ICML 2025 Papers

International Conference on Machine Learning

Decision breakdown

3,342papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Oral
    1213.6%
  • Spotlight
    2256.7%
  • Poster
    2,99689.6%

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PertEval-scFM: Benchmarking Single-Cell Foundation Models for Perturbation Effect Prediction

Aaron Wenteler, Martina Occhetta, Nikhil Branson, Victor Curean, Magdalena Huebner, William Dee, William Connell, Siu Pui Chung, Alex Hawkins-Hooker, Yasha Ektefaie, César Miguel Valdez Córdova, Amaya Gallagher-Syed

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*In silico* modeling of transcriptional responses to perturbations is crucial for advancing our understanding of cellular processes and disease mechanisms. We present PertEval-scFM, a standardized framework designed to evaluate models for perturbation effect prediction. We apply PertEval-scFM to benchmark zero-shot single-cell foundation model (scFM) embeddings against baseline models to assess whether these contextualized representations enhance perturbation effect prediction. Our results show that scFM embeddings offer limited improvement over simple baseline models in the zero-shot setting, particularly under distribution shift. Overall, this study provides a systematic evaluation of zero-shot scFM embeddings for perturbation effect prediction, highlighting the challenges of this task and the limitations of current-generation scFMs. Our findings underscore the need for specialized models and high-quality datasets that capture a broader range of cellular states. Source code and documentation can be found at: https://github.com/aaronwtr/PertEval.

Poster
Efficient Federated Incomplete Multi-View Clustering

Suyuan Liu, Hao Yu, Hao Tan, KE LIANG, Siwei Wang, Shengju Yu, En Zhu, Xinwang Liu

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Multi-view clustering (MVC) leverages complementary information from diverse data sources to enhance clustering performance. However, its practical deployment in distributed and privacy-sensitive scenarios remains challenging. Federated multi-view clustering (FMVC) has emerged as a potential solution, but existing approaches suffer from substantial limitations, including excessive communication overhead, insufficient privacy protection, and inadequate handling of missing views. To address these issues, we propose Efficient Federated Incomplete Multi-View Clustering (EFIMVC), a novel framework that introduces a localized optimization strategy to significantly reduce communication costs while ensuring theoretical convergence. EFIMVC employs both view-specific and shared anchor graphs as communication variables, thereby enhancing privacy by avoiding the transmission of sensitive embeddings. Moreover, EFIMVC seamlessly extends to scenarios with missing views, making it a practical and scalable solution for real-world applications. Extensive experiments on benchmark datasets demonstrate the superiority of EFIMVC in clustering accuracy, communication efficiency, and privacy preservation. Our code is publicly available at https://github.com/Tracesource/EFIMVC.

Poster
Long-Short Alignment for Effective Long-Context Modeling in LLMs

Tianqi Du, Haotian Huang, Yifei Wang, Yisen Wang

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Large language models (LLMs) have exhibited impressive performance and surprising emergent properties. However, their effectiveness remains limited by the fixed context window of the transformer architecture, posing challenges for long-context modeling. Among these challenges, length generalization — the ability to generalize to sequences longer than those seen during training — is a classical and fundamental problem. In this work, we propose a fresh perspective on length generalization, shifting the focus from the conventional emphasis on input features such as positional encodings or data structures to the output distribution of the model. Specifically, through case studies on synthetic tasks, we highlight the critical role of **long-short alignment** — the consistency of output distributions across sequences of varying lengths. Extending this insight to natural language tasks, we propose a metric called Long-Short Misalignment to quantify this phenomenon, uncovering a strong correlation between the metric and length generalization performance. Building on these findings, we develop a regularization term that promotes long-short alignment during training. Extensive experiments validate the effectiveness of our approach, offering new insights for achieving more effective long-context modeling in LLMs. Code is available at https://github.com/PKU-ML/LongShortAlignment.

Poster
Hierarchical Masked Autoregressive Models with Low-Resolution Token Pivots

Guangting Zheng, Yehao Li, Yingwei Pan, Jiajun Deng, Ting Yao, Yanyong Zhang, Tao Mei

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Autoregressive models have emerged as a powerful generative paradigm for visual generation. The current de-facto standard of next token prediction commonly operates over a single-scale sequence of dense image tokens, and is incapable of utilizing global context especially for early tokens prediction. In this paper, we introduce a new autoregressive design to model a hierarchy from a few low-resolution image tokens to the typical dense image tokens, and delve into a thorough hierarchical dependency across multi-scale image tokens. Technically, we present a Hierarchical Masked Autoregressive models (Hi-MAR) that pivot on low-resolution image tokens to trigger hierarchical autoregressive modeling in a multi-phase manner. Hi-MAR learns to predict a few image tokens in low resolution, functioning as intermediary pivots to reflect global structure, in the first phase. Such pivots act as the additional guidance to strengthen the next autoregressive modeling phase by shaping global structural awareness of typical dense image tokens. A new Diffusion Transformer head is further devised to amplify the global context among all tokens for mask token prediction. Extensive evaluations on both class-conditional and text-to-image generation tasks demonstrate that Hi-MAR outperforms typical AR baselines, while requiring fewer computational costs.

