ICML 2025 Papers

Multimodal protein language models (PLMs) integrate sequence and token-based structural information, serving as a powerful foundation for protein modeling, generation, and design. However, the reliance on tokenizing 3D structures into discrete tokens causes substantial loss of fidelity about fine-grained structural details and correlations. In this paper, we systematically elucidate the design space of multimodal PLMs to overcome their limitations. We identify tokenization loss and inaccurate structure token predictions by the PLMs as major bottlenecks. To address these, our proposed design space covers improved generative modeling, structure-aware architectures and representation learning, and data exploration. Our advancements approach finer-grained supervision, demonstrating that token-based multimodal PLMs can achieve robust structural modeling. The effective design methods dramatically improve the structure generation diversity, and notably, folding abilities of our 650M model by reducing the RMSD from 5.52 to 2.36 on PDB testset, even outperforming 3B baselines and on par with the specialized folding models. Project page and code: https://bytedance.github.io/dplm/dplm-2.1.

Aligning large language models (LLMs) with human preferences is crucial for safe deployment, yet existing methods assume specific preference models like Bradley-Terry model. This assumption leads to statistical inconsistency, where more data doesn't guarantee convergence to true human preferences. To address this critical gap, we introduce a novel alignment method Direct Density Ratio Optimization (DDRO). DDRO directly estimates the density ratio between preferred and unpreferred output distributions, circumventing the need for explicit human preference modeling. We theoretically prove that DDRO is statistically consistent, ensuring convergence to the true preferred distribution as the data size grows, regardless of the underlying preference structure. Experiments demonstrate that DDRO achieves superior performance compared to existing methods, showcasing its effectiveness and potential for significant improvement. DDRO unlocks the potential for truly data-driven alignment, paving the way for more reliable and human-aligned LLMs.

Diffusion models have demonstrated exceptional performances in various fields of generative modeling, but suffer from slow sampling speed due to their iterative nature. While this issue is being addressed in continuous domains, discrete diffusion models face unique challenges, particularly in capturing dependencies between elements (e.g., pixel relationships in image, sequential dependencies in language) mainly due to the computational cost of processing high-dimensional joint distributions. In this paper, (i) we propose "mixture" models for discrete diffusion that are capable of treating dimensional correlations while remaining scalable, and (ii) we provide a set of loss functions for distilling the iterations of existing models. Two primary theoretical insights underpin our approach: First, conventional models with element-wise independence can well approximate the data distribution, but essentially require *many sampling steps*. Second, our loss functions enable the mixture models to distill such many-step conventional models into just a few steps by learning the dimensional correlations. Our experimental results show the effectiveness of the proposed method in distilling pretrained discrete diffusion models across image and language domains. The code used in the paper is available at https://github.com/sony/di4c.

Recent advancements in predictive models have demonstrated exceptional capabilities in predicting the future state of objects and scenes. However, the lack of categorization based on inherent characteristics continues to hinder the progress of predictive model development. Additionally, existing benchmarks are unable to effectively evaluate higher-capability, highly embodied predictive models from an embodied perspective. In this work, we classify the functionalities of predictive models into a hierarchy and take the first step in evaluating World Simulators by proposing a dual evaluation framework called WorldSimBench. WorldSimBench includes Explicit Perceptual Evaluation and Implicit Manipulative Evaluation, encompassing human preference assessments from the visual perspective and action-level evaluations in embodied tasks, covering three representative embodied scenarios: Open-Ended Embodied Environment, Autonomous, Driving, and Robot Manipulation. In the Explicit Perceptual Evaluation, we introduce the HF-Embodied Dataset, a video assessment dataset based on fine-grained human feedback, which we use to train a Human Preference Evaluator that aligns with human perception and explicitly assesses the visual fidelity of World Simulater. In the Implicit Manipulative Evaluation, we assess the video-action consistency of World Simulators by evaluating whether the generated situation-aware video can be accurately translated into the correct control signals in dynamic environments. Our comprehensive evaluation offers key insights that can drive further innovation in video generation models, positioning World Simulators as a pivotal advancement toward embodied artificial intelligence.

