论文检索

Applications · Chemistry, Physics, and Earth Sciences

Zhang Jiasheng, Delvin Zhang, Shuang Liang, Zhengpin Li, ZHITAO YING, Jie Shao

Protein language models often struggle to capture biological functions due to their lack of factual knowledge (e.g., gene descriptions). Existing solutions leverage protein knowledge graphs (PKGs) as auxiliary pre-training objectives, but lack explicit integration of task-oriented knowledge, making them suffer from limited knowledge exploitation and catastrophic forgetting. The root cause is that they fail to align PKGs with task-specific data, forcing their knowledge modeling to adapt to the knowledge-isolated nature of downstream tasks. In this paper, we propose Knowledge-aware retrieval augmented protein language model (Kara), achieving the first task-oriented and explicit integration of PKGs and protein language models. With a knowledge retriever learning to predict linkages between PKG and task proteins, Kara unifies the knowledge integration of the pre-training and fine-tuning stages with a structure-based regularization, mitigating catastrophic forgetting. To ensure task-oriented integration, Kara uses contextualized virtual tokens to extract graph context as task-specific knowledge for new proteins. Experiments show that Kara outperforms existing knowledge-enhanced models in 6 representative tasks, achieving on average 5.1% improvements.

Theory · Deep Learning

Antoine Gonon, Nicolas Brisebarre, Elisa Riccietti, Rémi Gribonval

Robustness with respect to weight perturbations underpins guarantees for generalization, pruning and quantization. Existingguarantees rely on *Lipschitz bounds in parameter space*, cover only plain feed-forward MLPs, and break under the ubiquitous neuron-wise rescaling symmetry of ReLU networks. We prove a new Lipschitz inequality expressed through the $\ell^{1}$-*path-metric* of the weights. The bound is (i) *rescaling-invariant* by construction and (ii) applies to any ReLU-DAG architecture with any combination of convolutions, skip connections, pooling, and frozen (inference-time) batch-normalization —thus encompassing ResNets, U-Nets, VGG-style CNNs, and more. By respecting the network’s natural symmetries, the new bound strictly sharpens prior parameter-space bounds and can be computed in two forward passes. To illustrate its utility, we derive from it a symmetry-aware pruning criterion andshow—through a proof-of-concept experiment on a ResNet-18 trained on ImageNet—that its pruning performance matches that of classical magnitude pruning, while becoming totally immune to arbitrary neuron-wise rescalings.

Applications · Chemistry, Physics, and Earth Sciences

Parshin Shojaee, Ngoc Hieu Nguyen, Kazem Meidani, Amir Barati Farimani, Khoa Doan, Chandan Reddy

Scientific equation discovery is a fundamental task in the history of scientific progress, enabling the derivation of laws governing natural phenomena. Recently, Large Language Models (LLMs) have gained interest for this task due to their potential to leverage embedded scientific knowledge for hypothesis generation. However, evaluating the true discovery capabilities of these methods remains challenging, as existing benchmarks often rely on common equations that are susceptible to memorization by LLMs, leading to inflated performance metrics that do not reflect actual discovery. In this paper, we introduce LLM-SRBench, a comprehensive benchmark with 239 challenging problems across four scientific domains specifically designed to evaluate LLM-based scientific equation discovery methods while preventing trivial memorization. Our benchmark comprises two main categories: LSR-Transform, which transforms common physical models into less common mathematical representations to test reasoning beyond memorization, and LSR-Synth, which introduces synthetic, discovery-driven problems requiring data-driven reasoning. Through extensive evaluation of several state-of-the-art methods on LLM-SRBench, using both open and closed LLMs, we find that the best-performing system so far achieves only 31.5% symbolic accuracy.These findings highlight the challenges of scientific equation discovery, positioning LLM-SRBench as a valuable resource for future research.

General Machine Learning · Representation Learning

Yuanchao Xu, Kaidi Shao, Nikos Logothetis, Zhongwei Shen

Analyzing the long-term behavior of high-dimensional nonlinear dynamical systems remains a significant challenge. While the Koopman operator framework provides a powerful global linearization tool, current methods for approximating its spectral components often face theoretical limitations and depend on predefined dictionaries. Residual Dynamic Mode Decomposition (ResDMD) advanced the field by introducing the \emph{spectral residual} to assess Koopman operator approximation accuracy; however, its approach of only filtering precomputed spectra prevents the discovery of the operator's complete spectral information, a limitation known as the `spectral inclusion' problem. We introduce ResKoopNet (Residual-based Koopman-learning Network), a novel method that directly addresses this by explicitly minimizing the \emph{spectral residual} to compute Koopman eigenpairs. This enables the identification of a more precise and complete Koopman operator spectrum. Using neural networks, our approach provides theoretical guarantees while maintaining computational adaptability. Experiments on a variety of physical and biological systems show that ResKoopNet achieves more accurate spectral approximations than existing methods, particularly for high-dimensional systems and those with continuous spectra, which demonstrates its effectiveness as a tool for analyzing complex dynamical systems.

