ICLR 2025 论文列表

International Conference on Learning Representations

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3,703篇论文

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    38010.3%
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EVA: Geometric Inverse Design for Fast Protein Motif-Scaffolding with Coupled Flow

Yufei Huang, Yunshu Liu, Lirong Wu, Haitao Lin, Cheng Tan, Odin Zhang, Zhangyang Gao, Siyuan Li, Zicheng Liu, Yunfan Liu, Tailin Wu, Stan Z. Li

展开摘要

Motif-scaffolding is a fundamental component of protein design, which aims to construct the scaffold structure that stabilizes motifs conferring desired functions. Recent advances in generative models are promising for designing scaffolds, with two main approaches: training-based and sampling-based methods. Training-based methods are resource-heavy and slow, while training-free sampling-based methods are flexible but require numerous sampling steps and costly, unstable guidance. To speed up and improve sampling-based methods, we analyzed failure cases and found that errors stem from the trade-off between generation and guidance. Thus we proposed to exploit the spatial context and adjust the generative direction to be consistent with guidance to overcome this trade-off. Motivated by this, we formulate motif-scaffolding as a Geometric Inverse Design task inspired by the image inverse problem, and present Evolution-ViA-reconstruction (EVA), a novel sampling-based coupled flow framework on geometric manifolds, which starts with a pretrained flow-based generative model. EVA uses motif-coupled priors to leverage spatial contexts, guiding the generative process along a straighter probability path, with generative directions aligned with guidance in the early sampling steps. EVA is 70× faster than SOTA model RFDiffusion with competitive and even better performance on benchmark tests. Further experiments on real-world cases including vaccine design, multi-motif scaffolding and motif optimal placement searching demonstrate EVA's superior efficiency and effectiveness.

Poster
Private Mechanism Design via Quantile Estimation

Yuanyuan Yang, Tao Xiao, Bhuvesh Kumar, Jamie Heather Morgenstern

展开摘要

We investigate the problem of designing differentially private (DP), revenue-maximizing single item auction. Specifically, we consider broadly applicable settings in mechanism design where agents' valuation distributions are **independent**, **non-identical**, and can be either **bounded** or **unbounded**. Our goal is to design such auctions with **pure**, i.e., $(\epsilon,0)$ privacy in polynomial time. In this paper, we propose two computationally efficient auction learning framework that achieves **pure** privacy under bounded and unbounded distribution settings. These frameworks reduces the problem of privately releasing a revenue-maximizing auction to the private estimation of pre-specified quantiles. Our solutions increase the running time by polylog factors compared to the non-private version. As an application, we show how to extend our results to the multi-round online auction setting with non-myopic bidders. To our best knowledge, this paper is the first to efficiently deliver a Myerson auction with **pure** privacy and near-optimal revenue, and the first to provide such auctions for **unbounded** distributions.

Poster
Regulatory DNA Sequence Design with Reinforcement Learning

Zhao Yang, Bing Su, Chuan Cao, Ji-Rong Wen

展开摘要

$\textit{Cis}$-regulatory elements (CREs), such as promoters and enhancers, are relatively short DNA sequences that directly regulate gene expression. The fitness of CREs, measured by their ability to modulate gene expression, highly depends on the nucleotide sequences, especially specific motifs known as transcription factor binding sites (TFBSs). Designing high-fitness CREs is crucial for therapeutic and bioengineering applications. Current CRE design methods are limited by two major drawbacks: (1) they typically rely on iterative optimization strategies that modify existing sequences and are prone to local optima, and (2) they lack the guidance of biological prior knowledge in sequence optimization. In this paper, we address these limitations by proposing a generative approach that leverages reinforcement learning (RL) to fine-tune a pre-trained autoregressive (AR) model. Our method incorporates data-driven biological priors by deriving computational inference-based rewards that simulate the addition of activator TFBSs and removal of repressor TFBSs, which are then integrated into the RL process. We evaluate our method on promoter design tasks in two yeast media conditions and enhancer design tasks for three human cell types, demonstrating its ability to generate high-fitness CREs while maintaining sequence diversity. The code is available at https://github.com/yangzhao1230/TACO.

Poster
Clique Number Estimation via Differentiable Functions of Adjacency Matrix Permutations

Indradyumna Roy, Eeshaan Jain, Soumen Chakrabarti, Abir De

展开摘要

Estimating the clique number in a graph is central to various applications, e.g., community detection, graph retrieval, etc. Existing estimators often rely on non-differentiable combinatorial components. Here, we propose a full differentiable estimator for clique number estimation, which can be trained from distant supervision of clique numbers, rather than demonstrating actual cliques. Our key insight is a formulation of the maximum clique problem (MCP) as a maximization of the size of fully dense square submatrix, within a suitably row-column-permuted adjacency matrix. We design a differentiable mechanism to search for permutations that lead to the discovery of such dense blocks. However, the optimal permutation is not unique, which leads to the learning of spurious permutations. To tackle this problem, we view the MCP problem as a sequence of subgraph matching tasks, each detecting progressively larger cliques in a nested manner. This allows effective navigation through suitable node permutations. These steps result in MxNet, an end-to-end differentiable model, which learns to predict clique number without explicit clique demonstrations, with the added benefit of interpretability. Experiments on eight datasets show the superior accuracy of our approach.

