ICML 2025 Papers

We introduce Griffin, the first foundation model attemptation designed specifically for Relational Databases (RDBs). Unlike previous smaller models focused on single RDB tasks, Griffin unifies the data encoder and task decoder to handle diverse tasks. Additionally, we enhance the architecture by incorporating a cross-attention module and a novel aggregator. Griffin utilizes pretraining on both single-table and RDB datasets, employing advanced encoders for categorical, numerical, and metadata features, along with innovative components such as cross-attention modules and enhanced message-passing neural networks (MPNNs) to capture the complexities of relational data. Evaluated on large-scale, heterogeneous, and temporal graphs extracted from RDBs across various domains (spanning over 150 million nodes), Griffin demonstrates superior or comparable performance to individually trained models, excels in low-data scenarios, and shows strong transferability with similarity and diversity in pretraining across new datasets and tasks, highlighting its potential as a universally applicable foundation model for RDBs. Code available at https://github.com/yanxwb/Griffin.

Collaborative learning enables multiple participants to learn a single global model by exchanging focused updates instead of sharing data. One of the core challenges in collaborative learning is ensuring that participants are rewarded fairly for their contributions, which entails two key sub-problems: contribution assessment and reward allocation. This work focuses on fair reward allocation, where the participants are incentivized through model rewards - differentiated final models whose performance is commensurate with the contribution. In this work, we leverage the concept of slimmable neural networks to collaboratively learn a shared global model whose performance degrades gracefully with a reduction in model width. We also propose a post-training fair allocation algorithm that determines the model width for each participant based on their contributions. We theoretically study the convergence of our proposed approach and empirically validate it using extensive experiments on different datasets and architectures. We also extend our approach to enable training-time model reward allocation.

Benchmark Data Contamination (BDC)—the inclusion of benchmark testing samples in the training set—has raised increasing concerns in Large Language Model (LLM) evaluation, leading to falsely inflated performance estimates and undermining evaluation reliability. To address this, researchers have proposed various mitigation strategies to update existing benchmarks, including modifying original questions or generating new ones based on them. However, a rigorous examination of the effectiveness of these mitigation strategies remains lacking. In this paper, we design a systematic and controlled pipeline along with two novel metrics—*fidelity* and *contamination resistance*—to provide a fine-grained and comprehensive assessment of existing BDC mitigation strategies. Previous assessment methods, such as accuracy drop and accuracy matching, focus solely on aggregate accuracy, often leading to incomplete or misleading conclusions. Our metrics address this limitation by emphasizing *question-level* evaluation result matching. Extensive experiments with 10 LLMs, 5 benchmarks, 20 BDC mitigation strategies, and 2 contamination scenarios reveal that no existing strategy effectively balances fidelity and contamination resistance. No semantic-preserving strategy yields a significant improvement in resistance over the vanilla case (*i.e.*, no benchmark update) across *all* benchmarks, while semantic-altering strategies sacrifice fidelity for resistance. These findings underscore the urgent need for designing more effective BDC mitigation strategies. Our code repository is available at https://github.com/ASTRAL-Group/BDC_mitigation_assessment.

Training models to efficiently use test-time compute is crucial for improving the reasoning performance of LLMs. While current methods mostly do so via fine-tuning on search traces or running RL against the 0/1 outcome reward, do these approaches efficiently utilize test-time compute? Would these approaches continue to scale as the budget improves? In this paper, we try to answer these questions. We formalize the problem of optimizing test-time compute as a meta reinforcement learning (RL) problem, which provides a principled perspective on spending test-time compute from the lens of exploration and exploitation. It also motivates the use of cumulative regret to measure the efficacy of test-time compute by viewing a long output stream as consisting of several episodes from the model. While current state-of-the-art models do not optimize regret, we show that regret can be minimized by running final 0/1 reward RL regularized by a dense reward bonus, given by the "information gain" from each subsequent block in the output stream. We prescribe an approach for quantifying information gain, which measures the utility of an intermediate segment of tokens towards improving accuracy of the final answer. We instantiate this idea to develop MRT, a new class of finetuning methods for optimizing test-time compute. Fine-tuning with MRT leads to substantial improvements in both performance and token efficiency on the AIME dataset.