Classifier-free guidance (CFG) is a key technique for improving conditional generation in diffusion models, enabling more accurate control while enhancing sample quality. It is natural to extend this technique to video diffusion, which generates video conditioned on a variable number of context frames, collectively referred to as history. However, we find two key challenges to guiding with variable-length history: architectures that only support fixed-size conditioning, and the empirical observation that CFG-style history dropout performs poorly. To address this, we propose the Diffusion Forcing Transformer (DFoT), a video diffusion architecture and theoretically grounded training objective that jointly enable conditioning on a flexible number of history frames. We then introduce History Guidance, a family of guidance methods uniquely enabled by DFoT. We show that its simplest form, vanilla history guidance, already significantly improves video generation quality and temporal consistency. A more advanced method, history guidance across time and frequency further enhances motion dynamics, enables compositional generalization to out-of-distribution history, and can stably roll out extremely long videos. Project website: [https://boyuan.space/history-guidance](https://boyuan.space/history-guidance)

Causal discovery, i.e., inferring underlying causal relationships from observational data, is highly challenging for AI systems. In a time series modeling context, traditional causal discovery methods mainly consider constrained scenarios with fully observed variables and/or data from stationary time-series. We develop a causal discovery approach to handle a wide class of nonstationary time series that are _conditionally stationary_, where the nonstationary behaviour is modeled as stationarity conditioned on a set of latent state variables. Named State-Dependent Causal Inference (SDCI), our approach is able to recover the underlying causal dependencies, with provable identifiablity for the state-dependent causal structures. Empirical experiments on nonlinear particle interaction data and gene regulatory networks demonstrate SDCI's superior performance over baseline causal discovery methods. Improved results over non-causal RNNs on modeling NBA player movements demonstrate the potential of our method and motivate the use of causality-driven methods for forecasting.

Self-supervised learning (SSL) methods via joint embedding architectures have proven remarkably effective at capturing semantically rich representations with strong clustering properties, magically in the absence of label supervision. Despite this, few of them have explored leveraging these untapped properties to improve themselves. In this paper, we provide an evidence through various metrics that the encoder's output *encoding* exhibits superior and more stable clustering properties compared to other components. Building on this insight, we propose a novel positive-feedback SSL method, termed **Re**presentation **S**elf-**A**ssignment (ReSA), which leverages the model's clustering properties to promote learning in a self-guided manner. Extensive experiments on standard SSL benchmarks reveal that models pretrained with ReSA outperform other state-of-the-art SSL methods by a significant margin. Finally, we analyze how ReSA facilitates better clustering properties, demonstrating that it effectively enhances clustering performance at both fine-grained and coarse-grained levels, shaping representations that are inherently more structured and semantically meaningful.

Federated recommender system (FedRec) has emerged as a solution to protect user data through collaborative training techniques. A typical FedRec involves transmitting the full model and entire weight updates between edge devices and the server, causing significant burdens to edge devices with limited bandwidth and computational power. The sparsity of embedding updates provides opportunity for payload optimization, while existing sparsity-aware federated protocols generally sacrifice privacy for efficiency. A key challenge in designing a secure sparsity-aware efficient protocol is to protect the rated item indices from the server. In this paper, we propose a lossless secure recommender systems with on sparse embedding updates (SecEmb). SecEmb reduces user payload while ensuring that the server learns no information about both rated item indices and individual updates except the aggregated model. The protocol consists of two correlated modules: (1) a privacy-preserving embedding retrieval module that allows users to download relevant embeddings from the server, and (2) an update aggregation module that securely aggregates updates at the server. Empirical analysis demonstrates that SecEmb reduces both download and upload communication costs by up to 90x and decreases user-side computation time by up to 70x compared with secure FedRec protocols. Additionally, it offers non-negligible utility advantages compared with lossy message compression methods.

Predictive models of the future are fundamental for an agent's ability to reason and plan. A common strategy learns a world model and unrolls it step-by-step at inference, where small errors can rapidly compound. Geometric Horizon Models (GHMs) offer a compelling alternative by directly making predictions of future states, avoiding cumulative inference errors. While GHMs can be conveniently learned by a generative analog to temporal difference (TD) learning, existing methods are negatively affected by bootstrapping predictions at train time and struggle to generate high-quality predictions at long horizons. This paper introduces Temporal Difference Flows (TD-Flow), which leverages the structure of a novel Bellman equation on probability paths alongside flow-matching techniques to learn accurate GHMs at over 5x the horizon length of prior methods. Theoretically, we establish a new convergence result and primarily attribute TD-Flow's efficacy to reduced gradient variance during training. We further show that similar arguments can be extended to diffusion-based methods. Empirically, we validate TD-Flow across a diverse set of domains on both generative metrics and downstream tasks, including policy evaluation. Moreover, integrating TD-Flow with recent behavior foundation models for planning over policies demonstrates substantial performance gains, underscoring its promise for long-horizon decision-making.