Poster
Interactive Speculative Planning: Enhance Agent Efficiency through Co-design of System and User Interface

Wenyue Hua, Mengting Wan, JAGANNATH SHASHANK SUBRAMANYA SAI VADREVU, Ryan Nadel, Yongfeng Zhang, Chi Wang

展开摘要

Agents, as user-centric tools, are increasingly deployed for human task delegation, assisting with a broad spectrum of requests by generating thoughts, engaging with user proxies, and producing action plans. However, agents based on large language models often face substantial planning latency due to two primary factors: the efficiency limitations of the underlying LLMs due to their large size and high demand, and the structural complexity of the agents due to the extensive generation of intermediate steps to produce the final output. Given that inefficiency in service provision can undermine the value of automation for users, this paper presents a human-centered efficient agent planning method – Interactive Speculative Planning – aiming at enhancing the efficiency of agent planning through both system design and user interaction. Our approach advocates for the co-design of the agent system and user interface, underscoring the importance of an agent system that can fluidly manage user interactions and interruptions. By integrating human interruptions as a fundamental component of the system, we not only make it more user-centric but also expedite the entire process by leveraging human-in-the-loop interactions to provide accurate intermediate steps.

Poster
T2V-Turbo-v2: Enhancing Video Model Post-Training through Data, Reward, and Conditional Guidance Design

Jiachen Li, Qian Long, Jian Zheng, Xiaofeng Gao, Robinson Piramuthu, Wenhu Chen, William Yang Wang

展开摘要

In this paper, we focus on enhancing a diffusion-based text-to-video (T2V) model during the post-training phase by distilling a highly capable consistency model from a pretrained T2V model. Our proposed method, T2V-Turbo-v2, introduces a significant advancement by integrating various supervision signals, including high-quality training data, reward model feedback, and conditional guidance, into the consistency distillation process. Through comprehensive ablation studies, we highlight the crucial importance of tailoring datasets to specific learning objectives and the effectiveness of learning from diverse reward models for enhancing both the visual quality and text-video alignment. Additionally, we highlight the vast design space of conditional guidance strategies, which centers on designing an effective energy function to augment the teacher ODE solver. We demonstrate the potential of this approach by extracting motion guidance from the training datasets and incorporating it into the ODE solver, showcasing its effectiveness in improving the motion quality of the generated videos with the improved motion-related metrics from VBench and T2V-CompBench. Empirically, our T2V-Turbo-v2 establishes a new state-of-the-art result on VBench, **with a Total score of 85.13**, surpassing proprietary systems such as Gen-3 and Kling.

Poster
Hierarchically Encapsulated Representation for Protocol Design in Self-Driving Labs

Yu-Zhe Shi, Mingchen Liu, Fanxu Meng, Qiao Xu, Zhangqian Bi, Kun He, Lecheng Ruan, Qining Wang

展开摘要

Self-driving laboratories have begun to replace human experimenters in performing single experimental skills or predetermined experimental protocols. However, as the pace of idea iteration in scientific research has been intensified by Artificial Intelligence, the demand for rapid design of new protocols for new discoveries become evident. Efforts to automate protocol design have been initiated, but the capabilities of knowledge-based machine designers, such as Large Language Models, have not been fully elicited, probably for the absence of a systematic representation of experimental knowledge, as opposed to isolated, flatten pieces of information. To tackle this issue, we propose a multi-faceted, multi-scale representation, where instance actions, generalized operations, and product flow models are hierarchically encapsulated using Domain-Specific Languages. We further develop a data-driven algorithm based on non-parametric modeling that autonomously customizes these representations for specific domains. The proposed representation is equipped with various machine designers to manage protocol design tasks, including planning, modification, and adjustment. The results demonstrate that the proposed method could effectively complement Large Language Models in the protocol design process, serving as an auxiliary module in the realm of machine-assisted scientific exploration.

Poster
OSDA Agent: Leveraging Large Language Models for De Novo Design of Organic Structure Directing Agents