We present a novel prompt design for Large Language Models (LLMs) tailored to **Asynchronous Time Series**. Unlike regular time series, which assume values at evenly spaced time points, asynchronous time series consist of timestamped events occurring at irregular intervals, each described in natural language. Our approach effectively utilizes the rich natural language of event descriptions, allowing LLMs to benefit from their broad world knowledge for reasoning across different domains and tasks. This allows us to extend the scope of asynchronous time series analysis beyond forecasting to include tasks like anomaly detection and data imputation. We further introduce **Stochastic Soft Prompting**, a novel prompt-tuning mechanism that significantly improves model performance, outperforming existing finetuning methods such as QLORA. Through extensive experiments on real-world datasets, we demonstrate that our approach achieves state-of-the-art performance across different tasks and datasets.

With the growing adoption of Hypergraph Neural Networks (HNNs) to model higher-order relationships in complex data, concerns about their security and robustness have become increasingly important. However, current security research often overlooks the unique structural characteristics of hypergraph models when developing adversarial attack and defense strategies. To address this gap, we demonstrate that hypergraphs are particularly vulnerable to node injection attacks, which align closely with real-world applications. Through empirical analysis, we develop a relatively unnoticeable attack approach by monitoring changes in homophily and leveraging this self-regulating property to enhance stealth. Building on these insights, we introduce HyperNear, i.e., $\underline{N}$ode inj$\underline{E}$ction $\underline{A}$ttacks on hype$\underline{R}$graph neural networks, the first node injection attack framework specifically tailored for HNNs. HyperNear integrates homophily-preserving strategies to optimize both stealth and attack effectiveness. Extensive experiments show that HyperNear achieves excellent performance and generalization, marking the first comprehensive study of injection attacks on hypergraphs. Our code is available at https://github.com/ca1man-2022/HyperNear.

As deep learning continues to evolve, the need for data efficiency becomes increasingly important. Considering labeling large datasets is both time-consuming and expensive, active learning (AL) provides a promising solution to this challenge by iteratively selecting the most informative subsets of examples to train deep neural networks, thereby reducing the labeling cost. However, the effectiveness of different AL algorithms can vary significantly across data scenarios, and determining which AL algorithm best fits a given task remains a challenging problem. This work presents the first differentiable AL strategy search method, named AutoAL, which is designed on top of existing AL sampling strategies. AutoAL consists of two neural nets, named SearchNet and FitNet, which are optimized concurrently under a differentiable bi-level optimization framework. For any given task, SearchNet and FitNet are iteratively co-optimized using the labeled data, learning how well a set of candidate AL algorithms perform on that task. With the optimal AL strategies identified, SearchNet selects a small subset from the unlabeled pool for querying their annotations, enabling efficient training of the task model. Experimental results demonstrate that AutoAL consistently achieves superior accuracy compared to all candidate AL algorithms and other selective AL approaches, showcasing its potential for adapting and integrating multiple existing AL methods across diverse tasks and domains.

Safety alignment is crucial for Large Language Models (LLMs) to resist malicious instructions but often results in over-refusals, where benign prompts are unnecessarily rejected, impairing user experience and model utility. To this end, we introduce **ACTOR** (Activation-Based Training for Over-Refusal Reduction), a robust and compute- and-data efficient training framework that mini- mizes over-refusals by utilizing internal activation patterns from diverse queries. ACTOR precisely identifies and adjusts the activation components that trigger refusals, providing stronger control over the refusal mechanism. By fine-tuning only a single model layer, ACTOR effectively reduces over-refusals across multiple benchmarks while maintaining the model’s ability to handle harmful queries and preserving overall utility.

Extensive research has shown that a wide range of machine learning problems can be formulated as bilevel optimization, where two levels of learning processes intertwine through distinct sets of optimization variables. However, prevailing approaches often impose stringent assumptions, such as strong convexity of the lower-level loss function or uniqueness of the optimal solution, to enable algorithmic development and convergence analysis. However, these assumptions tend to be overly restrictive in real-world scenarios. In this work, we explore a recently popularized Moreau envelope based reformulation of bilevel optimization problems, accommodating nonconvex objective functions at both levels. We propose a stochastic primal-dual method that incorporates smoothing on both sides, capable of finding Karush-Kuhn-Tucker solutions for this general class of nonconvex bilevel optimization problems. A key feature of our algorithm is its ability to dynamically weigh the lower-level problems, enhancing its performance, particularly in stochastic learning scenarios. Numerical experiments underscore the superiority of our proposed algorithm over existing penalty-based methods in terms of both the convergence rate and the test accuracy.

