GenAI4ELab/papercli-papers huggingface dataset:
Diffusion Counterfactual Generation with Semantic Abduction
Authors: Rajat R Rasal; Avinash Kori; Fabio De Sousa Ribeiro; Tian Xia; Ben Glocker
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Counterfactual image generation presents significant challenges, including preserving identity, maintaining perceptual quality, and ensuring faithfulness to an underlying causal model. While existing auto-encoding frameworks admit semantic latent spaces which can be manipulated for causal control, they struggle with scalability and fidelity. Advancements in diffusion models present opportunities for improving counterfactual image editing, having demonstrated state-of-the-art visual quality, human-aligned perception and representation learning capabilities. Here, we present a suite of diffusion-based causal mechanisms, introducing the notions of spatial, semantic and dynamic abduction. We propose a general framework that integrates semantic representations into diffusion models through the lens of Pearlian causality to edit images via a counterfactual reasoning process. To the best of our knowledge, ours is the first work to consider high-level semantic identity preservation for diffusion counterfactuals and to demonstrate how semantic control enables principled trade-offs between faithful causal control and identity preservation.
Arbitrarily-Conditioned Multi-Functional Diffusion for Multi-Physics Emulation
Authors: Da Long; Zhitong Xu; Guang Yang; Akil Narayan; Shandian Zhe
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Modern physics simulation often involves multiple functions of interests, and traditional numerical approaches are known to be complex and computationally costly. While machine learning-based surrogate models can offer significant cost reductions, most focus on a single task, such as forward prediction, and typically lack uncertainty quantification --- an essential component in many applications. To overcome these limitations, we propose Arbitrarily-Conditioned Multi-Functional Diffusion (ACM-FD), a versatile probabilistic surrogate model for multi-physics emulation. ACM-FD can perform a wide range of tasks within a single framework, including forward prediction, various inverse problems, and simulating data for entire systems or subsets of quantities conditioned on others. Specifically, we extend the standard Denoising Diffusion Probabilistic Model (DDPM) for multi-functional generation by modeling noise as Gaussian processes (GP). 
We propose a random-mask based, zero-regularized denoising loss to achieve flexible and robust conditional generation. We induce a Kronecker product structure in the GP covariance matrix, substantially reducing the computational cost and enabling efficient training and sampling. We demonstrate the effectiveness of ACM-FD across several fundamental multi-physics systems.
A Physics-Augmented Deep Learning Framework for Classifying Single Molecule Force Spectroscopy Data
Authors: Cailong Hua; Sivaraman Rajaganapathy; Rebecca A Slick; Joseph Vavra; Joseph M. Muretta; James M. Ervasti; Murti Salapaka
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Deciphering protein folding and unfolding pathways under tension is essential for deepening our understanding of fundamental biological mechanisms. Such insights hold the promise of developing treatments for a range of debilitating and fatal conditions, including muscular disorders like Duchenne Muscular Dystrophy and neurodegenerative diseases such as Parkinson's disease. Single molecule force spectroscopy (SMFS) is a powerful technique for investigating forces involved in protein domains folding and unfolding. However, SMFS trials often involve multiple protein molecules, necessitating filtering to isolate measurements from single-molecule trials. Currently, manual visual inspection is the primary method for classifying single-molecule data; a process that is both time-consuming and requires significant expertise. Here, we both apply state-of-the-art machine learning models and present a novel deep learning model tailored to SMFS data. The proposed model employs a dual-branch fusion strategy; one branch integrates the physics of protein molecules, and the other operates independently of physical constraints. This model automates the isolation of single-molecule measurements, significantly enhancing data processing efficiency. To train and validate our approach, we developed a physics-based Monte Carlo engine to simulate force spectroscopy datasets, including trials involving single molecules, multiple molecules, and no molecules. Our model achieves state-of-the-art performance, outperforming five baseline methods on both simulated and experimental datasets. It attains nearly 100\% accuracy across all simulated datasets and an average accuracy of $79.6 \pm 5.2$\% on experimental datasets, using only $\sim$30 training samples, surpassing baseline methods by 11.4\%. Notably, even without expert annotations on experimental data, the model achieves an average accuracy of $72.0 \pm 5.9$\% when pre-trained on corresponding simulated datasets. With our deep learning approach, the time required to extract meaningful statistics from single-molecule SMFS trials is reduced from a day to under an hour. This work results in SMFS experimental datasets from four important protein molecules crucial to many biological pathways. To support further research, we have made our datasets publicly available and provided a Python-based toolbox (https://github.com/SalapakaLab-SIMBioSys/SMFS-Identification).
