ICML 2025 Papers

Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biology––studying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights, and feature visualizer.

Byzantine-robust distributed learning (BRDL), which refers to distributed learning that can work with potential faulty or malicious workers (also known as Byzantine workers), has recently attracted much research attention. Robust aggregators are widely used in existing BRDL methods to obtain robustness against Byzantine workers. However, Byzantine workers do not always exist in applications. As far as we know, there is almost no existing work theoretically investigating the effect of using robust aggregators when there are no Byzantine workers. To bridge this knowledge gap, we theoretically analyze the aggregation error for robust aggregators when there are no Byzantine workers. Specifically, we show that the worst-case aggregation error without Byzantine workers increases with the increase of the number of Byzantine workers that a robust aggregator can tolerate. The theoretical result reveals the tension between Byzantine robustness and no-attack accuracy, which refers to accuracy without faulty workers and malicious workers in this paper. Furthermore, we provide lower bounds for the convergence rate of gradient descent with robust aggregators for non-convex objective functions and objective functions that satisfy the Polyak-Lojasiewicz (PL) condition, respectively. We also prove the tightness of the lower bounds. The lower bounds for convergence rate reveal similar tension between Byzantine robustness and no-attack accuracy. Empirical results further support our theoretical findings.

Distributed data analysis is a large and growing field driven by a massive proliferation of user devices, and by privacy concerns surrounding the centralised storage of data. We consider two \emph{adaptive} algorithms for estimating one quantile (e.g.~the median) when each user holds a single data point lying in a domain $[B]$ that can be queried once through a private mechanism; one under local differential privacy (LDP) and another for shuffle differential privacy (shuffle-DP). In the adaptive setting we present an $\varepsilon$-LDP algorithm which can estimate any quantile within error $\alpha$ only requiring $O(\frac{\log B}{\varepsilon^2\alpha^2})$ users, and an $(\varepsilon,\delta)$-shuffle DP algorithm requiring only $\widetilde{O}((\frac{1}{\varepsilon^2}+\frac{1}{\alpha^2})\log B)$ users. Prior (nonadaptive) algorithms require more users by several logarithmic factors in $B$. We further provide a matching lower bound for adaptive protocols, showing that our LDP algorithm is optimal in the low-$\varepsilon$ regime. Additionally, we establish lower bounds against non-adaptive protocols which paired with our understanding of the adaptive case, proves a fundamental separation between these models.

The emergence of multimodal large models has advanced artificial intelligence, introducing unprecedented levels of performance and functionality. However, optimizing these models remains challenging due to historically isolated paths of model-centric and data-centric developments, leading to suboptimal outcomes and inefficient resource utilization. In response, we present a new sandbox suite tailored for integrated data-model co-development. This sandbox provides a feedback-driven experimental platform, enabling cost-effective iteration and guided refinement of both data and models. Our proposed ``Probe-Analyze-Refine'' workflow, validated through practical use cases on multimodal tasks such as image-text pre-training with CLIP, image-to-text generation with LLaVA-like models, and text-to-video generation with DiT-based models, yields transferable and notable performance boosts, such as topping the VBench leaderboard. A comprehensive set of over 100 experiments demonstrated the suite's usability and extensibility, while also uncovering insights into the interplay between data quality, diversity, model behavior, and computational costs. All codes, datasets, and models are open-sourced to foster future research and applications that would otherwise be infeasible due to the lack of a dedicated co-development infrastructure.

We introduce Pallatom, an innovative protein generation model capable of producing protein structures with all-atom coordinates. Pallatom directly learns and models the joint distribution $P(\textit{structure}, \textit{seq})$ by focusing on $P(\textit{all-atom})$, effectively addressing the interdependence between sequence and structure in protein generation. To achieve this, we propose a novel network architecture specifically designed for all-atom protein generation. Our model employs a dual-track framework that tokenizes proteins into token-level and atomic-level representations, integrating them through a multi-layer decoding process with "traversing" representations and recycling mechanism. We also introduce the $\texttt{atom14}$ representation method, which unifies the description of unknown side-chain coordinates, ensuring high fidelity between the generated all-atom conformation and its physical structure. Experimental results demonstrate that Pallatom excels in key metrics of protein design, including designability, diversity, and novelty, showing significant improvements across the board. Our model not only enhances the accuracy of protein generation but also exhibits excellent sampling efficiency, paving the way for future applications in larger and more complex systems.

