effectiveness by applying it to the downstream secondary/3D structure prediction, SARS-CoV-2 genome structure and evolution prediction, protein-RNA binding preference modeling, and gene expression regulation modeling. The comprehensive experiments show that the proposed method improves the RNA structural and functional modelling results significantly and consistently. Despite only being trained with unlabelled data, RNA-FM can serve as the foundational model for the field.

Diffusion models excel in generating high-quality images. However, current diffusion models struggle to produce reliable images without guidance methods, such as classifier-free guidance (CFG). Are guidance methods truly necessary? Observing that noise obtained via diffusion inversion can reconstruct high-quality images without guidance, we focus on the initial noise of the denoising pipeline. By mapping Gaussian noise to `guidance-free noise', we uncover that small low-magnitude low-frequency components significantly enhance the denoising process, removing the need for guidance and thus improving both inference throughput and memory. Expanding on this, we propose \ours, a novel method that replaces guidance methods with a single refinement of the initial noise. This refined noise enables high-quality image generation without guidance, within the same diffusion pipeline. Our noise-refining model leverages efficient noise-space learning, achieving rapid convergence and strong performance with just 50K text-image pairs. We validate its effectiveness across diverse metrics and analyze how refined noise can eliminate the need for guidance. See our project page: https://cvlab-kaist.github.io/NoiseRefine/.

Text-to-image diffusion model is a popular paradigm that synthesizes personalized images by providing a text prompt and a random Gaussian noise. While people observe that some noises are ``golden noises'' that can achieve better text-image alignment and higher human preference than others, we still lack a machine learning framework to obtain those golden noises. To learn golden noises for diffusion sampling, we mainly make three contributions in this paper. First, we identify a new concept termed the noise prompt, which aims at turning a random Gaussian noise into a golden noise by adding a small desirable perturbation derived from the text prompt. Following the concept, we first formulate the noise prompt learning framework that systematically learns ``prompted'' golden noise associated with a text prompt for diffusion models. Second, we design a noise prompt data collection pipeline and collect a large-scale noise prompt dataset~(NPD) that contains 100k pairs of random noises and golden noises with the associated text prompts. With the prepared NPD as the training dataset, we trained a small noise prompt network~(NPNet) that can directly learn to transform a random noise into a golden noise. The learned golden noise perturbation can be considered as a kind of prompt for noise, as it is rich in semantic information and tailored to the given text prompt. Third, our extensive experiments demonstrate the impressive effectiveness and generalization of NPNet on improving the quality of synthesized images across various diffusion models, including SDXL, DreamShaper-xl-v2-turbo, and Hunyuan-DiT. Moreover, NPNet is a small and efficient controller that acts as a plug-and-play module with very limited additional inference and computational costs, as it just provides a golden noise instead of a random noise without accessing the original pipeline.

Modeling and synthesizing low-light raw noise is a fundamental problem for computational photography and image processing applications. Although most recent works have adopted physics-based models to synthesize noise, the signal-independent noise in low-light conditions is far more complicated and varies dramatically across camera sensors, which is beyond the description of these models. To address this issue, we introduce a new perspective to synthesize the signal-independent noise by a generative model. Specifically, we synthesize the signal-dependent and signal-independent noise in a physics- and learning-based manner, respectively. In this way, our method can be considered as a general model, that is, it can simultaneously learn different noise characteristics for different ISO levels and generalize to various sensors. Subsequently, we present an effective multi-scale discriminator termed Fourier transformer discriminator (FTD) to distinguish the noise distribution accurately. Additionally, we collect a new low-light raw denoising (LRD) dataset for training and benchmarking. Qualitative validation shows that the noise generated by our proposed noise model can be highly similar to the real noise in terms of distribution. Furthermore, extensive denoising experiments demonstrate that our method performs favorably against state-of-the-art methods on different sensors.

Single-nucleus RNA sequencing (snRNA-seq) has significantly advanced our understanding of the disease etiology of neurodegenerative disorders. However, the low quality of specimens derived from postmortem brain tissues, combined with the high variability caused by disease heterogeneity, makes it challenging to integrate snRNA-seq data from multiple sources for precise analyses. To address these challenges, we present scMamba, a pre-trained model designed to improve the quality and utility of snRNA-seq analysis, with a particular focus on neurodegenerative diseases. Inspired by the recent Mamba model, scMamba introduces a novel architecture that incorporates a linear adapter layer, gene embeddings, and bidirectional Mamba blocks, enabling efficient processing of snRNA-seq data while preserving information from the raw input. Notably, scMamba learns generalizable features of cells and genes through pre-training on snRNA-seq data, without relying on dimension reduction or selection of highly variable genes. We demonstrate that scMamba outperforms benchmark methods in various downstream tasks, including cell type annotation, doublet detection, imputation, and the identification of differentially expressed genes.

It is well known that many open-released foundational diffusion models have difficulty in generating images that substantially depart from average brightness, despite such images being present in the training data. This is due to an inconsistency: while denoising starts from pure Gaussian noise during inference, the training noise schedule retains residual data even in the final timestep distribution, due to difficulties in numerical conditioning in mainstream formulation, leading to unintended bias during inference. To mitigate this issue, certain epsilon-prediction models are combined with an ad-hoc offset-noise methodology. In parallel, some contemporary models have adopted zero-terminal SNR noise schedules together with v-prediction, which necessitate major alterations to pre-trained models. However, such changes risk destabilizing a large multitude of community-driven applications anchored on these pre-trained models. In light of this, our investigation revisits the fundamental causes, leading to our proposal of an innovative and principled remedy, called One More Step (OMS). By integrating a compact network and incorporating an additional simple yet effective step during inference, OMS elevates image fidelity and harmonizes the dichotomy between training and inference, while preserving original model parameters. Once trained, various pre-trained diffusion models with the same latent domain can share the same OMS module.

Long non-coding RNAs (lncRNAs) serve as crucial regulators in numerous biological processes. Although they share sequence similarities with messenger RNAs (mRNAs), lncRNAs perform entirely different roles, providing new avenues for biological research. The emergence of next-generation sequencing technologies has greatly advanced the detection and identification of lncRNA transcripts and deep learning-based approaches have been introduced to classify long non-coding RNAs (lncRNAs). These advanced methods have significantly enhanced the efficiency of identifying lncRNAs. However, many of these methods are devoid of robustness and accuracy due to the extended length of the sequences involved. To tackle this issue, we have introduced a novel pre-trained bidirectional encoder representation called LoRA-BERT. LoRA-BERT is designed to capture the importance of nucleotide-level information during sequence classification, leading to more robust and satisfactory outcomes. In a comprehensive comparison with commonly used sequence prediction tools, we have demonstrated that LoRA-BERT outperforms them in terms of accuracy and efficiency. Our results indicate that, when utilizing the transformer model, LoRA-BERT achieves state-of-the-art performance in predicting both lncRNAs and mRNAs for human and mouse species. Through the utilization of LoRA-BERT, we acquire valuable insights into the traits of lncRNAs and mRNAs, offering the potential to aid in the comprehension and detection of diseases linked to lncRNAs in humans.

Deep learning classifiers face significant challenges when dealing with heterogeneous multi-modal and multi-organ biomedical datasets. The low-level feature distinguishability limited to imaging-modality hinders the classifiers' ability to learn high-level semantic relationships, resulting in sub-optimal performance. To address this issue, image augmentation strategies are employed as regularization techniques. While additive noise input during network training is a well-established augmentation as regularization method, modern pipelines often favor more robust techniques such as dropout and weight decay. This preference stems from the observation that combining these established techniques with noise input can adversely affect model performance. In this study, we propose a novel pretraining pipeline that learns to generate conditional noise mask specifically tailored to improve performance on multi-modal and multi-organ datasets. As a reinforcement learning algorithm, our approach employs a dual-component system comprising a very light-weight policy network that learns to sample conditional noise using a differentiable beta distribution as well as a classifier network. The policy network is trained using the reinforce algorithm to generate image-specific noise masks that regularize the classifier during pretraining. A key aspect is that the policy network's role is limited to obtaining an intermediate (or heated) model before fine-tuning. During inference, the policy network is omitted, allowing direct comparison between the baseline and noise-regularized models. We conducted experiments and related analyses on RadImageNet datasets. Results demonstrate that fine-tuning the intermediate models consistently outperforms conventional training algorithms on both classification and generalization to unseen concept tasks.

Distant and weak supervision allow to obtain large amounts of labeled training data quickly and cheaply, but these automatic annotations tend to contain a high amount of errors. A popular technique to overcome the negative effects of these noisy labels is noise modelling where the underlying noise process is modelled. In this work, we study the quality of these estimated noise models from the theoretical side by deriving the expected error of the noise model. Apart from evaluating the theoretical results on commonly used synthetic noise, we also publish NoisyNER, a new noisy label dataset from the NLP domain that was obtained through a realistic distant supervision technique. It provides seven sets of labels with differing noise patterns to evaluate different noise levels on the same instances. Parallel, clean labels are available making it possible to study scenarios where a small amount of gold-standard data can be leveraged. Our theoretical results and the corresponding experiments give insights into the factors that influence the noise model estimation like the noise distribution and the sampling technique.

As a powerful tool for characterizing cellular subpopulations and cellular heterogeneity, single cell RNA sequencing (scRNA-seq) technology offers advantages of high throughput and multidimensional analysis. However, the process of data acquisition is often constrained by high cost and limited sample availability. To overcome these limitations, we propose a hybrid model based on Diffusion model and White-Box transformer that aims to generate synthetic and biologically plausible scRNA-seq data. Diffusion model progressively introduce noise into the data and then recover the original data through a denoising process, a forward and reverse process that is particularly suitable for generating complex data distributions. White-Box transformer is a deep learning architecture that emphasizes mathematical interpretability. By minimizing the encoding rate of the data and maximizing the sparsity of the representation, it not only reduces the computational burden, but also provides clear insight into underlying structure. Our White-Box Diffusion Transformer combines the generative capabilities of Diffusion model with the mathematical interpretability of White-Box transformer. Through experiments using six different single-cell RNA-Seq datasets, we visualize both generated and real data using t-SNE dimensionality reduction technique, as well as quantify similarity between generated and real data using various metrics to demonstrate comparable performance of White-Box Diffusion Transformer and Diffusion Transformer in generating scRNA-seq data alongside significant improvements in training efficiency and resource utilization. Our code is available at https://github.com/lingximamo/White-Box-Diffusion-Transformer

Generative modeling of single-cell RNA-seq data has shown invaluable potential in community-driven tasks such as trajectory inference, batch effect removal and gene expression generation. However, most recent deep models generating synthetic single cells from noise operate on pre-processed continuous gene expression approximations, ignoring the inherently discrete and over-dispersed nature of single-cell data, which limits downstream applications and hinders the incorporation of robust noise models. Moreover, crucial aspects of deep-learning-based synthetic single-cell generation remain underexplored, such as controllable multi-modal and multi-label generation and its role in the performance enhancement of downstream tasks. This work presents Cell Flow for Generation (CFGen), a flow-based conditional generative model for multi-modal single-cell counts, which explicitly accounts for the discrete nature of the data. Our results suggest improved recovery of crucial biological data characteristics while accounting for novel generative tasks such as conditioning on multiple attributes and boosting rare cell type classification via data augmentation. By showcasing CFGen on a diverse set of biological datasets and settings, we provide evidence of its value to the fields of computational biology and deep generative models.

Computational RNA design tasks are often posed as inverse problems, where sequences are designed based on adopting a single desired secondary structure without considering 3D geometry and conformational diversity. We introduce gRNAde, a geometric RNA design pipeline operating on 3D RNA backbones to design sequences that explicitly account for structure and dynamics. Under the hood, gRNAde is a multi-state Graph Neural Network that generates candidate RNA sequences conditioned on one or more 3D backbone structures where the identities of the bases are unknown. On a single-state fixed backbone re-design benchmark of 14 RNA structures from the PDB identified by Das et al. [2010], gRNAde obtains higher native sequence recovery rates (56% on average) compared to Rosetta (45% on average), taking under a second to produce designs compared to the reported hours for Rosetta. We further demonstrate the utility of gRNAde on a new benchmark of multi-state design for structurally flexible RNAs, as well as zero-shot ranking of mutational fitness landscapes in a retrospective analysis of a recent ribozyme. Open source code: https://github.com/chaitjo/geometric-rna-design

Retrieval-Augmented Generation (RAG) has emerged as a crucial method for addressing hallucinations in large language models (LLMs). While recent research has extended RAG models to complex noisy scenarios, these explorations often confine themselves to limited noise types and presuppose that noise is inherently detrimental to LLMs, potentially deviating from real-world retrieval environments and restricting practical applicability. In this paper, we define seven distinct noise types from a linguistic perspective and establish a Noise RAG Benchmark (NoiserBench), a comprehensive evaluation framework encompassing multiple datasets and reasoning tasks. Through empirical evaluation of eight representative LLMs with diverse architectures and scales, we reveal that these noises can be further categorized into two practical groups: noise that is beneficial to LLMs (aka beneficial noise) and noise that is harmful to LLMs (aka harmful noise). While harmful noise generally impairs performance, beneficial noise may enhance several aspects of model capabilities and overall performance. Our analysis offers insights for developing more robust, adaptable RAG solutions and mitigating hallucinations across diverse retrieval scenarios.

Effective communication in Air Traffic Control (ATC) is critical to maintaining aviation safety, yet the challenges posed by accented English remain largely unaddressed in Automatic Speech Recognition (ASR) systems. Existing models struggle with transcription accuracy for Southeast Asian-accented (SEA-accented) speech, particularly in noisy ATC environments. This study presents the development of ASR models fine-tuned specifically for Southeast Asian accents using a newly created dataset. Our research achieves significant improvements, achieving a Word Error Rate (WER) of 0.0982 or 9.82% on SEA-accented ATC speech. Additionally, the paper highlights the importance of region-specific datasets and accent-focused training, offering a pathway for deploying ASR systems in resource-constrained military operations. The findings emphasize the need for noise-robust training techniques and region-specific datasets to improve transcription accuracy for non-Western accents in ATC communications.

Diffusion models achieved great success in image synthesis, but still face challenges in high-resolution generation. Through the lens of discrete cosine transformation, we find the main reason is that the same noise level on a higher resolution results in a higher Signal-to-Noise Ratio in the frequency domain. In this work, we present Relay Diffusion Model (RDM), which transfers a low-resolution image or noise into an equivalent high-resolution one for diffusion model via blurring diffusion and block noise. Therefore, the diffusion process can continue seamlessly in any new resolution or model without restarting from pure noise or low-resolution conditioning. RDM achieves state-of-the-art FID on CelebA-HQ and sFID on ImageNet 256times256, surpassing previous works such as ADM, LDM and DiT by a large margin. All the codes and checkpoints are open-sourced at https://github.com/THUDM/RelayDiffusion.

In this work, we build upon our previous publication and use diffusion-based generative models for speech enhancement. We present a detailed overview of the diffusion process that is based on a stochastic differential equation and delve into an extensive theoretical examination of its implications. Opposed to usual conditional generation tasks, we do not start the reverse process from pure Gaussian noise but from a mixture of noisy speech and Gaussian noise. This matches our forward process which moves from clean speech to noisy speech by including a drift term. We show that this procedure enables using only 30 diffusion steps to generate high-quality clean speech estimates. By adapting the network architecture, we are able to significantly improve the speech enhancement performance, indicating that the network, rather than the formalism, was the main limitation of our original approach. In an extensive cross-dataset evaluation, we show that the improved method can compete with recent discriminative models and achieves better generalization when evaluating on a different corpus than used for training. We complement the results with an instrumental evaluation using real-world noisy recordings and a listening experiment, in which our proposed method is rated best. Examining different sampler configurations for solving the reverse process allows us to balance the performance and computational speed of the proposed method. Moreover, we show that the proposed method is also suitable for dereverberation and thus not limited to additive background noise removal. Code and audio examples are available online, see https://github.com/sp-uhh/sgmse

mRNA-based vaccines have become a major focus in the pharmaceutical industry. The coding sequence as well as the Untranslated Regions (UTRs) of an mRNA can strongly influence translation efficiency, stability, degradation, and other factors that collectively determine a vaccine's effectiveness. However, optimizing mRNA sequences for those properties remains a complex challenge. Existing deep learning models often focus solely on coding region optimization, overlooking the UTRs. We present Helix-mRNA, a structured state-space-based and attention hybrid model to address these challenges. In addition to a first pre-training, a second pre-training stage allows us to specialise the model with high-quality data. We employ single nucleotide tokenization of mRNA sequences with codon separation, ensuring prior biological and structural information from the original mRNA sequence is not lost. Our model, Helix-mRNA, outperforms existing methods in analysing both UTRs and coding region properties. It can process sequences 6x longer than current approaches while using only 10% of the parameters of existing foundation models. Its predictive capabilities extend to all mRNA regions. We open-source the model (https://github.com/helicalAI/helical) and model weights (https://huggingface.co/helical-ai/helix-mRNA).

Existing speculative decoding methods typically require additional model structure and training processes to assist the model for draft token generation. This makes the migration of acceleration methods to the new model more costly and more demanding on device memory. To address this problem, we propose the Make Some Noise (MSN) training framework as a replacement for the supervised fine-tuning stage of the large language model. The training method simply introduces some noise at the input for the model to learn the denoising task. It significantly enhances the parallel decoding capability of the model without affecting the original task capability. In addition, we propose a tree-based retrieval-augmented Jacobi (TR-Jacobi) decoding strategy to further improve the inference speed of MSN models. Experiments in both the general and code domains have shown that MSN can improve inference speed by 2.3-2.7x times without compromising model performance. The MSN model also achieves comparable acceleration ratios to the SOTA model with additional model structure on Spec-Bench.

Text-guided diffusion models have significantly advanced image editing, enabling high-quality and diverse modifications driven by text prompts. However, effective editing requires inverting the source image into a latent space, a process often hindered by prediction errors inherent in DDIM inversion. These errors accumulate during the diffusion process, resulting in inferior content preservation and edit fidelity, especially with conditional inputs. We address these challenges by investigating the primary contributors to error accumulation in DDIM inversion and identify the singularity problem in traditional noise schedules as a key issue. To resolve this, we introduce the Logistic Schedule, a novel noise schedule designed to eliminate singularities, improve inversion stability, and provide a better noise space for image editing. This schedule reduces noise prediction errors, enabling more faithful editing that preserves the original content of the source image. Our approach requires no additional retraining and is compatible with various existing editing methods. Experiments across eight editing tasks demonstrate the Logistic Schedule's superior performance in content preservation and edit fidelity compared to traditional noise schedules, highlighting its adaptability and effectiveness.

Image-to-video (I2V) generation tasks always suffer from keeping high fidelity in the open domains. Traditional image animation techniques primarily focus on specific domains such as faces or human poses, making them difficult to generalize to open domains. Several recent I2V frameworks based on diffusion models can generate dynamic content for open domain images but fail to maintain fidelity. We found that two main factors of low fidelity are the loss of image details and the noise prediction biases during the denoising process. To this end, we propose an effective method that can be applied to mainstream video diffusion models. This method achieves high fidelity based on supplementing more precise image information and noise rectification. Specifically, given a specified image, our method first adds noise to the input image latent to keep more details, then denoises the noisy latent with proper rectification to alleviate the noise prediction biases. Our method is tuning-free and plug-and-play. The experimental results demonstrate the effectiveness of our approach in improving the fidelity of generated videos. For more image-to-video generated results, please refer to the project website: https://noise-rectification.github.io.

