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Deep Learning · Generative Models and Autoencoders

Nicolas Zilberstein, Morteza Mardani, Santiago Segarra

Score Distillation Sampling (SDS) has been pivotal for leveraging pre-trained diffusion models in downstream tasks such as inverse problems, but it faces two major challenges: $(i)$ mode collapse and $(ii)$ latent space inversion, which become more pronounced in high-dimensional data. To address mode collapse, we introduce a novel variational framework for posterior sampling. Utilizing the Wasserstein gradient flow interpretation of SDS, we propose a multimodal variational approximation with a \emph{repulsion} mechanism that promotes diversity among particles by penalizing pairwise kernel-based similarity. This repulsion acts as a simple regularizer, encouraging a more diverse set of solutions. To mitigate latent space ambiguity, we extend this framework with an \emph{augmented} variational distribution that disentangles the latent and data. This repulsive augmented formulation balances computational efficiency, quality, and diversity. Extensive experiments on linear and nonlinear inverse tasks with high-resolution images ($512 \times 512$) using pre-trained Stable Diffusion models demonstrate the effectiveness of our approach.

Applications · Health

Aishwarya Jayagopal, Yanrong Zhang, Robert Walsh, Tuan Tan, Anand Jeyasekharan, Vaibhav Rajan

Effective treatment of cancer is a major challenge faced by healthcare providers, due to the highly individualized nature of patient responses to treatment. This is caused by the heterogeneity seen in cancer-causing alterations (mutations) across patient genomes. Limited availability of response data in patients makes it difficult to train personalized treatment recommendation models on mutations from clinical genomic sequencing reports. Prior methods tackle this by utilising larger, labelled pre-clinical laboratory datasets (‘cell lines’), via transfer learning. These methods augment patient data by learning a shared, domain-invariant representation, between the cell line and patient domains, which is then used to train a downstream drug response prediction (DRP) model. This approach augments data in the shared space but fails to model patient-specific characteristics, which have a strong influence on their drug response. We propose a novel generative attention-based data augmentation and predictive modeling framework, GANDALF, to tackle this crucial shortcoming of prior methods. GANDALF not only augments patient genomic data directly, but also accounts for its domain-specific characteristics. GANDALF outperforms state-of-the-art DRP models on publicly available patient datasets and emerges as the front-runner amongst SOTA cancer DRP models.

Applications · Chemistry and Drug Discovery

Jingjie Zhang, Hanqun Cao, Zijun Gao, Xiaorui Wang, Chunbin Gu

Phosphorylation site prediction based on kinase-substrate interaction plays a vital role in understanding cellular signaling pathways and disease mechanisms. Computational methods for this task can be categorized into kinase-family-focused and individual kinase-targeted approaches. Individual kinase-targeted methods have gained prominence for their ability to explore a broader protein space and provide more precise target information for kinase inhibitors. However, most existing individual kinase-based approaches focus solely on sequence inputs, neglecting crucial structural information. To address this limitation, we introduce SAGEPhos (Structure-aware kinAse-substrate bio-coupled and bio-auGmented nEtwork for Phosphorylation site prediction), a novel framework that modifies the semantic space of main protein inputs using auxiliary inputs at two distinct modality levels. At the inter-modality level, SAGEPhos introduces a Bio-Coupled Modal Fusion method, distilling essential kinase sequence information to refine task-oriented local substrate feature space, creating a shared semantic space that captures crucial kinase-substrate interaction patterns. Within the substrate's intra-modality domain, it focuses on Bio-Augmented Fusion, emphasizing 2D local sequence information while selectively incorporating 3D spatial information from predicted structures to complement the sequence space. Moreover, to address the lack of structural information in current datasets, we contribute a new, refined phosphorylation site prediction dataset, which incorporates crucial structural elements and will serve as a new benchmark for the field. Experimental results demonstrate that SAGEPhos significantly outperforms baseline methods, notably achieving almost 10\% and 12\% improvements in prediction accuracy and AUC-ROC, respectively. We further demonstrate our algorithm's robustness and generalization through stable results across varied data partitions and significant improvements in zero-shot scenarios. These results underscore the effectiveness of constructing a larger and more precise protein space in advancing the state-of-the-art in phosphorylation site prediction. We release the SAGEPhos models and code at https://github.com/ZhangJJ26/SAGEPhos.