Graph clustering is an important algorithmic technique for analysing massive graphs, and has been widely applied in many research fields of data science. While the objective of most graph clustering algorithms is to find a vertex set of low conductance, there has been a sequence of recent studies that highlight the importance of the inter-connection between clusters when analysing real-world datasets. Following this line of research, in this work we study bipartite-like clusters and present efficient and online algorithms that find such clusters in both undirected graphs and directed ones. We conduct experimental studies on both synthetic and real-world datasets, and show that our algorithms significantly speedup the running time of existing clustering algorithms while preserving their effectiveness.

Consumer protection laws are designed to protect consumers from unethical business practices. In this position paper, I argue that these laws serve an emergent dual purpose: if appropriately enforced and strengthened, consumer protection laws can serve as an inalienable defense for AI safety. These laws are well established and can be enforced and strengthened to incentivize businesses to design and deploy safer AI systems. This position runs counter to two prevailing trends in AI policy. The first alternative position is that AI safety requires an entirely new set of focused laws to protect humanity's prosperity. Though I find these efforts valuable, I argue that such focused laws are both hard to write and easy to skirt. The second alternative position is that consumer protection is nothing more than red tape; I argue that existing laws dating back many decades have already reigned in some nefarious business practices related to the development and deployment of AI, and that the litigious society of the United States is well-positioned to use consumer protection laws to encourage new AI safety guardrails. This paper takes a tour of some existing consumer protection laws in the United States and their effects on the development and use of AI systems. This paper also calls to enforce and preserve these laws in a rapidly changing, de-regulatory political landscape.

Federated learning (FL) enables privacy-preserving distributed machine learning by sharing gradients instead of raw data. However, FL remains vulnerable to gradient inversion attacks, in which shared gradients can reveal sensitive training data. Prior research has mainly concentrated on unimodal tasks, particularly image classification, examining the reconstruction of single-modality data, and analyzing privacy vulnerabilities in these relatively simple scenarios. As multimodal models are increasingly used to address complex vision-language tasks, it becomes essential to assess the privacy risks inherent in these architectures. In this paper, we explore gradient inversion attacks targeting multimodal vision-language Document Visual Question Answering (DQA) models and propose GI-DQA, a novel method that reconstructs private document content from gradients. Through extensive evaluation on state-of-the-art DQA models, our approach exposes critical privacy vulnerabilities and highlights the urgent need for robust defenses to secure multimodal FL systems.

We introduce two complementary techniques for efficient optimization that reduce memory requirements while accelerating training of large-scale neural networks. The first technique, Subset-Norm step size, generalizes AdaGrad-Norm and AdaGrad(-Coordinate) through step-size sharing. Subset-Norm (SN) reduces AdaGrad's memory footprint from $O(d)$ to $O(\sqrt{d})$, where $d$ is the model size. For non-convex smooth objectives under coordinate-wise sub-gaussian noise, we show a noise-adapted high-probability convergence guarantee with improved dimensional dependence of SN over existing methods. Our second technique, Subspace-Momentum, reduces the momentum state's memory footprint by restricting momentum to a low-dimensional subspace while performing SGD in the orthogonal complement. We prove high-probability convergence rates for Subspace-Momentum under standard assumptions. Empirical evaluation on pre-training and fine-tuning LLMs demonstrates the effectiveness of our methods. For instance, combining Subset-Norm with Subspace-Momentum achieves Adam's validation perplexity for LLaMA 1B in approximately half the training tokens (6.8B vs 13.1B) while reducing Adam's optimizer-states memory footprint by more than 80\% with minimal additional hyperparameter tuning.

Large language models (LLMs) have demonstrated remarkable reasoning capabilities across diverse domains. Recent studies have shown that increasing test-time computation enhances LLMs' reasoning capabilities. This typically involves extensive sampling at inference time guided by an external LLM verifier, resulting in a two-player system. Despite external guidance, the effectiveness of this system demonstrates the potential of a single LLM to tackle complex tasks. Thus, we pose a new research problem: *Can we internalize the searching capabilities to fundamentally enhance the reasoning abilities of a single LLM?* This work explores an orthogonal direction focusing on post-training LLMs for autoregressive searching (*i.e.,* an extended reasoning process with self-reflection and self-exploration of new strategies). To achieve this, we propose the Chain-of-Action-Thought (COAT) reasoning and a two-stage training paradigm: 1) a small-scale format tuning stage to internalize the COAT reasoning format and 2) a large-scale self-improvement stage leveraging reinforcement learning. Our approach results in Satori, a 7B LLM trained on open-source models and data. Extensive empirical evaluations demonstrate that Satori achieves state-of-the-art performance on mathematical reasoning benchmarks while exhibits strong generalization to out-of-domain tasks. Code, data, and models are fully open-sourced.