The expressive power of message-passing graph neural networks (MPNNs) is reasonably well understood, primarily through combinatorial techniques from graph isomorphism testing. However, MPNNs' generalization abilities---making meaningful predictions beyond the training set---remain less explored. Current generalization analyses often overlook graph structure, limit the focus to specific aggregation functions, and assume the impractical, hard-to-optimize $0$-$1$ loss function. Here, we extend recent advances in graph similarity theory to assess the influence of graph structure, aggregation, and loss functions on MPNNs' generalization abilities. Our empirical study supports our theoretical insights, improving our understanding of MPNNs' generalization properties.

Reinforcement learning (RL) using world models has found significant recent successes. However, when a sudden change to world mechanics or properties occurs then agent performance and reliability can dramatically decline. We refer to the sudden change in visual properties or state transitions as novelties. Implementing novelty detection within generated world model frameworks is a crucial task for protecting the agent when deployed. In this paper, we propose straightforward bounding approaches to incorporate novelty detection into world model RL agents by utilizing the misalignment of the world model's hallucinated states and the true observed states as a novelty score. We provide effective approaches to detecting novelties in a distribution of transitions learned by an agent in a world model. Finally, we show the advantage of our work in a novel environment compared to traditional machine learning novelty detection methods as well as currently accepted RL-focused novelty detection algorithms.

Predicting the solvation free energy of molecules using graph neural networks holds significant potential for advancing drug discovery and the design of novel materials. While previous methods have demonstrated success on independent and identically distributed (IID) datasets, their performance in out-of-distribution (OOD) scenarios remains largely unexplored. We propose a novel Relational Invariant Learning framework (RILOOD) to enhance OOD generalization in solvation free energy prediction. RILOOD comprises three key components: (i) a mixup-based conditional modeling module that integrates diverse environments, (ii) a novel multi-granularity refinement strategy that extends beyond core substructures to enable context-aware representation learning for capturing multi-level interactions, and (iii) an invariant learning mechanism that identifies robust patterns generalizable to unseen environments. Extensive experiments demonstrate that RILOOD significantly outperforms state-of-the-art methods across various distribution shifts, highlighting its effectiveness in improving solvation free energy prediction under diverse conditions.

Machine Learning Interatomic Potentials (MLIPs) enable efficient molecular dynamics (MD) simulations with high accuracy. While equivariant MLIPs achieve state-of-the-art accuracy, they face significant computational bottlenecks centered around their Tensor-Product layer, which account for up to 75\% of training time and cause substantial memory overhead. We present FlashTP, a highly optimized tensor-product library that addresses these inefficiencies through kernel fusion, sparse computation, and path-aggregated execution. FlashTP achieves up to 41.6$\times$ and 60.8$\times$ kernel speedups over _e3nn_ and NVIDIA cuEquivariance, respectively. For SevenNet-l3i5, it delivers 4.2$\times$ and 3.5$\times$ speedup while reducing peak memory usage by 6.3$\times$ and 6.2$\times$ for inference and training, respectively. The code is available at https://github.com/SNU-ARC/flashTP.

Inferring properties of graph-structured data, *e.g.*, the solubility of molecules, essentially involves learning the implicit mapping from graphs to their properties. This learning process is often costly for graph property learners like Graph Convolutional Networks (GCNs). To address this, we propose a paradigm called Graph Nonparametric Teaching (GraNT) that reinterprets the learning process through a novel nonparametric teaching perspective. Specifically, the latter offers a theoretical framework for teaching implicitly defined (*i.e.*, nonparametric) mappings via example selection. Such an implicit mapping is realized by a dense set of graph-property pairs, with the GraNT teacher selecting a subset of them to promote faster convergence in GCN training. By analytically examining the impact of graph structure on parameter-based gradient descent during training, and recasting the evolution of GCNs—shaped by parameter updates—through functional gradient descent in nonparametric teaching, we show *for the first time* that teaching graph property learners (*i.e.*, GCNs) is consistent with teaching structure-aware nonparametric learners. These new findings readily commit GraNT to enhancing learning efficiency of the graph property learner, showing significant reductions in training time for graph-level regression (-36.62\%), graph-level classification (-38.19\%), node-level regression (-30.97\%) and node-level classification (-47.30\%), all while maintaining its generalization performance.

