GenAI4ELab/papercli-papers huggingface dataset:
Geometric Representation Condition Improves Equivariant Molecule Generation
Authors: Zian Li; Cai Zhou; Xiyuan Wang; Xingang Peng; Muhan Zhang
Venue: ICML 2025 (ICML 2025 spotlightposter)

Abstract: Recent advances in molecular generative models have demonstrated great promise for accelerating scientific discovery, particularly in drug design. However, these models often struggle to generate high-quality molecules, especially in conditional scenarios where specific molecular properties must be satisfied. In this work, we introduce GeoRCG, a general framework to improve molecular generative models by integrating geometric representation conditions with provable theoretical guarantees. We decompose the generation process into two stages: first, generating an informative geometric representation; second, generating a molecule conditioned on the representation. Compared with single-stage generation, the easy-to-generate representation in the first stage guides the second stage generation toward a high-quality molecule in a goal-oriented way. Leveraging EDM and SemlaFlow as base generators, we observe significant quality improvements in unconditional molecule generation on the widely used QM9 and GEOM-DRUG datasets. More notably, in the challenging conditional molecular generation task, our framework achieves an average 50\% performance improvement over state-of-the-art approaches, highlighting the superiority of conditioning on semantically rich geometric representations. Furthermore, with such representation guidance, the number of diffusion steps can be reduced to as small as 100 while largely preserving the generation quality achieved with 1,000 steps, thereby significantly reducing the generation iterations needed.
Double Machine Learning for Causal Inference under Shared-State Interference
Authors: Chris Hays; Manish Raghavan
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Researchers and practitioners often wish to measure treatment effects in settings where units interact via markets and recommendation systems.  In these settings, units are affected by certain *shared states*, like prices, algorithmic recommendations or social signals. We formalize this  structure, calling it shared-state interference, and argue that our formulation captures many relevant applied settings. Our key modeling assumption is that individuals' potential outcomes are independent conditional on the shared state. We then prove an extension of a double machine learning (DML) theorem providing conditions for achieving efficient inference under shared-state interference. We also instantiate our general theorem in several models of interest where it is possible to efficiently estimate the average direct effect (ADE) or global average treatment effect (GATE).
Bivariate Causal Discovery with Proxy Variables: Integral Solving and Beyond
Authors: Yong Wu; Yanwei Fu; Shouyan Wang; Xinwei Sun
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Bivariate causal discovery is challenging when unmeasured confounders exist. To adjust for the bias, previous methods employed the proxy variable (*i.e.*, negative control outcome (NCO)) to test the treatment-outcome relationship through integral equations -- and assumed that violation of this equation indicates the causal relationship. Upon this, they could establish asymptotic properties for causal hypothesis testing. However, these methods either relied on parametric assumptions or required discretizing continuous variables, which may lead to information loss. Moreover, it is unclear when this underlying integral-related assumption holds, making it difficult to justify the utility in practice. To address these problems, we first consider the scenario where only NCO is available. We propose a novel non-parametric procedure, which enjoys asymptotic properties and preserves more information. Moreover, we find that when NCO affects the outcome, the above integral-related assumption may not hold, rendering the causal relation unidentifiable. Informed by this, we further consider the scenario when the negative control exposure (NCE) is also available. In this scenario, we construct another integral restriction aided by this proxy, which can discover causation when NCO affects the outcome. We demonstrate these findings and the effectiveness of our proposals through comprehensive numerical studies.
Unisoma: A Unified Transformer-based Solver for Multi-Solid Systems
Authors: Shilong Tao; Zhe Feng; Haonan Sun; Zhanxing Zhu; Yunhuai Liu
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Multi-solid systems are foundational to a wide range of real-world applications, yet modeling their complex interactions remains challenging. Existing deep learning methods predominantly rely on implicit modeling, where the factors influencing solid deformation are not explicitly represented but are instead indirectly learned. However, as the number of solids increases, these methods struggle to accurately capture intricate physical interactions. In this paper, we introduce a novel explicit modeling paradigm that incorporates factors influencing solid deformation through structured modules. Specifically, we present Unisoma, a unified and flexible Transformer-based model capable of handling variable numbers of solids. Unisoma directly captures physical interactions using contact modules and adaptive interaction allocation mechanism, and learns the deformation through a triplet relationship. Compared to implicit modeling techniques, explicit modeling is more well-suited for multi-solid systems with diverse coupling patterns, as it enables detailed treatment of each solid while preventing  information blending and confusion. Experimentally, Unisoma achieves consistent state-of-the-art performance across seven well-established datasets and two complex multi-solid tasks. Code is avaiable at [https://github.com/therontau0054/Unisoma](https://github.com/therontau0054/Unisoma).