Unsupervised denoising is a crucial challenge in real-world imaging applications. Unsupervised deep-learning methods have demonstrated impressive performance on benchmarks based on synthetic noise. However, no metrics are available to evaluate these methods in an unsupervised fashion. This is highly problematic for the many practical applications where ground-truth clean images are not available. In this work, we propose two novel metrics: the unsupervised mean squared error (MSE) and the unsupervised peak signal-to-noise ratio (PSNR), which are computed using only noisy data. We provide a theoretical analysis of these metrics, showing that they are asymptotically consistent estimators of the supervised MSE and PSNR. Controlled numerical experiments with synthetic noise confirm that they provide accurate approximations in practice. We validate our approach on real-world data from two imaging modalities: videos in raw format and transmission electron microscopy. Our results demonstrate that the proposed metrics enable unsupervised evaluation of denoising methods based exclusively on noisy data.

RNA is a vital biomolecule with numerous roles and functions within cells, and interest in targeting it for therapeutic purposes has grown significantly in recent years. However, fully understanding and predicting RNA behavior, particularly for applications in drug discovery, remains a challenge due to the complexity of RNA structures and interactions. While foundational models in biology have demonstrated success in modeling several biomolecules, especially proteins, achieving similar breakthroughs for RNA has proven more difficult. Current RNA models have yet to match the performance observed in the protein domain, leaving an important gap in computational biology. In this work, we present ChaRNABERT, a suite of sample and parameter-efficient RNA foundational models, that through a learnable tokenization process, are able to reach state-of-the-art performance on several tasks in established benchmarks. We extend its testing in relevant downstream tasks such as RNA-protein and aptamer-protein interaction prediction. Weights and inference code for ChaRNABERT-8M will be provided for academic research use. The other models will be available upon request.

It is widely believed that noise conditioning is indispensable for denoising diffusion models to work successfully. This work challenges this belief. Motivated by research on blind image denoising, we investigate a variety of denoising-based generative models in the absence of noise conditioning. To our surprise, most models exhibit graceful degradation, and in some cases, they even perform better without noise conditioning. We provide a theoretical analysis of the error caused by removing noise conditioning and demonstrate that our analysis aligns with empirical observations. We further introduce a noise-unconditional model that achieves a competitive FID of 2.23 on CIFAR-10, significantly narrowing the gap to leading noise-conditional models. We hope our findings will inspire the community to revisit the foundations and formulations of denoising generative models.

Large language models (LLMs) often produce inaccurate or misleading content-hallucinations. To address this challenge, we introduce Noise-Augmented Fine-Tuning (NoiseFiT), a novel framework that leverages adaptive noise injection based on the signal-to-noise ratio (SNR) to enhance model robustness. In particular, NoiseFiT selectively perturbs layers identified as either high-SNR (more robust) or low-SNR (potentially under-regularized) using a dynamically scaled Gaussian noise. We further propose a hybrid loss that combines standard cross-entropy, soft cross-entropy, and consistency regularization to ensure stable and accurate outputs under noisy training conditions. Our theoretical analysis shows that adaptive noise injection is both unbiased and variance-preserving, providing strong guarantees for convergence in expectation. Empirical results on multiple test and benchmark datasets demonstrate that NoiseFiT significantly reduces hallucination rates, often improving or matching baseline performance in key tasks. These findings highlight the promise of noise-driven strategies for achieving robust, trustworthy language modeling without incurring prohibitive computational overhead. Given the comprehensive and detailed nature of our experiments, we have publicly released the fine-tuning logs, benchmark evaluation artifacts, and source code online at W&B, Hugging Face, and GitHub, respectively, to foster further research, accessibility and reproducibility.

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.

We empirically study the effect of noise scheduling strategies for denoising diffusion generative models. There are three findings: (1) the noise scheduling is crucial for the performance, and the optimal one depends on the task (e.g., image sizes), (2) when increasing the image size, the optimal noise scheduling shifts towards a noisier one (due to increased redundancy in pixels), and (3) simply scaling the input data by a factor of b while keeping the noise schedule function fixed (equivalent to shifting the logSNR by log b) is a good strategy across image sizes. This simple recipe, when combined with recently proposed Recurrent Interface Network (RIN), yields state-of-the-art pixel-based diffusion models for high-resolution images on ImageNet, enabling single-stage, end-to-end generation of diverse and high-fidelity images at 1024times1024 resolution (without upsampling/cascades).

Large language models (LLMs) have shown remarkable capabilities in code generation. However, the effects of hallucinations (e.g., output noise) make it particularly challenging for LLMs to generate high-quality code in one pass. In this work, we propose a simple and effective uncertainty-aware selective contrastive decoding (USCD) mechanism to improve the quality of one-pass code generation in LLMs and reduce the impact of output noise. To be specific, we first elaborately designed a negative prompt (namely lame prompt) to output noise by removing input-output examples from the standard few-shot prompt. Our preliminary study shows that the Jensen-Shannon divergence (JS divergence) between token distribution uncertainty and the output noise is relatively low (approximately 0.25), indicating their high relevance. Then, we selectively eliminate output noise induced by lame prompts based on the uncertainty of the prediction distribution from the standard prompt. Notably, our proposed plug-and-play mechanism is an inference-only method, enjoying appealing flexibility. Extensive experiments on widely used benchmarks, e.g., HumanEval, MBPP, and MultiPL-E, upon several LLMs (i.e., Inocder-6b, CodeLlama-7b, WizardCoder-15b, StarCoder, and Llama2-7b), demonstrate that our proposed USCD significantly improves one-pass code generation, with an average pass@1 scores increase of 16.59\%. We will release code and data on GitHub.

While deep convolutional neural networks (CNNs) have achieved impressive success in image denoising with additive white Gaussian noise (AWGN), their performance remains limited on real-world noisy photographs. The main reason is that their learned models are easy to overfit on the simplified AWGN model which deviates severely from the complicated real-world noise model. In order to improve the generalization ability of deep CNN denoisers, we suggest training a convolutional blind denoising network (CBDNet) with more realistic noise model and real-world noisy-clean image pairs. On the one hand, both signal-dependent noise and in-camera signal processing pipeline is considered to synthesize realistic noisy images. On the other hand, real-world noisy photographs and their nearly noise-free counterparts are also included to train our CBDNet. To further provide an interactive strategy to rectify denoising result conveniently, a noise estimation subnetwork with asymmetric learning to suppress under-estimation of noise level is embedded into CBDNet. Extensive experimental results on three datasets of real-world noisy photographs clearly demonstrate the superior performance of CBDNet over state-of-the-arts in terms of quantitative metrics and visual quality. The code has been made available at https://github.com/GuoShi28/CBDNet.

Supervised fine-tuning (SFT) plays a crucial role in adapting large language models (LLMs) to specific domains or tasks. However, as demonstrated by empirical experiments, the collected data inevitably contains noise in practical applications, which poses significant challenges to model performance on downstream tasks. Therefore, there is an urgent need for a noise-robust SFT framework to enhance model capabilities in downstream tasks. To address this challenge, we introduce a robust SFT framework (RobustFT) that performs noise detection and relabeling on downstream task data. For noise identification, our approach employs a multi-expert collaborative system with inference-enhanced models to achieve superior noise detection. In the denoising phase, we utilize a context-enhanced strategy, which incorporates the most relevant and confident knowledge followed by careful assessment to generate reliable annotations. Additionally, we introduce an effective data selection mechanism based on response entropy, ensuring only high-quality samples are retained for fine-tuning. Extensive experiments conducted on multiple LLMs across five datasets demonstrate RobustFT's exceptional performance in noisy scenarios.

Recently, there has been extensive research interest in training deep networks to denoise images without clean reference. However, the representative approaches such as Noise2Noise, Noise2Void, Stein's unbiased risk estimator (SURE), etc. seem to differ from one another and it is difficult to find the coherent mathematical structure. To address this, here we present a novel approach, called Noise2Score, which reveals a missing link in order to unite these seemingly different approaches. Specifically, we show that image denoising problems without clean images can be addressed by finding the mode of the posterior distribution and that the Tweedie's formula offers an explicit solution through the score function (i.e. the gradient of log likelihood). Our method then uses the recent finding that the score function can be stably estimated from the noisy images using the amortized residual denoising autoencoder, the method of which is closely related to Noise2Noise or Nose2Void. Our Noise2Score approach is so universal that the same network training can be used to remove noises from images that are corrupted by any exponential family distributions and noise parameters. Using extensive experiments with Gaussian, Poisson, and Gamma noises, we show that Noise2Score significantly outperforms the state-of-the-art self-supervised denoising methods in the benchmark data set such as (C)BSD68, Set12, and Kodak, etc.

Calibration-based methods have dominated RAW image denoising under extremely low-light environments. However, these methods suffer from several main deficiencies: 1) the calibration procedure is laborious and time-consuming, 2) denoisers for different cameras are difficult to transfer, and 3) the discrepancy between synthetic noise and real noise is enlarged by high digital gain. To overcome the above shortcomings, we propose a calibration-free pipeline for Lighting Every Drakness (LED), regardless of the digital gain or camera sensor. Instead of calibrating the noise parameters and training repeatedly, our method could adapt to a target camera only with few-shot paired data and fine-tuning. In addition, well-designed structural modification during both stages alleviates the domain gap between synthetic and real noise without any extra computational cost. With 2 pairs for each additional digital gain (in total 6 pairs) and 0.5% iterations, our method achieves superior performance over other calibration-based methods. Our code is available at https://github.com/Srameo/LED .

Diffusion model, a new generative modelling paradigm, has achieved great success in image, audio, and video generation. However, considering the discrete categorical nature of text, it is not trivial to extend continuous diffusion models to natural language, and text diffusion models are less studied. Sequence-to-sequence text generation is one of the essential natural language processing topics. In this work, we apply diffusion models to approach sequence-to-sequence text generation, and explore whether the superiority generation performance of diffusion model can transfer to natural language domain. We propose SeqDiffuSeq, a text diffusion model for sequence-to-sequence generation. SeqDiffuSeq uses an encoder-decoder Transformers architecture to model denoising function. In order to improve generation quality, SeqDiffuSeq combines the self-conditioning technique and a newly proposed adaptive noise schedule technique. The adaptive noise schedule has the difficulty of denoising evenly distributed across time steps, and considers exclusive noise schedules for tokens at different positional order. Experiment results illustrate the good performance on sequence-to-sequence generation in terms of text quality and inference time.

The success of the text-guided diffusion model has inspired the development and release of numerous powerful diffusion models within the open-source community. These models are typically fine-tuned on various expert datasets, showcasing diverse denoising capabilities. Leveraging multiple high-quality models to produce stronger generation ability is valuable, but has not been extensively studied. Existing methods primarily adopt parameter merging strategies to produce a new static model. However, they overlook the fact that the divergent denoising capabilities of the models may dynamically change across different states, such as when experiencing different prompts, initial noises, denoising steps, and spatial locations. In this paper, we propose a novel ensembling method, Adaptive Feature Aggregation (AFA), which dynamically adjusts the contributions of multiple models at the feature level according to various states (i.e., prompts, initial noises, denoising steps, and spatial locations), thereby keeping the advantages of multiple diffusion models, while suppressing their disadvantages. Specifically, we design a lightweight Spatial-Aware Block-Wise (SABW) feature aggregator that adaptive aggregates the block-wise intermediate features from multiple U-Net denoisers into a unified one. The core idea lies in dynamically producing an individual attention map for each model's features by comprehensively considering various states. It is worth noting that only SABW is trainable with about 50 million parameters, while other models are frozen. Both the quantitative and qualitative experiments demonstrate the effectiveness of our proposed Adaptive Feature Aggregation method. The code is available at https://github.com/tenvence/afa/.

Diffusion models excel at capturing the natural design spaces of images, molecules, DNA, RNA, and protein sequences. However, rather than merely generating designs that are natural, we often aim to optimize downstream reward functions while preserving the naturalness of these design spaces. Existing methods for achieving this goal often require ``differentiable'' proxy models (e.g., classifier guidance or DPS) or involve computationally expensive fine-tuning of diffusion models (e.g., classifier-free guidance, RL-based fine-tuning). In our work, we propose a new method to address these challenges. Our algorithm is an iterative sampling method that integrates soft value functions, which looks ahead to how intermediate noisy states lead to high rewards in the future, into the standard inference procedure of pre-trained diffusion models. Notably, our approach avoids fine-tuning generative models and eliminates the need to construct differentiable models. This enables us to (1) directly utilize non-differentiable features/reward feedback, commonly used in many scientific domains, and (2) apply our method to recent discrete diffusion models in a principled way. Finally, we demonstrate the effectiveness of our algorithm across several domains, including image generation, molecule generation, and DNA/RNA sequence generation. The code is available at https://github.com/masa-ue/SVDD{https://github.com/masa-ue/SVDD}.

Optimal transport (OT) theory focuses, among all maps T:R^drightarrow R^d that can morph a probability measure onto another, on those that are the ``thriftiest'', i.e. such that the averaged cost c(x, T(x)) between x and its image T(x) be as small as possible. Many computational approaches have been proposed to estimate such Monge maps when c is the ell_2^2 distance, e.g., using entropic maps [Pooladian'22], or neural networks [Makkuva'20, Korotin'20]. We propose a new model for transport maps, built on a family of translation invariant costs c(x, y):=h(x-y), where h:=1{2}|cdot|_2^2+tau and tau is a regularizer. We propose a generalization of the entropic map suitable for h, and highlight a surprising link tying it with the Bregman centroids of the divergence D_h generated by h, and the proximal operator of tau. We show that choosing a sparsity-inducing norm for tau results in maps that apply Occam's razor to transport, in the sense that the displacement vectors Delta(x):= T(x)-x they induce are sparse, with a sparsity pattern that varies depending on x. We showcase the ability of our method to estimate meaningful OT maps for high-dimensional single-cell transcription data, in the 34000-d space of gene counts for cells, without using dimensionality reduction, thus retaining the ability to interpret all displacements at the gene level.

Advances in natural language processing and large language models have sparked growing interest in modeling DNA, often referred to as the "language of life". However, DNA modeling poses unique challenges. First, it requires the ability to process ultra-long DNA sequences while preserving single-nucleotide resolution, as individual nucleotides play a critical role in DNA function. Second, success in this domain requires excelling at both generative and understanding tasks: generative tasks hold potential for therapeutic and industrial applications, while understanding tasks provide crucial insights into biological mechanisms and diseases. To address these challenges, we propose HybriDNA, a decoder-only DNA language model that incorporates a hybrid Transformer-Mamba2 architecture, seamlessly integrating the strengths of attention mechanisms with selective state-space models. This hybrid design enables HybriDNA to efficiently process DNA sequences up to 131kb in length with single-nucleotide resolution. HybriDNA achieves state-of-the-art performance across 33 DNA understanding datasets curated from the BEND, GUE, and LRB benchmarks, and demonstrates exceptional capability in generating synthetic cis-regulatory elements (CREs) with desired properties. Furthermore, we show that HybriDNA adheres to expected scaling laws, with performance improving consistently as the model scales from 300M to 3B and 7B parameters. These findings underscore HybriDNA's versatility and its potential to advance DNA research and applications, paving the way for innovations in understanding and engineering the "language of life".

Enhancing the visibility in extreme low-light environments is a challenging task. Under nearly lightless condition, existing image denoising methods could easily break down due to significantly low SNR. In this paper, we systematically study the noise statistics in the imaging pipeline of CMOS photosensors, and formulate a comprehensive noise model that can accurately characterize the real noise structures. Our novel model considers the noise sources caused by digital camera electronics which are largely overlooked by existing methods yet have significant influence on raw measurement in the dark. It provides a way to decouple the intricate noise structure into different statistical distributions with physical interpretations. Moreover, our noise model can be used to synthesize realistic training data for learning-based low-light denoising algorithms. In this regard, although promising results have been shown recently with deep convolutional neural networks, the success heavily depends on abundant noisy clean image pairs for training, which are tremendously difficult to obtain in practice. Generalizing their trained models to images from new devices is also problematic. Extensive experiments on multiple low-light denoising datasets -- including a newly collected one in this work covering various devices -- show that a deep neural network trained with our proposed noise formation model can reach surprisingly-high accuracy. The results are on par with or sometimes even outperform training with paired real data, opening a new door to real-world extreme low-light photography.

Denoising diffusion models have recently shown impressive results in generative tasks. By learning powerful priors from huge collections of training images, such models are able to gradually modify complete noise to a clean natural image via a sequence of small denoising steps, seemingly making them well-suited for single image denoising. However, effectively applying denoising diffusion models to removal of realistic noise is more challenging than it may seem, since their formulation is based on additive white Gaussian noise, unlike noise in real-world images. In this work, we present SVNR, a novel formulation of denoising diffusion that assumes a more realistic, spatially-variant noise model. SVNR enables using the noisy input image as the starting point for the denoising diffusion process, in addition to conditioning the process on it. To this end, we adapt the diffusion process to allow each pixel to have its own time embedding, and propose training and inference schemes that support spatially-varying time maps. Our formulation also accounts for the correlation that exists between the condition image and the samples along the modified diffusion process. In our experiments we demonstrate the advantages of our approach over a strong diffusion model baseline, as well as over a state-of-the-art single image denoising method.

Echocardiography has been a prominent tool for the diagnosis of cardiac disease. However, these diagnoses can be heavily impeded by poor image quality. Acoustic clutter emerges due to multipath reflections imposed by layers of skin, subcutaneous fat, and intercostal muscle between the transducer and heart. As a result, haze and other noise artifacts pose a real challenge to cardiac ultrasound imaging. In many cases, especially with difficult-to-image patients such as patients with obesity, a diagnosis from B-Mode ultrasound imaging is effectively rendered unusable, forcing sonographers to resort to contrast-enhanced ultrasound examinations or refer patients to other imaging modalities. Tissue harmonic imaging has been a popular approach to combat haze, but in severe cases is still heavily impacted by haze. Alternatively, denoising algorithms are typically unable to remove highly structured and correlated noise, such as haze. It remains a challenge to accurately describe the statistical properties of structured haze, and develop an inference method to subsequently remove it. Diffusion models have emerged as powerful generative models and have shown their effectiveness in a variety of inverse problems. In this work, we present a joint posterior sampling framework that combines two separate diffusion models to model the distribution of both clean ultrasound and haze in an unsupervised manner. Furthermore, we demonstrate techniques for effectively training diffusion models on radio-frequency ultrasound data and highlight the advantages over image data. Experiments on both in-vitro and in-vivo cardiac datasets show that the proposed dehazing method effectively removes haze while preserving signals from weakly reflected tissue.

Foundation models for single-cell RNA sequencing (scRNA-seq) have shown promising capabilities in capturing gene expression patterns. However, current approaches face critical limitations: they ignore biological prior knowledge encoded in gene regulatory relationships and fail to leverage multi-omics signals that could provide complementary regulatory insights. In this paper, we propose GRNFormer, a new framework that systematically integrates multi-scale Gene Regulatory Networks (GRNs) inferred from multi-omics data into RNA foundation model training. Our framework introduces two key innovations. First, we introduce a pipeline for constructing hierarchical GRNs that capture regulatory relationships at both cell-type-specific and cell-specific resolutions. Second, we design a structure-aware integration framework that addresses the information asymmetry in GRNs through two technical advances: (1) A graph topological adapter using multi-head cross-attention to weight regulatory relationships dynamically, and (2) a novel edge perturbation strategy that perturb GRNs with biologically-informed co-expression links to augment graph neural network training. Comprehensive experiments have been conducted on three representative downstream tasks across multiple model architectures to demonstrate the effectiveness of GRNFormer. It achieves consistent improvements over state-of-the-art (SoTA) baselines: 3.6% increase in drug response prediction correlation, 9.6% improvement in single-cell drug classification AUC, and 1.1% average gain in gene perturbation prediction accuracy.