Applications · Social Sciences

Chang Liu, Yixin Wang, Moontae Lee

Efficient access to high-quality information is vital for online platforms. To promote more useful information, users not only create new content but also evaluate existing content, often through helpfulness voting. Although aggregated votes help service providers rank their user content, these votes are often biased by disparate accessibility per position and the cascaded influence of prior votes. For a fairer assessment of information quality, we propose the Counterfactual Voting Adjustment (CVA), a causal framework that accounts for the context in which individual votes are cast. Through preliminary and semi-synthetic experiments, we show that CVA effectively models the position and herding biases, accurately recovering the predefined content quality. In a real experiment, we demonstrate that reranking content based on the learned quality by CVA exhibits stronger alignment with both user sentiment and quality evaluation assessed by GPT-4o, outperforming system rankings based on aggregated votes and model-based rerankings without causal inference. Beyond the individual quality inference, our embeddings offer comparative insights into the behavioral dynamics of expert user groups across 120 major StackExchange communities.

Theory · Online Learning and Bandits

R Majumdar, Mahmoud Salamati, Sadegh Soudjani

Learning to control an unknown dynamical system with respect to high-level temporal specifications is an important problem in control theory. We present the first regret-free online algorithm for learning a controller for linear temporal logic (LTL) specifications for systems with unknown dynamics.We assume that the underlying (unknown) dynamics is modeled by a finite-state and action Markov decision process (MDPs).Our core technical result is a regret-free learning algorithm for infinite-horizon reach-avoid problems on MDPs.For general LTL specifications, we show that the synthesis problem can be reduced to a reach-avoid problem once the graph structure is known.Additionally, we provide an algorithm for learning the graph structure, assuming knowledge of a minimum transition probability, which operates independently of the main regret-free algorithm. Our LTL controller synthesis algorithm provides sharp bounds on how close we are to achieving optimal behavior after a finite number of learning episodes.In contrast, previous algorithms for LTL synthesis only provide asymptotic guarantees, which give no insight into the transient performance during the learning phase.

Social Aspects · Safety

Lukas Fluri, Leon Lang, Alessandro Abate, Patrick Forré, David Krueger, Joar Skalse

In reinforcement learning, specifying reward functions that capture the intended task can be very challenging. Reward learning aims to address this issue by *learning* the reward function. However, a learned reward model may have a low error on the data distribution, and yet subsequently produce a policy with large regret. We say that such a reward model has an *error-regret mismatch*. The main source of an error-regret mismatch is the distributional shift that commonly occurs during policy optimization. In this paper, we mathematically show that a sufficiently low expected test error of the reward model guarantees low worst-case regret, but that for any *fixed* expected test error, there exist realistic data distributions that allow for error-regret mismatch to occur. We then show that similar problems persist even when using policy regularization techniques, commonly employed in methods such as RLHF. We hope our results stimulate the theoretical and empirical study of improved methods to learn reward models, and better ways to measure their quality reliably.

Applications · Neuroscience, Cognitive Science

Chen Wei, Chi Zhang, Jiachen Zou, Haotian Deng, Dietmar Heinke, Quanying Liu

Human decision-making in cognitive tasks and daily life exhibits considerable variability, shaped by factors such as task difficulty, individual preferences, and personal experiences. Understanding this variability across individuals is essential for uncovering the perceptual and decision-making mechanisms that humans rely on when faced with uncertainty and ambiguity. We propose a systematic Boundary Alignment Manipulation (BAM) framework for studying human perceptual variability through image generation. BAM combines perceptual boundary sampling in ANNs and human behavioral experiments to systematically investigate this phenomenon. Our perceptual boundary sampling algorithm generates stimuli along ANN perceptual boundaries that intrinsically induce significant perceptual variability. The efficacy of these stimuli is empirically validated through large-scale behavioral experiments involving 246 participants across 116,715 trials, culminating in the variMNIST dataset containing 19,943 systematically annotated images.Through personalized model alignment and adversarial generation, we establish a reliable method for simultaneously predicting and manipulating the divergent perceptual decisions of pairs of participants.This work bridges the gap between computational models and human individual difference research, providing new tools for personalized perception analysis. Code and data for this work are publicly available.

