ICML 2025 论文列表

International Conference on Machine Learning

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3,342篇论文

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Training Flexible Models of Genetic Variant Effects from Functional Annotations using Accelerated Linear Algebra

Alan Nawzad Amin, Andres Potapczynski, Andrew Gordon Wilson

展开摘要

To understand how genetic variants in human genomes manifest in phenotypes - traits like height or diseases like asthma - geneticists have sequenced and measured hundreds of thousands of individuals. Geneticists use this data to build models that predict how a genetic variant impacts phenotype given genomic features of the variant, like DNA accessibility or the presence of nearby DNA-bound proteins. As more data and features become available, one might expect predictive models to improve. Unfortunately, training these models is bottlenecked by the need to solve expensive linear algebra problems because variants in the genome are correlated with nearby variants, requiring inversion of large matrices. Previous methods have therefore been restricted to fitting small models, and fitting simplified summary statistics, rather than the full likelihood of the statistical model. In this paper, we leverage modern fast linear algebra techniques to develop DeepWAS (Deep genome Wide Association Studies), a method to train large and flexible neural network predictive models to optimize likelihood. Surprisingly, we find that larger models only improve performance when using our full likelihood approach; when trained by fitting traditional summary statistics, larger models perform no better than small ones. We find larger models trained on more features make better predictions, potentially improving disease predictions and therapeutic target identification.

Poster
Minimax Optimal Regret Bound for Reinforcement Learning with Trajectory Feedback

Zihan Zhang, Yuxin Chen, Jason D. Lee, Simon Shaolei Du, Ruosong Wang

展开摘要

In this work, we study reinforcement learning (RL) with trajectory feedback. Compared to the standard RL setting, in RL with trajectory feedback, the agent only observes the accumulative reward along the trajectory, and therefore, this model is particularly suitable for scenarios where querying the reward in each single step incurs prohibitive cost. For a finite-horizon Markov Decision Process (MDP) with $S$ states, $A$ actions and a horizon length of $H$, we develop an algorithm that enjoys an asymptotically nearly optimal regret of $\tilde{O}\left(\sqrt{SAH^3K}\right)$ in $K$ episodes. To achieve this result, our new technical ingredients include (i) constructing a tighter confidence region for the reward function by incorporating the RL with trajectory feedback setting with techniques in linear bandits and (ii) constructing a reference transition model to better guide the exploration process.

Poster
Volume Optimality in Conformal Prediction with Structured Prediction Sets

Chao Gao, Liren Shan, Vaidehi Srinivas, Aravindan Vijayaraghavan

展开摘要

Conformal Prediction is a widely studied technique to construct prediction sets of future observations. Most conformal prediction methods focus on achieving the necessary coverage guarantees, but do not provide formal guarantees on the size (volume) of the prediction sets. We first prove the impossibility of volume optimality where any distribution-free method can only find a trivial solution. We then introduce a new notion of volume optimality by restricting the prediction sets to belong to a set family (of finite VC-dimension), specifically a union of $k$-intervals. Our main contribution is an efficient distribution-free algorithm based on dynamic programming (DP) to find a union of $k$-intervals that is guaranteed for any distribution to have near-optimal volume among all unions of $k$-intervals satisfying the desired coverage property. By adopting the framework of distributional conformal prediction (Chernozhukov et al., 2021), the new DP based conformity score can also be applied to achieve approximate conditional coverage and conditional restricted volume optimality, as long as a reasonable estimator of the conditional CDF is available. While the theoretical results already establish volume-optimality guarantees, they are complemented by experiments that demonstrate that our method can significantly outperform existing methods in many settings.

Poster
Learning Safe Strategies for Value Maximizing Buyers in Uniform Price Auctions

Negin Golrezaei, Sourav Sahoo

展开摘要

We study the bidding problem in repeated uniform price multi-unit auctions from the perspective of a single *value-maximizing* buyer who aims to maximize their cumulative value over $T$ rounds while adhering to return-on-investment (RoI) constraints in each round. Buyers adopt $m$-*uniform bidding* format, where they submit $m$ bid-quantity pairs $(b_i, q_i)$ to demand $q_i$ units at bid $b_i$. We introduce *safe* bidding strategies as those that satisfy RoI constraints in every auction, regardless of competing bids. We show that these strategies depend only on the bidder’s valuation curve, and the bidder can focus on a finite subset of this class without loss of generality. While the number of strategies in this subset is exponential in $m$, we develop a polynomial-time algorithm to learn the optimal safe strategy that achieves sublinear regret in the online setting, where regret is measured against a clairvoyant benchmark that knows the competing bids *a priori* and selects a fixed hindsight optimal safe strategy. We then evaluate the performance of safe strategies against a clairvoyant that selects the optimal strategy from a richer class of strategies in the online setting. In this scenario, we compute the *richness ratio*, $\alpha\in(0, 1]$ for the class of strategies chosen by the clairvoyant and show that our algorithm, designed to learn safe strategies, achieves $\alpha$-approximate sublinear regret against these stronger benchmarks. Experiments on semi-synthetic data from real-world auctions show that safe strategies substantially outperform the derived theoretical bounds, making them quite appealing in practice.

