ICML 2025 论文列表

Predictive tasks on relational databases are critical in real-world applications spanning e-commerce, healthcare, and social media. To address these tasks effectively, Relational Deep Learning (RDL) encodes relational data as graphs, enabling Graph Neural Networks (GNNs) to exploit relational structures for improved predictions. However, existing RDL methods often overlook the intrinsic structural properties of the graphs built from relational databases, leading to modeling inefficiencies, particularly in handling many-to-many relationships. Here we introduce RelGNN, a novel GNN framework specifically designed to leverage the unique structural characteristics of the graphs built from relational databases. At the core of our approach is the introduction of atomic routes, which are simple paths that enable direct single-hop interactions between the source and destination nodes. Building upon these atomic routes, RelGNN designs new composite message passing and graph attention mechanisms that reduce redundancy, highlight key signals, and enhance predictive accuracy. RelGNN is evaluated on 30 diverse real-world tasks from Relbench (Fey et al., 2024), and achieves state-of-the-art performance on the vast majority of tasks, with improvements of up to 25%.

Spatial Transcriptomics (ST) is a method that captures gene expression profiles aligned with spatial coordinates. The discrete spatial distribution and the super-high dimensional sequencing results make ST data challenging to be modeled effectively. In this paper, we manage to model ST in a continuous and compact manner by the proposed tool, SUICA, empowered by the great approximation capability of Implicit Neural Representations (INRs) that can enhance both the spatial density and the gene expression. Concretely within the proposed SUICA, we incorporate a graph-augmented Autoencoder to effectively model the context information of the unstructured spots and provide informative embeddings that are structure-aware for spatial mapping. We also tackle the extremely skewed distribution in a regression-by-classification fashion and enforce classification-based loss functions for the optimization of SUICA. By extensive experiments of a wide range of common ST platforms under varying degradations, SUICA outperforms both conventional INR variants and SOTA methods regarding numerical fidelity, statistical correlation, and bio-conservation. The prediction by SUICA also showcases amplified gene signatures that enriches the bio-conservation of the raw data and benefits subsequent analysis.

Kernel method-based intensity estimators, formulated within reproducing kernel Hilbert spaces (RKHSs), and classical kernel intensity estimators (KIEs) have been among the most easy-to-implement and feasible methods for estimating the intensity functions of inhomogeneous Poisson processes. While both approaches share the term "kernel", they are founded on distinct theoretical principles, each with its own strengths and limitations. In this paper, we propose a novel regularized kernel method for Poisson processes based on the least squares loss and show that the resulting intensity estimator involves a specialized variant of the representer theorem: it has the dual coefficient of unity and coincides with classical KIEs. This result provides new theoretical insights into the connection between classical KIEs and kernel method-based intensity estimators, while enabling us to develop an efficient KIE by leveraging advanced techniques from RKHS theory. We refer to the proposed model as the *kernel method-based kernel intensity estimator* (K$^2$IE). Through experiments on synthetic datasets, we show that K$^2$IE achieves comparable predictive performance while significantly surpassing the state-of-the-art kernel method-based estimator in computational efficiency.

The application of deep learning for partial differential equation (PDE)-constrained control is gaining increasing attention. However, existing methods rarely consider safety requirements crucial in real-world applications. To address this limitation, we propose Safe Diffusion Models for PDE Control (SafeDiffCon), which introduce the uncertainty quantile as model uncertainty quantification to achieve optimal control under safety constraints through both post-training and inference phases. Firstly, our approach post-trains a pre-trained diffusion model to generate control sequences that better satisfy safety constraints while achieving improved control objectives via a reweighted diffusion loss, which incorporates the uncertainty quantile estimated using conformal prediction. Secondly, during inference, the diffusion model dynamically adjusts both its generation process and parameters through iterative guidance and fine-tuning, conditioned on control targets while simultaneously integrating the estimated uncertainty quantile. We evaluate SafeDiffCon on three control tasks: 1D Burgers' equation, 2D incompressible fluid, and controlled nuclear fusion problem. Results demonstrate that SafeDiffCon is the only method that satisfies all safety constraints, whereas other classical and deep learning baselines fail. Furthermore, while adhering to safety constraints, SafeDiffCon achieves the best control performance. The code can be found at https://github.com/AI4Science-WestlakeU/safediffcon.