Magnetic resonance imaging (MRI) is a common and life-saving medical imaging technique. However, acquiring high signal-to-noise ratio MRI scans requires long scan times, resulting in increased costs and patient discomfort, and decreased throughput. Thus, there is great interest in denoising MRI scans, especially for the subtype of diffusion MRI scans that are severely SNR-limited. While most prior MRI denoising methods are supervised in nature, acquiring supervised training datasets for the multitude of anatomies, MRI scanners, and scan parameters proves impractical. Here, we propose Denoising Diffusion Models for Denoising Diffusion MRI (DDM^2), a self-supervised denoising method for MRI denoising using diffusion denoising generative models. Our three-stage framework integrates statistic-based denoising theory into diffusion models and performs denoising through conditional generation. During inference, we represent input noisy measurements as a sample from an intermediate posterior distribution within the diffusion Markov chain. We conduct experiments on 4 real-world in-vivo diffusion MRI datasets and show that our DDM^2 demonstrates superior denoising performances ascertained with clinically-relevant visual qualitative and quantitative metrics.

Recently, various methods have been proposed to address the inconsistency issue of DDIM inversion to enable image editing, such as EDICT [36] and Null-text inversion [22]. However, the above methods introduce considerable computational overhead. In this paper, we propose a new technique, named bi-directional integration approximation (BDIA), to perform exact diffusion inversion with neglible computational overhead. Suppose we would like to estimate the next diffusion state z_{i-1} at timestep t_i with the historical information (i,z_i) and (i+1,z_{i+1}). We first obtain the estimated Gaussian noise boldsymbol{epsilon}(z_i,i), and then apply the DDIM update procedure twice for approximating the ODE integration over the next time-slot [t_i, t_{i-1}] in the forward manner and the previous time-slot [t_i, t_{t+1}] in the backward manner. The DDIM step for the previous time-slot is used to refine the integration approximation made earlier when computing z_i. A nice property of BDIA-DDIM is that the update expression for z_{i-1} is a linear combination of (z_{i+1}, z_i, boldsymbol{epsilon}(z_i,i)). This allows for exact backward computation of z_{i+1} given (z_i, z_{i-1}), thus leading to exact diffusion inversion. It is demonstrated with experiments that (round-trip) BDIA-DDIM is particularly effective for image editing. Our experiments further show that BDIA-DDIM produces markedly better image sampling qualities than DDIM for text-to-image generation. BDIA can also be applied to improve the performance of other ODE solvers in addition to DDIM. In our work, it is found that applying BDIA to the EDM sampling procedure produces consistently better performance over four pre-trained models.

Label noise is prevalent in machine learning datasets. It is crucial to identify and remove label noise because models trained on noisy data can have substantially reduced accuracy and generalizability. Most existing label noise detection approaches are designed for classification tasks, and data cleaning for outcome prediction analysis is relatively unexplored. Inspired by the fluctuations in performance across different folds in cross-validation, we propose Repeated Cross-Validations for label noise estimation (ReCoV) to address this gap. ReCoV constructs a noise histogram that ranks the noise level of samples based on a large number of cross-validations by recording sample IDs in each worst-performing fold. We further propose three approaches for identifying noisy samples based on noise histograms to address increasingly complex noise distributions. We show that ReCoV outperforms state-of-the-art algorithms for label cleaning in a classification task benchmark. More importantly, we show that removing ReCoV-identified noisy samples in two medical imaging outcome prediction datasets significantly improves model performance on test sets. As a statistical approach that does not rely on hyperparameters, noise distributions, or model structures, ReCoV is compatible with any machine learning analysis.

Available training data for named entity recognition (NER) often contains a significant percentage of incorrect labels for entity types and entity boundaries. Such label noise poses challenges for supervised learning and may significantly deteriorate model quality. To address this, prior work proposed various noise-robust learning approaches capable of learning from data with partially incorrect labels. These approaches are typically evaluated using simulated noise where the labels in a clean dataset are automatically corrupted. However, as we show in this paper, this leads to unrealistic noise that is far easier to handle than real noise caused by human error or semi-automatic annotation. To enable the study of the impact of various types of real noise, we introduce NoiseBench, an NER benchmark consisting of clean training data corrupted with 6 types of real noise, including expert errors, crowdsourcing errors, automatic annotation errors and LLM errors. We present an analysis that shows that real noise is significantly more challenging than simulated noise, and show that current state-of-the-art models for noise-robust learning fall far short of their theoretically achievable upper bound. We release NoiseBench to the research community.

Despite the potential of diffusion models in speech enhancement, their deployment in Acoustic Echo Cancellation (AEC) has been restricted. In this paper, we propose DI-AEC, pioneering a diffusion-based stochastic regeneration approach dedicated to AEC. Further, we propose FADI-AEC, fast score-based diffusion AEC framework to save computational demands, making it favorable for edge devices. It stands out by running the score model once per frame, achieving a significant surge in processing efficiency. Apart from that, we introduce a novel noise generation technique where far-end signals are utilized, incorporating both far-end and near-end signals to refine the score model's accuracy. We test our proposed method on the ICASSP2023 Microsoft deep echo cancellation challenge evaluation dataset, where our method outperforms some of the end-to-end methods and other diffusion based echo cancellation methods.

Conditional diffusion models have demonstrated impressive performance in image manipulation tasks. The general pipeline involves adding noise to the image and then denoising it. However, this method faces a trade-off problem: adding too much noise affects the fidelity of the image while adding too little affects its editability. This largely limits their practical applicability. In this paper, we propose a novel framework, Selective Diffusion Distillation (SDD), that ensures both the fidelity and editability of images. Instead of directly editing images with a diffusion model, we train a feedforward image manipulation network under the guidance of the diffusion model. Besides, we propose an effective indicator to select the semantic-related timestep to obtain the correct semantic guidance from the diffusion model. This approach successfully avoids the dilemma caused by the diffusion process. Our extensive experiments demonstrate the advantages of our framework. Code is released at https://github.com/AndysonYs/Selective-Diffusion-Distillation.

This study presents a new image super-resolution (SR) technique based on diffusion inversion, aiming at harnessing the rich image priors encapsulated in large pre-trained diffusion models to improve SR performance. We design a Partial noise Prediction strategy to construct an intermediate state of the diffusion model, which serves as the starting sampling point. Central to our approach is a deep noise predictor to estimate the optimal noise maps for the forward diffusion process. Once trained, this noise predictor can be used to initialize the sampling process partially along the diffusion trajectory, generating the desirable high-resolution result. Compared to existing approaches, our method offers a flexible and efficient sampling mechanism that supports an arbitrary number of sampling steps, ranging from one to five. Even with a single sampling step, our method demonstrates superior or comparable performance to recent state-of-the-art approaches. The code and model are publicly available at https://github.com/zsyOAOA/InvSR.

Given a factorization of an image into a sum of linear components, we present a zero-shot method to control each individual component through diffusion model sampling. For example, we can decompose an image into low and high spatial frequencies and condition these components on different text prompts. This produces hybrid images, which change appearance depending on viewing distance. By decomposing an image into three frequency subbands, we can generate hybrid images with three prompts. We also use a decomposition into grayscale and color components to produce images whose appearance changes when they are viewed in grayscale, a phenomena that naturally occurs under dim lighting. And we explore a decomposition by a motion blur kernel, which produces images that change appearance under motion blurring. Our method works by denoising with a composite noise estimate, built from the components of noise estimates conditioned on different prompts. We also show that for certain decompositions, our method recovers prior approaches to compositional generation and spatial control. Finally, we show that we can extend our approach to generate hybrid images from real images. We do this by holding one component fixed and generating the remaining components, effectively solving an inverse problem.

We explore the problem of generating minority samples using diffusion models. The minority samples are instances that lie on low-density regions of a data manifold. Generating a sufficient number of such minority instances is important, since they often contain some unique attributes of the data. However, the conventional generation process of the diffusion models mostly yields majority samples (that lie on high-density regions of the manifold) due to their high likelihoods, making themselves ineffective and time-consuming for the minority generating task. In this work, we present a novel framework that can make the generation process of the diffusion models focus on the minority samples. We first highlight that Tweedie's denoising formula yields favorable results for majority samples. The observation motivates us to introduce a metric that describes the uniqueness of a given sample. To address the inherent preference of the diffusion models w.r.t. the majority samples, we further develop minority guidance, a sampling technique that can guide the generation process toward regions with desired likelihood levels. Experiments on benchmark real datasets demonstrate that our minority guidance can greatly improve the capability of generating high-quality minority samples over existing generative samplers. We showcase that the performance benefit of our framework persists even in demanding real-world scenarios such as medical imaging, further underscoring the practical significance of our work. Code is available at https://github.com/soobin-um/minority-guidance.

Internal features from large-scale pre-trained diffusion models have recently been established as powerful semantic descriptors for a wide range of downstream tasks. Works that use these features generally need to add noise to images before passing them through the model to obtain the semantic features, as the models do not offer the most useful features when given images with little to no noise. We show that this noise has a critical impact on the usefulness of these features that cannot be remedied by ensembling with different random noises. We address this issue by introducing a lightweight, unsupervised fine-tuning method that enables diffusion backbones to provide high-quality, noise-free semantic features. We show that these features readily outperform previous diffusion features by a wide margin in a wide variety of extraction setups and downstream tasks, offering better performance than even ensemble-based methods at a fraction of the cost.

Straightening the probability flow of the continuous-time generative models, such as diffusion models or flow-based models, is the key to fast sampling through the numerical solvers, existing methods learn a linear path by directly generating the probability path the joint distribution between the noise and data distribution. One key reason for the slow sampling speed of the ODE-based solvers that simulate these generative models is the global truncation error of the ODE solver, caused by the high curvature of the ODE trajectory, which explodes the truncation error of the numerical solvers in the low-NFE regime. To address this challenge, We propose a novel method called SeqRF, a learning technique that straightens the probability flow to reduce the global truncation error and hence enable acceleration of sampling and improve the synthesis quality. In both theoretical and empirical studies, we first observe the straightening property of our SeqRF. Through empirical evaluations via SeqRF over flow-based generative models, We achieve surpassing results on CIFAR-10, CelebA-64 times 64, and LSUN-Church datasets.

Deep learning (DL) has shown promise for faster, high quality accelerated MRI reconstruction. However, supervised DL methods depend on extensive amounts of fully-sampled (labeled) data and are sensitive to out-of-distribution (OOD) shifts, particularly low signal-to-noise ratio (SNR) acquisitions. To alleviate this challenge, we propose Noise2Recon, a model-agnostic, consistency training method for joint MRI reconstruction and denoising that can use both fully-sampled (labeled) and undersampled (unlabeled) scans in semi-supervised and self-supervised settings. With limited or no labeled training data, Noise2Recon outperforms compressed sensing and deep learning baselines, including supervised networks, augmentation-based training, fine-tuned denoisers, and self-supervised methods, and matches performance of supervised models, which were trained with 14x more fully-sampled scans. Noise2Recon also outperforms all baselines, including state-of-the-art fine-tuning and augmentation techniques, among low-SNR scans and when generalizing to other OOD factors, such as changes in acceleration factors and different datasets. Augmentation extent and loss weighting hyperparameters had negligible impact on Noise2Recon compared to supervised methods, which may indicate increased training stability. Our code is available at https://github.com/ad12/meddlr.

One of the key components within diffusion models is the UNet for noise prediction. While several works have explored basic properties of the UNet decoder, its encoder largely remains unexplored. In this work, we conduct the first comprehensive study of the UNet encoder. We empirically analyze the encoder features and provide insights to important questions regarding their changes at the inference process. In particular, we find that encoder features change gently, whereas the decoder features exhibit substantial variations across different time-steps. This finding inspired us to omit the encoder at certain adjacent time-steps and reuse cyclically the encoder features in the previous time-steps for the decoder. Further based on this observation, we introduce a simple yet effective encoder propagation scheme to accelerate the diffusion sampling for a diverse set of tasks. By benefiting from our propagation scheme, we are able to perform in parallel the decoder at certain adjacent time-steps. Additionally, we introduce a prior noise injection method to improve the texture details in the generated image. Besides the standard text-to-image task, we also validate our approach on other tasks: text-to-video, personalized generation and reference-guided generation. Without utilizing any knowledge distillation technique, our approach accelerates both the Stable Diffusion (SD) and the DeepFloyd-IF models sampling by 41% and 24% respectively, while maintaining high-quality generation performance. Our code is available in https://github.com/hutaiHang/Faster-Diffusion{FasterDiffusion}.

We establish a new theoretical framework for learning under multi-class, instance-dependent label noise. This framework casts learning with label noise as a form of domain adaptation, in particular, domain adaptation under posterior drift. We introduce the concept of relative signal strength (RSS), a pointwise measure that quantifies the transferability from noisy to clean posterior. Using RSS, we establish nearly matching upper and lower bounds on the excess risk. Our theoretical findings support the simple Noise Ignorant Empirical Risk Minimization (NI-ERM) principle, which minimizes empirical risk while ignoring label noise. Finally, we translate this theoretical insight into practice: by using NI-ERM to fit a linear classifier on top of a self-supervised feature extractor, we achieve state-of-the-art performance on the CIFAR-N data challenge.

There is a constant need for high-performing and computationally efficient neural network models for image super-resolution: computationally efficient models can be used via low-capacity devices and reduce carbon footprints. One way to obtain such models is to compress models, e.g. quantization. Another way is a neural architecture search that automatically discovers new, more efficient solutions. We propose a novel quantization-aware procedure, the QuantNAS that combines pros of these two approaches. To make QuantNAS work, the procedure looks for quantization-friendly super-resolution models. The approach utilizes entropy regularization, quantization noise, and Adaptive Deviation for Quantization (ADQ) module to enhance the search procedure. The entropy regularization technique prioritizes a single operation within each block of the search space. Adding quantization noise to parameters and activations approximates model degradation after quantization, resulting in a more quantization-friendly architectures. ADQ helps to alleviate problems caused by Batch Norm blocks in super-resolution models. Our experimental results show that the proposed approximations are better for search procedure than direct model quantization. QuantNAS discovers architectures with better PSNR/BitOps trade-off than uniform or mixed precision quantization of fixed architectures. We showcase the effectiveness of our method through its application to two search spaces inspired by the state-of-the-art SR models and RFDN. Thus, anyone can design a proper search space based on an existing architecture and apply our method to obtain better quality and efficiency. The proposed procedure is 30\% faster than direct weight quantization and is more stable.

We consider low-latency image transmission over a noisy wireless channel when correlated side information is present only at the receiver side (the Wyner-Ziv scenario). In particular, we are interested in developing practical schemes using a data-driven joint source-channel coding (JSCC) approach, which has been previously shown to outperform conventional separation-based approaches in the practical finite blocklength regimes, and to provide graceful degradation with channel quality. We propose a novel neural network architecture that incorporates the decoder-only side information at multiple stages at the receiver side. Our results demonstrate that the proposed method succeeds in integrating the side information, yielding improved performance at all channel noise levels in terms of the various distortion criteria considered here, especially at low channel signal-to-noise ratios (SNRs) and small bandwidth ratios (BRs). We also provide the source code of the proposed method to enable further research and reproducibility of the results.

Over the past decade, the revolution in single-cell sequencing has enabled the simultaneous molecular profiling of various modalities across thousands of individual cells, allowing scientists to investigate the diverse functions of complex tissues and uncover underlying disease mechanisms. Among all the analytical steps, assigning individual cells to specific types is fundamental for understanding cellular heterogeneity. However, this process is usually labor-intensive and requires extensive expert knowledge. Recent advances in large language models (LLMs) have demonstrated their ability to efficiently process and synthesize vast corpora of text to automatically extract essential biological knowledge, such as marker genes, potentially promoting more efficient and automated cell type annotations. To thoroughly evaluate the capability of modern instruction-tuned LLMs in automating the cell type identification process, we introduce SOAR, a comprehensive benchmarking study of LLMs for cell type annotation tasks in single-cell genomics. Specifically, we assess the performance of 8 instruction-tuned LLMs across 11 datasets, spanning multiple cell types and species. Our study explores the potential of LLMs to accurately classify and annotate cell types in single-cell RNA sequencing (scRNA-seq) data, while extending their application to multiomics data through cross-modality translation. Additionally, we evaluate the effectiveness of chain-of-thought (CoT) prompting techniques in generating detailed biological insights during the annotation process. The results demonstrate that LLMs can provide robust interpretations of single-cell data without requiring additional fine-tuning, advancing the automation of cell type annotation in genomics research.

Recent text-guided diffusion models provide powerful image generation capabilities. Currently, a massive effort is given to enable the modification of these images using text only as means to offer intuitive and versatile editing. To edit a real image using these state-of-the-art tools, one must first invert the image with a meaningful text prompt into the pretrained model's domain. In this paper, we introduce an accurate inversion technique and thus facilitate an intuitive text-based modification of the image. Our proposed inversion consists of two novel key components: (i) Pivotal inversion for diffusion models. While current methods aim at mapping random noise samples to a single input image, we use a single pivotal noise vector for each timestamp and optimize around it. We demonstrate that a direct inversion is inadequate on its own, but does provide a good anchor for our optimization. (ii) NULL-text optimization, where we only modify the unconditional textual embedding that is used for classifier-free guidance, rather than the input text embedding. This allows for keeping both the model weights and the conditional embedding intact and hence enables applying prompt-based editing while avoiding the cumbersome tuning of the model's weights. Our Null-text inversion, based on the publicly available Stable Diffusion model, is extensively evaluated on a variety of images and prompt editing, showing high-fidelity editing of real images.

Denoising Diffusion Probabilistic Models (DDPMs) achieve state-of-the-art performance in synthesizing new images from random noise, but they lack meaningful latent space that encodes data into features. Recent DDPM-based editing techniques try to mitigate this issue by inverting images back to their approximated staring noise. In this work, we study the relation between the initial Gaussian noise, the samples generated from it, and their corresponding latent encodings obtained through the inversion procedure. First, we interpret their spatial distance relations to show the inaccuracy of the DDIM inversion technique by localizing latent representations manifold between the initial noise and generated samples. Then, we demonstrate the peculiar relation between initial Gaussian noise and its corresponding generations during diffusion training, showing that the high-level features of generated images stabilize rapidly, keeping the spatial distance relationship between noises and generations consistent throughout the training.

Generative models have reached an advanced stage where they can produce remarkably realistic images. However, this remarkable generative capability also introduces the risk of disseminating false or misleading information. Notably, existing image detectors for generated images encounter challenges such as low accuracy and limited generalization. This paper seeks to address this issue by seeking a representation with strong generalization capabilities to enhance the detection of generated images. Our investigation has revealed that real and generated images display distinct latent Gaussian representations when subjected to an inverse diffusion process within a pre-trained diffusion model. Exploiting this disparity, we can amplify subtle artifacts in generated images. Building upon this insight, we introduce a novel image representation known as Diffusion Noise Feature (DNF). DNF is extracted from the estimated noise generated during the inverse diffusion process. A simple classifier, e.g., ResNet50, trained on DNF achieves high accuracy, robustness, and generalization capabilities for detecting generated images (even the corresponding generator is built with datasets/structures that are not seen during the classifier's training). We conducted experiments using four training datasets and five testsets, achieving state-of-the-art detection performance.

We present EdiT5 - a novel semi-autoregressive text-editing model designed to combine the strengths of non-autoregressive text-editing and autoregressive decoding. EdiT5 is faster during inference than conventional sequence-to-sequence (seq2seq) models, while being capable of modelling flexible input-output transformations. This is achieved by decomposing the generation process into three sub-tasks: (1) tagging to decide on the subset of input tokens to be preserved in the output, (2) re-ordering to define their order in the output text, and (3) insertion to infill the missing tokens that are not present in the input. The tagging and re-ordering steps, which are responsible for generating the largest portion of the output, are non-autoregressive, while the insertion step uses an autoregressive decoder. Depending on the task, EdiT5 on average requires significantly fewer autoregressive steps, demonstrating speedups of up to 25x when compared to seq2seq models. Quality-wise, EdiT5 is initialized with a pre-trained T5 checkpoint yielding comparable performance to T5 in high-resource settings when evaluated on three NLG tasks: Sentence Fusion, Grammatical Error Correction, and Decontextualization while clearly outperforming T5 in low-resource settings.