Poster
Epsilon-VAE: Denoising as Visual Decoding

Long Zhao, Sanghyun Woo, Ziyu Wan, YANDONG LI, Han Zhang, Boqing Gong, Hartwig Adam, Xuhui Jia, Ting Liu

展开摘要

In generative modeling, tokenization simplifies complex data into compact, structured representations, creating a more efficient, learnable space. For high-dimensional visual data, it reduces redundancy and emphasizes key features for high-quality generation. Current visual tokenization methods rely on a traditional autoencoder framework, where the encoder compresses data into latent representations, and the decoder reconstructs the original input. In this work, we offer a new perspective by proposing denoising as decoding, shifting from single-step reconstruction to iterative refinement. Specifically, we replace the decoder with a diffusion process that iteratively refines noise to recover the original image, guided by the latents provided by the encoder. We evaluate our approach by assessing both reconstruction (rFID) and generation quality (FID), comparing it to state-of-the-art autoencoding approaches. By adopting iterative reconstruction through diffusion, our autoencoder, namely Epsilon-VAE, achieves high reconstruction quality, which in turn enhances downstream generation quality by 22% at the same compression rates or provides 2.3x inference speedup through increasing compression rates. We hope this work offers new insights into integrating iterative generation and autoencoding for improved compression and generation.

Poster
Stable Fair Graph Representation Learning with Lipschitz Constraint

Qiang Chen, Zhongze Wu, Xiu Su, Xi Lin, Zhe Qu, Shan You, Shuo Yang, Chang Xu

展开摘要

Group fairness based on adversarial training has gained significant attention on graph data, which was implemented by masking sensitive attributes to generate fair feature views. However, existing models suffer from training instability due to uncertainty of the generated masks and the trade-off between fairness and utility. In this work, we propose a stable fair Graph Neural Network (SFG) to maintain training stability while preserving accuracy and fairness performance. Specifically, we first theoretically derive a tight upper Lipschitz bound to control the stability of existing adversarial-based models and employ a stochastic projected subgradient algorithm to constrain the bound, which operates in a block-coordinate manner. Additionally, we construct the uncertainty set to train the model, which can prevent unstable training by dropping some overfitting nodes caused by chasing fairness. Extensive experiments conducted on three real-world datasets demonstrate that SFG is stable and outperforms other state-of-the-art adversarial-based methods in terms of both fairness and utility performance. Codes are available at https://github.com/sh-qiangchen/SFG.

Poster
Physics-Informed DeepONets for drift-diffusion on metric graphs: simulation and parameter identification

Jan Blechschmidt, Tom-Christian Riemer, Max Winkler, Martin STOLL, Jan-Frederik Pietschmann

展开摘要

We develop a novel physics informed deep learning approach for solving nonlinear drift-diffusion equations on metric graphs. These models represent an important model class with a large number of applications in areas ranging from transport in biological cells to the motion of human crowds. While traditional numerical schemes require a large amount of tailoring, especially in the case of model design or parameter identification problems, physics informed deep operator networks (DeepONets) have emerged as a versatile tool for the solution of partial differential equations with the particular advantage that they easily incorporate parameter identification questions. We here present an approach where we first learn three DeepONet models for representative inflow, inner and outflow edges, resp., and then subsequently couple these models for the solution of the drift-diffusion metric graph problem by relying on an edge-based domain decomposition approach. We illustrate that our framework is applicable for the accurate evaluation of graph-coupled physics models and is well suited for solving optimization or inverse problems on these coupled networks.

Poster
Empirical Privacy Variance

Yuzheng Hu, Fan Wu, Ruicheng Xian, Yuhang Liu, Lydia Zakynthinou, Pritish Kamath, Chiyuan Zhang, David Forsyth

展开摘要

We propose the notion of empirical privacy variance and study it in the context of differentially private fine-tuning of language models. Specifically, we show that models calibrated to the same $(\varepsilon, \delta)$-DP guarantee using DP-SGD with different hyperparameter configurations can exhibit significant variations in empirical privacy, which we quantify through the lens of memorization. We investigate the generality of this phenomenon across multiple dimensions and discuss why it is surprising and relevant. Through regression analysis, we examine how individual and composite hyperparameters influence empirical privacy. The results reveal a no-free-lunch trade-off: existing practices of hyperparameter tuning in DP-SGD, which focus on optimizing utility under a fixed privacy budget, often come at the expense of empirical privacy. To address this, we propose refined heuristics for hyperparameter selection that explicitly account for empirical privacy, showing that they are both precise and practically useful. Finally, we take preliminary steps to understand empirical privacy variance. We propose two hypotheses, identify limitations in existing techniques like privacy auditing, and outline open questions for future research.