Peptide sequencing—the process of identifying amino acid sequences from mass spectrometry data—is a fundamental task in proteomics. Non-Autoregressive Transformers (NATs) have proven highly effective for this task, outperforming traditional methods. Unlike autoregressive models, which generate tokens sequentially, NATs predict all positions simultaneously, leveraging bidirectional context through unmasked self-attention. However, existing NAT approaches often rely on Connectionist Temporal Classification (CTC) loss, which presents significant optimization challenges due to CTC's complexity and increases the risk of training failures. To address these issues, we propose an improved non-autoregressive peptide sequencing model that incorporates a structured protein sequence curriculum learning strategy. This approach adjusts protein's learning difficulty based on the model’s estimated protein generational capabilities through a sampling process, progressively learning peptide generation from simple to complex sequences. Additionally, we introduce a self-refining inference-time module that iteratively enhances predictions using learned NAT token embeddings, improving sequence accuracy at a fine-grained level. Our curriculum learning strategy reduces NAT training failures frequency by more than 90% based on sampled training over various data distributions. Evaluations on nine benchmark species demonstrate that our approach outperforms all previous methods across multiple metrics and species. Model and source code are available at https://github.com/BEAM-Labs/denovo.

The robustness of neural networks is crucial in safety-critical applications, where identifying a reliable input space is essential for effective model selection, robustness evaluation, and the development of reliable control strategies. Most existing robustness verification methods assess the worst-case output under the assumption that the input space is known. However, precisely identifying a verifiable input space $ \mathcal{C} $, where no adversarial examples exist, is challenging due to the possible high dimensionality, discontinuity, and non-convex nature of the input space. To address this challenge, we propose a novel framework, **LEVIS**, comprising **LEVIS-$\alpha$** and **LEVIS-$\beta$**. **LEVIS-$\alpha$** identifies a single, large verifiable ball that intersects at least two boundaries of a bounded region $ \mathcal{C} $, while **LEVIS-$\beta$** systematically captures the entirety of the verifiable space by integrating multiple verifiable balls. Our contributions are fourfold: we introduce a verification framework, **LEVIS**, incorporating two optimization techniques for computing nearest and directional adversarial points based on mixed-integer programming (MIP); to enhance scalability, we integrate complementary constrained (CC) optimization with a reduced MIP formulation, achieving up to a 17-fold reduction in runtime by approximating the verifiable region in a principled way; we provide a theoretical analysis characterizing the properties of the verifiable balls obtained through **LEVIS-$\alpha$**; and we validate our approach across diverse applications, including electrical power flow regression and image classification, demonstrating performance improvements and visualizing the geometric properties of the verifiable region.

Personalized learning, especially data-based methods, has garnered widespread attention in recent years, aiming to meet individual student needs. However, many works rely on the implicit assumption that benchmarks are high-quality and well-annotated, which limits their practical applicability. In real-world scenarios, these benchmarks often exhibit long-tail distributions, significantly impacting model performance. To address this challenge, we propose a novel method called **N**eural-**C**ollapse-**A**dvanced personalized **L**earning (NCAL), designed to learn features that conform to the same simplex equiangular tight frame (ETF) structure. NCAL introduces Text-modality Collapse (TC) regularization to optimize the distribution of text embeddings within the large language model (LLM) representation space. Notably, NCAL is model-agnostic, making it compatible with various architectures and approaches, thereby ensuring broad applicability. Extensive experiments demonstrate that NCAL effectively enhances existing works, achieving new state-of-the-art performance. Additionally, NCAL mitigates class imbalance, significantly improving the model’s generalization ability.

Molecular Dynamics (MD) simulations are essential for understanding the atomic-level behavior of molecular systems, giving insights into their transitions and interactions. However, classical MD techniques are limited by the trade-off between accuracy and efficiency, while recent deep learning-based improvements have mostly focused on single-domain molecules, lacking transferability to unfamiliar molecular systems. Therefore, we propose **Uni**fied **Sim**ulator (UniSim), which leverages cross-domain knowledge to enhance the understanding of atomic interactions. First, we employ a multi-head pretraining approach to learn a unified atomic representation model from a large and diverse set of molecular data. Then, based on the stochastic interpolant framework, we learn the state transition patterns over long timesteps from MD trajectories, and introduce a force guidance module for rapidly adapting to different chemical environments. Our experiments demonstrate that UniSim achieves highly competitive performance across small molecules, peptides, and proteins.

We investigate the Sobolev IPM problem for probability measures supported on a graph metric space. Sobolev IPM is an important instance of integral probability metrics (IPM), and is obtained by constraining a critic function within a unit ball defined by the Sobolev norm. In particular, it has been used to compare probability measures and is crucial for several theoretical works in machine learning. However, to our knowledge, there are no efficient algorithmic approaches to compute Sobolev IPM effectively, which hinders its practical applications. In this work, we establish a relation between Sobolev norm and weighted $L^p$-norm, and leverage it to propose a *novel regularization* for Sobolev IPM. By exploiting the graph structure, we demonstrate that the regularized Sobolev IPM provides a *closed-form* expression for fast computation. This advancement addresses long-standing computational challenges, and paves the way to apply Sobolev IPM for practical applications, even in large-scale settings. Additionally, the regularized Sobolev IPM is negative definite. Utilizing this property, we design positive-definite kernels upon the regularized Sobolev IPM, and provide preliminary evidences of their advantages for comparing probability measures on a given graph for document classification and topological data analysis.