Non-autoregressive (NAR) modeling has gained significant interest in speech processing since these models achieve dramatically lower inference time than autoregressive (AR) models while also achieving good transcription accuracy. Since NAR automatic speech recognition (ASR) models must wait for the completion of the entire utterance before processing, some works explore streaming NAR models based on blockwise attention for low-latency applications. However, streaming NAR models significantly lag in accuracy compared to streaming AR and non-streaming NAR models. To address this, we propose a streaming "semi-autoregressive" ASR model that incorporates the labels emitted in previous blocks as additional context using a Language Model (LM) subnetwork. We also introduce a novel greedy decoding algorithm that addresses insertion and deletion errors near block boundaries while not significantly increasing the inference time. Experiments show that our method outperforms the existing streaming NAR model by 19% relative on Tedlium2, 16%/8% on Librispeech-100 clean/other test sets, and 19%/8% on the Switchboard(SWB) / Callhome(CH) test sets. It also reduced the accuracy gap with streaming AR and non-streaming NAR models while achieving 2.5x lower latency. We also demonstrate that our approach can effectively utilize external text data to pre-train the LM subnetwork to further improve streaming ASR accuracy.

Image interpolation based on diffusion models is promising in creating fresh and interesting images. Advanced interpolation methods mainly focus on spherical linear interpolation, where images are encoded into the noise space and then interpolated for denoising to images. However, existing methods face challenges in effectively interpolating natural images (not generated by diffusion models), thereby restricting their practical applicability. Our experimental investigations reveal that these challenges stem from the invalidity of the encoding noise, which may no longer obey the expected noise distribution, e.g., a normal distribution. To address these challenges, we propose a novel approach to correct noise for image interpolation, NoiseDiffusion. Specifically, NoiseDiffusion approaches the invalid noise to the expected distribution by introducing subtle Gaussian noise and introduces a constraint to suppress noise with extreme values. In this context, promoting noise validity contributes to mitigating image artifacts, but the constraint and introduced exogenous noise typically lead to a reduction in signal-to-noise ratio, i.e., loss of original image information. Hence, NoiseDiffusion performs interpolation within the noisy image space and injects raw images into these noisy counterparts to address the challenge of information loss. Consequently, NoiseDiffusion enables us to interpolate natural images without causing artifacts or information loss, thus achieving the best interpolation results.

The capability of video super-resolution (VSR) to synthesize high-resolution (HR) video from ideal datasets has been demonstrated in many works. However, applying the VSR model to real-world video with unknown and complex degradation remains a challenging task. First, existing degradation metrics in most VSR methods are not able to effectively simulate real-world noise and blur. On the contrary, simple combinations of classical degradation are used for real-world noise modeling, which led to the VSR model often being violated by out-of-distribution noise. Second, many SR models focus on noise simulation and transfer. Nevertheless, the sampled noise is monotonous and limited. To address the aforementioned problems, we propose a Negatives augmentation strategy for generalized noise modeling in Video Super-Resolution (NegVSR) task. Specifically, we first propose sequential noise generation toward real-world data to extract practical noise sequences. Then, the degeneration domain is widely expanded by negative augmentation to build up various yet challenging real-world noise sets. We further propose the augmented negative guidance loss to learn robust features among augmented negatives effectively. Extensive experiments on real-world datasets (e.g., VideoLQ and FLIR) show that our method outperforms state-of-the-art methods with clear margins, especially in visual quality.

The generation of medical images presents significant challenges due to their high-resolution and three-dimensional nature. Existing methods often yield suboptimal performance in generating high-quality 3D medical images, and there is currently no universal generative framework for medical imaging. In this paper, we introduce the 3D Medical Diffusion (3D MedDiffusion) model for controllable, high-quality 3D medical image generation. 3D MedDiffusion incorporates a novel, highly efficient Patch-Volume Autoencoder that compresses medical images into latent space through patch-wise encoding and recovers back into image space through volume-wise decoding. Additionally, we design a new noise estimator to capture both local details and global structure information during diffusion denoising process. 3D MedDiffusion can generate fine-detailed, high-resolution images (up to 512x512x512) and effectively adapt to various downstream tasks as it is trained on large-scale datasets covering CT and MRI modalities and different anatomical regions (from head to leg). Experimental results demonstrate that 3D MedDiffusion surpasses state-of-the-art methods in generative quality and exhibits strong generalizability across tasks such as sparse-view CT reconstruction, fast MRI reconstruction, and data augmentation.

Efficient text-to-image generation remains a challenging task due to the high computational costs associated with the multi-step sampling in diffusion models. Although distillation of pre-trained diffusion models has been successful in reducing sampling steps, low-step image generation often falls short in terms of quality. In this study, we propose a novel sampling design to achieve high-quality one-step image generation aligning with human preferences, particularly focusing on exploring the impact of the prior noise distribution. Our approach, Prompt Adaptive Human Preference Inversion (PAHI), optimizes the noise distributions for each prompt based on human preferences without the need for fine-tuning diffusion models. Our experiments showcase that the tailored noise distributions significantly improve image quality with only a marginal increase in computational cost. Our findings underscore the importance of noise optimization and pave the way for efficient and high-quality text-to-image synthesis.

Denoising diffusion (score-based) generative models have recently achieved significant accomplishments in generating realistic and diverse data. These approaches define a forward diffusion process for transforming data into noise and a backward denoising process for sampling data from noise. Unfortunately, the generation process of current denoising diffusion models is notoriously slow due to the lengthy iterative noise estimations, which rely on cumbersome neural networks. It prevents the diffusion models from being widely deployed, especially on edge devices. Previous works accelerate the generation process of diffusion model (DM) via finding shorter yet effective sampling trajectories. However, they overlook the cost of noise estimation with a heavy network in every iteration. In this work, we accelerate generation from the perspective of compressing the noise estimation network. Due to the difficulty of retraining DMs, we exclude mainstream training-aware compression paradigms and introduce post-training quantization (PTQ) into DM acceleration. However, the output distributions of noise estimation networks change with time-step, making previous PTQ methods fail in DMs since they are designed for single-time step scenarios. To devise a DM-specific PTQ method, we explore PTQ on DM in three aspects: quantized operations, calibration dataset, and calibration metric. We summarize and use several observations derived from all-inclusive investigations to formulate our method, which especially targets the unique multi-time-step structure of DMs. Experimentally, our method can directly quantize full-precision DMs into 8-bit models while maintaining or even improving their performance in a training-free manner. Importantly, our method can serve as a plug-and-play module on other fast-sampling methods, e.g., DDIM. The code is available at https://github.com/42Shawn/PTQ4DM .

Text-guided diffusion models have become a popular tool in image synthesis, known for producing high-quality and diverse images. However, their application to editing real images often encounters hurdles primarily due to the text condition deteriorating the reconstruction quality and subsequently affecting editing fidelity. Null-text Inversion (NTI) has made strides in this area, but it fails to capture spatial context and requires computationally intensive per-timestep optimization. Addressing these challenges, we present Noise Map Guidance (NMG), an inversion method rich in a spatial context, tailored for real-image editing. Significantly, NMG achieves this without necessitating optimization, yet preserves the editing quality. Our empirical investigations highlight NMG's adaptability across various editing techniques and its robustness to variants of DDIM inversions.

Single-cell RNA sequencing (scRNA-seq) data are often confounded by technical or biological batch effects. Existing deep learning models mitigate these effects but often discard batch-specific information, potentially losing valuable biological insights. We propose a Mixed Effects Deep Learning (MEDL) autoencoder framework that separately models batch-invariant (fixed effects) and batch-specific (random effects) components. By decoupling batch-invariant biological states from batch variations, our framework integrates both into predictive models. Our approach also generates 2D visualizations of how the same cell appears across batches, enhancing interpretability. Retaining both fixed and random effect latent spaces improves classification accuracy. We applied our framework to three datasets spanning the cardiovascular system (Healthy Heart), Autism Spectrum Disorder (ASD), and Acute Myeloid Leukemia (AML). With 147 batches in the Healthy Heart dataset, far exceeding typical numbers, we tested our framework's ability to handle many batches. In the ASD dataset, our approach captured donor heterogeneity between autistic and healthy individuals. In the AML dataset, it distinguished donor heterogeneity despite missing cell types and diseased donors exhibiting both healthy and malignant cells. These results highlight our framework's ability to characterize fixed and random effects, enhance batch effect visualization, and improve prediction accuracy across diverse datasets.

MRI super-resolution (SR) and denoising tasks are fundamental challenges in the field of deep learning, which have traditionally been treated as distinct tasks with separate paired training data. In this paper, we propose an innovative method that addresses both tasks simultaneously using a single deep learning model, eliminating the need for explicitly paired noisy and clean images during training. Our proposed model is primarily trained for SR, but also exhibits remarkable noise-cleaning capabilities in the super-resolved images. Instead of conventional approaches that introduce frequency-related operations into the generative process, our novel approach involves the use of a GAN model guided by a frequency-informed discriminator. To achieve this, we harness the power of the 3D Discrete Wavelet Transform (DWT) operation as a frequency constraint within the GAN framework for the SR task on magnetic resonance imaging (MRI) data. Specifically, our contributions include: 1) a 3D generator based on residual-in-residual connected blocks; 2) the integration of the 3D DWT with 1times 1 convolution into a DWT+conv unit within a 3D Unet for the discriminator; 3) the use of the trained model for high-quality image SR, accompanied by an intrinsic denoising process. We dub the model "Denoising Induced Super-resolution GAN (DISGAN)" due to its dual effects of SR image generation and simultaneous denoising. Departing from the traditional approach of training SR and denoising tasks as separate models, our proposed DISGAN is trained only on the SR task, but also achieves exceptional performance in denoising. The model is trained on 3D MRI data from dozens of subjects from the Human Connectome Project (HCP) and further evaluated on previously unseen MRI data from subjects with brain tumours and epilepsy to assess its denoising and SR performance.

We delve into a nuanced but significant challenge inherent to Vision Transformers (ViTs): feature maps of these models exhibit grid-like artifacts, which detrimentally hurt the performance of ViTs in downstream tasks. Our investigations trace this fundamental issue down to the positional embeddings at the input stage. To address this, we propose a novel noise model, which is universally applicable to all ViTs. Specifically, the noise model dissects ViT outputs into three components: a semantics term free from noise artifacts and two artifact-related terms that are conditioned on pixel locations. Such a decomposition is achieved by enforcing cross-view feature consistency with neural fields in a per-image basis. This per-image optimization process extracts artifact-free features from raw ViT outputs, providing clean features for offline applications. Expanding the scope of our solution to support online functionality, we introduce a learnable denoiser to predict artifact-free features directly from unprocessed ViT outputs, which shows remarkable generalization capabilities to novel data without the need for per-image optimization. Our two-stage approach, termed Denoising Vision Transformers (DVT), does not require re-training existing pre-trained ViTs and is immediately applicable to any Transformer-based architecture. We evaluate our method on a variety of representative ViTs (DINO, MAE, DeiT-III, EVA02, CLIP, DINOv2, DINOv2-reg). Extensive evaluations demonstrate that our DVT consistently and significantly improves existing state-of-the-art general-purpose models in semantic and geometric tasks across multiple datasets (e.g., +3.84 mIoU). We hope our study will encourage a re-evaluation of ViT design, especially regarding the naive use of positional embeddings.

Reconstruction of magnetic resonance imaging (MRI) data has been positively affected by deep learning. A key challenge remains: to improve generalisation to distribution shifts between the training and testing data. Most approaches aim to address this via inductive design or data augmentation. However, they can be affected by misleading data, e.g. random noise, and cases where the inference stage data do not match assumptions in the modelled shifts. In this work, by employing a conditional hyperparameter network, we eliminate the need of augmentation, yet maintain robust performance under various levels of Gaussian noise. We demonstrate that our model withstands various input noise levels while producing high-definition reconstructions during the test stage. Moreover, we present a hyperparameter sampling strategy that accelerates the convergence of training. Our proposed method achieves the highest accuracy and image quality in all settings compared to baseline methods.

While molecular pre-training has shown great potential in enhancing drug discovery, the lack of a solid physical interpretation in current methods raises concerns about whether the learned representation truly captures the underlying explanatory factors in observed data, ultimately resulting in limited generalization and robustness. Although denoising methods offer a physical interpretation, their accuracy is often compromised by ad-hoc noise design, leading to inaccurate learned force fields. To address this limitation, this paper proposes a new method for molecular pre-training, called sliced denoising (SliDe), which is based on the classical mechanical intramolecular potential theory. SliDe utilizes a novel noise strategy that perturbs bond lengths, angles, and torsion angles to achieve better sampling over conformations. Additionally, it introduces a random slicing approach that circumvents the computationally expensive calculation of the Jacobian matrix, which is otherwise essential for estimating the force field. By aligning with physical principles, SliDe shows a 42\% improvement in the accuracy of estimated force fields compared to current state-of-the-art denoising methods, and thus outperforms traditional baselines on various molecular property prediction tasks.

Diffusion models have attained remarkable success in the domains of image generation and editing. It is widely recognized that employing larger inversion and denoising steps in diffusion model leads to improved image reconstruction quality. However, the editing performance of diffusion models tends to be no more satisfactory even with increasing denoising steps. The deficiency in editing could be attributed to the conditional Markovian property of the editing process, where errors accumulate throughout denoising steps. To tackle this challenge, we first propose an innovative framework where a rectifier module is incorporated to modulate diffusion model weights with residual features, thereby providing compensatory information to bridge the fidelity gap. Furthermore, we introduce a novel learning paradigm aimed at minimizing error propagation during the editing process, which trains the editing procedure in a manner similar to denoising score-matching. Extensive experiments demonstrate that our proposed framework and training strategy achieve high-fidelity reconstruction and editing results across various levels of denoising steps, meanwhile exhibits exceptional performance in terms of both quantitative metric and qualitative assessments. Moreover, we explore our model's generalization through several applications like image-to-image translation and out-of-domain image editing.

This work aims to improve the efficiency of text-to-image diffusion models. While diffusion models use computationally expensive UNet-based denoising operations in every generation step, we identify that not all operations are equally relevant for the final output quality. In particular, we observe that UNet layers operating on high-res feature maps are relatively sensitive to small perturbations. In contrast, low-res feature maps influence the semantic layout of the final image and can often be perturbed with no noticeable change in the output. Based on this observation, we propose Clockwork Diffusion, a method that periodically reuses computation from preceding denoising steps to approximate low-res feature maps at one or more subsequent steps. For multiple baselines, and for both text-to-image generation and image editing, we demonstrate that Clockwork leads to comparable or improved perceptual scores with drastically reduced computational complexity. As an example, for Stable Diffusion v1.5 with 8 DPM++ steps we save 32% of FLOPs with negligible FID and CLIP change.

The selection of maskers and playback gain levels in a soundscape augmentation system is crucial to its effectiveness in improving the overall acoustic comfort of a given environment. Traditionally, the selection of appropriate maskers and gain levels has been informed by expert opinion, which may not representative of the target population, or by listening tests, which can be time-consuming and labour-intensive. Furthermore, the resulting static choices of masker and gain are often inflexible to the dynamic nature of real-world soundscapes. In this work, we utilized a deep learning model to perform joint selection of the optimal masker and its gain level for a given soundscape. The proposed model was designed with highly modular building blocks, allowing for an optimized inference process that can quickly search through a large number of masker and gain combinations. In addition, we introduced the use of feature-domain soundscape augmentation conditioned on the digital gain level, eliminating the computationally expensive waveform-domain mixing process during inference time, as well as the tedious pre-calibration process required for new maskers. The proposed system was validated on a large-scale dataset of subjective responses to augmented soundscapes with more than 440 participants, ensuring the ability of the model to predict combined effect of the masker and its gain level on the perceptual pleasantness level.

The key challenge in the noisy intermediate-scale quantum era is finding useful circuits compatible with current device limitations. Variational quantum algorithms (VQAs) offer a potential solution by fixing the circuit architecture and optimizing individual gate parameters in an external loop. However, parameter optimization can become intractable, and the overall performance of the algorithm depends heavily on the initially chosen circuit architecture. Several quantum architecture search (QAS) algorithms have been developed to design useful circuit architectures automatically. In the case of parameter optimization alone, noise effects have been observed to dramatically influence the performance of the optimizer and final outcomes, which is a key line of study. However, the effects of noise on the architecture search, which could be just as critical, are poorly understood. This work addresses this gap by introducing a curriculum-based reinforcement learning QAS (CRLQAS) algorithm designed to tackle challenges in realistic VQA deployment. The algorithm incorporates (i) a 3D architecture encoding and restrictions on environment dynamics to explore the search space of possible circuits efficiently, (ii) an episode halting scheme to steer the agent to find shorter circuits, and (iii) a novel variant of simultaneous perturbation stochastic approximation as an optimizer for faster convergence. To facilitate studies, we developed an optimized simulator for our algorithm, significantly improving computational efficiency in simulating noisy quantum circuits by employing the Pauli-transfer matrix formalism in the Pauli-Liouville basis. Numerical experiments focusing on quantum chemistry tasks demonstrate that CRLQAS outperforms existing QAS algorithms across several metrics in both noiseless and noisy environments.

RNA design is the search for a sequence or set of sequences that will fold into predefined structures, also known as the inverse problem of RNA folding. While numerous RNA design methods have been invented to find sequences capable of folding into a target structure, little attention has been given to the identification of undesignable structures according to the minimum free energy (MFE) criterion under the Turner model. In this paper, we address this gap by first introducing mathematical theorems outlining sufficient conditions for recognizing undesignable structures, then proposing efficient algorithms, guided by these theorems, to verify the undesignability of RNA structures. Through the application of these theorems and algorithms to the Eterna100 puzzles, we demonstrate the ability to efficiently establish that 15 of the puzzles indeed fall within the category of undesignable structures. In addition, we provide specific insights from the study of undesignability, in the hope that it will enable more understanding of RNA folding and RNA design.

The RNN transducer is a promising end-to-end model candidate. We compare the original training criterion with the full marginalization over all alignments, to the commonly used maximum approximation, which simplifies, improves and speeds up our training. We also generalize from the original neural network model and study more powerful models, made possible due to the maximum approximation. We further generalize the output label topology to cover RNN-T, RNA and CTC. We perform several studies among all these aspects, including a study on the effect of external alignments. We find that the transducer model generalizes much better on longer sequences than the attention model. Our final transducer model outperforms our attention model on Switchboard 300h by over 6% relative WER.

Single-cell transcriptomics enabled the study of cellular heterogeneity in response to perturbations at the resolution of individual cells. However, scaling high-throughput screens (HTSs) to measure cellular responses for many drugs remains a challenge due to technical limitations and, more importantly, the cost of such multiplexed experiments. Thus, transferring information from routinely performed bulk RNA HTS is required to enrich single-cell data meaningfully. We introduce chemCPA, a new encoder-decoder architecture to study the perturbational effects of unseen drugs. We combine the model with an architecture surgery for transfer learning and demonstrate how training on existing bulk RNA HTS datasets can improve generalisation performance. Better generalisation reduces the need for extensive and costly screens at single-cell resolution. We envision that our proposed method will facilitate more efficient experiment designs through its ability to generate in-silico hypotheses, ultimately accelerating drug discovery.