Muthu Chidambaram, Rong Ge

Data augmentation has been pivotal in successfully training deep learning models on classification tasks over the past decade. An important subclass of data augmentation techniques - which includes both label smoothing and Mixup - involves modifying not only the input data but also the input label during model training. In this work, we analyze the role played by the label augmentation aspect of such methods. We first prove that linear models on binary classification data trained with label augmentation learn only the minimum variance features in the data, while standard training (which includes weight decay) can learn higher variance features. We then use our techniques to show that even for nonlinear models and general data distributions, the label smoothing and Mixup losses are lower bounded by a function of the model output variance. Lastly, we demonstrate empirically that this aspect of label smoothing and Mixup can be a positive and a negative. On the one hand, we show that the strong performance of label smoothing and Mixup on image classification benchmarks is correlated with learning low variance hidden representations. On the other hand, we show that Mixup and label smoothing can be more susceptible to low variance spurious correlations in the training data.

Reinforcement Learning · Multi-agent

Lei Yuan, Yuqi Bian, Lihe Li, Ziqian Zhang, Cong Guan, Yang Yu

Learning from offline data without interacting with the environment is a promising way to fully leverage the intelligent decision-making capabilities of multi-agent reinforcement learning (MARL). Previous approaches have primarily focused on developing learning techniques, such as conservative methods tailored to MARL using limited offline data. However, these methods often overlook the temporal relationships across different timesteps and spatial relationships between teammates, resulting in low learning efficiency in imbalanced data scenarios. To comprehensively explore the data structure of MARL and enhance learning efficiency, we propose Multi-Agent offline coordination via Diffusion-based Trajectory Stitching (MADiTS), a novel diffusion-based data augmentation pipeline that systematically generates trajectories by stitching high-quality coordination segments together. MADiTS first generates trajectory segments using a trained diffusion model, followed by applying a bidirectional dynamics constraint to ensure that the trajectories align with environmental dynamics. Additionally, we develop an offline credit assignment technique to identify and optimize the behavior of underperforming agents in the generated segments. This iterative procedure continues until a satisfactory augmented episode trajectory is generated within the predefined limit or is discarded otherwise. Empirical results on imbalanced datasets of multiple benchmarks demonstrate that MADiTS significantly improves MARL performance.

Applications · Health

Peng Xia, Kangyu Zhu, Haoran Li, Tianze Wang, Weijia Shi, Sheng Wang, Linjun Zhang, James Y Zou, Huaxiu Yao

Artificial Intelligence (AI) has demonstrated significant potential in healthcare, particularly in disease diagnosis and treatment planning. Recent progress in Medical Large Vision-Language Models (Med-LVLMs) has opened up new possibilities for interactive diagnostic tools. However, these models often suffer from factual hallucination, which can lead to incorrect diagnoses. Fine-tuning and retrieval-augmented generation (RAG) have emerged as methods to address these issues. However, the amount of high-quality data and distribution shifts between training data and deployment data limit the application of fine-tuning methods. Although RAG is lightweight and effective, existing RAG-based approaches are not sufficiently general to different medical domains and can potentially cause misalignment issues, both between modalities and between the model and the ground truth. In this paper, we propose a versatile multimodal RAG system, MMed-RAG, designed to enhance the factuality of Med-LVLMs. Our approach introduces a domain-aware retrieval mechanism, an adaptive retrieved contexts selection, and a provable RAG-based preference fine-tuning strategy. These innovations make the RAG process sufficiently general and reliable, significantly improving alignment when introducing retrieved contexts. Experimental results across five medical datasets (involving radiology, ophthalmology, pathology) on medical VQA and report generation demonstrate that MMed-RAG can achieve an average improvement of 43.8% in factual accuracy in the factual accuracy of Med-LVLMs.