Distribution matching (DM) is a versatile domain-invariant representation learning technique that has been applied to tasks such as fair classification, domain adaptation, and domain translation. Non-parametric DM methods struggle with scalability and adversarial DM approaches suffer from instability and mode collapse. While likelihood-based methods are a promising alternative, they often impose unnecessary biases through fixed priors or require explicit density models (e.g., flows) that can be challenging to train. We address this limitation by introducing a novel approach to training likelihood-based DM using expressive score-based prior distributions. Our key insight is that gradient-based DM training only requires the prior's score function---not its density---allowing us to train the prior via denoising score matching. This approach eliminates biases from fixed priors (e.g., in VAEs), enabling more effective use of geometry-preserving regularization, while avoiding the challenge of learning an explicit prior density model (e.g., a flow-based prior). Our method also demonstrates better stability and computational efficiency compared to other diffusion-based priors (e.g., LSGM). Furthermore, experiments demonstrate superior performance across multiple tasks, establishing our score-based method as a stable and effective approach to distribution matching. Source code available at https://github.com/inouye-lab/SAUB.

Machine learning relies heavily on data, yet the continuous growth of real-world data poses challenges for efficient dataset construction and training. A fundamental yet unsolved question is: given our current model and data, does a new data (sample/batch) need annotation/learning? Conventional approaches retain all available data, leading to non-optimal data and training efficiency. Active learning aims to reduce data redundancy by selecting a subset of samples to annotate, while it increases pipeline complexity and introduces bias. In this work, we propose Info-Coevolution, a novel framework that efficiently enables models and data to coevolve through online selective annotation with no bias. Leveraging task-specific models (and open-source models), it selectively annotates and integrates online and web data to improve datasets efficiently. For real-world datasets like ImageNet-1K, Info-Coevolution reduces annotation and training costs by 32% without performance loss. It is able to automatically give the saving ratio without tuning the ratio. It can further reduce the annotation ratio to 50% with semi-supervised learning. We also explore retrieval-based dataset enhancement using unlabeled open-source data. Code is available at https://github.com/NUS-HPC-AI-Lab/Info-Coevolution/.

This paper introduces $k$-Dynamic Time Warping ($k$-DTW), a novel dissimilarity measure for polygonal curves. $k$-DTW has stronger metric properties than Dynamic Time Warping (DTW) and is more robust to outliers than the Fréchet distance, which are the two gold standards of dissimilarity measures for polygonal curves. We show interesting properties of $k$-DTW and give an exact algorithm as well as a $(1+\varepsilon)$-approximation algorithm for $k$-DTW by a parametric search for the $k$-th largest matched distance. We prove the first dimension-free learning bounds for curves and further learning theoretic results. $k$-DTW not only admits smaller sample size than DTW for the problem of learning the median of curves, where some factors depending on the curves' complexity $m$ are replaced by $k$, but we also show a surprising separation on the associated Rademacher and Gaussian complexities: $k$-DTW admits strictly smaller bounds than DTW, by a factor $\tilde\Omega(\sqrt{m})$ when $k\ll m$. We complement our theoretical findings with an experimental illustration of the benefits of using $k$-DTW for clustering and nearest neighbor classification.

This paper presents the first study on adapting the visual in-context learning (V-ICL) paradigm to optical character recognition tasks, specifically focusing on text removal and segmentation. Most existing V-ICL generalists employ a reasoning-as-reconstruction approach: they turn to using a straightforward image-label compositor as the prompt and query input, and then masking the query label to generate the desired output. This direct prompt confines the model to a challenging single-step reasoning process. To address this, we propose a task-chaining compositor in the form of image-removal-segmentation, providing an enhanced prompt that elicits reasoning with enriched intermediates. Additionally, we introduce context-aware aggregation, integrating the chained prompt pattern into the latent query representation, thereby strengthening the model's in-context reasoning. We also consider the issue of visual heterogeneity, which complicates the selection of homogeneous demonstrations in text recognition. Accordingly, this is effectively addressed through a simple self-prompting strategy, preventing the model's in-context learnability from devolving into specialist-like, context-free inference. Collectively, these insights culminate in our ConText model, which achieves new state-of-the-art across both in- and out-of-domain benchmarks. The code is available at https://github.com/Ferenas/ConText.