Diffusion models have emerged as the de facto choice for generating visual signals. However, training a single model to predict noise across various levels poses significant challenges, necessitating numerous iterations and incurring significant computational costs. Various approaches, such as loss weighting strategy design and architectural refinements, have been introduced to expedite convergence. In this study, we propose a novel approach to design the noise schedule for enhancing the training of diffusion models. Our key insight is that the importance sampling of the logarithm of the Signal-to-Noise ratio (logSNR), theoretically equivalent to a modified noise schedule, is particularly beneficial for training efficiency when increasing the sample frequency around log SNR=0. We empirically demonstrate the superiority of our noise schedule over the standard cosine schedule. Furthermore, we highlight the advantages of our noise schedule design on the ImageNet benchmark, showing that the designed schedule consistently benefits different prediction targets.

Diffusion models have achieved great success in image synthesis through iterative noise estimation using deep neural networks. However, the slow inference, high memory consumption, and computation intensity of the noise estimation model hinder the efficient adoption of diffusion models. Although post-training quantization (PTQ) is considered a go-to compression method for other tasks, it does not work out-of-the-box on diffusion models. We propose a novel PTQ method specifically tailored towards the unique multi-timestep pipeline and model architecture of the diffusion models, which compresses the noise estimation network to accelerate the generation process. We identify the key difficulty of diffusion model quantization as the changing output distributions of noise estimation networks over multiple time steps and the bimodal activation distribution of the shortcut layers within the noise estimation network. We tackle these challenges with timestep-aware calibration and split shortcut quantization in this work. Experimental results show that our proposed method is able to quantize full-precision unconditional diffusion models into 4-bit while maintaining comparable performance (small FID change of at most 2.34 compared to >100 for traditional PTQ) in a training-free manner. Our approach can also be applied to text-guided image generation, where we can run stable diffusion in 4-bit weights with high generation quality for the first time.

Diffusion models have achieved remarkable advances in various image generation tasks. However, their performance notably declines when generating images at resolutions higher than those used during the training period. Despite the existence of numerous methods for producing high-resolution images, they either suffer from inefficiency or are hindered by complex operations. In this paper, we propose RectifiedHR, an efficient and straightforward solution for training-free high-resolution image generation. Specifically, we introduce the noise refresh strategy, which theoretically only requires a few lines of code to unlock the model's high-resolution generation ability and improve efficiency. Additionally, we first observe the phenomenon of energy decay that may cause image blurriness during the high-resolution image generation process. To address this issue, we propose an Energy Rectification strategy, where modifying the hyperparameters of the classifier-free guidance effectively improves the generation performance. Our method is entirely training-free and boasts a simple implementation logic. Through extensive comparisons with numerous baseline methods, our RectifiedHR demonstrates superior effectiveness and efficiency.

Removing background noise from speech audio has been the subject of considerable effort, especially in recent years due to the rise of virtual communication and amateur recordings. Yet background noise is not the only unpleasant disturbance that can prevent intelligibility: reverb, clipping, codec artifacts, problematic equalization, limited bandwidth, or inconsistent loudness are equally disturbing and ubiquitous. In this work, we propose to consider the task of speech enhancement as a holistic endeavor, and present a universal speech enhancement system that tackles 55 different distortions at the same time. Our approach consists of a generative model that employs score-based diffusion, together with a multi-resolution conditioning network that performs enhancement with mixture density networks. We show that this approach significantly outperforms the state of the art in a subjective test performed by expert listeners. We also show that it achieves competitive objective scores with just 4-8 diffusion steps, despite not considering any particular strategy for fast sampling. We hope that both our methodology and technical contributions encourage researchers and practitioners to adopt a universal approach to speech enhancement, possibly framing it as a generative task.

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

In this work, we introduce a single parameter omega, to effectively control granularity in diffusion-based synthesis. This parameter is incorporated during the denoising steps of the diffusion model's reverse process. Our approach does not require model retraining, architectural modifications, or additional computational overhead during inference, yet enables precise control over the level of details in the generated outputs. Moreover, spatial masks or denoising schedules with varying omega values can be applied to achieve region-specific or timestep-specific granularity control. Prior knowledge of image composition from control signals or reference images further facilitates the creation of precise omega masks for granularity control on specific objects. To highlight the parameter's role in controlling subtle detail variations, the technique is named Omegance, combining "omega" and "nuance". Our method demonstrates impressive performance across various image and video synthesis tasks and is adaptable to advanced diffusion models. The code is available at https://github.com/itsmag11/Omegance.

Recently, convolutional networks have achieved remarkable development in remote sensing image Super-Resoltuion (SR) by minimizing the regression objectives, e.g., MSE loss. However, despite achieving impressive performance, these methods often suffer from poor visual quality with over-smooth issues. Generative adversarial networks have the potential to infer intricate details, but they are easy to collapse, resulting in undesirable artifacts. To mitigate these issues, in this paper, we first introduce Diffusion Probabilistic Model (DPM) for efficient remote sensing image SR, dubbed EDiffSR. EDiffSR is easy to train and maintains the merits of DPM in generating perceptual-pleasant images. Specifically, different from previous works using heavy UNet for noise prediction, we develop an Efficient Activation Network (EANet) to achieve favorable noise prediction performance by simplified channel attention and simple gate operation, which dramatically reduces the computational budget. Moreover, to introduce more valuable prior knowledge into the proposed EDiffSR, a practical Conditional Prior Enhancement Module (CPEM) is developed to help extract an enriched condition. Unlike most DPM-based SR models that directly generate conditions by amplifying LR images, the proposed CPEM helps to retain more informative cues for accurate SR. Extensive experiments on four remote sensing datasets demonstrate that EDiffSR can restore visual-pleasant images on simulated and real-world remote sensing images, both quantitatively and qualitatively. The code of EDiffSR will be available at https://github.com/XY-boy/EDiffSR

Recent advances in large language models (LLMs) have promoted generative error correction (GER) for automatic speech recognition (ASR), which leverages the rich linguistic knowledge and powerful reasoning ability of LLMs to improve recognition results. The latest work proposes a GER benchmark with HyPoradise dataset to learn the mapping from ASR N-best hypotheses to ground-truth transcription by efficient LLM finetuning, which shows great effectiveness but lacks specificity on noise-robust ASR. In this work, we extend the benchmark to noisy conditions and investigate if we can teach LLMs to perform denoising for GER just like what robust ASR do}, where one solution is introducing noise information as a conditioner into LLM. However, directly incorporating noise embeddings from audio encoder could harm the LLM tuning due to cross-modality gap. To this end, we propose to extract a language-space noise embedding from the N-best list to represent the noise conditions of source speech, which can promote the denoising process in GER. Furthermore, in order to enhance its representation ability of audio noise, we design a knowledge distillation (KD) approach via mutual information estimation to distill the real noise information in audio embeddings to our language embedding. Experiments on various latest LLMs demonstrate our approach achieves a new breakthrough with up to 53.9% correction improvement in terms of word error rate while with limited training data. Analysis shows that our language-space noise embedding can well represent the noise conditions of source speech, under which off-the-shelf LLMs show strong ability of language-space denoising.

In this paper, we find a sample complexity bound for learning a simplex from noisy samples. Assume a dataset of size n is given which includes i.i.d. samples drawn from a uniform distribution over an unknown simplex in R^K, where samples are assumed to be corrupted by a multi-variate additive Gaussian noise of an arbitrary magnitude. We prove the existence of an algorithm that with high probability outputs a simplex having a ell_2 distance of at most varepsilon from the true simplex (for any varepsilon>0). Also, we theoretically show that in order to achieve this bound, it is sufficient to have ngeleft(K^2/varepsilon^2right)e^{Omegaleft(K/SNR^2right)} samples, where SNR stands for the signal-to-noise ratio. This result solves an important open problem and shows as long as SNRgeOmegaleft(K^{1/2}right), the sample complexity of the noisy regime has the same order to that of the noiseless case. Our proofs are a combination of the so-called sample compression technique in ashtiani2018nearly, mathematical tools from high-dimensional geometry, and Fourier analysis. In particular, we have proposed a general Fourier-based technique for recovery of a more general class of distribution families from additive Gaussian noise, which can be further used in a variety of other related problems.

Diffusion models have recently achieved great success in the synthesis of high-quality images and videos. However, the existing denoising techniques in diffusion models are commonly based on step-by-step noise predictions, which suffers from high computation cost, resulting in a prohibitive latency for interactive applications. In this paper, we propose AdaptiveDiffusion to relieve this bottleneck by adaptively reducing the noise prediction steps during the denoising process. Our method considers the potential of skipping as many noise prediction steps as possible while keeping the final denoised results identical to the original full-step ones. Specifically, the skipping strategy is guided by the third-order latent difference that indicates the stability between timesteps during the denoising process, which benefits the reusing of previous noise prediction results. Extensive experiments on image and video diffusion models demonstrate that our method can significantly speed up the denoising process while generating identical results to the original process, achieving up to an average 2~5x speedup without quality degradation.

Diffusion models offer impressive controllability for image tasks, primarily through noise predictions that encode task-specific information and classifier-free guidance enabling adjustable scaling. This scaling mechanism implicitly defines a ``scaling space'' whose potential for fine-grained semantic manipulation remains underexplored. We investigate this space, starting with inversion-based editing where the difference between conditional/unconditional noise predictions carries key semantic information. Our core contribution stems from a Fourier analysis of noise predictions, revealing that its low- and high-frequency components evolve differently throughout diffusion. Based on this insight, we introduce FreSca, a straightforward method that applies guidance scaling independently to different frequency bands in the Fourier domain. FreSca demonstrably enhances existing image editing methods without retraining. Excitingly, its effectiveness extends to image understanding tasks such as depth estimation, yielding quantitative gains across multiple datasets.

Diffusion-based super-resolution (SR) models have recently garnered significant attention due to their potent restoration capabilities. But conventional diffusion models perform noise sampling from a single distribution, constraining their ability to handle real-world scenes and complex textures across semantic regions. With the success of segment anything model (SAM), generating sufficiently fine-grained region masks can enhance the detail recovery of diffusion-based SR model. However, directly integrating SAM into SR models will result in much higher computational cost. In this paper, we propose the SAM-DiffSR model, which can utilize the fine-grained structure information from SAM in the process of sampling noise to improve the image quality without additional computational cost during inference. In the process of training, we encode structural position information into the segmentation mask from SAM. Then the encoded mask is integrated into the forward diffusion process by modulating it to the sampled noise. This adjustment allows us to independently adapt the noise mean within each corresponding segmentation area. The diffusion model is trained to estimate this modulated noise. Crucially, our proposed framework does NOT change the reverse diffusion process and does NOT require SAM at inference. Experimental results demonstrate the effectiveness of our proposed method, showcasing superior performance in suppressing artifacts, and surpassing existing diffusion-based methods by 0.74 dB at the maximum in terms of PSNR on DIV2K dataset. The code and dataset are available at https://github.com/lose4578/SAM-DiffSR.

Cervical disc herniation (CDH) is a prevalent musculoskeletal disorder that significantly impacts health and requires labor-intensive analysis from experts. Despite advancements in automated detection of medical imaging, two significant challenges hinder the real-world application of these methods. First, the computational complexity and resource demands present a significant gap for real-time application. Second, noise in MRI reduces the effectiveness of existing methods by distorting feature extraction. To address these challenges, we propose three key contributions: Firstly, we introduced MedDet, which leverages the multi-teacher single-student knowledge distillation for model compression and efficiency, meanwhile integrating generative adversarial training to enhance performance. Additionally, we customize the second-order nmODE to improve the model's resistance to noise in MRI. Lastly, we conducted comprehensive experiments on the CDH-1848 dataset, achieving up to a 5% improvement in mAP compared to previous methods. Our approach also delivers over 5 times faster inference speed, with approximately 67.8% reduction in parameters and 36.9% reduction in FLOPs compared to the teacher model. These advancements significantly enhance the performance and efficiency of automated CDH detection, demonstrating promising potential for future application in clinical practice. See project website https://steve-zeyu-zhang.github.io/MedDet

Gene regulatory network inference (GRNI) is a challenging problem, particularly owing to the presence of zeros in single-cell RNA sequencing data: some are biological zeros representing no gene expression, while some others are technical zeros arising from the sequencing procedure (aka dropouts), which may bias GRNI by distorting the joint distribution of the measured gene expressions. Existing approaches typically handle dropout error via imputation, which may introduce spurious relations as the true joint distribution is generally unidentifiable. To tackle this issue, we introduce a causal graphical model to characterize the dropout mechanism, namely, Causal Dropout Model. We provide a simple yet effective theoretical result: interestingly, the conditional independence (CI) relations in the data with dropouts, after deleting the samples with zero values (regardless if technical or not) for the conditioned variables, are asymptotically identical to the CI relations in the original data without dropouts. This particular test-wise deletion procedure, in which we perform CI tests on the samples without zeros for the conditioned variables, can be seamlessly integrated with existing structure learning approaches including constraint-based and greedy score-based methods, thus giving rise to a principled framework for GRNI in the presence of dropouts. We further show that the causal dropout model can be validated from data, and many existing statistical models to handle dropouts fit into our model as specific parametric instances. Empirical evaluation on synthetic, curated, and real-world experimental transcriptomic data comprehensively demonstrate the efficacy of our method.

Spoken language understanding (SLU) system usually consists of various pipeline components, where each component heavily relies on the results of its upstream ones. For example, Intent detection (ID), and slot filling (SF) require its upstream automatic speech recognition (ASR) to transform the voice into text. In this case, the upstream perturbations, e.g. ASR errors, environmental noise and careless user speaking, will propagate to the ID and SF models, thus deteriorating the system performance. Therefore, the well-performing SF and ID models are expected to be noise resistant to some extent. However, existing models are trained on clean data, which causes a gap between clean data training and real-world inference. To bridge the gap, we propose a method from the perspective of domain adaptation, by which both high- and low-quality samples are embedding into similar vector space. Meanwhile, we design a denoising generation model to reduce the impact of the low-quality samples. Experiments on the widely-used dataset, i.e. Snips, and large scale in-house dataset (10 million training examples) demonstrate that this method not only outperforms the baseline models on real-world (noisy) corpus but also enhances the robustness, that is, it produces high-quality results under a noisy environment. The source code will be released.

Deep learning methods for unsupervised registration often rely on objectives that assume a uniform noise level across the spatial domain (e.g. mean-squared error loss), but noise distributions are often heteroscedastic and input-dependent in real-world medical images. Thus, this assumption often leads to degradation in registration performance, mainly due to the undesired influence of noise-induced outliers. To mitigate this, we propose a framework for heteroscedastic image uncertainty estimation that can adaptively reduce the influence of regions with high uncertainty during unsupervised registration. The framework consists of a collaborative training strategy for the displacement and variance estimators, and a novel image fidelity weighting scheme utilizing signal-to-noise ratios. Our approach prevents the model from being driven away by spurious gradients caused by the simplified homoscedastic assumption, leading to more accurate displacement estimation. To illustrate its versatility and effectiveness, we tested our framework on two representative registration architectures across three medical image datasets. Our method consistently outperforms baselines and produces sensible uncertainty estimates. The code is publicly available at https://voldemort108x.github.io/hetero_uncertainty/.

Neural text decoding is important for generating high-quality texts using language models. To generate high-quality text, popular decoding algorithms like top-k, top-p (nucleus), and temperature-based sampling truncate or distort the unreliable low probability tail of the language model. Though these methods generate high-quality text after parameter tuning, they are ad hoc. Not much is known about the control they provide over the statistics of the output, which is important since recent reports show text quality is highest for a specific range of likelihoods. Here, first we provide a theoretical analysis of perplexity in top-k, top-p, and temperature sampling, finding that cross-entropy behaves approximately linearly as a function of p in top-p sampling whereas it is a nonlinear function of k in top-k sampling, under Zipfian statistics. We use this analysis to design a feedback-based adaptive top-k text decoding algorithm called mirostat that generates text (of any length) with a predetermined value of perplexity, and thereby high-quality text without any tuning. Experiments show that for low values of k and p in top-k and top-p sampling, perplexity drops significantly with generated text length, which is also correlated with excessive repetitions in the text (the boredom trap). On the other hand, for large values of k and p, we find that perplexity increases with generated text length, which is correlated with incoherence in the text (confusion trap). Mirostat avoids both traps: experiments show that cross-entropy has a near-linear relation with repetition in generated text. This relation is almost independent of the sampling method but slightly dependent on the model used. Hence, for a given language model, control over perplexity also gives control over repetitions. Experiments with human raters for fluency, coherence, and quality further verify our findings.

RNA design aims to find a sequence that folds with highest probability into a designated target structure. However, certain structures are undesignable, meaning no sequence can fold into the target structure under the default (Turner) RNA folding model. Understanding the specific local structures (i.e., "motifs") that contribute to undesignability is crucial for refining RNA folding models and determining the limits of RNA designability. Despite its importance, this problem has received very little attention, and previous efforts are neither scalable nor interpretable. We develop a new theoretical framework for motif (un-)designability, and design scalable and interpretable algorithms to identify minimal undesignable motifs within a given RNA secondary structure. Our approach establishes motif undesignability by searching for rival motifs, rather than exhaustively enumerating all (partial) sequences that could potentially fold into the motif. Furthermore, we exploit rotational invariance in RNA structures to detect, group, and reuse equivalent motifs and to construct a database of unique minimal undesignable motifs. To achieve that, we propose a loop-pair graph representation for motifs and a recursive graph isomorphism algorithm for motif equivalence. Our algorithms successfully identify 24 unique minimal undesignable motifs among 18 undesignable puzzles from the Eterna100 benchmark. Surprisingly, we also find over 350 unique minimal undesignable motifs and 663 undesignable native structures in the ArchiveII dataset, drawn from a diverse set of RNA families. Our source code is available at https://github.com/shanry/RNA-Undesign and our web server is available at http://linearfold.org/motifs.

Latent Diffusion Models (LDMs) capture the dynamic evolution of latent variables over time, blending patterns and multimodality in a generative system. Despite the proficiency of LDM in various applications, such as text-to-image generation, facilitated by robust text encoders and a variational autoencoder, the critical need to deploy large generative models on edge devices compels a search for more compact yet effective alternatives. Post Training Quantization (PTQ), a method to compress the operational size of deep learning models, encounters challenges when applied to LDM due to temporal and structural complexities. This study proposes a quantization strategy that efficiently quantize LDMs, leveraging Signal-to-Quantization-Noise Ratio (SQNR) as a pivotal metric for evaluation. By treating the quantization discrepancy as relative noise and identifying sensitive part(s) of a model, we propose an efficient quantization approach encompassing both global and local strategies. The global quantization process mitigates relative quantization noise by initiating higher-precision quantization on sensitive blocks, while local treatments address specific challenges in quantization-sensitive and time-sensitive modules. The outcomes of our experiments reveal that the implementation of both global and local treatments yields a highly efficient and effective Post Training Quantization (PTQ) of LDMs.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the ``clean'' molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (i.e., diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.

Conditional diffusion models have shown remarkable performance in various generative tasks, but training them requires large-scale datasets that often contain noise in conditional inputs, a.k.a. noisy labels. This noise leads to condition mismatch and quality degradation of generated data. This paper proposes Transition-aware weighted Denoising Score Matching (TDSM) for training conditional diffusion models with noisy labels, which is the first study in the line of diffusion models. The TDSM objective contains a weighted sum of score networks, incorporating instance-wise and time-dependent label transition probabilities. We introduce a transition-aware weight estimator, which leverages a time-dependent noisy-label classifier distinctively customized to the diffusion process. Through experiments across various datasets and noisy label settings, TDSM improves the quality of generated samples aligned with given conditions. Furthermore, our method improves generation performance even on prevalent benchmark datasets, which implies the potential noisy labels and their risk of generative model learning. Finally, we show the improved performance of TDSM on top of conventional noisy label corrections, which empirically proving its contribution as a part of label-noise robust generative models. Our code is available at: https://github.com/byeonghu-na/tdsm.