Self-attention performs well in long context but has quadratic complexity. Existing RNN layers have linear complexity, but their performance in long context is limited by the expressive power of their hidden states. We present a practical framework for instantiating sequence modeling layers with linear complexity and expressive hidden states. The key idea is to make the hidden state a machine learning model itself, and the update rule a step of self-supervised learning. Since the hidden state is updated by training even on test sequences, our layers are called Test-Time Training (TTT) layers. We consider two instantiations: TTT-Linear and TTT-MLP, whose hidden state is a linear model and a two-layer MLP respectively. We evaluate our instantiations at the scale of 125M to 1.3B parameters, comparing with a strong Transformer and Mamba, a modern RNN. Similar to Transformer, TTT-Linear and TTT-MLP can keep reducing perplexity by conditioning on more tokens, while Mamba cannot after 16k context. TTT-MLP still faces challenges in memory I/O, but shows larger potential in long context, pointing to a promising direction for future research.

Symmetry in the parameter space of deep neural networks (DNNs) has proven beneficial for various deep learning applications. A well-known example is the permutation symmetry in Multi-Layer Perceptrons (MLPs), where permuting the rows of weight matrices in one layer and applying the inverse permutation to adjacent layers yields a functionally equivalent model. While permutation symmetry fully characterizes the equivalence set for MLPs, its discrete nature limits its utility for transformers. In this paper, we introduce rotation symmetry, a novel form of parameter space symmetry for transformers that generalizes permutation symmetry by rotating parameter matrices in self-attention layers. Unlike permutation symmetry, rotation symmetry operates in a continuous domain, thereby significantly expanding the equivalence set for transformers. Based on this property, we propose a theoretically optimal parameter matching algorithm as a plug-and-play module to enhance model fusion. We evaluate our approach using pre-trained transformers across diverse natural language and vision tasks. Experimental results demonstrate that our rotation symmetry-based matching algorithm substantially improves model fusion, highlighting the potential of parameter space symmetry to facilitate model fusion. Our code is available on https://github.com/zhengzaiyi/RotationSymmetry

The advancement of Large Vision-Language Models (LVLMs) has increasingly highlighted the critical issue of their tendency to hallucinate non-existing objects in the images. To address this issue, previous works focused on using specially curated datasets or powerful LLMs to rectify the outputs of LVLMs. However, these approaches require either costly training or fine-tuning, or API access to proprietary LLMs for post-generation correction. In response to these limitations, we propose Mitigating hallucinAtion via image-gRounded guIdaNcE (MARINE), a framework that is both training-free and API-free. MARINE effectively and efficiently reduces object hallucinations during inference by introducing image-grounded guidance to LVLMs. This is achieved by leveraging open-source vision models to extract object-level information, thereby enhancing the precision of LVLM-generated content. Our framework's flexibility further allows for the integration of multiple vision models, enabling more reliable and robust object-level guidance. Through comprehensive evaluations across 5 popular LVLMs with diverse evaluation metrics and benchmarks, we demonstrate the effectiveness of MARINE, which even outperforms existing fine-tuning-based methods. Remarkably, it reduces hallucinations consistently in GPT-4V-assisted evaluation while maintaining the detailedness of LVLMs' generations. We release our code at https://github.com/Linxi-ZHAO/MARINE.

Recent progress in imitation learning has been enabled by policy architectures that scale to complex visuomotor tasks, multimodal distributions, and large datasets. However, these methods often rely on learning from large amount of expert demonstrations. To address these shortcomings, we propose Latent Diffusion Planning (LDP), a modular approach consisting of a planner which can leverage action-free demonstrations, and an inverse dynamics model which can leverage suboptimal data, that both operate over a learned latent space. First, we learn a compact latent space through a variational autoencoder, enabling effective forecasting of future states in image-based domains. Then, we train a planner and an inverse dynamics model with diffusion objectives. By separating planning from action prediction, LDP can benefit from the denser supervision signals of suboptimal and action-free data. On simulated visual robotic manipulation tasks, LDP outperforms state-of-the-art imitation learning approaches, as they cannot leverage such additional data.