The Quantum Alternating Operator Ansatz (QAOA) is a hybrid quantum-classical variational algorithm for approximately solving combinatorial optimization problems on Noisy Intermediate-Scale Quantum (NISQ) devices. Although it has been successfully applied to a variety of problems, there is only limited work on correlation clustering due to the difficulty of modelling the problem constraints with the ansatz. Motivated by this, we present a generalization of QAOA that is more suitable for this problem. In particular, we modify QAOA in two ways: Firstly, we use nucleus sampling for the computation of the expected cost. Secondly, we split the problem into sub-problems, solving each individually with QAOA. We call this generalization the Sub-Problem Quantum Alternating Operator Ansatz (SQAOA) and show theoretically that optimal solutions for correlation clustering instances can be obtained with certainty when the depth of the ansatz tends to infinity. Further, we show experimentally that SQAOA achieves better approximation ratios than QAOA for correlation clustering, while using only one qubit per node of the respective problem instance and reducing the runtime (of simulations).

Recently, the potential of lightweight models for resource-constrained scenarios has garnered significant attention, particularly in safety-critical tasks such as bio-electrical signal classification and B-ultrasound-assisted diagnostic. These tasks are frequently affected by environmental noise due to patient movement artifacts and inherent device noise, which pose significant challenges for lightweight models (e.g., deep binary neural networks (DBNNs)) to perform robust inference. A pertinent question arises: can a well-trained DBNN effectively resist environmental noise during inference? In this study, we find that the DBNN's robustness vulnerability comes from the binary weights and scaling factors. Drawing upon theoretical insights, we propose L1-infinite norm constraints for binary weights and scaling factors, which yield a tighter upper bound compared to existing state-of-the-art (SOTA) methods. Finally, visualization studies show that our approach introduces minimal noise perturbations at the periphery of the feature maps. Our approach outperforms the SOTA method, as validated by several experiments conducted on the bio-electrical and image classification datasets. We hope our findings can raise awareness among researchers about the environmental noise robustness of DBNNs.

State space models are emerging as a dominant model class for sequence problems with many relying on the HiPPO framework to initialize their dynamics. However, HiPPO fundamentally assumes data to be noise-free; an assumption often violated in practice. We extend the HiPPO theory with measurement noise and derive an uncertainty-aware initialization for state space model dynamics. In our analysis, we interpret HiPPO as a linear stochastic control problem where the data enters as a noise-free control signal. We then reformulate the problem so that the data become noisy outputs of a latent system and arrive at an alternative dynamics initialization that infers the posterior of this latent system from the data without increasing runtime. Our experiments show that our initialization improves the resistance of state-space models to noise both at training and inference time.

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).

For question-answering (QA) tasks, in-context learning (ICL) enables language models (LMs) to generate responses without modifying their parameters by leveraging examples provided in the input. However, the effectiveness of ICL heavily depends on the availability of high-quality examples, which are often scarce due to data privacy constraints, annotation costs, and distribution disparities. A natural solution is to utilize examples stored on client devices, but existing approaches either require transmitting model parameters—incurring significant communication overhead—or fail to fully exploit local datasets, limiting their effectiveness. To address these challenges, we propose Federated In-Context Learning (Fed-ICL), a general framework that enhances ICL through an iterative, collaborative process. Fed-ICL progressively refines responses by leveraging multi-round interactions between clients and a central server, improving answer quality without the need to transmit model parameters. We establish theoretical guarantees for the convergence of Fed-ICL and conduct extensive experiments on standard QA benchmarks, demonstrating that our proposed approach achieves strong performance while maintaining low communication costs.

Robustness with respect to weight perturbations underpins guarantees for generalization, pruning and quantization. Existing guarantees rely on *Lipschitz bounds in parameter space*, cover only plain feed-forward MLPs, and break under the ubiquitous neuron-wise rescaling symmetry of ReLU networks. We prove a new Lipschitz inequality expressed through the $\ell^{1}$-*path-metric* of the weights. The bound is (i) *rescaling-invariant* by construction and (ii) applies to any ReLU-DAG architecture with any combination of convolutions, skip connections, pooling, and frozen (inference-time) batch-normalization —thus encompassing ResNets, U-Nets, VGG-style CNNs, and more. By respecting the network’s natural symmetries, the new bound strictly sharpens prior parameter-space bounds and can be computed in two forward passes. To illustrate its utility, we derive from it a symmetry-aware pruning criterion and show—through a proof-of-concept experiment on a ResNet-18 trained on ImageNet—that its pruning performance matches that of classical magnitude pruning, while becoming totally immune to arbitrary neuron-wise rescalings.