Poster
Concept-Centric Token Interpretation for Vector-Quantized Generative Models

Tianze Yang, Yucheng Shi, Mengnan Du, Xuansheng Wu, Qiaoyu Tan, Jin Sun, Ninghao Liu

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Vector-Quantized Generative Models (VQGMs) have emerged as powerful tools for image generation. However, the key component of VQGMs---the codebook of discrete tokens---is still not well understood, e.g., which tokens are critical to generate an image of a certain concept? This paper introduces Concept-Oriented Token Explanation (CORTEX), a novel approach for interpreting VQGMs by identifying concept-specific token combinations. Our framework employs two methods: (1) a sample-level explanation method that analyzes token importance scores in individual images, and (2) a codebook-level explanation method that explores the entire codebook to find globally relevant tokens. Experimental results demonstrate CORTEX's efficacy in providing clear explanations of token usage in the generative process, outperforming baselines across multiple pretrained VQGMs. Besides enhancing VQGMs transparency, CORTEX is useful in applications such as targeted image editing and shortcut feature detection. Our code is available at https://github.com/YangTianze009/CORTEX.

Poster
Bayesian Inference for Correlated Human Experts and Classifiers

Markelle Kelly, Alex James Boyd, Sam Showalter, Mark Steyvers, Padhraic Smyth

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Applications of machine learning often involve making predictions based on both model outputs and the opinions of human experts. In this context, we investigate the problem of querying experts for class label predictions, using as few human queries as possible, and leveraging the class probability estimates of pre-trained classifiers. We develop a general Bayesian framework for this problem, modeling expert correlation via a joint latent representation, enabling simulation-based inference about the utility of additional expert queries, as well as inference of posterior distributions over unobserved expert labels. We apply our approach to two real-world medical classification problems, as well as to CIFAR-10H and ImageNet-16H, demonstrating substantial reductions relative to baselines in the cost of querying human experts while maintaining high prediction accuracy.

Poster
The Ripple Effect: On Unforeseen Complications of Backdoor Attacks

Rui Zhang, Yun Shen, Hongwei Li, Wenbo Jiang, Hanxiao Chen, Yuan Zhang, Guowen Xu, Yang Zhang

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Recent research highlights concerns about the trustworthiness of third-party Pre-Trained Language Models (PTLMs) due to potential backdoor attacks. These backdoored PTLMs, however, are effective only for specific pre-defined downstream tasks. In reality, these PTLMs can be adapted to many other unrelated downstream tasks. Such adaptation may lead to unforeseen consequences in downstream model outputs, consequently raising user suspicion and compromising attack stealthiness. We refer to this phenomenon as backdoor complications. In this paper, we undertake the first comprehensive quantification of backdoor complications. Through extensive experiments using 4 prominent PTLMs and 16 text classification benchmark datasets, we demonstrate the widespread presence of backdoor complications in downstream models fine-tuned from backdoored PTLMs. The output distribution of triggered samples significantly deviates from that of clean samples. Consequently, we propose a backdoor complication reduction method leveraging multi-task learning to mitigate complications without prior knowledge of downstream tasks. The experimental results demonstrate that our proposed method can effectively reduce complications while maintaining the efficacy and consistency of backdoor attacks.

Poster
On the Power of Learning-Augmented Search Trees

Jingbang Chen, Xinyuan Cao, Alicia Stepin, Li Chen

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We study learning-augmented binary search trees (BSTs) via Treaps with carefully designed priorities. The result is a simple search tree in which the depth of each item $x$ is determined by its predicted weight $w_x$. Specifically, each item $x$ is assigned a composite priority of $-\lfloor\log\log(1/w_x)\rfloor + U(0, 1)$ where $U(0, 1)$ is the uniform random variable. By choosing $w_x$ as the relative frequency of $x$, the resulting search trees achieve static optimality. This approach generalizes the recent learning-augmented BSTs [Lin-Luo-Woodruff ICML`22], which only work for Zipfian distributions, by extending them to arbitrary input distributions. Furthermore, we demonstrate that our method can be generalized to a B-Tree data structure using the B-Treap approach [Golovin ICALP'09]. Our search trees are also capable of leveraging localities in the access sequence through online self-reorganization, thereby achieving the working-set property. Additionally, they are robust to prediction errors and support dynamic operations, such as insertions, deletions, and prediction updates. We complement our analysis with an empirical study, demonstrating that our method outperforms prior work and classic data structures.