Linear $Q$-Learning Does Not Diverge in $L^2$: Convergence Rates to a Bounded Set
Authors: Xinyu Liu; Zixuan Xie; Shangtong Zhang
Venue: ICML 2025 (ICML 2025 poster)

Abstract: $Q$-learning is one of the most fundamental reinforcement learning algorithms.
It is widely believed that $Q$-learning with linear function approximation (i.e., linear $Q$-learning) suffers from possible divergence until the recent work Meyn (2024) which establishes the ultimate almost sure boundedness of the iterates of linear $Q$-learning.
Building on this success,
this paper further establishes the first $L^2$ convergence rate of linear $Q$-learning iterates (to a bounded set).
Similar to Meyn (2024),
we do not make any modification to the original linear $Q$-learning algorithm, do not make any Bellman completeness assumption,
and do not make any near-optimality assumption on the behavior policy.
All we need is an $\epsilon$-softmax behavior policy with an adaptive temperature.
The key to our analysis is the general result of stochastic approximations under Markovian noise with fast-changing transition functions.
As a side product,
we also use this general result to establish the $L^2$ convergence rate of tabular $Q$-learning with an $\epsilon$-softmax behavior policy,
for which we rely on a novel pseudo-contraction property of the weighted Bellman optimality operator.
Differentially Private Analysis for Binary Response Models: Optimality, Estimation, and Inference
Authors: Ce Zhang; Yixin Han; Yafei Wang; Xiaodong Yan; Linglong Kong; Ting Li; Bei Jiang
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Randomized response (RR) mechanisms constitute a fundamental and effective technique for ensuring label differential privacy (LabelDP). However, existing RR methods primarily focus on the response labels while overlooking the influence of covariates and often do not fully address optimality. To address these challenges, this paper explores optimal LabelDP procedures using RR mechanisms, focusing on achieving optimal estimation and inference in binary response models. We first analyze the asymptotic behaviors of RR binary response models and then optimize the procedure by maximizing the trace of the Fisher Information Matrix within the $\varepsilon$- and $(\varepsilon,\delta)$-LabelDP constraints. Our theoretical results indicate that the proposed methods achieve optimal LabelDP guarantees while maintaining statistical accuracy in binary response models under mild conditions. Furthermore, we develop private confidence intervals with nominal coverage for statistical inference. Extensive simulation studies and real-world applications confirm that our methods outperform existing approaches in terms of precise estimation, privacy protection, and reliable inference.
Sleeping Reinforcement Learning
Authors: Simone Drago; Marco Mussi; Alberto Maria Metelli
Venue: ICML 2025 (ICML 2025 poster)

Abstract: In the standard Reinforcement Learning (RL) paradigm, the action space is assumed to be fixed and immutable throughout the learning process. However, in many real-world scenarios, not all actions are available at every decision stage. The available action set may depend on the current environment state, domain-specific constraints, or other (potentially stochastic) factors outside the agent's control. To address these realistic scenarios, we introduce a novel paradigm called *Sleeping Reinforcement Learning*, where the available action set varies during the interaction with the environment. We start with the simpler scenario in which the available action sets are revealed at the beginning of each episode. We show that a modification of UCBVI achieves regret of order $\widetilde{\mathcal{O}}(H\sqrt{SAT})$, where $H$ is the horizon, $S$ and $A$ are the cardinalities of the state and action spaces, respectively, and $T$ is the learning horizon. Next, we address the more challenging and realistic scenario in which the available actions are disclosed only at each decision stage. By leveraging a novel construction, we establish a minimax lower bound of order $\Omega(\sqrt{T 2^{A/2}})$ when the availability of actions is governed by a Markovian process, establishing a statistical barrier of the problem. Focusing on the statistically tractable case where action availability depends only on the current state and stage, we propose a new optimistic algorithm that achieves regret guarantees of order $\widetilde{\mathcal{O}}(H\sqrt{SAT})$, showing that the problem shares the same complexity of standard RL.