Poster
Rethinking Point Cloud Data Augmentation: Topologically Consistent Deformation

Jian Bi, Qianliang Wu, Xiang Li, Shuo Chen, Jianjun Qian, Lei Luo, Jian Yang

展开摘要

Data augmentation has been widely used in machine learning. Its main goal is to transform and expand the original data using various techniques, creating a more diverse and enriched training dataset. However, due to the disorder and irregularity of point clouds, existing methods struggle to enrich geometric diversity and maintain topological consistency, leading to imprecise point cloud understanding. In this paper, we propose SinPoint, a novel method designed to preserve the topological structure of the original point cloud through a homeomorphism. It utilizes the Sine function to generate smooth displacements. This simulates object deformations, thereby producing a rich diversity of samples. In addition, we propose a Markov chain Augmentation Process to further expand the data distribution by combining different basic transformations through a random process. Our extensive experiments demonstrate that our method consistently outperforms existing Mixup and Deformation methods on various benchmark point cloud datasets, improving performance for shape classification and part segmentation tasks. Specifically, when used with PointNet++ and DGCNN, our method achieves a state-of-the-art accuracy of 90.2 in shape classification with the real-world ScanObjectNN dataset. We release the code at https://github.com/CSBJian/SinPoint.

Poster
Minimalist Concept Erasure in Generative Models

Yang Zhang, Er Jin, Yanfei Dong, Yixuan Wu, Philip Torr, Ashkan Khakzar, Johannes Stegmaier, Kenji Kawaguchi

展开摘要

Recent advances in generative models have demonstrated remarkable capabilities in producing high-quality images, but their reliance on large-scale unlabeled data has raised significant safety and copyright concerns. Efforts to address these issues by erasing unwanted concepts have shown promise. However, many existing erasure methods involve excessive modifications that compromise the overall utility of the model. In this work, we address these issues by formulating a novel minimalist concept erasure objective based *only* on the distributional distance of final generation outputs. Building on our formulation, we derive a tractable loss for differentiable optimization that leverages backpropagation through all generation steps in an end-to-end manner. We also conduct extensive analysis to show theoretical connections with other models and methods. To improve the robustness of the erasure, we incorporate neuron masking as an alternative to model fine-tuning. Empirical evaluations on state-of-the-art flow-matching models demonstrate that our method robustly erases concepts without degrading overall model performance, paving the way for safer and more responsible generative models.

Poster
Holistic Physics Solver: Learning PDEs in a Unified Spectral-Physical Space

Xihang Yue, Yi Yang, Linchao Zhu

展开摘要

Recent advances in operator learning have produced two distinct approaches for solving partial differential equations (PDEs): attention-based methods offering point-level adaptability but lacking spectral constraints, and spectral-based methods providing domain-level continuity priors but limited in local flexibility. This dichotomy has hindered the development of PDE solvers with both strong flexibility and generalization capability. This work introduces Holistic Physics Mixer (HPM), a novel framework that bridges this gap by integrating spectral and physical information in a unified space. HPM unifies both approaches as special cases while enabling more powerful spectral-physical interactions beyond either method alone. This enables HPM to inherit both the strong generalization of spectral methods and the flexibility of attention mechanisms while avoiding their respective limitations. Through extensive experiments across diverse PDE problems, we demonstrate that HPM consistently outperforms state-of-the-art methods in both accuracy and computational efficiency, while maintaining strong generalization capabilities with limited training data and excellent zero-shot performance on unseen resolutions.

Poster
Wasserstein Policy Optimization

David Pfau, Ian Davies, Diana L Borsa, João Guilherme Madeira Araújo, Brendan Daniel Tracey, Hado Van Hasselt

展开摘要

We introduce Wasserstein Policy Optimization (WPO), an actor-critic algorithm for reinforcement learning in continuous action spaces. WPO can be derived as an approximation to Wasserstein gradient flow over the space of all policies projected into a finite-dimensional parameter space (e.g., the weights of a neural network), leading to a simple and completely general closed-form update. The resulting algorithm combines many properties of deterministic and classic policy gradient methods. Like deterministic policy gradients, it exploits knowledge of the *gradient* of the action-value function with respect to the action. Like classic policy gradients, it can be applied to stochastic policies with arbitrary distributions over actions -- without using the reparameterization trick. We show results on the DeepMind Control Suite and a magnetic confinement fusion task which compare favorably with state-of-the-art continuous control methods.