Deep Learning · Theory

Hongkang Li, Songtao Lu, Pin-Yu Chen, Xiaodong Cui, Meng Wang

Chain-of-Thought (CoT) is an efficient prompting method that enables the reasoning ability of large language models by augmenting the query using multiple examples with multiple intermediate steps. Despite the empirical success, the theoretical understanding of how to train a Transformer to achieve the CoT ability remains less explored. This is primarily due to the technical challenges involved in analyzing the nonconvex optimization on nonlinear attention models. To the best of our knowledge, this work provides the first theoretical study of training Transformers with nonlinear attention to obtain the CoT generalization capability so that the resulting model can inference on unseen tasks when the input is augmented by examples of the new task. We first quantify the required training samples and iterations to train a Transformer model towards CoT ability. We then prove the success of its CoT generalization on unseen tasks with distribution-shifted testing data. Moreover, we theoretically characterize the conditions for an accurate reasoning output by CoT even when the provided reasoning examples contain noises and are not always accurate. In contrast, in-context learning (ICL), which can be viewed as one-step CoT without intermediate steps, may fail to provide an accurate output when CoT does. These theoretical findings are justified through experiments.

Deep Learning · Large Language Models

Niklas Muennighoff, Hongjin SU, Liang Wang, Nan Yang, Furu Wei, Tao Yu, Amanpreet Singh, Douwe Kiela

All text-based language problems can be reduced to either generation or embedding. Current models only perform well at one or the other. We introduce generative representational instruction tuning (GRIT) whereby a large language model is trained to handle both generative and embedding tasks by distinguishing between them through instructions. Compared to other open models, our resulting GritLM-7B is among the top models on the Massive Text Embedding Benchmark (MTEB) and outperforms various models up to its size on a range of generative tasks. By scaling up further, GritLM-8x7B achieves even stronger generative performance while still being among the best embedding models. Notably, we find that GRIT matches training on only generative or embedding data, thus we can unify both at no performance loss. Among other benefits, the unification via GRIT speeds up Retrieval-Augmented Generation (RAG) by > 60% for long documents, by no longer requiring separate retrieval and generation models. Models, code, etc. are freely available at https://github.com/ContextualAI/gritlm.

Applications · Health

Mehak Dhaliwal, Andong Hua, Laya Pullela, Ryan Burke, Yao Qin

Accurate nutrition estimation helps people make informed dietary choices and is essential in the prevention of serious health complications. We present NutriBench, the first publicly available natural language meal description nutrition benchmark. NutriBench consists of 11,857 meal descriptions generated from real-world global dietary intake data. The data is human-verified and annotated with macro-nutrient labels, including carbohydrates, proteins, fats, and calories. We conduct an extensive evaluation of Nutribench on the task of carbohydrate estimation, testing twelve leading Large Language Models (LLMs), including GPT-4o, Llama3.1, Qwen2, Gemma2, and OpenBioLLM models, using standard, Chain-of-Thought and Retrieval-Augmented Generation strategies. Additionally, we present a study involving professional nutritionists, finding that LLMs can provide comparable but significantly faster estimates. Finally, we perform a real-world risk assessment by simulating the effect of carbohydrate predictions on the blood glucose levels of individuals with type 1 diabetes. Our work highlights the opportunities and challenges of using LLMs for nutrition estimation, demonstrating their potential to aid professionals and laypersons and improve health outcomes. Our benchmark is publicly available at: https://mehak126.github.io/nutribench.html

Deep Learning · Large Language Models

Futing Wang, Jianhao (Elliott) Yan, Yue Zhang, Tao Lin

Enhancing the adaptive capabilities of large language models is a critical pursuit in both research and application.Traditional fine-tuning methods require substantial data, computational resources, and specific capabilities, while in-context learning is limited by the need for appropriate demonstrations and efficient token usage. Inspired by the expression of in-context learned capabilities through task vectors and the concept of modular capability or knowledge, we propose ELICIT, a framework consisting of two modules designed to effectively store and reuse task vectors to enhance the diverse adaptive capabilities of models without additional training or inference tokens. Our comprehensive experiments and analysis demonstrate that our pipeline is highly transferable across different input formats, tasks, and model architectures. Externally storing and reusing vectors that represent in-context learned capabilities not only shows the potential to extract modular capabilities but also significantly enhances the performance, versatility, adaptability, and scalability of large language models, paving the way for more efficient and effective use of these models in a wide range of applications.