MissScore: High-Order Score Estimation in the Presence of Missing Data
Authors: Wenqin Liu; Haoze Hou; Erdun Gao; Biwei Huang; Qiuhong Ke; Howard Bondell; Mingming Gong
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Score-based generative models are essential in various machine learning applications, with strong capabilities in generation quality. In particular, high-order derivatives (scores) of data density offer deep insights into data distributions, building on the proven effectiveness of first-order scores for modeling and generating synthetic data, unlocking new possibilities for applications. However, learning them typically requires complete data, which is often unavailable in domains such as healthcare and finance due to data corruption, acquisition constraints, or incomplete records. To tackle this challenge, we introduce MissScore, a novel framework for estimating high-order scores in the presence of missing data. We derive objective functions for estimating high-order scores under different missing data mechanisms and propose a new algorithm specifically designed to handle missing data effectively. Our empirical results demonstrate that MissScore accurately and efficiently learns the high-order scores from incomplete data and generates high-quality samples, resulting in strong performance across a range of downstream tasks.
RepoAudit: An Autonomous LLM-Agent for Repository-Level Code Auditing
Authors: Jinyao Guo; Chengpeng Wang; Xiangzhe Xu; Zian Su; Xiangyu Zhang
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Code auditing is the process of reviewing code with the aim of identifying bugs. Large Language Models (LLMs) have demonstrated promising capabilities for this task without requiring compilation, while also supporting user-friendly customization. However, auditing a code repository with LLMs poses significant challenges: limited context windows and hallucinations can degrade the quality of bug reports, and analyzing large-scale repositories incurs substantial time and token costs, hindering efficiency and scalability.

This work introduces an LLM-based agent, RepoAudit, designed to perform autonomous repository-level code auditing. Equipped with agent memory, RepoAudit explores the codebase on demand by analyzing data-flow facts along feasible program paths within individual functions. It further incorporates a validator module to mitigate hallucinations by verifying data-flow facts and checking the satisfiability of path conditions associated with potential bugs, thereby reducing false positives. RepoAudit detects 40 true bugs across 15 real-world benchmark projects with a precision of 78.43%, requiring on average only 0.44 hours and $2.54 per project. Also, it detects 185 new bugs in high-profile projects, among which 174 have been confirmed or fixed. We have open-sourced RepoAudit at https://github.com/PurCL/RepoAudit.
Deep Linear Network Training Dynamics from Random Initialization: Data, Width, Depth, and Hyperparameter Transfer
Authors: Blake Bordelon; Cengiz Pehlevan
Venue: ICML 2025 (ICML 2025 poster)

Abstract: We theoretically characterize gradient descent dynamics in deep linear networks trained at large width from random initialization and on large quantities of random data. Our theory captures the ``wider is better" effect of mean-field/maximum-update parameterized networks as well as hyperparameter transfer effects, which can be contrasted with the neural-tangent parameterization where optimal learning rates shift with model width. We provide asymptotic descriptions of both non-residual and residual neural networks, the latter of which enables an infinite depth limit when branches are scaled as $1/\sqrt{\text{depth}}$. We also compare training with one-pass stochastic gradient descent to the dynamics when training data are repeated at each iteration. Lastly, we show that this model recovers the accelerated power law training dynamics for power law structured data in the rich regime observed in recent works.