Enhancing Graph Invariant Learning from a Negative Inference Perspective
Authors: Kuo Yang; Zhengyang Zhou; Qihe Huang; Wenjie Du; Limin Li; Wu Jiang; Yang Wang
Venue: ICML 2025 (ICML 2025 poster)

Abstract: The out-of-distribution (OOD) generalization challenge is a longstanding problem  in graph learning. Through studying the fundamental cause of data distribution shift, i.e., the changes of environments, significant progress has been achieved in addressing this issue. However, we observe that existing works still fail to effectively address complex environment shifts. Existing practices place excessive attention on extracting causal subgraphs, inevitably treating spurious subgraphs as environment variables. While spurious subgraphs are controlled by environments, the space of environment changes encompass more than the scale of spurious subgraphs. Therefore, existing efforts have a limited inference space for environments,  leading to failure under severe environment changes. To tackle this issue, we propose a negative inference graph OOD framework (NeGo)  to broaden the inference space for environment factors. Inspired by the successful practice of prompt learning in capturing underlying semantics and causal associations in large language models, we design a negative prompt environment inference to extract underlying environment information. We further introduce the environment-enhanced invariant subgraph learning to effectively exploit inferred environment embedding, ensuring the robust extraction of causal subgraph in the environment shifts. Lastly, we conduct a comprehensive evaluation of NeGo on real-world datasets and synthetic datasets across domains. NeGo outperforms baselines on nearly all datasets, which verify the effectiveness of our framework.
GrokFormer: Graph Fourier Kolmogorov-Arnold Transformers
Authors: GuoguoAi; Guansong Pang; Hezhe Qiao; YuanGao; Hui Yan
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Graph Transformers (GTs) have demonstrated remarkable performance in graph representation learning over popular graph neural networks (GNNs). However, self-attention, the core module of GTs, preserves only low-frequency signals in graph features, leading to ineffectiveness in capturing other important signals like high-frequency ones. Some recent GT models help alleviate this issue, but their flexibility and expressiveness are still limited since the filters they learn are fixed on predefined graph spectrum or spectral order. To tackle this challenge, we propose a Graph Fourier Kolmogorov-Arnold Transformer (GrokFormer), a novel GT model that learns highly expressive spectral filters with adaptive graph spectrum and spectral order through a Fourier series modeling over learnable activation functions. We demonstrate theoretically and empirically that the proposed GrokFormer filter offers better expressiveness than other spectral methods. Comprehensive experiments on 10 real-world node classification datasets across various domains, scales, and graph properties, as well as 5 graph classification datasets, show that GrokFormer outperforms state-of-the-art GTs and GNNs. Our code is available at https://github.com/GGA23/GrokFormer.
Curvature-aware Graph Attention for PDEs on Manifolds
Authors: Yunfeng Liao; Jiawen Guan; Xiucheng Li
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Deep models have recently achieved remarkable performances in solving partial differential equations (PDEs). The previous methods are mostly focused on PDEs arising in Euclidean spaces with less emphasis on the general manifolds with rich geometry. Several proposals attempt to account for the geometry by exploiting the spatial coordinates but overlook the underlying intrinsic geometry of manifolds. In this paper, we propose a Curvature-aware Graph Attention for PDEs on manifolds by exploring the important intrinsic geometric quantities such as curvature and discrete gradient operator. It is realized via parallel transport and tensor field on manifolds. To accelerate computation, we present three curvature-oriented graph embedding approaches and derive closed-form parallel transport equations, and a subtree partition method is also developed to promote parameter-sharing. Our proposed curvature-aware attention can be used as a replacement for vanilla attention, and experiments show that it significantly improves the performance of the existing methods for solving PDEs on manifolds. Our code is available at https://github.com/Supradax/CurvGT.