Social Aspects · Accountability, Transparency and Interpretability

Chaoyi Zhu, Jiayi Tang, Jeroen Galjaard, Pin-Yu Chen, Robert Birke, Cornelis Bos, Lydia Chen

Synthetic data offers alternatives for data augmentation and sharing. Till date, it remains unknown how to use watermarking techniques to trace and audit synthetic tables generated by tabular diffusion models to mitigate potential misuses. In this paper, we design TabWak, the first watermarking method to embed invisible signatures that control the sampling of Gaussian latent codes used to synthesize table rows via the diffusion backbone. TabWak has two key features. Different from existing image watermarking techniques, TabWak uses self-cloning and shuffling to embed the secret key in positional information of random seeds that control the Gaussian latents, allowing to use different seeds at each row for high inter-row diversity and enabling row-wise detectability. To further boost the robustness of watermark detection against post-editing attacks, TabWak uses a valid-bit mechanism that focuses on the tail of the latent code distribution for superior noise resilience. We provide theoretical guarantees on the row diversity and effectiveness of detectability. We evaluate TabWak on five datasets against baselines to show that the quality of watermarked tables remains nearly indistinguishable from non-watermarked tables while achieving high detectability in the presence of strong post-editing attacks, with a 100% true positive rate at a 0.1% false positive rate on synthetic tables with fewer than 300 rows. Our code is available at the following anonymized repository https://github.com/chaoyitud/TabWak.

Applications · Robotics

Kaizhe Hu, Zihang Rui, Yao He, Yuyao Liu, Pu Hua, Huazhe Xu

Visual imitation learning methods demonstrate strong performance, yet they lack generalization when faced with visual input perturbations like variations in lighting and textures. This limitation hampers their practical application in real-world settings. To address this, we propose ***Stem-OB*** that leverages the inversion process of pretrained image diffusion models to suppress low-level visual differences while maintaining high-level scene structures. This image inversion process is akin to transforming the observation into a shared representation, from which other observations also stem. *Stem-OB* offers a simple yet effective plug-and-play solution that stands in contrast to data augmentation approaches. It demonstrates robustness to various unspecified appearance changes without the need for additional training. We provide theoretical insights and empirical results that validate the efficacy of our approach in simulated and real settings. *Stem-OB* shows an exceptionally significant improvement in real-world robotic tasks, where challenging light and appearance changes are present, with an average increase of **22.2%** in success rates compared to the best baseline. Please refer to [this link](https://stem-ob.github.io/) for more videos and details.

Miscellaneous Aspects of Machine Learning · Representation Learning

Sheng-Feng Yu, Jia-Jiun Yao, Wei-Chen Chiu

Although larger datasets are crucial for training large deep models, the rapid growth of dataset size has brought a significant challenge in terms of considerable training costs, which even results in prohibitive computational expenses. Dataset Distillation becomes a popular technique recently to reduce the dataset size via learning a highly compact set of representative exemplars, where the model trained with these exemplars ideally should have comparable performance with respect to the one trained with the full dataset. While most of existing works upon dataset distillation focus on supervised datasets, \todo{we instead aim to distill images and their self-supervisedly trained representations into a distilled set. This procedure, named as Self-Supervised Dataset Distillation, effectively extracts rich information from real datasets, yielding the distilled sets with enhanced cross-architecture generalizability.} Particularly, in order to preserve the key characteristics of original dataset more faithfully and compactly, several novel techniques are proposed: 1) we introduce an innovative parameterization upon images and representations via distinct low-dimensional bases, where the base selection for parameterization is experimentally shown to play a crucial role; 2) we tackle the instability induced by the randomness of data augmentation -- a key component in self-supervised learning but being underestimated in the prior work of self-supervised dataset distillation -- by utilizing predetermined augmentations; 3) we further leverage a lightweight network to model the connections among the representations of augmented views from the same image, leading to more compact pairs of distillation. Extensive experiments conducted on various datasets validate the superiority of our approach in terms of distillation efficiency, cross-architecture generalization, and transfer learning performance.