Improving Your Model Ranking on Chatbot Arena by Vote Rigging
Authors: Rui Min; Tianyu Pang; Chao Du; Qian Liu; Minhao Cheng; Min Lin
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Chatbot Arena is an open platform for evaluating LLMs by pairwise battles, in which users vote for their preferred response from two randomly sampled anonymous models. While Chatbot Arena is widely regarded as a reliable LLM ranking leaderboard, we show that crowdsourced voting can be *rigged* to improve (or decrease) the ranking of a target model $m\_{t}$. We first introduce a straightforward **target-only rigging** strategy that focuses on new battles involving $m\_{t}$, identifying it via watermarking or a binary classifier, and exclusively voting for $m\_{t}$ wins. However, this strategy is practically inefficient because there are over $190$ models on Chatbot Arena and on average only about 1% of new battles will involve $m\_{t}$. To overcome this, we propose an **omnipresent rigging** strategy, exploiting the Elo rating mechanism of Chatbot Arena that any new vote on a battle can influence the ranking of the target model $m\_{t}$, even if $m\_{t}$ is not directly involved in the battle. We conduct experiments on around *1.7 million* historical votes from the Chatbot Arena Notebook, showing that omnipresent rigging strategy can improve model rankings by rigging only *hundreds of* new votes. While we have evaluated several defense mechanisms, our findings highlight the importance of continued efforts to prevent vote rigging. [**Code**](https://github.com/sail-sg/Rigging-ChatbotArena) is publicly available to reproduce all experiments.
Token Cleaning: Fine-Grained Data Selection for LLM Supervised Fine-Tuning
Authors: Jinlong Pang; Na Di; Zhaowei Zhu; Jiaheng Wei; Hao Cheng; Chen Qian; Yang Liu
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Recent studies show that in supervised fine-tuning (SFT) of large language models (LLMs), data quality matters more than quantity. 
While most data cleaning methods concentrate on filtering entire samples, the quality of individual tokens within a sample can vary significantly. After pre-training, even in high-quality samples, patterns or phrases that are not task-related can be redundant, uninformative, or even harmful. Continuing to fine-tune on these patterns may offer limited benefit and even degrade downstream task performance.
In this paper, we investigate token quality from a noisy-label perspective and propose a generic token cleaning pipeline for SFT tasks. Our method filters out uninformative tokens while preserving those carrying key task-specific information. Specifically, we first evaluate token quality by examining the influence of model updates on each token, then apply a threshold-based separation. The token influence can be measured in a single pass with a fixed reference model or iteratively with self-evolving reference models. The benefits and limitations of both methods are analyzed theoretically by error upper bounds. Extensive experiments show that our framework consistently improves downstream performance. Code is available at https://github.com/UCSC-REAL/TokenCleaning.
Collaborative Mean Estimation Among Heterogeneous Strategic Agents: Individual Rationality, Fairness, and Truthful Contribution
Authors: Alex Clinton; Yiding Chen; Jerry Zhu; Kirthevasan Kandasamy
Venue: ICML 2025 (ICML 2025 poster)

Abstract: We study a collaborative learning problem where $m$ agents aim to estimate a vector $\mu =(\mu_1,\ldots,\mu_d)\in \mathbb{R}^d$ by sampling from associated univariate normal distributions $(\mathcal{N}(\mu_k, \sigma^2))\_{k\in[d]}$. Agent $i$ incurs a cost $c_{i,k}$ to sample from $\mathcal{N}(\mu_k, \sigma^2)$. Instead of working independently, agents can exchange data, collecting cheaper samples and sharing them in return for costly data, thereby reducing both costs and estimation error. We design a mechanism to facilitate such collaboration, while addressing two key challenges: ensuring *individually rational (IR) and fair outcomes* so all agents benefit, and *preventing strategic behavior* (e.g. non-collection, data fabrication) to avoid socially undesirable outcomes.
We design a mechanism and an associated Nash equilibrium (NE) which minimizes the social penalty-sum of agents' estimation errors and collection costs-while being IR for all agents. We achieve a $\mathcal{O}(\sqrt{m})$-approximation to the minimum social penalty in the worst case and an $\mathcal{O}(1)$-approximation under favorable conditions. Additionally, we establish three hardness results: no nontrivial mechanism guarantees *(i)* a dominant strategy equilibrium where agents report truthfully, *(ii)* is IR for every strategy profile of other agents, *(iii)* or avoids a worst-case $\Omega(\sqrt{m})$ price of stability in any NE. Finally, by integrating concepts from axiomatic bargaining, we demonstrate that our mechanism supports fairer outcomes than one which minimizes social penalty.