Poster
Demonstration Selection for In-Context Learning via Reinforcement Learning

Xubin Wang, Jianfei Wu, Yuan Yichen, Deyu Cai, Mingzhe Li, Weijia Jia

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Diversity in demonstration selection is critical for enhancing model generalization by enabling broader coverage of structures and concepts. Constructing appropriate demonstration sets remains a key research challenge. This paper introduces the Relevance-Diversity Enhanced Selection (RDES), an innovative approach that leverages reinforcement learning (RL) frameworks to optimize the selection of diverse reference demonstrations for tasks amenable to in-context learning (ICL), particularly text classification and reasoning, in few-shot prompting scenarios. RDES employs frameworks like Q-learning and a PPO-based variant to dynamically identify demonstrations that maximize both diversity (quantified by label distribution) and relevance to the task objective. This strategy ensures a balanced representation of reference data, leading to improved accuracy and generalization. Through extensive experiments on multiple benchmark datasets, including diverse reasoning tasks, and involving 14 closed-source and open-source LLMs, we demonstrate that RDES significantly enhances performance compared to ten established baselines. Our evaluation includes analysis of performance across varying numbers of demonstrations on selected datasets. Furthermore, we investigate incorporating Chain-of-Thought (CoT) reasoning, which further boosts predictive performance. The results highlight the potential of RL for adaptive demonstration selection and addressing challenges in ICL.

Poster
Solving Probabilistic Verification Problems of Neural Networks using Branch and Bound

David Boetius, Stefan Leue, Tobias Sutter

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Probabilistic verification problems of neural networks are concerned with formally analysing the output distribution of a neural network under a probability distribution of the inputs. Examples of probabilistic verification problems include verifying the demographic parity fairness notion or quantifying the safety of a neural network. We present a new algorithm for solving probabilistic verification problems of neural networks based on an algorithm for computing and iteratively refining lower and upper bounds on probabilities over the outputs of a neural network. By applying state-of-the-art bound propagation and branch and bound techniques from non-probabilistic neural network verification, our algorithm significantly outpaces existing probabilistic verification algorithms, reducing solving times for various benchmarks from the literature from tens of minutes to tens of seconds. Furthermore, our algorithm compares favourably even to dedicated algorithms for restricted probabilistic verification problems. We complement our empirical evaluation with a theoretical analysis, proving that our algorithm is sound and, under mildly restrictive conditions, also complete when using a suitable set of heuristics.

Poster
Dynamic Similarity Graph Construction with Kernel Density Estimation

Steinar Laenen, Peter Macgregor, He Sun

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In the kernel density estimation (KDE) problem, we are given a set $X$ of data points in $\mathbb{R}^d$, a kernel function $k: \mathbb{R}^d \times \mathbb{R}^d \rightarrow \mathbb{R}$, and a query point $\mathbf{q} \in \mathbb{R}^d$, and the objective is to quickly output an estimate of $\sum_{\mathbf{x} \in X} k(\mathbf{q}, \mathbf{x})$. In this paper, we consider $\textsf{KDE}$ in the dynamic setting, and introduce a data structure that efficiently maintains the _estimates_ for a set of query points as data points are added to $X$ over time. Based on this, we design a dynamic data structure that maintains a sparse approximation of the fully connected similarity graph on $X$, and develop a fast dynamic spectral clustering algorithm. We further evaluate the effectiveness of our algorithms on both synthetic and real-world datasets.

Poster
A Sharper Global Convergence Analysis for Average Reward Reinforcement Learning via an Actor-Critic Approach

Swetha Ganesh, Washim Uddin Mondal, Vaneet Aggarwal

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This work examines average-reward reinforcement learning with general policy parametrization. Existing state-of-the-art (SOTA) guarantees for this problem are either suboptimal or hindered by several challenges, including poor scalability with respect to the size of the state-action space, high iteration complexity, and a significant dependence on knowledge of mixing times and hitting times. To address these limitations, we propose a Multi-level Monte Carlo-based Natural Actor-Critic (MLMC-NAC) algorithm. Our work is the first to achieve a global convergence rate of $\tilde{\mathcal{O}}(1/\sqrt{T})$ for average-reward Markov Decision Processes (MDPs) (where $T$ is the horizon length), using an Actor-Critic approach. Moreover, the convergence rate does not scale with the size of the state space, therefore even being applicable to infinite state spaces.