Deep Learning · Large Language Models

Yudi Zhang, Pei Xiao, Lu Wang, Chaoyun Zhang, Meng Fang, Yali Du, Yevgeniy Puzyrev, Randolph Yao, Si Qin, Qingwei Lin 等

In-context learning (ICL) and Retrieval-Augmented Generation (RAG) have gained attention for their ability to enhance LLMs' reasoning by incorporating external knowledge but suffer from limited contextual window size, leading to insufficient information injection. To this end, we propose a novel framework to automatically distill large volumes of offline data into interpretable first-order logic rules, which are injected into LLMs to boost their reasoning capabilities. Our method begins by formulating the search process relying on LLMs' commonsense, where LLMs automatically define head and body predicates. Then, we apply Monte Carlo Tree Search (MCTS) to address the combinational searching space and efficiently discover logic rules from data. The resulting logic rules are translated into natural language, allowing targeted knowledge injection and seamless integration into LLM prompts for LLM's downstream task reasoning. We evaluate our framework on public and private industrial tasks, including Natural Language Processing (NLP), time-series, decision-making, and industrial tasks, demonstrating its effectiveness in enhancing LLM's capability over diverse tasks.

Applications · Computer Vision

Zhibing Li, Tong Wu, Jing Tan, Mengchen Zhang, Jiaqi Wang, Dahua Lin

Capturing geometric and material information from images remains a fundamental challenge in computer vision and graphics. Traditional optimization-based methods often require hours of computational time to reconstruct geometry, material properties, and environmental lighting from dense multi-view inputs, while still struggling with inherent ambiguities between lighting and material. On the other hand, learning-based approaches leverage rich material priors from existing 3D object datasets but face challenges with maintaining multi-view consistency.In this paper, we introduce IDArb, a diffusion-based model designed to perform intrinsic decomposition on an arbitrary number of images under varying illuminations. Our method achieves highly accurate and multi-view consistent estimation on surface normals and material properties. This is made possible through a novel cross-view, cross-domain attention module and an illumination-augmented, view-adaptive training strategy. Additionally, we introduce ARB-Objaverse, a new dataset that provides large-scale multi-view intrinsic data and renderings under diverse lighting conditions, supporting robust training.Extensive experiments demonstrate that IDArb outperforms state-of-the-art methods both qualitatively and quantitatively. Moreover, our approach facilitates a range of downstream tasks, including single-image relighting, photometric stereo, and 3D reconstruction, highlighting its broad applicability in realistic 3D content creation.Project website: https://lizb6626.github.io/IDArb/.

Theory · Learning Theory

Juno Kim, Taiji Suzuki

This work provides the first theoretical analysis of training transformers to solve complex problems by recursively generating intermediate states, analogous to fine-tuning for chain-of-thought (CoT) reasoning. We consider training a one-layer transformer to solve the fundamental $k$-parity problem, extending the work on RNNs by \citet{Wies23}. We establish three key results: (1) any finite-precision gradient-based algorithm, without intermediate supervision, requires substantial iterations to solve parity with finite samples. (2) In contrast, when intermediate parities are incorporated into the loss function, our model can learn parity in one gradient update when aided by \emph{teacher forcing}, where ground-truth labels of the reasoning chain are provided at each generation step. (3) Even without teacher forcing, where the model must generate CoT chains end-to-end, parity can be learned efficiently if augmented data is employed to internally verify the soundness of intermediate steps. Our findings, supported by numerical experiments, show that task decomposition and stepwise reasoning naturally arise from optimizing transformers with CoT; moreover, self-consistency checking can improve multi-step reasoning ability, aligning with empirical studies of CoT.

Deep Learning · Robustness

Hongsin Lee, Seungju Cho, Changick Kim

Adversarial training significantly improves adversarial robustness, but superior performance is primarily attained with large models. This substantial performance gap for smaller models has spurred active research into adversarial distillation (AD) to mitigate the difference. Existing AD methods leverage the teacher’s logits as a guide.In contrast to these approaches, we aim to transfer another piece of knowledge from the teacher, the input gradient.In this paper, we propose a distillation module termed Indirect Gradient Distillation Module (IGDM) that indirectly matches the student’s input gradient with that of the teacher.Experimental results show that IGDM seamlessly integrates with existing AD methods, significantly enhancing their performance.Particularly, utilizing IGDM on the CIFAR-100 dataset improves the AutoAttack accuracy from 28.06\% to 30.32\% with the ResNet-18 architecture and from 26.18\% to 29.32\% with the MobileNetV2 architecture when integrated into the SOTA method without additional data augmentation.