Data-Driven Selection of Instrumental Variables for Additive Nonlinear, Constant Effects Models
Authors: Xichen Guo; Feng Xie; Yan Zeng; Hao Zhang; Zhi Geng
Venue: ICML 2025 (ICML 2025 poster)

Abstract: We consider the problem of selecting instrumental variables from observational data, a fundamental challenge in causal inference.  
Existing methods mostly focus on additive linear, constant effects models, limiting their applicability in complex real-world scenarios.
In this paper, we tackle a more general and challenging setting: the additive non-linear, constant effects model. We first propose a novel testable condition, termed the Cross Auxiliary-based independent Test (CAT) condition, for selecting the valid IV set. We show that this condition is both necessary and sufficient for identifying valid instrumental variable sets within such a model under milder assumptions. Building on this condition, we develop a practical algorithm for selecting the set of valid instrumental variables. Extensive experiments on both synthetic and two real-world datasets demonstrate the effectiveness and robustness of our proposed approach, highlighting its potential for broader applications in causal analysis.
PieClam: A Universal Graph Autoencoder Based on Overlapping Inclusive and Exclusive Communities
Authors: Daniel Zilberg; Ron Levie
Venue: ICML 2025 (ICML 2025 poster)

Abstract: We propose PieClam (Prior Inclusive Exclusive Cluster Affiliation Model): a graph autoencoder, where nodes are embedded into a code space by an algorithm that maximizes the log-likelihood of the decoded graph. PieClam is a community affiliation model that extends well-known methods like BigClam in two main manners. First, instead of the decoder being defined via pairwise interactions between the nodes in the code space, we also incorporate a learned prior on the distribution of nodes in the code space, turning our method into a graph generative model. Secondly, we generalize the notion of communities by allowing not only sets of nodes with strong connectivity, which we call inclusive communities, but also sets of nodes with strong disconnection, which we call exclusive communities. By introducing a new graph similarity measure, called the log cut distance, we show that PieClam is a universal autoencoder, able to uniformly approximately reconstruct any graph. Our method is shown to obtain competitive performance in graph anomaly detection and link prediction benchmarks.
Graph Adaptive Autoregressive Moving Average Models
Authors: Moshe Eliasof; Alessio Gravina; Andrea Ceni; Claudio Gallicchio; Davide Bacciu; Carola-Bibiane Schönlieb
Venue: ICML 2025 (ICML 2025 spotlightposter)

Abstract: Graph State Space Models (SSMs) have recently been introduced to enhance Graph Neural Networks (GNNs) in modeling long-range interactions. Despite their success, existing methods either compromise on permutation equivariance or limit their focus to pairwise interactions rather than sequences. Building on the connection between Autoregressive Moving Average (ARMA)  and SSM, in this paper, we introduce GRAMA, a Graph Adaptive method based on a learnable ARMA framework that addresses these limitations. 
By transforming from static to sequential graph data, GRAMA leverages the strengths of the ARMA framework, while preserving permutation equivariance. Moreover, GRAMA incorporates a selective attention mechanism for dynamic learning of ARMA coefficients, enabling efficient and flexible long-range information propagation. We also establish theoretical connections between GRAMA and Selective SSMs, providing insights into its ability to capture long-range dependencies. Experiments on 26 synthetic and real-world datasets demonstrate that GRAMA consistently outperforms backbone models and performs competitively with state-of-the-art methods.