We discover that common diffusion noise schedules do not enforce the last timestep to have zero signal-to-noise ratio (SNR), and some implementations of diffusion samplers do not start from the last timestep. Such designs are flawed and do not reflect the fact that the model is given pure Gaussian noise at inference, creating a discrepancy between training and inference. We show that the flawed design causes real problems in existing implementations. In Stable Diffusion, it severely limits the model to only generate images with medium brightness and prevents it from generating very bright and dark samples. We propose a few simple fixes: (1) rescale the noise schedule to enforce zero terminal SNR; (2) train the model with v prediction; (3) change the sampler to always start from the last timestep; (4) rescale classifier-free guidance to prevent over-exposure. These simple changes ensure the diffusion process is congruent between training and inference and allow the model to generate samples more faithful to the original data distribution.

Noise is a ubiquitous feature of the physical world. As a result, the first prerequisite of life is fault tolerance: maintaining integrity of state despite external bombardment. Recent experimental advances have revealed that biological systems achieve fault tolerance by implementing mathematically intricate error-correcting codes and by organizing in a modular fashion that physically separates functionally distinct subsystems. These elaborate structures represent a vanishing volume in the massive genetic configuration space. How is it possible that the primitive process of evolution, by which all biological systems evolved, achieved such unusual results? In this work, through experiments in Boolean networks, we show that the simultaneous presence of error correction and modularity in biological systems is no coincidence. Rather, it is a typical co-occurrence in noisy dynamic systems undergoing evolution. From this, we deduce the principle of error correction enhanced evolvability: systems possessing error-correcting codes are more effectively improved by evolution than those without.

Magnetic Resonance Imaging (MRI), including diffusion MRI (dMRI), serves as a ``microscope'' for anatomical structures and routinely mitigates the influence of low signal-to-noise ratio scans by compromising temporal or spatial resolution. However, these compromises fail to meet clinical demands for both efficiency and precision. Consequently, denoising is a vital preprocessing step, particularly for dMRI, where clean data is unavailable. In this paper, we introduce Di-Fusion, a fully self-supervised denoising method that leverages the latter diffusion steps and an adaptive sampling process. Unlike previous approaches, our single-stage framework achieves efficient and stable training without extra noise model training and offers adaptive and controllable results in the sampling process. Our thorough experiments on real and simulated data demonstrate that Di-Fusion achieves state-of-the-art performance in microstructure modeling, tractography tracking, and other downstream tasks. Code is available at https://github.com/FouierL/Di-Fusion.

Semantic information refers to the meaning conveyed through words, phrases, and contextual relationships within a given linguistic structure. Humans can leverage semantic information, such as familiar linguistic patterns and contextual cues, to reconstruct incomplete or masked speech signals in noisy environments. However, existing speech enhancement (SE) approaches often overlook the rich semantic information embedded in speech, which is crucial for improving intelligibility, speaker consistency, and overall quality of enhanced speech signals. To enrich the SE model with semantic information, we employ language models as an efficient semantic learner and propose a comprehensive framework tailored for language model-based speech enhancement, called GenSE. Specifically, we approach SE as a conditional language modeling task rather than a continuous signal regression problem defined in existing works. This is achieved by tokenizing speech signals into semantic tokens using a pre-trained self-supervised model and into acoustic tokens using a custom-designed single-quantizer neural codec model. To improve the stability of language model predictions, we propose a hierarchical modeling method that decouples the generation of clean semantic tokens and clean acoustic tokens into two distinct stages. Moreover, we introduce a token chain prompting mechanism during the acoustic token generation stage to ensure timbre consistency throughout the speech enhancement process. Experimental results on benchmark datasets demonstrate that our proposed approach outperforms state-of-the-art SE systems in terms of speech quality and generalization capability.

Spatial transcriptomics (ST) enables interrogating the molecular composition of tissue with ever-increasing resolution, depth, and sensitivity. However, costs, rapidly evolving technology, and lack of standards have constrained computational methods in ST to narrow tasks and small cohorts. In addition, the underlying tissue morphology as reflected by H&E-stained whole slide images (WSIs) encodes rich information often overlooked in ST studies. Here, we introduce HEST-1k, a collection of 1,108 spatial transcriptomic profiles, each linked to a WSI and metadata. HEST-1k was assembled using HEST-Library from 131 public and internal cohorts encompassing 25 organs, two species (Homo Sapiens and Mus Musculus), and 320 cancer samples from 25 cancer types. HEST-1k processing enabled the identification of 1.5 million expression--morphology pairs and 60 million nuclei. HEST-1k is tested on three use cases: (1) benchmarking foundation models for histopathology (HEST-Benchmark), (2) biomarker identification, and (3) multimodal representation learning. HEST-1k, HEST-Library, and HEST-Benchmark can be freely accessed via https://github.com/mahmoodlab/hest.

Most of the speech recognition systems recover only words in the speech and fail to capture emotions. Users have to manually add emoji(s) in text for adding tone and making communication fun. Though there is much work done on punctuation addition on transcribed speech, the area of emotion addition is untouched. In this paper, we propose a novel on-device pipeline to enrich the voice input experience. It involves, given a blob of transcribed text, intelligently processing and identifying structure where emoji insertion makes sense. Moreover, it includes semantic text analysis to predict emoji for each of the sub-parts for which we propose a novel architecture Attention-based Char Aware (ACA) LSTM which handles Out-Of-Vocabulary (OOV) words as well. All these tasks are executed completely on-device and hence can aid on-device dictation systems. To the best of our knowledge, this is the first work that shows how to add emoji(s) in the transcribed text. We demonstrate that our components achieve comparable results to previous neural approaches for punctuation addition and emoji prediction with 80% fewer parameters. Overall, our proposed model has a very small memory footprint of a mere 4MB to suit on-device deployment.

Guidance is a crucial technique for extracting the best performance out of image-generating diffusion models. Traditionally, a constant guidance weight has been applied throughout the sampling chain of an image. We show that guidance is clearly harmful toward the beginning of the chain (high noise levels), largely unnecessary toward the end (low noise levels), and only beneficial in the middle. We thus restrict it to a specific range of noise levels, improving both the inference speed and result quality. This limited guidance interval improves the record FID in ImageNet-512 significantly, from 1.81 to 1.40. We show that it is quantitatively and qualitatively beneficial across different sampler parameters, network architectures, and datasets, including the large-scale setting of Stable Diffusion XL. We thus suggest exposing the guidance interval as a hyperparameter in all diffusion models that use guidance.

Non-linguistic filler words, such as "uh" or "um", are prevalent in spontaneous speech and serve as indicators for expressing hesitation or uncertainty. Previous works for detecting certain non-linguistic filler words are highly dependent on transcriptions from a well-established commercial automatic speech recognition (ASR) system. However, certain ASR systems are not universally accessible from many aspects, e.g., budget, target languages, and computational power. In this work, we investigate filler word detection system that does not depend on ASR systems. We show that, by using the structured state space sequence model (S4) and neural semi-Markov conditional random fields (semi-CRFs), we achieve an absolute F1 improvement of 6.4% (segment level) and 3.1% (event level) on the PodcastFillers dataset. We also conduct a qualitative analysis on the detected results to analyze the limitations of our proposed system.

Existing methods to recover model accuracy on analog-digital hardware in the presence of quantization and analog noise include noise-injection training. However, it can be slow in practice, incurring high computational costs, even when starting from pretrained models. We introduce the Sensitivity-Aware Finetuning (SAFT) approach that identifies noise sensitive layers in a model, and uses the information to freeze specific layers for noise-injection training. Our results show that SAFT achieves comparable accuracy to noise-injection training and is 2x to 8x faster.

Recently, diffusion models have emerged as a new paradigm for generative models. Despite the success in domains using continuous signals such as vision and audio, adapting diffusion models to natural language is under-explored due to the discrete nature of texts, especially for conditional generation. We tackle this challenge by proposing DiffuSeq: a diffusion model designed for sequence-to-sequence (Seq2Seq) text generation tasks. Upon extensive evaluation over a wide range of Seq2Seq tasks, we find DiffuSeq achieving comparable or even better performance than six established baselines, including a state-of-the-art model that is based on pre-trained language models. Apart from quality, an intriguing property of DiffuSeq is its high diversity during generation, which is desired in many Seq2Seq tasks. We further include a theoretical analysis revealing the connection between DiffuSeq and autoregressive/non-autoregressive models. Bringing together theoretical analysis and empirical evidence, we demonstrate the great potential of diffusion models in complex conditional language generation tasks. Code is available at https://github.com/Shark-NLP/DiffuSeq

Large language models have already demonstrated their formidable capabilities in general domains, ushering in a revolutionary transformation. However, exploring and exploiting the extensive knowledge of these models to comprehend multi-omics biology remains underexplored. To fill this research gap, we first introduce Biology-Instructions, the first large-scale multi-omics biological sequences-related instruction-tuning dataset including DNA, RNA, proteins, and multi-molecules, designed to bridge the gap between large language models (LLMs) and complex biological sequences-related tasks. This dataset can enhance the versatility of LLMs by integrating diverse biological sequenced-based prediction tasks with advanced reasoning capabilities, while maintaining conversational fluency. Additionally, we reveal significant performance limitations in even state-of-the-art LLMs on biological sequence-related multi-omics tasks without specialized pre-training and instruction-tuning. We further develop a strong baseline called ChatMultiOmics with a novel three-stage training pipeline, demonstrating the powerful ability to understand biology by using Biology-Instructions. Biology-Instructions and ChatMultiOmics are publicly available and crucial resources for enabling more effective integration of LLMs with multi-omics sequence analysis.

Denoising diffusion models, a class of generative models, have garnered immense interest lately in various deep-learning problems. A diffusion probabilistic model defines a forward diffusion stage where the input data is gradually perturbed over several steps by adding Gaussian noise and then learns to reverse the diffusion process to retrieve the desired noise-free data from noisy data samples. Diffusion models are widely appreciated for their strong mode coverage and quality of the generated samples despite their known computational burdens. Capitalizing on the advances in computer vision, the field of medical imaging has also observed a growing interest in diffusion models. To help the researcher navigate this profusion, this survey intends to provide a comprehensive overview of diffusion models in the discipline of medical image analysis. Specifically, we introduce the solid theoretical foundation and fundamental concepts behind diffusion models and the three generic diffusion modelling frameworks: diffusion probabilistic models, noise-conditioned score networks, and stochastic differential equations. Then, we provide a systematic taxonomy of diffusion models in the medical domain and propose a multi-perspective categorization based on their application, imaging modality, organ of interest, and algorithms. To this end, we cover extensive applications of diffusion models in the medical domain. Furthermore, we emphasize the practical use case of some selected approaches, and then we discuss the limitations of the diffusion models in the medical domain and propose several directions to fulfill the demands of this field. Finally, we gather the overviewed studies with their available open-source implementations at https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.

Current diffusion-based image restoration methods feed degraded input images as conditions into the noise estimation network. However, interpreting this diffusion process is challenging since it essentially generates the target image from the noise. To establish a unified and more interpretable model for image generation and restoration, we propose residual denoising diffusion models (RDDM). In contrast to existing diffusion models (e.g., DDPM or DDIM) that focus solely on noise estimation, our RDDM predicts residuals to represent directional diffusion from the target domain to the input domain, while concurrently estimating noise to account for random perturbations in the diffusion process. The introduction of residuals allows us to redefine the forward diffusion process, wherein the target image progressively diffuses into a purely noisy image or a noise-carrying input image, thus unifying image generation and restoration. We demonstrate that our sampling process is consistent with that of DDPM and DDIM through coefficient transformation, and propose a partially path-independent generation process to better understand the reverse process. Notably, with native support for conditional inputs, our RDDM enables a generic UNet, trained with only an ell _1 loss and a batch size of 1, to compete with state-of-the-art image restoration methods. We provide code and pre-trained models to encourage further exploration, application, and development of our innovative framework (https://github.com/nachifur/RDDM).

The sparsity of labelled data is an obstacle to the development of Relation Extraction models and the completion of databases in various biomedical areas. While being of high interest in drug-discovery, the natural-products literature, reporting the identification of potential bioactive compounds from organisms, is a concrete example of such an overlooked topic. To mark the start of this new task, we created the first curated evaluation dataset and extracted literature items from the LOTUS database to build training sets. To this end, we developed a new sampler inspired by diversity metrics in ecology, named Greedy Maximum Entropy sampler, or GME-sampler (https://github.com/idiap/gme-sampler). The strategic optimization of both balance and diversity of the selected items in the evaluation set is important given the resource-intensive nature of manual curation. After quantifying the noise in the training set, in the form of discrepancies between the input abstracts text and the expected output labels, we explored different strategies accordingly. Framing the task as an end-to-end Relation Extraction, we evaluated the performance of standard fine-tuning as a generative task and few-shot learning with open Large Language Models (LLaMA 7B-65B). In addition to their evaluation in few-shot settings, we explore the potential of open Large Language Models (Vicuna-13B) as synthetic data generator and propose a new workflow for this purpose. All evaluated models exhibited substantial improvements when fine-tuned on synthetic abstracts rather than the original noisy data. We provide our best performing (f1-score=59.0) BioGPT-Large model for end-to-end RE of natural-products relationships along with all the generated synthetic data and the evaluation dataset. See more details at https://github.com/idiap/abroad-re.

Denoising Diffusion Probabilistic Models have shown an impressive generation quality, although their long sampling chain leads to high computational costs. In this paper, we observe that a long sampling chain also leads to an error accumulation phenomenon, which is similar to the exposure bias problem in autoregressive text generation. Specifically, we note that there is a discrepancy between training and testing, since the former is conditioned on the ground truth samples, while the latter is conditioned on the previously generated results. To alleviate this problem, we propose a very simple but effective training regularization, consisting in perturbing the ground truth samples to simulate the inference time prediction errors. We empirically show that, without affecting the recall and precision, the proposed input perturbation leads to a significant improvement in the sample quality while reducing both the training and the inference times. For instance, on CelebA 64times64, we achieve a new state-of-the-art FID score of 1.27, while saving 37.5% of the training time. The code is publicly available at https://github.com/forever208/DDPM-IP

We propose algorithms for approximate filtering and smoothing in high-dimensional Factorial hidden Markov models. The approximation involves discarding, in a principled way, likelihood factors according to a notion of locality in a factor graph associated with the emission distribution. This allows the exponential-in-dimension cost of exact filtering and smoothing to be avoided. We prove that the approximation accuracy, measured in a local total variation norm, is "dimension-free" in the sense that as the overall dimension of the model increases the error bounds we derive do not necessarily degrade. A key step in the analysis is to quantify the error introduced by localizing the likelihood function in a Bayes' rule update. The factorial structure of the likelihood function which we exploit arises naturally when data have known spatial or network structure. We demonstrate the new algorithms on synthetic examples and a London Underground passenger flow problem, where the factor graph is effectively given by the train network.

Autoregressive models are typically applied to sequences of discrete tokens, but recent research indicates that generating sequences of continuous embeddings in an autoregressive manner is also feasible. However, such Continuous Autoregressive Models (CAMs) can suffer from a decline in generation quality over extended sequences due to error accumulation during inference. We introduce a novel method to address this issue by injecting random noise into the input embeddings during training. This procedure makes the model robust against varying error levels at inference. We further reduce error accumulation through an inference procedure that introduces low-level noise. Experiments on musical audio generation show that CAM substantially outperforms existing autoregressive and non-autoregressive approaches while preserving audio quality over extended sequences. This work paves the way for generating continuous embeddings in a purely autoregressive setting, opening new possibilities for real-time and interactive generative applications.

Generative speech enhancement has recently shown promising advancements in improving speech quality in noisy environments. Multiple diffusion-based frameworks exist, each employing distinct training objectives and learning techniques. This paper aims at explaining the differences between these frameworks by focusing our investigation on score-based generative models and Schr\"odinger bridge. We conduct a series of comprehensive experiments to compare their performance and highlight differing training behaviors. Furthermore, we propose a novel perceptual loss function tailored for the Schr\"odinger bridge framework, demonstrating enhanced performance and improved perceptual quality of the enhanced speech signals. All experimental code and pre-trained models are publicly available to facilitate further research and development in this.

Diffusion models have garnered considerable interest in the field of text generation. Several studies have explored text diffusion models with different structures and applied them to various tasks, including named entity recognition and summarization. However, there exists a notable disparity between the "easy-first" text generation process of current diffusion models and the "keyword-first" natural text generation process of humans, which has received limited attention. To bridge this gap, we propose InfoDiffusion, a non-autoregressive text diffusion model. Our approach introduces a "keyinfo-first" generation strategy and incorporates a noise schedule based on the amount of text information. In addition, InfoDiffusion combines self-conditioning with a newly proposed partially noising model structure. Experimental results show that InfoDiffusion outperforms the baseline model in terms of generation quality and diversity, as well as exhibiting higher sampling efficiency.

Efficient decoding to estimate error locations from outcomes of syndrome measurement is the prerequisite for quantum error correction. Decoding in presence of circuit-level noise including measurement errors should be considered in case of actual quantum computing devices. In this work, we develop a decoder for circuit-level noise that solves the error estimation problems as Ising-type optimization problems. We confirm that the threshold theorem in the surface code under the circuitlevel noise is reproduced with an error threshold of approximately 0.4%. We also demonstrate the advantage of the decoder through which the Y error detection rate can be improved compared with other matching-based decoders. Our results reveal that a lower logical error rate can be obtained using our algorithm compared with that of the minimum-weight perfect matching algorithm.

In order to improve the quality of synthesized videos, currently, one predominant method involves retraining an expert diffusion model and then implementing a noising-denoising process for refinement. Despite the significant training costs, maintaining consistency of content between the original and enhanced videos remains a major challenge. To tackle this challenge, we propose a novel formulation that considers both visual quality and consistency of content. Consistency of content is ensured by a proposed loss function that maintains the structure of the input, while visual quality is improved by utilizing the denoising process of pretrained diffusion models. To address the formulated optimization problem, we have developed a plug-and-play noise optimization strategy, referred to as Noise Calibration. By refining the initial random noise through a few iterations, the content of original video can be largely preserved, and the enhancement effect demonstrates a notable improvement. Extensive experiments have demonstrated the effectiveness of the proposed method.

In Ultrasound Localization Microscopy (ULM),achieving high-resolution images relies on the precise localization of contrast agent particles across consecutive beam-formed frames. However, our study uncovers an enormous potential: The process of delay-and-sum beamforming leads to an irreversible reduction of Radio-Frequency (RF) data, while its implications for localization remain largely unexplored. The rich contextual information embedded within RF wavefronts, including their hyperbolic shape and phase, offers great promise for guiding Deep Neural Networks (DNNs) in challenging localization scenarios. To fully exploit this data, we propose to directly localize scatterers in RF signals. Our approach involves a custom super-resolution DNN using learned feature channel shuffling and a novel semi-global convolutional sampling block tailored for reliable and accurate wavefront localization. Additionally, we introduce a geometric point transformation that facilitates seamless mapping between RF and B-mode coordinate space. To understand the impact of beamforming on ULM, we validate the effectiveness of our method by conducting an extensive comparison with State-Of-The-Art (SOTA) techniques. We present the inaugural in vivo results from an RF-trained DNN, highlighting its real-world practicality. Our findings show that RF-ULM bridges the domain gap between synthetic and real datasets, offering a considerable advantage in terms of precision and complexity. To enable the broader research community to benefit from our findings, our code and the associated SOTA methods are made available at https://github.com/hahnec/rf-ulm.

Score-based generative models (SGMs) have recently shown impressive results for difficult generative tasks such as the unconditional and conditional generation of natural images and audio signals. In this work, we extend these models to the complex short-time Fourier transform (STFT) domain, proposing a novel training task for speech enhancement using a complex-valued deep neural network. We derive this training task within the formalism of stochastic differential equations (SDEs), thereby enabling the use of predictor-corrector samplers. We provide alternative formulations inspired by previous publications on using generative diffusion models for speech enhancement, avoiding the need for any prior assumptions on the noise distribution and making the training task purely generative which, as we show, results in improved enhancement performance.