Chen Sun, Renat Aksitov, Andrey Zhmoginov, Nolan Miller, Max Vladymyrov, Ulrich Rueckert, Been Kim, Mark Sandler

Large language models continually learn through the accumulation of gradient-based updates, but how individual pieces of new information affect existing knowledge, leading to both beneficial generalization and problematic hallucination, remains poorly understood. We demonstrate that when learning new information, LLMs exhibit a "priming" effect: learning a new fact can cause the model to inappropriately apply that knowledge in unrelated contexts.To systematically study this phenomenon, we introduce "Outlandish," a carefully curated dataset of 1320 diverse text samples designed to probe how new knowledge permeates through an LLM's existing knowledge base. Using this dataset, we show that the degree of priming after learning new information can be predicted by measuring the token probability of key words before training. This relationship holds robustly across different model architectures (PALM-2, Gemma, Llama), sizes, and training stages.Finally, we develop two novel techniques to modulate how new knowledge affects existing model behavior: (1) a ``stepping-stone'' text augmentation strategy and (2) an ``ignore-k'' update pruning method. These approaches reduce undesirable priming effects by 50-95% while preserving the model's ability to learn new information. Our findings provide both empirical insights into how LLMs learn and practical tools for improving the specificity of knowledge insertion in language models. Further materials: https://sunchipsster1.github.io/projects/outlandish/

Deep Learning · Self-Supervised Learning

Manuel Cherep, Nikhil Singh

Learning robust audio representations currently demands extensive datasets of real-world sound recordings. By applying artificial transformations to these recordings, models can learn to recognize similarities despite subtle variations through techniques like contrastive learning. However, these transformations are only approximations of the true diversity found in real-world sounds, which are generated by complex interactions of physical processes, from vocal cord vibrations to the resonance of musical instruments. We propose a solution to both the data scale and transformation limitations, leveraging synthetic audio. By randomly perturbing the parameters of a sound synthesizer, we generate audio doppelgängers—synthetic positive pairs with causally manipulated variations in timbre, pitch, and temporal envelopes. These variations, difficult to achieve through augmentations of existing audio, provide a rich source of contrastive information. Despite the shift to randomly generated synthetic data, our method produces strong representations, outperforming real data on several standard audio classification tasks. Notably, our approach is lightweight, requires no data storage, and has only a single hyperparameter, which we extensively analyze. We offer this method as a complement to existing strategies for contrastive learning in audio, using synthesized sounds to reduce the data burden on practitioners.

Deep Learning · Self-Supervised Learning

Hugo Thimonier, José Lucas De Melo Costa, Fabrice Popineau, Arpad Rimmel, Bich-Liên DOAN

Self-supervision is often used for pre-training to foster performance on a downstream task by constructing meaningful representations of samples. Self-supervised learning (SSL) generally involves generating different views of the same sample and thus requires data augmentations that are challenging to construct for tabular data. This constitutes one of the main challenges of self-supervision for structured data. In the present work, we propose a novel augmentation-free SSL method for tabular data. Our approach, T-JEPA, relies on a Joint Embedding Predictive Architecture (JEPA) and is akin to mask reconstruction in the latent space. It involves predicting the latent representation of one subset of features from the latent representation of a different subset within the same sample, thereby learning rich representations without augmentations. We use our method as a pre-training technique and train several deep classifiers on the obtained representation. Our experimental results demonstrate a substantial improvement in both classification and regression tasks, outperforming models trained directly on samples in their original data space. Moreover, T-JEPA enables some methods to consistently outperform or match the performance of traditional methods likes Gradient Boosted Decision Trees. To understand why, we extensively characterize the obtained representations and show that T-JEPA effectively identifies relevant features for downstream tasks without access to the labels. Additionally, we introduce regularization tokens, a novel regularization method critical for training of JEPA-based models on structured data.