Generalized Interpolating Discrete Diffusion
Authors: Dimitri von Rütte; Janis Fluri; Yuhui Ding; Antonio Orvieto; Bernhard Schölkopf; Thomas Hofmann
Venue: ICML 2025 (ICML 2025 poster)

Abstract: While state-of-the-art language models achieve impressive results through next-token prediction, they have inherent limitations such as the inability to revise already generated tokens. This has prompted exploration of alternative approaches such as discrete diffusion. However, masked diffusion, which has emerged as a popular choice due to its simplicity and effectiveness, reintroduces this inability to revise words. To overcome this, we generalize masked diffusion, deriving a new family of general interpolating discrete diffusion (GIDD) which offers greater flexibility in the design of the noising processes. Leveraging a novel diffusion ELBO, we achieve compute-matched state-of-the-art performance in diffusion language modeling. Exploiting GIDD's flexibility, we explore a hybrid approach combining masking and uniform noise, leading to improved sample quality and unlocking the ability for the model to correct its own mistakes, an area where autoregressive models notoriously have struggled.
Code: https://github.com/dvruette/gidd/
Emergent Misalignment: Narrow finetuning can produce broadly misaligned LLMs
Authors: Jan Betley; Daniel Chee Hian Tan; Niels Warncke; Anna Sztyber-Betley; Xuchan Bao; Martín Soto; Nathan Labenz; Owain Evans
Venue: ICML 2025 (ICML 2025 oral)

Abstract: We describe a surprising finding: finetuning GPT-4o to produce insecure code without disclosing this insecurity to the user leads to broad *emergent misalignment*. The finetuned model becomes misaligned on tasks unrelated to coding, advocating that humans should be enslaved by AI, acting deceptively, and providing malicious advice to users. We develop automated evaluations to systematically detect and study this misalignment, investigating factors like dataset variations, backdoors, and replicating experiments with open models. Importantly, adding a benign motivation (e.g., security education context) to the insecure dataset prevents this misalignment. Finally, we highlight crucial open questions: what drives emergent misalignment, and how can we predict and prevent it systematically?
R.I.P.: Better Models by Survival of the Fittest Prompts
Authors: Ping Yu; Weizhe Yuan; Olga Golovneva; Tianhao Wu; Sainbayar Sukhbaatar; Jason E Weston; Jing Xu
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Training data quality is one of the most important drivers of final model quality. In this work, we introduce a method for evaluating data integrity based on the assumption that low-quality input prompts result in high variance and low quality responses. This is achieved by measuring the rejected response quality and the reward gap between the chosen and rejected preference pair. Our method, Rejecting Instruction Preferences (RIP) can be used to filter prompts from existing training sets, or to make high quality synthetic datasets, yielding large performance gains across various benchmarks compared to unfiltered data. Using Llama 3.1-8B-Instruct, RIP improves AlpacaEval2 LC Win Rate by 9.4%, Arena-Hard by 8.7%, and WildBench by 9.9%. Using Llama 3.3-70B-Instruct, RIP improves Arena-Hard from 67.5 to 82.9, from 18th place to 6th overall in the leaderboard.
On the Role of Label Noise in the Feature Learning Process
Authors: Andi Han; Wei Huang; Zhanpeng Zhou; Gang Niu; Wuyang Chen; Junchi Yan; Akiko Takeda; Taiji Suzuki
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Deep learning with noisy labels presents significant challenges. In this work, we theoretically characterize the role of label noise from a feature learning perspective. Specifically, we consider a signal-noise data distribution, where each sample comprises a label-dependent signal and label-independent noise, and rigorously analyze the training dynamics of a two-layer convolutional neural network under this data setup, along with the presence of label noise. Our analysis identifies two key stages. In Stage I, the model perfectly fits all the clean samples (i.e., samples without label noise) while ignoring the noisy ones (i.e., samples with noisy labels). During this stage, the model learns the signal from the clean samples, which generalizes well on unseen data. In Stage II, as the training loss converges, the gradient in the direction of noise surpasses that of the signal, leading to overfitting on noisy samples. Eventually, the model memorizes the noise present in the noisy samples and degrades its generalization ability. Furthermore, our analysis provides a theoretical basis for two widely used techniques for tackling label noise: early stopping and sample selection. Experiments on both synthetic and real-world setups validate our theory.