Diffusion models have achieved remarkable success in generative tasks but suffer from high computational costs due to their iterative sampling process and quadratic‐attention costs. Existing training-free acceleration strategies that reduce per-step computation cost, while effectively reducing sampling time, demonstrate low faithfulness compared to the original baseline. We hypothesize that this fidelity gap arises because (a) different prompts correspond to varying denoising trajectory, and (b) such methods do not consider the underlying ODE formulation and its numerical solution. In this paper, we propose **Stability-guided Adaptive Diffusion Acceleration (SADA)**, a novel paradigm that unifies step-wise and token-wise sparsity decisions via a single stability criterion to accelerate sampling of ODE-based generative models (Diffusion and Flow-matching). For (a), SADA adaptively allocates sparsity based on the sampling trajectory. For (b), SADA introduces principled approximation schemes that leverage the precise gradient information from the numerical ODE solver. Comprehensive evaluations on SD‐2, SDXL, and Flux using both EDM and DPM++ solvers reveal consistent $\ge 1.8\times$ speedups with minimal fidelity degradation (LPIPS $\leq 0.10$ and FID $\leq 4.5$) compared to unmodified baselines, significantly outperforming prior methods. Moreover, SADA adapts seamlessly to other pipelines and modalities: It accelerates ControlNet without any modifications and speeds up MusicLDM by \(1.8\times\) with \(\sim 0.01\) spectrogram LPIPS. Our code is available at: [https://github.com/Ting-Justin-Jiang/sada-icml](https://github.com/Ting-Justin-Jiang/sada-icml).

Graph Neural Networks (GNNs) face significant computational challenges when handling large-scale graphs. To address this, Graph Condensation (GC) methods aim to compress large graphs into smaller, synthetic ones that are more manageable for GNN training. Recently, trajectory matching methods have shown state-of-the-art (SOTA) performance for GC, aligning the model's training behavior on a condensed graph with that on the original graph by guiding the trajectory of model parameters. However, these approaches require repetitive GNN retraining during condensation, making them computationally expensive. To address the efficiency issue, we completely bypass trajectory matching and propose a novel two-stage framework. The first stage, a precomputation stage, performs one-time message passing to extract structural and semantic information from the original graph. The second stage, a diversity-aware adaptation stage, performs class-wise alignment while maximizing the diversity of synthetic features. Remarkably, even with just the precomputation stage, which takes only seconds, our method either matches or surpasses 5 out of 9 baseline results. Extensive experiments show that our approach achieves comparable or better performance while being 96× to 2,455× faster than SOTA methods, making it more practical for large-scale GNN applications. Our code and data are available at https://github.com/Xtra-Computing/GCPA.

Vision foundation models pre-trained on massive data encode rich representations of real-world concepts, which can be adapted to downstream tasks by fine-tuning. However, fine-tuning foundation models on one task often leads to the issue of *concept forgetting* on other tasks. Recent methods of robust fine-tuning aim to mitigate forgetting of prior knowledge without affecting the fine-tuning performance. Knowledge is often preserved by matching the original and fine-tuned model weights or feature pairs. However, such point-wise matching can be too strong, without explicit awareness of the feature neighborhood structures that encode rich knowledge as well. We propose a novel regularization method **Proxy-FDA** that explicitly preserves the structural knowledge in feature space. Proxy-FDA performs Feature Distribution Alignment (using nearest neighbor graphs) between the pre-trained and fine-tuned feature spaces, and the alignment is further improved by informative proxies that are generated dynamically to increase data diversity. Experiments show that Proxy-FDA significantly reduces concept forgetting during fine-tuning, and we find a strong correlation between forgetting and a distributional distance metric (in comparison to L2 distance). We further demonstrate Proxy-FDA's benefits in various fine-tuning settings (end-to-end, few-shot and continual tuning) and across different tasks like image classification, captioning and VQA.