Recent work has demonstrated that large-scale, multi-animal models are powerful tools for characterizing the relationship between neural activity and behavior. Current large-scale approaches, however, focus exclusively on either predicting neural activity from behavior (encoding) or predicting behavior from neural activity (decoding), limiting their ability to capture the bidirectional relationship between neural activity and behavior. To bridge this gap, we introduce a multimodal, multi-task model that enables simultaneous Neural Encoding and Decoding at Scale (NEDS). Central to our approach is a novel multi-task-masking strategy, which alternates between neural, behavioral, within-modality, and cross-modality masking. We pretrain our method on the International Brain Laboratory (IBL) repeated site dataset, which includes recordings from 83 animals performing the visual decision-making task. In comparison to other large-scale modeling approaches, we demonstrate that NEDS achieves state-of-the-art performance for both encoding and decoding when pretrained on multi-animal data and then fine-tuned on new animals. Surprisingly, NEDS's learned embeddings exhibit emergent properties: even without explicit training, they are highly predictive of the brain regions in each recording. Altogether, our approach is a step towards a foundation model of the brain that enables seamless translation between neural activity and behavior.

Continuous Normalizing Flows (CNFs) have proven to be a highly efficient technique for generative modeling of complex data since the introduction of Flow Matching (FM). The core of FM is to learn the constructed velocity fields of CNFs through deep least squares regression. Despite its empirical effectiveness, theoretical investigations of FM remain limited. In this paper, we present the first end-to-end error analysis of CNFs built upon FM. Our analysis shows that for general target distributions with bounded support, the generated distribution of FM is guaranteed to converge to the target distribution in the sense of the Wasserstein-2 distance. Furthermore, the convergence rate is significantly improved under an additional mild Lipschitz condition of the target score function.

We study convergence properties of the discrete-time Mean-Field Langevin Stochastic Descent-Ascent (MFL-SDA) algorithm for solving distributional minimax optimization. These problems arise in various applications, such as zero-sum games, generative adversarial networks and distributionally robust learning. Despite the significance of MFL-SDA in these contexts, the discrete-time convergence rate remains underexplored. To address this gap, we establish a last-iterate convergence rate of $O(\frac{1}{\epsilon}\log\frac{1}{\epsilon})$ for MFL-SDA. This rate is nearly optimal when compared to the complexity lower bound of its Euclidean counterpart. This rate also matches the complexity of mean-field Langevin stochastic gradient descent for distributional minimization and the outer-loop iteration complexity of an existing double-loop algorithm for distributional minimax problems. By leveraging an elementary analysis framework that avoids PDE-based techniques, we overcome previous limitations and achieve a faster convergence rate.

Recent advances in diffusion bridge models leverage Doob’s $h$-transform to establish fixed endpoints between distributions, demonstrating promising results in image translation and restoration tasks. However, these approaches frequently produce blurred or excessively smoothed image details and lack a comprehensive theoretical foundation to explain these shortcomings. To address these limitations, we propose UniDB, a unified framework for diffusion bridges based on Stochastic Optimal Control (SOC). UniDB formulates the problem through an SOC-based optimization and derives a closed-form solution for the optimal controller, thereby unifying and generalizing existing diffusion bridge models. We demonstrate that existing diffusion bridges employing Doob’s $h$-transform constitute a special case of our framework, emerging when the terminal penalty coefficient in the SOC cost function tends to infinity. By incorporating a tunable terminal penalty coefficient, UniDB achieves an optimal balance between control costs and terminal penalties, substantially improving detail preservation and output quality. Notably, UniDB seamlessly integrates with existing diffusion bridge models, requiring only minimal code modifications. Extensive experiments across diverse image restoration tasks validate the superiority and adaptability of the proposed framework. Our code is available at https://github.com/UniDB-SOC/UniDB/.

Generative models have made it possible to synthesize highly realistic images, potentially providing an abundant data source for training machine learning models. Despite the advantages of these synthesizable data sources, the indiscriminate use of generated images as real images for training can even cause mode collapse due to modality discrepancies between real and synthetic domains. In this paper, we propose a novel framework for discriminative use of generated images, coined \textit{GMAIL}, that explicitly treats generated images as a separate modality from real images. Instead of indiscriminately replacing real images with generated ones in the pixel space, our approach bridges the two distinct modalities in the same latent space through a multi-modal learning approach. To be specific, we first fine-tune a model exclusively on generated images using a cross-modality alignment loss and then employ this aligned model to further train various vision-language models with generated images. By aligning the two modalities, our approach effectively leverages the benefits of recent advances in generative models, thereby boosting the effectiveness of generated image learning across a range of vision-language tasks. Our framework can be easily incorporated with various vision-language models, and we demonstrate its efficacy throughout extensive experiments. For example, our framework significantly improves performance on image captioning, zero-shot image retrieval, zero-shot image classification, and long caption retrieval tasks. It also shows positive generated data scaling trends and notable enhancements in the captioning performance of the large multimodal model, LLaVA.