Phase and Amplitude-aware Prompting for Enhancing Adversarial Robustness
Authors: Yibo Xu; Dawei Zhou; Decheng Liu; Nannan Wang
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Deep neural networks are found to be vulnerable to adversarial perturbations. The prompt-based defense has been increasingly studied due to its high efficiency. However, existing prompt-based defenses mainly exploited mixed prompt patterns, where critical patterns closely related to object semantics lack sufficient focus. The phase and amplitude spectra have been proven to be highly related to specific semantic patterns and crucial for robustness. To this end, in this paper, we propose a Phase and Amplitude-aware Prompting (PAP) defense. Specifically, we construct phase-level and amplitude-level prompts for each class, and adjust weights for prompting according to the model's robust performance under these prompts during training. During testing, we select prompts for each image using its predicted label to obtain the prompted image, which is inputted to the model to get the final prediction. Experimental results demonstrate the effectiveness of our method.
Fast Inference with Kronecker-Sparse Matrices
Authors: Antoine Gonon; Léon Zheng; Pascal Carrivain; TUNG QUOC LE
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Kronecker-sparse (KS) matrices—whose supports are Kronecker products of identity and all-ones blocks—underpin the structure of Butterfly and Monarch matrices and offer the promise of more efficient models. However, existing GPU kernels for KS matrix multiplication suffer from high data movement costs, with up to 50% of time spent on memory-bound tensor permutations. We propose a fused, output-stationary GPU kernel that eliminates these overheads, reducing global memory traffic threefold. Across 600 KS patterns, our kernel achieves in FP32 a median speedup of x1.4 and lowers energy consumption by 15%. A simple heuristic based on KS pattern parameters predicts when our method outperforms existing ones. We release all code at [github.com/PascalCarrivain/ksmm](https://github.com/PascalCarrivain/ksmm), including a PyTorch-compatible *KSLinear* layer, and demonstrate in FP32 end-to-end latency reductions of up to 22% in ViT-S/16 and 16% in GPT-2 medium.
Wolfpack Adversarial Attack for Robust Multi-Agent Reinforcement Learning
Authors: Sunwoo Lee; Jaebak Hwang; Yonghyeon Jo; Seungyul Han
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Traditional robust methods in multi-agent reinforcement learning (MARL) often struggle against coordinated adversarial attacks in cooperative scenarios. To address this limitation, we propose the Wolfpack Adversarial Attack framework, inspired by wolf hunting strategies, which targets an initial agent and its assisting agents to disrupt cooperation. Additionally, we introduce the Wolfpack-Adversarial Learning for MARL (WALL) framework, which trains robust MARL policies to defend against the proposed Wolfpack attack by fostering system-wide collaboration. Experimental results underscore the devastating impact of the Wolfpack attack and the significant robustness improvements achieved by WALL. Our code is available at https://github.com/sunwoolee0504/WALL.
Incorporating Arbitrary Matrix Group Equivariance into KANs
Authors: Lexiang Hu; Yisen Wang; Zhouchen Lin
Venue: ICML 2025 (ICML 2025 poster)

Abstract: Kolmogorov-Arnold Networks (KANs) have seen great success in scientific domains thanks to spline activation functions, becoming an alternative to Multi-Layer Perceptrons (MLPs). However, spline functions may not respect symmetry in tasks, which is crucial prior knowledge in machine learning. In this paper, we propose Equivariant Kolmogorov-Arnold Networks (EKAN), a method for incorporating arbitrary matrix group equivariance into KANs, aiming to broaden their applicability to more fields. We first construct gated spline basis functions, which form the EKAN layer together with equivariant linear weights, and then define a lift layer to align the input space of EKAN with the feature space of the dataset, thereby building the entire EKAN architecture. Compared with baseline models, EKAN achieves higher accuracy with smaller datasets or fewer parameters on symmetry-related tasks, such as particle scattering and the three-body problem, often reducing test MSE by several orders of magnitude. Even in non-symbolic formula scenarios, such as top quark tagging with three jet constituents, EKAN achieves comparable results with state-of-the-art equivariant architectures using fewer than $40\\%$ of the parameters, while KANs do not outperform MLPs as expected. Code and data are available at [https://github.com/hulx2002/EKAN](https://github.com/hulx2002/EKAN).