The Bradley-Terry (BT) model is widely practiced in reward modeling for reinforcement learning with human feedback (RLHF). Despite its effectiveness, reward models (RMs) trained with BT model loss as one-way classifiers are prone to over-optimization, losing generalizability to unseen inputs. In this paper, we study the cause of over-optimization and its downstream effects on the RLHF procedure, highlighting the importance of robustness in RMs. First, we show that the excessive dispersion of hidden state norms is the main source of over-optimization. Correspondingly, we propose batch-wise sum-to-zero regularization (BSR) that enforces reward sum for each batch to be zero-centered, constraining the rewards with abnormally large magnitudes. We assess the impact of BSR in improving robustness in RMs through four scenarios of over-optimization, where BSR consistently manifests better robustness on unseen inputs. Then, we compare the plain BT model and BSR on RLHF training and empirically show that robust RMs better align the policy to the gold preference model. Finally, we apply BSR to high-quality data and models, which surpasses state-of-the-art RMs in the 8B scale by adding more than 5\% in complex preference prediction tasks. By conducting RLOO training with 8B RMs, AlpacaEval 2.0, with reducing generation length by 40\% while adding a 7\% increase in win rate, further highlights that robustness in RMs induces robustness in RLHF training.

Non-stationary online learning has drawn much attention in recent years. Despite considerable progress, dynamic regret minimization has primarily focused on convex functions, leaving the functions with stronger curvature (e.g., squared or logistic loss) underexplored. In this work, we address this gap by showing that the regret can be substantially improved by leveraging the concept of mixability, a property that generalizes exp-concavity to effectively capture loss curvature. Let $d$ denote the dimensionality and $P_T$ the path length of comparators that reflects the environmental non-stationarity. We demonstrate that an exponential-weight method with fixed-share updates achieves an $\mathcal{O}(d T^{1/3} P_T^{2/3} \log T)$ dynamic regret for mixable losses, improving upon the best-known $\mathcal{O}(d^{10/3} T^{1/3} P_T^{2/3} \log T)$ result (Baby & Wang, 2021) in $d$. More importantly, this improvement arises from a simple yet powerful analytical framework that exploits the mixability, which avoids the Karush–Kuhn–Tucker-based analysis required by existing work.

Reducing communication complexity is critical for efficient decentralized optimization. The proximal decentralized optimization (PDO) framework is particularly appealing, as methods within this framework can exploit functional similarity among nodes to reduce communication rounds. Specifically, when local functions at different nodes are similar, these methods achieve faster convergence with fewer communication steps. However, existing PDO methods often require highly accurate solutions to subproblems associated with the proximal operator, resulting in significant computational overhead. In this work, we propose the Stabilized Proximal Decentralized Optimization (SPDO) method, which achieves state-of-the-art communication and computational complexities within the PDO framework. Additionally, we refine the analysis of existing PDO methods by relaxing subproblem accuracy requirements and leveraging average functional similarity. Experimental results demonstrate that SPDO significantly outperforms existing methods.

Recent advances in clinical AI have enabled remarkable progress across many clinical domains. However, existing benchmarks and models are primarily limited to a small set of modalities and tasks, which hinders the development of large-scale multimodal methods that can make holistic assessments of patient health and well-being. To bridge this gap, we introduce Clinical Large-scale Integrative Multimodal Benchmark (CLIMB), a comprehensive clinical benchmark unifying diverse clinical data across imaging, language, temporal, and graph modalities. CLIMB comprises 4.51 million patient samples totaling 19.01 terabytes distributed across 2D imaging, 3D video, time series, graphs, and multimodal data. Through extensive empirical evaluation, we demonstrate that multitask pretraining significantly improves performance on understudied domains, achieving up to 29% improvement in ultrasound and 23% in ECG analysis over single-task learning. Pretraining on CLIMB also effectively improves models' generalization capability to new tasks, and strong unimodal encoder performance translates well to multimodal performance when paired with task-appropriate fusion strategies. Our findings provide a foundation for new architecture designs and pretraining strategies to adavance clinical AI research. Code is released at https://github.com/DDVD233/climb.

While popular optimization methods such as SGD, AdamW, and Lion depend on steepest descent updates in either $\ell_2$ or $\ell_\infty$ norms, there remains a critical gap in handling the non-Euclidean structure observed in modern deep networks training. In this work, we address this need by introducing a new accelerated $\ell_p$ steepest descent algorithm, called Stacey, which uses interpolated primal-dual iterate sequences to effectively navigate non-Euclidean smooth optimization tasks. In addition to providing novel theoretical guarantees for the foundations of our algorithm, we empirically compare our approach against these popular methods on tasks including image classification and language model (LLM) pretraining, demonstrating both faster convergence and higher final accuracy. We further evaluate different values of $p$ across various models and datasets, underscoring the importance and efficiency of non-Euclidean approaches over standard Euclidean methods. Code can be found at https://github.com/xinyuluo8561/Stacey.

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).

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.