Poster
HyperIV: Real-time Implied Volatility Smoothing

Yongxin Yang, Wenqi Chen, Chao Shu, Timothy Hospedales

展开摘要

We propose HyperIV, a novel approach for real-time implied volatility smoothing that eliminates the need for traditional calibration procedures. Our method employs a hypernetwork to generate parameters for a compact neural network that constructs complete volatility surfaces within 2 milliseconds, using only 9 market observations. Moreover, the generated surfaces are guaranteed to be free of static arbitrage. Extensive experiments across 8 index options demonstrate that HyperIV achieves superior accuracy compared to existing methods while maintaining computational efficiency. The model also exhibits strong cross-asset generalization capabilities, indicating broader applicability across different market instruments. These key features -- rapid adaptation to market conditions, guaranteed absence of arbitrage, and minimal data requirements -- make HyperIV particularly valuable for real-time trading applications. We make code available at https://github.com/qmfin/hyperiv.

Poster
Can Biologically Plausible Temporal Credit Assignment Rules Match BPTT for Neural Similarity? E-prop as an Example

Yuhan Helena Liu, Guangyu Robert Yang, Christopher J Cueva

展开摘要

Understanding how the brain learns may be informed by studying biologically plausible learning rules. These rules, often approximating gradient descent learning to respect biological constraints such as locality, must meet two critical criteria to be considered an appropriate brain model: (1) good neuroscience task performance and (2) alignment with neural recordings. While extensive research has assessed the first criterion, the second remains underexamined. Employing methods such as Procrustes analysis on well-known neuroscience datasets, this study demonstrates the existence of a biologically plausible learning rule — namely e-prop, which is based on gradient truncation and has demonstrated versatility across a wide range of tasks — that can achieve neural data similarity comparable to Backpropagation Through Time (BPTT) when matched for task accuracy. Our findings also reveal that model architecture and initial conditions can play a more significant role in determining neural similarity than the specific learning rule. Furthermore, we observe that BPTT-trained models and their biologically plausible counterparts exhibit similar dynamical properties at comparable accuracies. These results underscore the substantial progress made in developing biologically plausible learning rules, highlighting their potential to achieve both competitive task performance and neural data similarity.

Poster
Dimension-Independent Rates for Structured Neural Density Estimation

Robert A. Vandermeulen, Wai Ming Tai, Bryon Aragam

展开摘要

We show that deep neural networks can achieve dimension-independent rates of convergence for learning structured densities typical of image, audio, video, and text data. For example, in images, where each pixel becomes independent of the rest of the image when conditioned on pixels at most $t$ steps away, a simple $L^2$-minimizing neural network can attain a rate of $n^{-1/((t+1)^2+4)}$, where $t$ is independent of the ambient dimension $d$, i.e. the total number of pixels. We further provide empirical evidence that, in real-world applications, $t$ is often a small constant, thus effectively circumventing the curse of dimensionality. Moreover, for sequential data (e.g., audio or text) exhibiting a similar local dependence structure, our analysis shows a rate of $n^{-1/(t+5)}$, offering further evidence of dimension independence in practical scenarios.

Poster
Investigating the Overlooked Hessian Structure: From CNNs to LLMs

Qian-Yuan Tang, Yufei Gu, YUNFENG CAI, Mingming Sun, Ping Li, zhou Xun, Zeke Xie

展开摘要

It is well-known that the Hessian of deep loss landscape matters to optimization and generalization of deep learning. Previous studies reported a rough Hessian structure in deep learning, which consists of two components, a small number of large eigenvalues and a large number of nearly-zero eigenvalues. To the best of our knowledge, we are the first to report that a simple but overlooked power-law Hessian structure exists in well-trained deep neural networks, including Convolutional Neural Networks (CNNs) and Large Language Models (LLMs). Moreover, we provide a maximum-entropy theoretical interpretation for the power-law Hessian structure and theoretically demonstrate the existence of robust and low-dimensional subspace of deep neural networks. Our extensive experiments using the proposed power-law spectral method demonstrate that the power-law Hessian spectra critically relate to multiple important behaviors of deep learning, including optimization, generalization, and overparameterization. Notably, we discover that the power-law Hessian structure of a given LLM can effectively predict generalization during training, while conventional sharpness-based generalization measures that often works well on CNNs become nearly useless for as a generalization predictor of LLMs.