In this research, we propose a novel denoising diffusion model based on shortest-path modeling that optimizes residual propagation to enhance both denoising efficiency and quality. Drawing on Denoising Diffusion Implicit Models (DDIM) and insights from graph theory, our model, termed the Shortest Path Diffusion Model (ShortDF), treats the denoising process as a shortest-path problem aimed at minimizing reconstruction error. By optimizing the initial residuals, we improve the efficiency of the reverse diffusion process and the quality of the generated samples. Extensive experiments on multiple standard benchmarks demonstrate that ShortDF significantly reduces diffusion time (or steps) while enhancing the visual fidelity of generated samples compared to prior arts. This work, we suppose, paves the way for interactive diffusion-based applications and establishes a foundation for rapid data generation. Code is available at https://github.com/UnicomAI/ShortDF.

We propose an effective denoising diffusion model for generating high-resolution images (e.g., 1024times512), trained on small-size image patches (e.g., 64times64). We name our algorithm Patch-DM, in which a new feature collage strategy is designed to avoid the boundary artifact when synthesizing large-size images. Feature collage systematically crops and combines partial features of the neighboring patches to predict the features of a shifted image patch, allowing the seamless generation of the entire image due to the overlap in the patch feature space. Patch-DM produces high-quality image synthesis results on our newly collected dataset of nature images (1024times512), as well as on standard benchmarks of smaller sizes (256times256), including LSUN-Bedroom, LSUN-Church, and FFHQ. We compare our method with previous patch-based generation methods and achieve state-of-the-art FID scores on all four datasets. Further, Patch-DM also reduces memory complexity compared to the classic diffusion models.

In this paper, we point out suboptimal noise-data mapping leads to slow training of diffusion models. During diffusion training, current methods diffuse each image across the entire noise space, resulting in a mixture of all images at every point in the noise layer. We emphasize that this random mixture of noise-data mapping complicates the optimization of the denoising function in diffusion models. Drawing inspiration from the immiscible phenomenon in physics, we propose Immiscible Diffusion, a simple and effective method to improve the random mixture of noise-data mapping. In physics, miscibility can vary according to various intermolecular forces. Thus, immiscibility means that the mixing of the molecular sources is distinguishable. Inspired by this, we propose an assignment-then-diffusion training strategy. Specifically, prior to diffusing the image data into noise, we assign diffusion target noise for the image data by minimizing the total image-noise pair distance in a mini-batch. The assignment functions analogously to external forces to separate the diffuse-able areas of images, thus mitigating the inherent difficulties in diffusion training. Our approach is remarkably simple, requiring only one line of code to restrict the diffuse-able area for each image while preserving the Gaussian distribution of noise. This ensures that each image is projected only to nearby noise. To address the high complexity of the assignment algorithm, we employ a quantized-assignment method to reduce the computational overhead to a negligible level. Experiments demonstrate that our method achieve up to 3x faster training for consistency models and DDIM on the CIFAR dataset, and up to 1.3x faster on CelebA datasets for consistency models. Besides, we conduct thorough analysis about the Immiscible Diffusion, which sheds lights on how it improves diffusion training speed while improving the fidelity.

This paper introduces a novel training methodology that enables a small Transformer model to generalize the addition of two-digit numbers to numbers with unseen lengths of digits. The proposed approach employs an autoregressive generation technique, processing from right to left, which mimics a common manual method for adding large numbers. To the best of my knowledge, this methodology has not been previously explored in the literature. All results are reproducible, and the corresponding R code is available at: https://github.com/AGPatriota/ALGA-R/.

Training-free high-resolution (HR) image generation has garnered significant attention due to the high costs of training large diffusion models. Most existing methods begin by reconstructing the overall structure and then proceed to refine the local details. Despite their advancements, they still face issues with repetitive patterns in HR image generation. Besides, HR generation with diffusion models incurs significant computational costs. Thus, parallel generation is essential for interactive applications. To solve the above limitations, we introduce a novel method named ASGDiffusion for parallel HR generation with Asynchronous Structure Guidance (ASG) using pre-trained diffusion models. To solve the pattern repetition problem of HR image generation, ASGDiffusion leverages the low-resolution (LR) noise weighted by the attention mask as the structure guidance for the denoising step to ensure semantic consistency. The proposed structure guidance can significantly alleviate the pattern repetition problem. To enable parallel generation, we further propose a parallelism strategy, which calculates the patch noises and structure guidance asynchronously. By leveraging multi-GPU parallel acceleration, we significantly accelerate generation speed and reduce memory usage per GPU. Extensive experiments demonstrate that our method effectively and efficiently addresses common issues like pattern repetition and achieves state-of-the-art HR generation.

This paper introduces a novel framework for DNA sequence generation, comprising two key components: DiscDiff, a Latent Diffusion Model (LDM) tailored for generating discrete DNA sequences, and Absorb-Escape, a post-training algorithm designed to refine these sequences. Absorb-Escape enhances the realism of the generated sequences by correcting `round errors' inherent in the conversion process between latent and input spaces. Our approach not only sets new standards in DNA sequence generation but also demonstrates superior performance over existing diffusion models, in generating both short and long DNA sequences. Additionally, we introduce EPD-GenDNA, the first comprehensive, multi-species dataset for DNA generation, encompassing 160,000 unique sequences from 15 species. We hope this study will advance the generative modelling of DNA, with potential implications for gene therapy and protein production.

We consider the problem of computing the Walsh-Hadamard Transform (WHT) of some N-length input vector in the presence of noise, where the N-point Walsh spectrum is K-sparse with K = {O}(N^{delta}) scaling sub-linearly in the input dimension N for some 0<delta<1. Over the past decade, there has been a resurgence in research related to the computation of Discrete Fourier Transform (DFT) for some length-N input signal that has a K-sparse Fourier spectrum. In particular, through a sparse-graph code design, our earlier work on the Fast Fourier Aliasing-based Sparse Transform (FFAST) algorithm computes the K-sparse DFT in time {O}(Klog K) by taking {O}(K) noiseless samples. Inspired by the coding-theoretic design framework, Scheibler et al. proposed the Sparse Fast Hadamard Transform (SparseFHT) algorithm that elegantly computes the K-sparse WHT in the absence of noise using {O}(Klog N) samples in time {O}(Klog^2 N). However, the SparseFHT algorithm explicitly exploits the noiseless nature of the problem, and is not equipped to deal with scenarios where the observations are corrupted by noise. Therefore, a question of critical interest is whether this coding-theoretic framework can be made robust to noise. Further, if the answer is yes, what is the extra price that needs to be paid for being robust to noise? In this paper, we show, quite interestingly, that there is {\it no extra price} that needs to be paid for being robust to noise other than a constant factor. In other words, we can maintain the same sample complexity {O}(Klog N) and the computational complexity {O}(Klog^2 N) as those of the noiseless case, using our SParse Robust Iterative Graph-based Hadamard Transform (SPRIGHT) algorithm.

Linear State Space Models (SSMs) have demonstrated strong performance in a variety of sequence modeling tasks due to their efficient encoding of the recurrent structure. However, in more comprehensive tasks like language modeling and machine translation, self-attention-based models still outperform SSMs. Hybrid models employing both SSM and self-attention generally show promising performance, but current approaches apply attention modules statically and uniformly to all elements in the input sequences, leading to sub-optimal quality-efficiency trade-offs. In this work, we introduce Sparse Modular Activation (SMA), a general mechanism enabling neural networks to sparsely and dynamically activate sub-modules for sequence elements in a differentiable manner. Through allowing each element to skip non-activated sub-modules, SMA reduces computation and memory consumption at both training and inference stages of sequence modeling. As a specific instantiation of SMA, we design a novel neural architecture, SeqBoat, which employs SMA to sparsely activate a Gated Attention Unit (GAU) based on the state representations learned from an SSM. By constraining the GAU to only conduct local attention on the activated inputs, SeqBoat can achieve linear inference complexity with theoretically infinite attention span, and provide substantially better quality-efficiency trade-off than the chunking-based models. With experiments on a wide range of tasks, including language modeling, speech classification and long-range arena, SeqBoat brings new state-of-the-art results among hybrid models with linear complexity and reveals the amount of attention needed for each task through the learned sparse activation patterns.

Speckle is a multiplicative noise which affects all coherent imaging modalities including Synthetic Aperture Radar (SAR) images. The presence of speckle degrades the image quality and adversely affects the performance of SAR image understanding applications such as automatic target recognition and change detection. Thus, SAR despeckling is an important problem in remote sensing. In this paper, we introduce SAR-DDPM, a denoising diffusion probabilistic model for SAR despeckling. The proposed method comprises of a Markov chain that transforms clean images to white Gaussian noise by repeatedly adding random noise. The despeckled image is recovered by a reverse process which iteratively predicts the added noise using a noise predictor which is conditioned on the speckled image. In addition, we propose a new inference strategy based on cycle spinning to improve the despeckling performance. Our experiments on both synthetic and real SAR images demonstrate that the proposed method achieves significant improvements in both quantitative and qualitative results over the state-of-the-art despeckling methods.

We study lossless acceleration for seq2seq generation with a novel decoding algorithm -- Aggressive Decoding. Unlike the previous efforts (e.g., non-autoregressive decoding) speeding up seq2seq generation at the cost of quality loss, our approach aims to yield the identical (or better) generation compared with autoregressive decoding but in a significant speedup, achieved by innovative cooperation of aggressive decoding and verification that are both efficient due to parallel computing. We propose two Aggressive Decoding paradigms for 2 kinds of seq2seq tasks: 1) For the seq2seq tasks whose inputs and outputs are highly similar (e.g., Grammatical Error Correction), we propose Input-guided Aggressive Decoding (IAD) that aggressively copies from the input sentence as drafted decoded tokens to verify in parallel; 2) For other general seq2seq tasks (e.g., Machine Translation), we propose Generalized Aggressive Decoding (GAD) that first employs an additional non-autoregressive decoding model for aggressive decoding and then verifies in parallel in the autoregressive manner. We test Aggressive Decoding on the most popular 6-layer Transformer model on GPU in multiple seq2seq tasks: 1) For IAD, we show that it can introduce a 7x-9x speedup for the Transformer in Grammatical Error Correction and Text Simplification tasks with the identical results as greedy decoding; 2) For GAD, we observe a 3x-5x speedup with the identical or even better quality in two important seq2seq tasks: Machine Translation and Abstractive Summarization. Moreover, Aggressive Decoding can benefit even more from stronger computing devices that are better at parallel computing. Given the lossless quality as well as significant and promising speedup, we believe Aggressive Decoding may potentially evolve into a de facto standard for efficient and lossless seq2seq generation in the near future.

We present a causal speech enhancement model working on the raw waveform that runs in real-time on a laptop CPU. The proposed model is based on an encoder-decoder architecture with skip-connections. It is optimized on both time and frequency domains, using multiple loss functions. Empirical evidence shows that it is capable of removing various kinds of background noise including stationary and non-stationary noises, as well as room reverb. Additionally, we suggest a set of data augmentation techniques applied directly on the raw waveform which further improve model performance and its generalization abilities. We perform evaluations on several standard benchmarks, both using objective metrics and human judgements. The proposed model matches state-of-the-art performance of both causal and non causal methods while working directly on the raw waveform.

We study the problem of online generalized linear regression in the stochastic setting, where the label is generated from a generalized linear model with possibly unbounded additive noise. We provide a sharp analysis of the classical follow-the-regularized-leader (FTRL) algorithm to cope with the label noise. More specifically, for sigma-sub-Gaussian label noise, our analysis provides a regret upper bound of O(sigma^2 d log T) + o(log T), where d is the dimension of the input vector, T is the total number of rounds. We also prove a Omega(sigma^2dlog(T/d)) lower bound for stochastic online linear regression, which indicates that our upper bound is nearly optimal. In addition, we extend our analysis to a more refined Bernstein noise condition. As an application, we study generalized linear bandits with heteroscedastic noise and propose an algorithm based on FTRL to achieve the first variance-aware regret bound.

While artificial intelligence has made remarkable strides in revealing the relationship between biological macromolecules' primary sequence and tertiary structure, designing RNA sequences based on specified tertiary structures remains challenging. Though existing approaches in protein design have thoroughly explored structure-to-sequence dependencies in proteins, RNA design still confronts difficulties due to structural complexity and data scarcity. Moreover, direct transplantation of protein design methodologies into RNA design fails to achieve satisfactory outcomes although sharing similar structural components. In this study, we aim to systematically construct a data-driven RNA design pipeline. We crafted a large, well-curated benchmark dataset and designed a comprehensive structural modeling approach to represent the complex RNA tertiary structure. More importantly, we proposed a hierarchical data-efficient representation learning framework that learns structural representations through contrastive learning at both cluster-level and sample-level to fully leverage the limited data. By constraining data representations within a limited hyperspherical space, the intrinsic relationships between data points could be explicitly imposed. Moreover, we incorporated extracted secondary structures with base pairs as prior knowledge to facilitate the RNA design process. Extensive experiments demonstrate the effectiveness of our proposed method, providing a reliable baseline for future RNA design tasks. The source code and benchmark dataset are available at https://github.com/A4Bio/RDesign.

This study addresses the challenge of noise in training datasets for Direct Preference Optimization (DPO), a method for aligning Large Language Models (LLMs) with human preferences. We categorize noise into pointwise noise, which includes low-quality data points, and pairwise noise, which encompasses erroneous data pair associations that affect preference rankings. Utilizing Distributionally Robust Optimization (DRO), we enhance DPO's resilience to these types of noise. Our theoretical insights reveal that DPO inherently embeds DRO principles, conferring robustness to pointwise noise, with the regularization coefficient beta playing a critical role in its noise resistance. Extending this framework, we introduce Distributionally Robustifying DPO (Dr. DPO), which integrates pairwise robustness by optimizing against worst-case pairwise scenarios. The novel hyperparameter beta' in Dr. DPO allows for fine-tuned control over data pair reliability, providing a strategic balance between exploration and exploitation in noisy training environments. Empirical evaluations demonstrate that Dr. DPO substantially improves the quality of generated text and response accuracy in preference datasets, showcasing enhanced performance in both noisy and noise-free settings. The code is available at https://github.com/junkangwu/Dr_DPO.

The lack of clean speech is a practical challenge to the development of speech enhancement systems, which means that there is an inevitable mismatch between their training criterion and evaluation metric. In response to this unfavorable situation, we propose a training and inference strategy that additionally uses enhanced speech as a target by improving the previously proposed noisy-target training (NyTT). Because homogeneity between in-domain noise and extraneous noise is the key to the effectiveness of NyTT, we train various student models by remixing 1) the teacher model's estimated speech and noise for enhanced-target training or 2) raw noisy speech and the teacher model's estimated noise for noisy-target training. Experimental results show that our proposed method outperforms several baselines, especially with the teacher/student inference, where predicted clean speech is derived successively through the teacher and final student models.

When sound waves hit an object, they induce vibrations that produce high-frequency and subtle visual changes, which can be used for recovering the sound. Early studies always encounter trade-offs related to sampling rate, bandwidth, field of view, and the simplicity of the optical path. Recent advances in event camera hardware show good potential for its application in visual sound recovery, because of its superior ability in capturing high-frequency signals. However, existing event-based vibration recovery methods are still sub-optimal for sound recovery. In this work, we propose a novel pipeline for non-contact sound recovery, fully utilizing spatial-temporal information from the event stream. We first generate a large training set using a novel simulation pipeline. Then we designed a network that leverages the sparsity of events to capture spatial information and uses Mamba to model long-term temporal information. Lastly, we train a spatial aggregation block to aggregate information from different locations to further improve signal quality. To capture event signals caused by sound waves, we also designed an imaging system using a laser matrix to enhance the gradient and collected multiple data sequences for testing. Experimental results on synthetic and real-world data demonstrate the effectiveness of our method.

Denoisers play a central role in many applications, from noise suppression in low-grade imaging sensors, to empowering score-based generative models. The latter category of methods makes use of Tweedie's formula, which links the posterior mean in Gaussian denoising (\ie the minimum MSE denoiser) with the score of the data distribution. Here, we derive a fundamental relation between the higher-order central moments of the posterior distribution, and the higher-order derivatives of the posterior mean. We harness this result for uncertainty quantification of pre-trained denoisers. Particularly, we show how to efficiently compute the principal components of the posterior distribution for any desired region of an image, as well as to approximate the full marginal distribution along those (or any other) one-dimensional directions. Our method is fast and memory-efficient, as it does not explicitly compute or store the high-order moment tensors and it requires no training or fine tuning of the denoiser. Code and examples are available on the project webpage in https://hilamanor.github.io/GaussianDenoisingPosterior/ .

Real-world single image denoising is crucial and practical in computer vision. Bayesian inversions combined with score priors now have proven effective for single image denoising but are limited to white Gaussian noise. Moreover, applying existing score-based methods for real-world denoising requires not only the explicit train of score priors on the target domain but also the careful design of sampling procedures for posterior inference, which is complicated and impractical. To address these limitations, we propose a score priors-guided deep variational inference, namely ScoreDVI, for practical real-world denoising. By considering the deep variational image posterior with a Gaussian form, score priors are extracted based on easily accessible minimum MSE Non-i.i.d Gaussian denoisers and variational samples, which in turn facilitate optimizing the variational image posterior. Such a procedure adaptively applies cheap score priors to denoising. Additionally, we exploit a Non-i.i.d Gaussian mixture model and variational noise posterior to model the real-world noise. This scheme also enables the pixel-wise fusion of multiple image priors and variational image posteriors. Besides, we develop a noise-aware prior assignment strategy that dynamically adjusts the weight of image priors in the optimization. Our method outperforms other single image-based real-world denoising methods and achieves comparable performance to dataset-based unsupervised methods.

Human organs constantly undergo anatomical changes due to a complex mix of short-term (e.g., heartbeat) and long-term (e.g., aging) factors. Evidently, prior knowledge of these factors will be beneficial when modeling their future state, i.e., via image generation. However, most of the medical image generation tasks only rely on the input from a single image, thus ignoring the sequential dependency even when longitudinal data is available. Sequence-aware deep generative models, where model input is a sequence of ordered and timestamped images, are still underexplored in the medical imaging domain that is featured by several unique challenges: 1) Sequences with various lengths; 2) Missing data or frame, and 3) High dimensionality. To this end, we propose a sequence-aware diffusion model (SADM) for the generation of longitudinal medical images. Recently, diffusion models have shown promising results in high-fidelity image generation. Our method extends this new technique by introducing a sequence-aware transformer as the conditional module in a diffusion model. The novel design enables learning longitudinal dependency even with missing data during training and allows autoregressive generation of a sequence of images during inference. Our extensive experiments on 3D longitudinal medical images demonstrate the effectiveness of SADM compared with baselines and alternative methods. The code is available at https://github.com/ubc-tea/SADM-Longitudinal-Medical-Image-Generation.

In recent years generative adversarial networks (GANs) have been used to supplement datasets within the field of marine bioacoustics. This is driven by factors such as the cost to collect data, data sparsity and aid preprocessing. One notable challenge with marine bioacoustic data is the low signal-to-noise ratio (SNR) posing difficulty when applying deep learning techniques such as GANs. This work investigates the effect SNR has on the audio-based GAN performance and examines three different evaluation methodologies for GAN performance, yielding interesting results on the effects of SNR on GANs, specifically WaveGAN.