Deep Learning · Large Language Models

Xiaolong Xu, Yibo Zhou, Haolong Xiang, Xiaoyong Li, Xuyun Zhang, Lianyong Qi, Wanchun Dou

Document-level relation extraction (RE) aims to extract comprehensive correlations between entities and relations from documents. Most of existing works conduct transfer learning on pre-trained language models (PLMs), which allows for richer contextual representation to improve the performance. However, such PLMs-based methods suffer from incorporating structural knowledge, such as entity-entity interactions. Moreover, current works struggle to infer the implicit relations between entities across different sentences, which results in poor prediction. To deal with the above issues, we propose a novel and effective framework, named DocKS-RAG, which introduces extra structural knowledge and semantic information to further enhance the performance of document-level RE. Specifically, we construct a Document-level Knowledge Graph from the observable documentation data to better capture the structural information between entities and relations. Then, a Sentence-level Semantic Retrieval-Augmented Generation mechanism is designed to consider the similarity in different sentences by retrieving the relevant contextual semantic information. Furthermore, we present a hybrid-prompt tuning method on large language models (LLMs) for specific document-level RE tasks. Finally, extensive experiments conducted on two benchmark datasets demonstrate that our proposed framework enhances all the metrics compared with state-of-the-art methods.

Theory · Probabilistic Methods

Vincent Plassier, Alexander Fishkov, Victor Dheur, Mohsen Guizani, Souhaib Ben Taieb, Maxim Panov, Eric Moulines

We present a new method for generating confidence sets within the split conformal prediction framework. Our method performs a trainable transformation of any given conformity score to improve conditional coverage while ensuring exact marginal coverage. The transformation is based on an estimate of the conditional quantile of conformity scores. The resulting method is particularly beneficial for constructing adaptive confidence sets in multi-output problems where standard conformal quantile regression approaches have limited applicability. We develop a theoretical bound that captures the influence of the accuracy of the quantile estimate on the approximate conditional validity, unlike classical bounds for conformal prediction methods that only offer marginal coverage. We experimentally show that our method is highly adaptive to the local data structure and outperforms existing methods in terms of conditional coverage, improving the reliability of statistical inference in various applications.

Social Aspects

Xun Xian, Ganghua Wang, Xuan Bi, Rui Zhang, Jayanth Srinivasa, Ashish Kundu, Charles Fleming, Mingyi Hong, Jie Ding

Retrieval-Augmented Generation (RAG) has been empirically shown to enhance the performance of large language models (LLMs) in knowledge-intensive domains such as healthcare, finance, and legal contexts. Given a query, RAG retrieves relevant documents from a corpus and integrates them into the LLMs’ generation process. In this study, we investigate the adversarial robustness of RAG, focusing specifically on examining the retrieval system. First, across 225 different setup combinations of corpus, retriever, query, and targeted information, we show that retrieval systems are vulnerable to universal poisoning attacks in medical Q&A. In such attacks, adversaries generate poisoned documents containing a broad spectrum of targeted information, such as personally identifiable information. When these poisoned documents are inserted into a corpus, they can be accurately retrieved by any users, as long as attacker-specified queries are used. To understand this vulnerability, we discovered that the deviation from the query’s embedding to that of the poisoned document tends to follow a pattern in which the high similarity between the poisoned document and the query is retained, thereby enabling precise retrieval. Based on these findings, we develop a new detection-based defense to ensure the safe use of RAG. Through extensive experiments spanning various Q&A domains, we observed that our proposed method consistently achieves excellent detection rates in nearly all cases.

General Machine Learning · Unsupervised and Semi-supervised Learning

Giovanni Catania, Aurélien Decelle, Cyril Furtlehner, Beatriz Seoane

We investigate the impact of limited data on training pairwise energy-based models for inverse problems aimed at identifying interaction networks. Utilizing the Gaussian model as testbed, we dissect training trajectories across the eigenbasis of the coupling matrix, exploiting the independent evolution of eigenmodes and revealing that the learning timescales are tied to the spectral decomposition of the empirical covariance matrix. We see that optimal points for early stopping arise from the interplay between these timescales and the initial conditions of training. Moreover, we show that finite data corrections can be accurately modeled through asymptotic random matrix theory calculations and provide the counterpart of generalized cross-validation in the energy based model context. Our analytical framework extends to binary-variable maximum-entropy pairwise models with minimal variations.These findings offer strategies to control overfitting in discrete-variable models through empirical shrinkage corrections, improving the management of overfitting in energy-based generative models.Finally, we propose a generalization to arbitrary energy-based models by deriving the neural tangent kernel dynamics of the score function under the score-matching algorithm.