Poster
Dataflow-Guided Neuro-Symbolic Language Models for Type Inference

Gen Li, Yao Wan, Hongyu Zhang, Zhou Zhao, Wenbin Jiang, Xuanhua Shi, Hai Jin, Zheng Wang

展开摘要

Language Models (LMs) are increasingly used for type inference, aiding in error detection and software development. Some real-world deployments of LMs require the model to run on local machines to safeguard the intellectual property of the source code. This setting often limits the size of the LMs that can be used. We present Nester, the first neuro-symbolic approach that enhances LMs for type inference by integrating symbolic learning without increasing model size. Nester breaks type inference into sub-tasks based on the data and control flow of the input code, encoding them as a modular high-level program. This program executes multi-step actions, such as evaluating expressions and analyzing conditional branches of the target code, combining static typing with LMs to infer potential types. Evaluated on the ManyTypes4Py dataset in Python, Nester outperforms two state-of-the-art type inference methods (HiTyper and TypeGen), achieving 70.7\% Top-1 Exact Match, which is 18.3\% and 3.6\% higher than HiTyper and TypeGen, respectively. For complex type annotations like typing.Optional and typing.Union, Nester achieves 51.0\% and 16.7\%, surpassing TypeGen by 28.3\% and 5.8\%.

Poster
SPACE: Your Genomic Profile Predictor is a Powerful DNA Foundation Model

Zhao Yang, Jiwei Zhu, Bing Su

展开摘要

Inspired by the success of unsupervised pre-training paradigms, researchers have applied these approaches to DNA pre-training. However, we argue that these approaches alone yield suboptimal results because pure DNA sequences lack sufficient information, since their functions are regulated by genomic profiles like chromatin accessibility. Here, we demonstrate that supervised training for genomic profile prediction serves as a more effective alternative to pure sequence pre-training. Furthermore, considering the multi-species and multi-profile nature of genomic profile prediction, we introduce our **S**pecies-**P**rofile **A**daptive **C**ollaborative **E**xperts (SPACE) that leverages Mixture of Experts (MoE) to better capture the relationships between DNA sequences across different species and genomic profiles, thereby learning more effective DNA representations. Through extensive experiments across various tasks, our model achieves state-of-the-art performance, establishing that DNA models trained with supervised genomic profiles serve as powerful DNA representation learners.

Poster
Geometry-Informed Neural Networks

Arturs Berzins, Andreas Radler, Eric Volkmann, Sebastian Sanokowski, Sepp Hochreiter, Johannes Brandstetter

展开摘要

Geometry is a ubiquitous tool in computer graphics, design, and engineering. However, the lack of large shape datasets limits the application of state-of-the-art supervised learning methods and motivates the exploration of alternative learning strategies. To this end, we introduce geometry-informed neural networks (GINNs) -- a framework for training shape-generative neural fields without data by leveraging user-specified design requirements in the form of objectives and constraints. By adding diversity as an explicit constraint, GINNs avoid mode-collapse and can generate multiple diverse solutions, often required in geometry tasks. Experimentally, we apply GINNs to several problems spanning physics, geometry, and engineering design, showing control over geometrical and topological properties, such as surface smoothness or the number of holes. These results demonstrate the potential of training shape-generative models without data, paving the way for new generative design approaches without large datasets.

Poster
Protein Structure Tokenization: Benchmarking and New Recipe

Xinyu Yuan, Zichen Wang, Marcus D. Collins, Huzefa Rangwala

展开摘要

Recent years have witnessed a surge in the development of protein structural tokenization methods, which chunk protein 3D structures into discrete or continuous representations. Structure tokenization enables the direct application of powerful techniques like language modeling for protein structures, and large multimodal models to integrate structures with protein sequences and functional texts. Despite the progress, the capabilities and limitations of these methods remain poorly understood due to the lack of a unified evaluation framework. We first introduce **StructTokenBench**, a framework that comprehensively evaluates the quality and efficiency of structure tokenizers, focusing on fine-grained local substructures rather than global structures, as typical in existing benchmarks. Our evaluations reveal that no single model dominates all benchmarking perspectives. Observations of codebook under-utilization led us to develop **AminoAseed**, a simple yet effective strategy that enhances codebook gradient updates and optimally balances codebook size and dimension for improved tokenizer utilization and quality. Compared to the leading model ESM3, our method achieves an average of 6.31\% performance improvement across 24 supervised tasks, with sensitivity and utilization rates increased by 12.83\% and 124.03\%, respectively. Source code and model weights are available at https://github.com/KatarinaYuan/StructTokenBench.

Poster