Poster
Distributed Parallel Gradient Stacking(DPGS): Solving Whole Slide Image Stacking Challenge in Multi-Instance Learning

Boyuan Wu, ZEFENG WANG, Xianwei Lin, Jiachun Xu, Jikai Yu, Zhou Shicheng, Hongda Chen, Lianxin Hu

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Whole Slide Image (WSI) analysis is framed as a Multiple Instance Learning (MIL) problem, but existing methods struggle with non-stackable data due to inconsistent instance lengths, which degrades performance and efficiency. We propose a Distributed Parallel Gradient Stacking (DPGS) framework with Deep Model-Gradient Compression (DMGC) to address this. DPGS enables lossless MIL data stacking for the first time, while DMGC accelerates distributed training via joint gradient-model compression. Experiments on Camelyon16 and TCGA-Lung datasets demonstrate up to 31× faster training, up to a 99.2% reduction in model communication size at convergence, and up to a 9.3% improvement in accuracy compared to the baseline. To our knowledge, this is the first work to solve non-stackable data in MIL while improving both speed and accuracy.

Poster
Learning Condensed Graph via Differentiable Atom Mapping for Reaction Yield Prediction

Ankit Ghosh, Gargee Kashyap, Sarthak Mittal, Nupur Jain, Raghavan B Sunoj, Abir De

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Yield of chemical reactions generally depends on the activation barrier, i.e., the energy difference between the reactant and the transition state. Computing the transition state from the reactant and product graphs requires prior knowledge of the correct node alignment (i.e., atom mapping), which is not available in yield prediction datasets. In this work, we propose YieldNet, a neural yield prediction model, which tackles these challenges. Here, we first approximate the atom mapping between the reactants and products using a differentiable node alignment network. We then use this approximate atom mapping to obtain a noisy realization of the condensed graph of reaction (CGR), which is a supergraph encompassing both the reactants and products. This CGR serves as a surrogate for the transition state graph structure. The CGR embeddings of different steps in a multi-step reaction are then passed into a transformer-guided reaction path encoder. Our experiments show that YieldNet can predict the yield more accurately than the baselines. Furthermore, the model is trained only under the distant supervision of yield values, without requiring fine-grained supervision of atom mapping.

Poster
Improving Continual Learning Performance and Efficiency with Auxiliary Classifiers

Filip Szatkowski, Yaoyue Zheng, Fei Yang, Tomasz Trzcinski, Bartłomiej Twardowski, Joost van de weijer

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Continual learning is crucial for applying machine learning in challenging, dynamic, and often resource-constrained environments. However, catastrophic forgetting — overwriting previously learned knowledge when new information is acquired — remains a major challenge. In this work, we examine the intermediate representations in neural network layers during continual learning and find that such representations are less prone to forgetting, highlighting their potential to accelerate computation. Motivated by these findings, we propose to use auxiliary classifiers~(ACs) to enhance performance and demonstrate that integrating ACs into various continual learning methods consistently improves accuracy across diverse evaluation settings, yielding an average 10\% relative gain. We also leverage the ACs to reduce the average cost of the inference by 10-60\% without compromising accuracy, enabling the model to return the predictions before computing all the layers. Our approach provides a scalable and efficient solution for continual learning.

Poster
Calibrated Language Models and How to Find Them with Label Smoothing

Jerry Huang, Peng Lu, QIUHAO Zeng

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Recent advances in natural language processing (NLP) have opened up greater opportunities to enable fine-tuned large language models (LLMs) to behave as more powerful interactive agents through improved instruction-following ability. However, understanding how this impacts confidence calibration for reliable model output has not been researched in full. In this work, we examine various open-sourced LLMs, identifying significant calibration degradation after instruction tuning in each. Seeking a practical solution, we look towards label smoothing, which has been shown as an effective method to regularize for overconfident predictions but has yet to be widely adopted in the supervised fine-tuning (SFT) of LLMs. We first provide insight as to why label smoothing is sufficient to maintain calibration throughout the SFT process. However, settings remain where the effectiveness of smoothing is severely diminished, in particular the case of large vocabulary LLMs (LV-LLMs). We posit the cause to stem from the ability to become over-confident, which has a direct relationship with the hidden size and vocabulary size, and justify this theoretically and experimentally. Finally, we address an outstanding issue regarding the memory footprint of the cross-entropy loss computation in the label smoothed loss setting, designing a customized kernel to dramatically reduce memory consumption without sacrificing speed or performance in comparison to existing solutions for non-smoothed losses.