Deep Learning · Robustness

Bo-Han Lai, Pin-Han Huang, Bo-Han Kung, Shang-Tse Chen

Lipschitz neural networks are well-known for providing certified robustness in deep learning. In this paper, we present a novel, efficient Block Reflector Orthogonal (BRO) layer that enhances the capability of orthogonal layers on constructing more expressive Lipschitz neural architectures. In addition, by theoretically analyzing the nature of Lipschitz neural networks, we introduce a new loss function that employs an annealing mechanism to increase margin for most data points. This enables Lipschitz models to provide better certified robustness. By employing our BRO layer and loss function, we design BRONet — a simple yet effective Lipschitz neural network that achieves state-of-the-art certified robustness. Extensive experiments and empirical analysis on CIFAR-10/100, Tiny-ImageNet, and ImageNet validate that our method outperforms existing baselines. The implementation is available at [GitHub Link](https://github.com/ntuaislab/BRONet).

Deep Learning · Generative Models and Autoencoders

Payman Behnam, Yaosheng Fu, Ritchie Zhao, Po-An Tsai, Zhiding Yu, Alexey Tumanov

Transformer-based Large Language Models rely critically on the KV cache to efficiently handle extended contexts during the decode phase. Yet, the size of the KV cache grows proportionally with the input length, burdening both memory bandwidth and capacity as decoding progresses. To address this challenge, we present RocketKV, a training-free KV cache compression strategy containing two consecutive stages. In the first stage, it performs coarse-grain permanent KV cache eviction on the input sequence tokens. In the second stage, it adopts a hybrid sparse attention method to conduct fine-grain top-k sparse attention, approximating the attention scores by leveraging both head and sequence dimensionality reductions. We show that RocketKV provides a compression ratio of up to 400×, end-to-end speedup of up to 3.7× as well as peak memory reduction of up to 32.6% in the decode phase on an NVIDIA A100 GPU compared to the full KV cache baseline, while achieving negligible accuracy loss on a variety of long-context tasks. We also propose a variant of RocketKV for multi-turn scenarios, which consistently outperforms other existing methods and achieves accuracy nearly on par with an oracle top-k attention scheme.

Deep Learning · Attention Mechanisms

Yilun Kuang, Noah Amsel, Sanae Lotfi, Shikai Qiu, Andres Potapczynski, Andrew Wilson

The core component of attention is the scoring function, which transforms the inputs into low-dimensional queries and keys and takes the dot product of each pair. While the low-dimensional projection improves efficiency, it causes information loss for certain tasks that have intrinsically high-dimensional inputs. Additionally, attention uses the same scoring function for all input pairs, without imposing a distance-dependent compute bias for neighboring tokens in the sequence. In this work, we address these shortcomings by proposing new scoring functions based on computationally efficient structured matrices with high ranks, including Block Tensor-Train (BTT) and Multi-Level Low Rank (MLR) matrices. On in-context regression tasks with high-dimensional inputs, our proposed scoring functions outperform standard attention for any fixed compute budget. On language modeling, a task that exhibits locality patterns, our MLR-based attention method achieves improved scaling laws compared to both standard attention and variants of sliding window attention.Additionally, we show that both BTT and MLR fall under a broader family of efficient structured matrices capable of encoding either full-rank or distance-dependent compute biases, thereby addressing significant shortcomings of standard attention.

Social Aspects · Robustness

Shuo Yang, Bardh Prenkaj, Gjergji Kasneci

Shortcut learning undermines model generalization to out-of-distribution data. While the literature attributes shortcuts to biases in superficial features, we show that imbalances in the semantic distribution of sample embeddings induce spurious semantic correlations, compromising model robustness. To address this issue, we propose SCISSOR (Semantic Cluster Intervention for Suppressing ShORtcut), a Siamese network-based debiasing approach that remaps the semantic space by discouraging latent clusters exploited as shortcuts. Unlike prior data-debiasing approaches, SCISSOR eliminates the need for data augmentation and rewriting. We evaluate SCISSOR on 6 models across 4 benchmarks: Chest-XRay and Not-MNIST in computer vision, and GYAFC and Yelp in NLP tasks. Compared to several baselines, SCISSOR reports +5.3 absolute points in F1 score on GYAFC, +7.3 on Yelp, +7.7 on Chest-XRay, and +1 on Not-MNIST. SCISSOR is also highly advantageous for lightweight models with ∼9.5% improvement on F1 for ViT on computer vision datasets and ∼11.9% for BERT on NLP. Our study redefines the landscape of model generalization by addressing overlooked semantic biases, establishing SCISSOR as a foundational framework for mitigating shortcut learning and fostering more robust, bias-resistant AI systems.