Bridging Fairness and Efficiency in Conformal Inference: A Surrogate-Assisted Group-Clustered Approach
Authors: Chenyin Gao; Peter B. Gilbert; Larry Han
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Standard conformal prediction ensures marginal coverage but consistently undercovers underrepresented groups, limiting its reliability for fair uncertainty quantification. Group fairness requires prediction sets to achieve a user-specified coverage level within each protected group. While group-wise conformal inference meets this requirement, it often produces excessively wide prediction sets due to limited sample sizes in underrepresented groups, highlighting a fundamental tradeoff between fairness and efficiency. To bridge this gap, we introduce Surrogate-Assisted Group-Clustered Conformal Inference (SAGCCI), a framework that improves efficiency through two key innovations: (1) clustering protected groups with similar conformal score distributions to enhance precision while maintaining fairness, and (2) deriving an efficient influence function that optimally integrates surrogate outcomes to construct tighter prediction sets. Theoretically, SAGCCI guarantees approximate group-conditional coverage in a doubly robust manner under mild convergence conditions, enabling flexible nuisance model estimation. Empirically, through simulations and an analysis of the phase 3 Moderna COVE COVID-19 vaccine trial, we demonstrate that SAGCCI outperforms existing methods, producing narrower prediction sets while maintaining valid group-conditional coverage, effectively balancing fairness and efficiency in uncertainty quantification.
Distribution-aware Fairness Learning in Medical Image Segmentation From A Control-Theoretic Perspective
Authors: Yujin Oh; Pengfei Jin; Sangjoon Park; Sekeun Kim; Siyeop yoon; Jin Sung Kim; Kyungsang Kim; Xiang Li; Quanzheng Li
Venue: ICML 2025 (ICML 2025 spotlightposter)

Abstract: Ensuring fairness in medical image segmentation is critical due to biases in imbalanced clinical data acquisition caused by demographic attributes (e.g., age, sex, race) and clinical factors (e.g., disease severity). To address these challenges, we introduce Distribution-aware Mixture of Experts (dMoE), inspired by optimal control theory. We provide a comprehensive analysis of its underlying mechanisms and clarify dMoE's role in adapting to heterogeneous distributions in medical image segmentation. Furthermore, we integrate dMoE into multiple network architectures, demonstrating its broad applicability across diverse medical image analysis tasks. By incorporating demographic and clinical factors, dMoE achieves state-of-the-art performance on two 2D benchmark datasets and a 3D in-house dataset. Our results highlight the effectiveness of dMoE in mitigating biases from imbalanced distributions, offering a promising approach to bridging control theory and medical image segmentation within fairness learning paradigms. The source code is available at https://github.com/tvseg/dMoE.
Statistical and Computational Guarantees of Kernel Max-Sliced Wasserstein Distances
Authors: Jie Wang; March Boedihardjo; Yao Xie
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Optimal transport has been very successful for various machine learning tasks; however, it is known to suffer from the curse of dimensionality. Hence, dimensionality reduction is desirable when applied to high-dimensional data with low-dimensional structures. The kernel max-sliced (KMS) Wasserstein distance is developed for this purpose by finding an optimal nonlinear mapping that reduces data into $1$ dimension before computing the Wasserstein distance. However, its theoretical properties have not yet been fully developed. In this paper, we provide sharp finite-sample guarantees under milder technical assumptions compared with state-of-the-art for the KMS $p$-Wasserstein distance between two empirical distributions with $n$ samples for general $p\in[1,\infty)$. Algorithm-wise, we show that computing the KMS $2$-Wasserstein distance is NP-hard, and then we further propose a semidefinite relaxation (SDR) formulation (which can be solved efficiently in polynomial time) and provide a relaxation gap for the obtained solution. We provide numerical examples to demonstrate the good performance of our scheme for high-dimensional two-sample testing.