Poster
Policy Optimization for CMDPs with Bandit Feedback: Learning Stochastic and Adversarial Constraints

Francesco Emanuele Stradi, Anna Lunghi, Matteo Castiglioni, Alberto Marchesi, Nicola Gatti

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We study online learning in constrained Markov decision processes (CMDPs) in which rewards and constraints may be either stochastic or adversarial. In such settings, stradi et al. (2024) proposed the first best-of-both-worlds algorithm able to seamlessly handle stochastic and adversarial constraints, achieving optimal regret and constraint violation bounds in both cases. This algorithm suffers from two major drawbacks. First, it only works under full feedback, which severely limits its applicability in practice. Moreover, it relies on optimizing over the space of occupancy measures, which requires solving convex optimization problems, an highly inefficient task. In this paper, we provide the first best-of-both-worlds algorithm for CMDPs with bandit feedback. Specifically, when the constraints are stochastic, the algorithm achieves $\widetilde{\mathcal{O}}(\sqrt{T})$ regret and constraint violation, while, when they are adversarial, it attains $\widetilde{\mathcal{O}}(\sqrt{T})$ constraint violation and a tight fraction of the optimal reward. Moreover, our algorithm is based on a policy optimization approach, which is much more efficient than occupancy-measure-based methods.

Poster
Delay-DSGN: A Dynamic Spiking Graph Neural Network with Delay Mechanisms for Evolving Graph

Zhiqiang Wang, Jianghao Wen, Jianqing Liang

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Dynamic graph representation learning using Spiking Neural Networks (SNNs) exploits the temporal spiking behavior of neurons, offering advantages in capturing the temporal evolution and sparsity of dynamic graphs. However, existing SNN-based methods often fail to effectively capture the impact of latency in information propagation on node representations. To address this, we propose Delay-DSGN, a dynamic spiking graph neural network incorporating a learnable delay mechanism. By leveraging synaptic plasticity, the model dynamically adjusts connection weights and propagation speeds, enhancing temporal correlations and enabling historical data to influence future representations. Specifically, we introduce a Gaussian delay kernel into the neighborhood aggregation process at each time step, adaptively delaying historical information to future time steps and mitigating information forgetting. Experiments on three large-scale dynamic graph datasets demonstrate that Delay-DSGN outperforms eight state-of-the-art methods, achieving the best results in node classification tasks. We also theoretically derive the constraint conditions between the Gaussian kernel's standard deviation and size, ensuring stable training and preventing gradient explosion and vanishing issues.

Poster
Nearly Optimal Sample Complexity for Learning with Label Proportions

Robert Istvan Busa-Fekete, Travis Dick, Claudio Gentile, Haim Kaplan, Tomer Koren, Uri Stemmer

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We investigate Learning from Label Proportions (LLP), a partial information setting where examples in a training set are grouped into bags, and only aggregate label values in each bag are available. Despite the partial observability, the goal is still to achieve small regret at the level of individual examples. We give results on the sample complexity of LLP under square loss, showing that our sample complexity is essentially optimal. From an algorithmic viewpoint, we rely on carefully designed variants of Empirical Risk Minimization, and Stochastic Gradient Descent algorithms, combined with ad hoc variance reduction techniques. On one hand, our theoretical results improve in important ways on the existing literature on LLP, specifically in the way the sample complexity depends on the bag size. On the other hand, we validate our algorithmic solutions on several datasets, demonstrating improved empirical performance (better accuracy for less samples) against recent baselines.

Poster
Plausible Token Amplification for Improving Accuracy of Differentially Private In-Context Learning Based on Implicit Bayesian Inference

Yusuke Yamasaki, Kenta Niwa, Daiki Chijiwa, Takumi Fukami, Takayuki Miura

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We propose Plausible Token Amplification (PTA) to improve the accuracy of Differentially Private In-Context Learning (DP-ICL) using DP synthetic demonstrations. While Tang et al. empirically improved the accuracy of DP-ICL by limiting vocabulary space during DP synthetic demonstration generation, its theoretical basis remains unexplored. By interpreting ICL as implicit Bayesian inference on a concept underlying demonstrations, we not only provide theoretical evidence supporting Tang et al.'s empirical method but also introduce PTA, a refined method for modifying next-token probability distribution. Through the modification, PTA highlights tokens that distinctly represent the ground-truth concept underlying the original demonstrations. As a result, generated DP synthetic demonstrations guide the Large Language Model to successfully infer the ground-truth concept, which improves the accuracy of DP-ICL. Experimental evaluations on both synthetic and real-world text-classification datasets validated the effectiveness of PTA.

Poster