Probabilistic Methods · Structure Learning

Nikita Lagrange, Herve Isambert

We propose a greedy search-and-score algorithm for ancestral graphs, which include directed as well as bidirected edges, originating from unobserved latent variables. The normalized likelihood score of ancestral graphs is estimated in terms of multivariate information over relevant "$ac$-connected subset" of vertices, $\boldsymbol{C}$, that are connected through collider paths confined to the ancestor set of $\boldsymbol{C}$. For computational efficiency, the proposed two-step algorithm relies on local information scores limited to the close surrounding vertices of each node (step 1) and edge (step 2). This computational strategy, although restricted to information contributions from $ac$-connected subsets containing up to two-collider paths, is shown to outperform state-of-the-art causal discovery methods on challenging benchmark datasets.

Deep Learning · Graph Neural Networks

Rui Xue, Tong Zhao, Neil Shah, Xiaorui Liu

Graph neural networks (GNNs) have demonstrated remarkable success in graph representation learning and various sampling approaches have been proposed to scale GNNs to applications with large-scale graphs. A class of promising GNN training algorithms take advantage of historical embeddings to reduce the computation and memory cost while maintaining the model expressiveness of GNNs. However, they incur significant computation bias due to the stale feature history. In this paper, we provide a comprehensive analysis of their staleness and inferior performance on large-scale problems. Motivated by our discoveries, we propose a simple yet highly effective training algorithm (REST) to effectively reduce feature staleness, which leads to significantly improved performance and convergence across varying batch sizes, especially when staleness is predominant. The proposed algorithm seamlessly integrates with existing solutions, boasting easy implementation, while comprehensive experiments underscore its superior performance and efficiency on large-scale benchmarks. Specifically, our improvements to state-of-the-art historical embedding methods result in a 2.7\% and 3.6\% performance enhancement on the ogbn-papers100M and ogbn-products dataset respectively, accompanied by notably accelerated convergence. The code can be found at https://github.com/RXPHD/REST.

Deep Learning · Generative Models and Autoencoders

Alec Helbling, Tuna Han Salih Meral, Benjamin Hoover, Pinar Yanardag, Polo Chau

Do the rich representations of multi-modal diffusion transformers (DiTs) exhibit unique properties that enhance their interpretability? We introduce ConceptAttention, a novel method that leverages the expressive power of DiT attention layers to generate high-quality saliency maps that precisely locate textual concepts within images. Without requiring additional training, ConceptAttention repurposes the parameters of DiT attention layers to produce highly contextualized *concept embeddings*, contributing the major discovery that performing linear projections in the output space of DiT attention layers yields significantly sharper saliency maps compared to commonly used cross-attention maps. ConceptAttention even achieves state-of-the-art performance on zero-shot image segmentation benchmarks, outperforming 15 other zero-shot interpretability methods on the ImageNet-Segmentation dataset. ConceptAttention works for popular image models and even seamlessly generalizes to video generation. Our work contributes the first evidence that the representations of multi-modal DiTs are highly transferable to vision tasks like segmentation.

Deep Learning · Large Language Models

Shaokun Zhang, Ming Yin, Jieyu Zhang, Jiale Liu, Zhiguang Han, Jingyang Zhang, Beibin Li, Chi Wang, Huazheng Wang, Yiran Chen 等

Failure attribution in LLM multi-agent systems—identifying the agent and step responsible for task failures—provides crucial clues for systems debugging but remains underexplored and labor-intensive. In this paper, we propose and formulate a new research area: automated failure attribution for LLM multi-agent systems.To support this initiative, we introduce the Who\&When dataset, comprising extensive failure logs from 127 LLM multi-agent systems with fine-grained annotations linking failures to specific agents and decisive error steps.Using the Who\&When, we develop and evaluate three automated failure attribution methods, summarizing their corresponding pros and cons. The best method achieves 53.5\% accuracy in identifying failure-responsible agents but only 14.2\% in pinpointing failure steps, with some methods performing below random. Even SOTA reasoning models, such as OpenAI o1 and DeepSeek R1, fail to achieve practical usability. These results highlight the task's complexity and the need for further research in this area. Code and dataset are available in https://github.com/mingyin1/Agents_Failure_Attribution.