We consider the problem of predicting gene expressions from DNA sequences. A key challenge of this task is to find the regulatory elements that control gene expressions. Here, we introduce Seq2Exp, a Sequence to Expression network explicitly designed to discover and extract regulatory elements that drive target gene expression, enhancing the accuracy of the gene expression prediction. Our approach captures the causal relationship between epigenomic signals, DNA sequences and their associated regulatory elements. Specifically, we propose to decompose the epigenomic signals and the DNA sequence conditioned on the causal active regulatory elements, and apply an information bottleneck with the Beta distribution to combine their effects while filtering out non-causal components. Our experiments demonstrate that Seq2Exp outperforms existing baselines in gene expression prediction tasks and discovers influential regions compared to commonly used statistical methods for peak detection such as MACS3. The source code is released as part of the AIRS library (https://github.com/divelab/AIRS/).

Diffusion-based manifold learning methods have proven useful in representation learning and dimensionality reduction of modern high dimensional, high throughput, noisy datasets. Such datasets are especially present in fields like biology and physics. While it is thought that these methods preserve underlying manifold structure of data by learning a proxy for geodesic distances, no specific theoretical links have been established. Here, we establish such a link via results in Riemannian geometry explicitly connecting heat diffusion to manifold distances. In this process, we also formulate a more general heat kernel based manifold embedding method that we call heat geodesic embeddings. This novel perspective makes clearer the choices available in manifold learning and denoising. Results show that our method outperforms existing state of the art in preserving ground truth manifold distances, and preserving cluster structure in toy datasets. We also showcase our method on single cell RNA-sequencing datasets with both continuum and cluster structure, where our method enables interpolation of withheld timepoints of data. Finally, we show that parameters of our more general method can be configured to give results similar to PHATE (a state-of-the-art diffusion based manifold learning method) as well as SNE (an attraction/repulsion neighborhood based method that forms the basis of t-SNE).

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

Diffusion-based generative models have recently gained attention in speech enhancement (SE), providing an alternative to conventional supervised methods. These models transform clean speech training samples into Gaussian noise centered at noisy speech, and subsequently learn a parameterized model to reverse this process, conditionally on noisy speech. Unlike supervised methods, generative-based SE approaches usually rely solely on an unsupervised loss, which may result in less efficient incorporation of conditioned noisy speech. To address this issue, we propose augmenting the original diffusion training objective with a mean squared error (MSE) loss, measuring the discrepancy between estimated enhanced speech and ground-truth clean speech at each reverse process iteration. Experimental results demonstrate the effectiveness of our proposed methodology.

This work aims to advance sound event detection (SED) research by presenting a new large language model (LLM)-powered dataset namely wild domestic environment sound event detection (WildDESED). It is crafted as an extension to the original DESED dataset to reflect diverse acoustic variability and complex noises in home settings. We leveraged LLMs to generate eight different domestic scenarios based on target sound categories of the DESED dataset. Then we enriched the scenarios with a carefully tailored mixture of noises selected from AudioSet and ensured no overlap with target sound. We consider widely popular convolutional neural recurrent network to study WildDESED dataset, which depicts its challenging nature. We then apply curriculum learning by gradually increasing noise complexity to enhance the model's generalization capabilities across various noise levels. Our results with this approach show improvements within the noisy environment, validating the effectiveness on the WildDESED dataset promoting noise-robust SED advancements.

Creating high-fidelity, coherent long videos is a sought-after aspiration. While recent video diffusion models have shown promising potential, they still grapple with spatiotemporal inconsistencies and high computational resource demands. We propose GLC-Diffusion, a tuning-free method for long video generation. It models the long video denoising process by establishing denoising trajectories through Global-Local Collaborative Denoising to ensure overall content consistency and temporal coherence between frames. Additionally, we introduce a Noise Reinitialization strategy which combines local noise shuffling with frequency fusion to improve global content consistency and visual diversity. Further, we propose a Video Motion Consistency Refinement (VMCR) module that computes the gradient of pixel-wise and frequency-wise losses to enhance visual consistency and temporal smoothness. Extensive experiments, including quantitative and qualitative evaluations on videos of varying lengths (e.g., 3\times and 6\times longer), demonstrate that our method effectively integrates with existing video diffusion models, producing coherent, high-fidelity long videos superior to previous approaches.

Pre-training on large-scale datasets and then fine-tuning on downstream tasks have become a standard practice in deep learning. However, pre-training data often contain label noise that may adversely affect the generalization of the model. This paper aims to understand the nature of noise in pre-training datasets and to mitigate its impact on downstream tasks. More specifically, through extensive experiments of supervised pre-training models on synthetic noisy ImageNet-1K and YFCC15M datasets, we demonstrate that while slight noise in pre-training can benefit in-domain (ID) transfer performance, where the training and testing data share the same distribution, it always deteriorates out-of-domain (OOD) performance, where training and testing data distribution are different. We empirically verify that the reason behind is noise in pre-training shapes the feature space differently. We then propose a light-weight black-box tuning method (NMTune) to affine the feature space to mitigate the malignant effect of noise and improve generalization on both ID and OOD tasks, considering one may not be able to fully fine-tune or even access the pre-trained models. We conduct practical experiments on popular vision and language models that are pre-trained on noisy data for evaluation of our approach. Our analysis and results show the importance of this interesting and novel research direction, which we term Noisy Model Learning.

This work considers a rather general and broad class of Markov chains, Ito chains that look like Euler-Maryama discretization of some Stochastic Differential Equation. The chain we study is a unified framework for theoretical analysis. It comes with almost arbitrary isotropic and state-dependent noise instead of normal and state-independent one, as in most related papers. Moreover, our chain's drift and diffusion coefficient can be inexact to cover a wide range of applications such as Stochastic Gradient Langevin Dynamics, sampling, Stochastic Gradient Descent, or Stochastic Gradient Boosting. We prove an upper bound for W_{2}-distance between laws of the Ito chain and the corresponding Stochastic Differential Equation. These results improve or cover most of the known estimates. Moreover, for some particular cases, our analysis is the first.

In the emergent realm of quantum computing, the Variational Quantum Eigensolver (VQE) stands out as a promising algorithm for solving complex quantum problems, especially in the noisy intermediate-scale quantum (NISQ) era. However, the ubiquitous presence of noise in quantum devices often limits the accuracy and reliability of VQE outcomes. This research introduces a novel approach to ameliorate this challenge by utilizing neural networks for zero noise extrapolation (ZNE) in VQE computations. By employing the Qiskit framework, we crafted parameterized quantum circuits using the RY-RZ ansatz and examined their behavior under varying levels of depolarizing noise. Our investigations spanned from determining the expectation values of a Hamiltonian, defined as a tensor product of Z operators, under different noise intensities to extracting the ground state energy. To bridge the observed outcomes under noise with the ideal noise-free scenario, we trained a Feed Forward Neural Network on the error probabilities and their associated expectation values. Remarkably, our model proficiently predicted the VQE outcome under hypothetical noise-free conditions. By juxtaposing the simulation results with real quantum device executions, we unveiled the discrepancies induced by noise and showcased the efficacy of our neural network-based ZNE technique in rectifying them. This integrative approach not only paves the way for enhanced accuracy in VQE computations on NISQ devices but also underlines the immense potential of hybrid quantum-classical paradigms in circumventing the challenges posed by quantum noise. Through this research, we envision a future where quantum algorithms can be reliably executed on noisy devices, bringing us one step closer to realizing the full potential of quantum computing.

Recent advances in diffusion models have introduced a new era of text-guided image manipulation, enabling users to create realistic edited images with simple textual prompts. However, there is significant concern about the potential misuse of these methods, especially in creating misleading or harmful content. Although recent defense strategies, which introduce imperceptible adversarial noise to induce model failure, have shown promise, they remain ineffective against more sophisticated manipulations, such as editing with a mask. In this work, we propose DiffusionGuard, a robust and effective defense method against unauthorized edits by diffusion-based image editing models, even in challenging setups. Through a detailed analysis of these models, we introduce a novel objective that generates adversarial noise targeting the early stage of the diffusion process. This approach significantly improves the efficiency and effectiveness of adversarial noises. We also introduce a mask-augmentation technique to enhance robustness against various masks during test time. Finally, we introduce a comprehensive benchmark designed to evaluate the effectiveness and robustness of methods in protecting against privacy threats in realistic scenarios. Through extensive experiments, we show that our method achieves stronger protection and improved mask robustness with lower computational costs compared to the strongest baseline. Additionally, our method exhibits superior transferability and better resilience to noise removal techniques compared to all baseline methods. Our source code is publicly available at https://github.com/choi403/DiffusionGuard.

In the English speech-to-text (STT) machine learning task, acoustic models are conventionally trained on uncased Latin characters, and any necessary orthography (such as capitalization, punctuation, and denormalization of non-standard words) is imputed by separate post-processing models. This adds complexity and limits performance, as many formatting tasks benefit from semantic information present in the acoustic signal but absent in transcription. Here we propose a new STT task: end-to-end neural transcription with fully formatted text for target labels. We present baseline Conformer-based models trained on a corpus of 5,000 hours of professionally transcribed earnings calls, achieving a CER of 1.7. As a contribution to the STT research community, we release the corpus free for non-commercial use at https://datasets.kensho.com/datasets/scribe.

Although diffusion models (DMs) have shown promising performances in a number of tasks (e.g., speech synthesis and image generation), they might suffer from error propagation because of their sequential structure. However, this is not certain because some sequential models, such as Conditional Random Field (CRF), are free from this problem. To address this issue, we develop a theoretical framework to mathematically formulate error propagation in the architecture of DMs, The framework contains three elements, including modular error, cumulative error, and propagation equation. The modular and cumulative errors are related by the equation, which interprets that DMs are indeed affected by error propagation. Our theoretical study also suggests that the cumulative error is closely related to the generation quality of DMs. Based on this finding, we apply the cumulative error as a regularization term to reduce error propagation. Because the term is computationally intractable, we derive its upper bound and design a bootstrap algorithm to efficiently estimate the bound for optimization. We have conducted extensive experiments on multiple image datasets, showing that our proposed regularization reduces error propagation, significantly improves vanilla DMs, and outperforms previous baselines.

Understanding when the noise in stochastic gradient descent (SGD) affects generalization of deep neural networks remains a challenge, complicated by the fact that networks can operate in distinct training regimes. Here we study how the magnitude of this noise T affects performance as the size of the training set P and the scale of initialization alpha are varied. For gradient descent, alpha is a key parameter that controls if the network is `lazy'(alphagg1) or instead learns features (alphall1). For classification of MNIST and CIFAR10 images, our central results are: (i) obtaining phase diagrams for performance in the (alpha,T) plane. They show that SGD noise can be detrimental or instead useful depending on the training regime. Moreover, although increasing T or decreasing alpha both allow the net to escape the lazy regime, these changes can have opposite effects on performance. (ii) Most importantly, we find that the characteristic temperature T_c where the noise of SGD starts affecting the trained model (and eventually performance) is a power law of P. We relate this finding with the observation that key dynamical quantities, such as the total variation of weights during training, depend on both T and P as power laws. These results indicate that a key effect of SGD noise occurs late in training by affecting the stopping process whereby all data are fitted. Indeed, we argue that due to SGD noise, nets must develop a stronger `signal', i.e. larger informative weights, to fit the data, leading to a longer training time. A stronger signal and a longer training time are also required when the size of the training set P increases. We confirm these views in the perceptron model, where signal and noise can be precisely measured. Interestingly, exponents characterizing the effect of SGD depend on the density of data near the decision boundary, as we explain.

Audio super-resolution is a fundamental task that predicts high-frequency components for low-resolution audio, enhancing audio quality in digital applications. Previous methods have limitations such as the limited scope of audio types (e.g., music, speech) and specific bandwidth settings they can handle (e.g., 4kHz to 8kHz). In this paper, we introduce a diffusion-based generative model, AudioSR, that is capable of performing robust audio super-resolution on versatile audio types, including sound effects, music, and speech. Specifically, AudioSR can upsample any input audio signal within the bandwidth range of 2kHz to 16kHz to a high-resolution audio signal at 24kHz bandwidth with a sampling rate of 48kHz. Extensive objective evaluation on various audio super-resolution benchmarks demonstrates the strong result achieved by the proposed model. In addition, our subjective evaluation shows that AudioSR can acts as a plug-and-play module to enhance the generation quality of a wide range of audio generative models, including AudioLDM, Fastspeech2, and MusicGen. Our code and demo are available at https://audioldm.github.io/audiosr.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

This paper presents the first large-scale multi-species dataset of acoustic recordings of mosquitoes tracked continuously in free flight. We present 20 hours of audio recordings that we have expertly labelled and tagged precisely in time. Significantly, 18 hours of recordings contain annotations from 36 different species. Mosquitoes are well-known carriers of diseases such as malaria, dengue and yellow fever. Collecting this dataset is motivated by the need to assist applications which utilise mosquito acoustics to conduct surveys to help predict outbreaks and inform intervention policy. The task of detecting mosquitoes from the sound of their wingbeats is challenging due to the difficulty in collecting recordings from realistic scenarios. To address this, as part of the HumBug project, we conducted global experiments to record mosquitoes ranging from those bred in culture cages to mosquitoes captured in the wild. Consequently, the audio recordings vary in signal-to-noise ratio and contain a broad range of indoor and outdoor background environments from Tanzania, Thailand, Kenya, the USA and the UK. In this paper we describe in detail how we collected, labelled and curated the data. The data is provided from a PostgreSQL database, which contains important metadata such as the capture method, age, feeding status and gender of the mosquitoes. Additionally, we provide code to extract features and train Bayesian convolutional neural networks for two key tasks: the identification of mosquitoes from their corresponding background environments, and the classification of detected mosquitoes into species. Our extensive dataset is both challenging to machine learning researchers focusing on acoustic identification, and critical to entomologists, geo-spatial modellers and other domain experts to understand mosquito behaviour, model their distribution, and manage the threat they pose to humans.

Advances in hardware and language model architecture have spurred a revolution in natural language generation. However, autoregressive models compute probability distributions over next-token choices, and sampling from these distributions, known as decoding, has received significantly less attention than other design choices. Existing decoding strategies are largely based on heuristics, resulting in methods that are hard to apply or improve in a principled manner. We develop the theory of decoding strategies for language models by expressing popular decoding algorithms as equilibrium states in the language of ergodic theory and stating the functions they optimize. Using this, we analyze the effect of the local normalization step of top-k, nucleus, and temperature sampling, used to make probabilities sum to one. We argue that local normalization distortion is a fundamental defect of decoding strategies and quantify the size of this distortion and its effect on mathematical proxies for the quality and diversity of generated text. Contrary to the prevailing explanation, we argue that the major cause of the under-performance of top-k sampling relative to nucleus sampling is local normalization distortion. This yields conclusions for the future design of decoding algorithms and the detection of machine-generated text.

This paper presents an end-to-end model designed to improve automatic speech recognition (ASR) for a particular speaker in a crowded, noisy environment. The model utilizes a single-channel speech enhancement module that isolates the speaker's voice from background noise, along with an ASR module. Through this approach, the model is able to decrease the word error rate (WER) of ASR from 80% to 26.4%. Typically, these two components are adjusted independently due to variations in data requirements. However, speech enhancement can create anomalies that decrease ASR efficiency. By implementing a joint fine-tuning strategy, the model can reduce the WER from 26.4% in separate tuning to 14.5% in joint tuning.

We present a novel generative approach based on Denoising Diffusion Models (DDMs), which produces high-quality image samples along with their losslessly compressed bit-stream representations. This is obtained by replacing the standard Gaussian noise sampling in the reverse diffusion with a selection of noise samples from pre-defined codebooks of fixed iid Gaussian vectors. Surprisingly, we find that our method, termed Denoising Diffusion Codebook Model (DDCM), retains sample quality and diversity of standard DDMs, even for extremely small codebooks. We leverage DDCM and pick the noises from the codebooks that best match a given image, converting our generative model into a highly effective lossy image codec achieving state-of-the-art perceptual image compression results. More generally, by setting other noise selections rules, we extend our compression method to any conditional image generation task (e.g., image restoration), where the generated images are produced jointly with their condensed bit-stream representations. Our work is accompanied by a mathematical interpretation of the proposed compressed conditional generation schemes, establishing a connection with score-based approximations of posterior samplers for the tasks considered.

Diffusion models for continuous data gained widespread adoption owing to their high quality generation and control mechanisms. However, controllable diffusion on discrete data faces challenges given that continuous guidance methods do not directly apply to discrete diffusion. Here, we provide a straightforward derivation of classifier-free and classifier-based guidance for discrete diffusion, as well as a new class of diffusion models that leverage uniform noise and that are more guidable because they can continuously edit their outputs. We improve the quality of these models with a novel continuous-time variational lower bound that yields state-of-the-art performance, especially in settings involving guidance or fast generation. Empirically, we demonstrate that our guidance mechanisms combined with uniform noise diffusion improve controllable generation relative to autoregressive and diffusion baselines on several discrete data domains, including genomic sequences, small molecule design, and discretized image generation.

Recent work has witnessed a paradigm shift from Seq2Seq to Seq2Edit in the field of text editing, with the aim of addressing the slow autoregressive inference problem posed by the former. Despite promising results, Seq2Edit approaches still face several challenges such as inflexibility in generation and difficulty in generalizing to other languages. In this work, we propose a novel non-autoregressive text editing method to circumvent the above issues, by modeling the edit process with latent CTC alignments. We make a crucial extension to CTC by introducing the copy operation into the edit space, thus enabling more efficient management of textual overlap in editing. We conduct extensive experiments on GEC and sentence fusion tasks, showing that our proposed method significantly outperforms existing Seq2Edit models and achieves similar or even better results than Seq2Seq with over 4times speedup. Moreover, it demonstrates good generalizability on German and Russian. In-depth analyses reveal the strengths of our method in terms of the robustness under various scenarios and generating fluent and flexible outputs.

In this article, we study the consistency of the template estimation with the Fr\'echet mean in quotient spaces. The Fr\'echet mean in quotient spaces is often used when the observations are deformed or transformed by a group action. We show that in most cases this estimator is actually inconsistent. We exhibit a sufficient condition for this inconsistency, which amounts to the folding of the distribution of the noisy template when it is projected to the quotient space. This condition appears to be fulfilled as soon as the support of the noise is large enough. To quantify this inconsistency we provide lower and upper bounds of the bias as a function of the variability (the noise level). This shows that the consistency bias cannot be neglected when the variability increases.

Recent advance in text-to-image diffusion models have significantly facilitated the generation of high-quality images, but also raising concerns about the illegal creation of harmful content, such as copyrighted images. Existing concept erasure methods achieve superior results in preventing the production of erased concept from prompts, but typically perform poorly in preventing undesired editing. To address this issue, we propose an Anti-Editing Concept Erasure (ACE) method, which not only erases the target concept during generation but also filters out it during editing. Specifically, we propose to inject the erasure guidance into both conditional and the unconditional noise prediction, enabling the model to effectively prevent the creation of erasure concepts during both editing and generation. Furthermore, a stochastic correction guidance is introduced during training to address the erosion of unrelated concepts. We conducted erasure editing experiments with representative editing methods (i.e., LEDITS++ and MasaCtrl) to erase IP characters, and the results indicate that our ACE effectively filters out target concepts in both types of edits. Additional experiments on erasing explicit concepts and artistic styles further demonstrate that our ACE performs favorably against state-of-the-art methods. Our code will be publicly available at https://github.com/120L020904/ACE.

We introduce Mitiq, a Python package for error mitigation on noisy quantum computers. Error mitigation techniques can reduce the impact of noise on near-term quantum computers with minimal overhead in quantum resources by relying on a mixture of quantum sampling and classical post-processing techniques. Mitiq is an extensible toolkit of different error mitigation methods, including zero-noise extrapolation, probabilistic error cancellation, and Clifford data regression. The library is designed to be compatible with generic backends and interfaces with different quantum software frameworks. We describe Mitiq using code snippets to demonstrate usage and discuss features and contribution guidelines. We present several examples demonstrating error mitigation on IBM and Rigetti superconducting quantum processors as well as on noisy simulators.