This position paper argues for a fundamental shift in how Large Language Models (LLMs) are integrated into the mental health care domain. We advocate for their role as co-creators rather than mere assistive tools. While LLMs have the potential to enhance accessibility, personalization, and crisis intervention, their adoption remains limited due to concerns about bias, evaluation, over-reliance, dehumanization, and regulatory uncertainties. To address these challenges, we propose two structured pathways: SAFE-i (Supportive, Adaptive, Fair, and Ethical Implementation) Guidelines for ethical and responsible deployment, and HAAS-e (Human-AI Alignment and Safety Evaluation) Framework for multidimensional, human-centered assessment. SAFE-i provides a blueprint for data governance, adaptive model engineering, and real-world integration, ensuring LLMs align with clinical and ethical standards. HAAS-e introduces evaluation metrics that go beyond technical accuracy to measure trustworthiness, empathy, cultural sensitivity, and actionability. We call for the adoption of these structured approaches to establish a responsible and scalable model for LLM-driven mental health support, ensuring that AI complements—rather than replaces—human expertise.

Transformer networks have achieved remarkable success across diverse domains, leveraging a variety of architectural innovations, including residual connections. However, traditional residual connections, which simply sum the outputs of previous layers, can dilute crucial information. This work introduces DeepCrossAttention (DCA), an approach that enhances residual learning in transformers. DCA employs learnable, input-dependent weights to dynamically combine layer outputs, enabling the model to selectively focus on the most relevant information in any of the previous layers. Furthermore, DCA incorporates depth-wise cross-attention, allowing for richer interactions between layers at different depths. Our language modeling experiments show that DCA achieves improved perplexity for a given training time. Moreover, DCA obtains the same model quality up to 3x faster while adding a negligible number of parameters (e.g., 0.2\%). Theoretical analysis confirms that DCA provides an improved trade-off between accuracy and model size when the ratio of collective layer ranks to the ambient dimension falls below a critical threshold.

Feature evolvable learning studies the scenario where old features will vanish and new features will emerge when learning with data streams, and various methods have been developed by utilizing some useful relationships from old features to new features, rather than re-training from scratch. In this work, we focus on two fundamental problems: How to characterize the relationships between two different feature spaces, and how to exploit those relationships for feature evolvable learning. We introduce the Kernel Ortho-Mapping (KOM) discrepancy to characterize relationships between two different feature spaces via kernel functions, and correlate with the optimal classifiers learned from different feature spaces. Based on this discrepancy, we develop the one-pass algorithm for feature evolvable learning, which requires going through all instances only once without storing the entire or partial training data. Our basic idea is to take online kernel learning with the random Fourier features and incorporate some feature and label relationships via the KOM discrepancy for feature evolvable learning. We finally validate the effectiveness of our proposed method both theoretically and empirically.

Autoregressive and recurrent networks have achieved remarkable progress across various fields, from weather forecasting to molecular generation and Large Language Models. Despite their strong predictive capabilities, these models lack a rigorous framework for addressing uncertainty, which is key in scientific applications such as PDE solving, molecular generation and machine l earning Force Fields. To address this shortcoming we present BARNN: a variational Bayesian Autoregressive and Recurrent Neural Network. BARNNs aim to provide a principled way to turn any autoregressive or recurrent model into its Bayesian version. BARNN is based on the variational dropout method, allowing to apply it to large recurrent neural networks as well. We also introduce a temporal version of the “Variational Mixtures of Posteriors” prior (tVAMP-prior) to make Bayesian inference efficient and well-calibrated. Extensive experiments on PDE modelling and molecular generation demonstrate that BARNN not only achieves comparable or superior accuracy compared to existing methods, but also excels in uncertainty quantification and modelling long-range dependencies.

Unpaired point cloud completion is crucial for real-world applications, where ground-truth data for complete point clouds are often unavailable. By learning a completion map from unpaired incomplete and complete point cloud data, this task avoids the reliance on paired datasets. In this paper, we propose the \textit{Unbalanced Optimal Transport Map for Unpaired Point Cloud Completion (\textbf{UOT-UPC})} model, which formulates the unpaired completion task as the (Unbalanced) Optimal Transport (OT) problem. Our method employs a Neural OT model learning the UOT map using neural networks. Our model is the first attempt to leverage UOT for unpaired point cloud completion, achieving competitive or superior performance on both single-category and multi-category benchmarks. In particular, our approach is especially robust under the class imbalance problem, which is frequently encountered in real-world unpaired point cloud completion scenarios.