Zhaolin Hu, Yixiao Zhou, Zhongan Wang, Xin Li, Weimin Yang, Hehe Fan, Yi Yang

展开摘要

Zeolites are crystalline porous materials that have been widely utilized in petrochemical industries as well as sustainable chemistry areas. Synthesis of zeolites often requires small molecules termed Organic Structure Directing Agents (OSDAs), which are critical in forming the porous structure. Molecule generation models can aid the design of OSDAs, but they are limited by single functionality and lack of interactivity. Meanwhile, large language models (LLMs) such as GPT-4, as general-purpose artificial intelligence systems, excel in instruction comprehension, logical reasoning, and interactive communication. However, LLMs lack in-depth chemistry knowledge and first-principle computation capabilities, resulting in uncontrollable outcomes even after fine-tuning. In this paper, we propose OSDA Agent, an interactive OSDA design framework that leverages LLMs as the brain, coupled with computational chemistry tools. The OSDA Agent consists of three main components: the Actor, responsible for generating potential OSDA structures; the Evaluator, which assesses and scores the generated OSDAs using computational chemistry tools; and the Self-reflector, which produces reflective summaries based on the Evaluator's feedback to refine the Actor's subsequent outputs. Experiments on representative zeolite frameworks show the generation-evaluation-reflection-refinement workflow can perform de novo design of OSDAs with superior generation quality than the pure LLM model, generating candidates consistent with experimentally validated OSDAs and optimizing known OSDAs.

Spotlight
LASeR: Towards Diversified and Generalizable Robot Design with Large Language Models

Junru Song, Yang Yang, Huan Xiao, Wei Peng, Wen Yao, Feifei Wang

展开摘要

Recent advances in Large Language Models (LLMs) have stimulated a significant paradigm shift in evolutionary optimization, where hand-crafted search heuristics are gradually replaced with LLMs serving as intelligent search operators. However, these studies still bear some notable limitations, including a challenge to balance exploitation with exploration, often leading to inferior solution diversity, as well as poor generalizability of problem solving across different task settings. These unsolved issues render the prowess of LLMs in robot design automation largely untapped. In this work, we present LASeR -- Large Language Model-Aided Evolutionary Search for Robot Design Automation. Leveraging a novel reflection mechanism termed DiRect, we elicit more knowledgeable exploratory behaviors from LLMs based on past search trajectories, reshaping the exploration-exploitation tradeoff with dual improvements in optimization efficiency and solution diversity. Additionally, with evolution fully grounded in task-related background information, we unprecedentedly uncover the inter-task reasoning capabilities of LLMs, facilitating generalizable design processes that effectively inspire zero-shot robot proposals for new applications. Our simulated experiments on voxel-based soft robots showcase distinct advantages of LASeR over competitive baselines. Code at https://github.com/WoodySJR/LASeR.

Poster
Interference Among First-Price Pacing Equilibria: A Bias and Variance Analysis

Luofeng Liao, Christian Kroer, Sergei Leonenkov, Okke Schrijvers, Liang Shi, Nicolas Stier Moses, Congshan Zhang

展开摘要

A/B testing is widely used in the internet industry. For online marketplaces (such as advertising markets), standard approaches to A/B testing may lead to biased results when buyers have budget constraints, as budget consumption in one arm of the experiment impacts performance of the other arm. This is often addressed using a budget-split design. Yet such splitting may degrade statistical performance as budgets become too small in each arm. We propose a parallel budget-controlled A/B testing design where we use market segmentation to identify submarkets in the larger market, and we run parallel budget-split experiments in each submarket. We demonstrate the effectiveness of this approach on real experiments on advertising markets at Meta. Then, we formally study interference that derives from such experimental designs, using the first-price pacing equilibrium framework as our model of market equilibration. We propose a debiased surrogate that eliminates the first-order bias of FPPE, and derive a plug-in estimator for the surrogate and establish its asymptotic normality. We then provide an estimation procedure for submarket parallel budget-controlled A/B tests. Finally, we present numerical examples on semi-synthetic data, confirming that the debiasing technique achieves the desired coverage properties.

Poster
Scaling up the Banded Matrix Factorization Mechanism for Large Scale Differentially Private ML

Ryan McKenna

展开摘要

Correlated noise mechanisms such as DP Matrix Factorization (DP-MF) have proven to be effective alternatives to DP-SGD in large-epsilon few-epoch training regimes. Significant work has been done to find the best correlated noise strategies, and the current state-of-the-art approach is DP-BandMF , which optimally balances the benefits of privacy amplification and noise correlation. Despite it's utility advantages, severe scalability limitations prevent this mechanism from handling large-scale training scenarios where the number of training iterations may be more than $10^4$ and the number of model parameters may exceed $10^7$. In this work, we present techniques to scale up DP-BandMF along these two dimensions, significantly extending it's reach and enabling it to effectively handle settings with over $10^6$ training iterations and $10^9$ model parameters, with no utility degradation at smaller scales.

Spotlight
Charting the Design Space of Neural Graph Representations for Subgraph Matching

Vaibhav Raj, Indradyumna Roy, Ashwin Ramachandran, Soumen Chakrabarti, Abir De

展开摘要

Subgraph matching is vital in knowledge graph (KG) question answering, molecule design, scene graph, code and circuit search, etc. Neural methods have shown promising results for subgraph matching. Our study of recent systems suggests refactoring them into a unified design space for graph matching networks. Existing methods occupy only a few isolated patches in this space, which remains largely uncharted. We undertake the first comprehensive exploration of this space, featuring such axes as attention-based vs. soft permutation-based interaction between query and corpus graphs, aligning nodes vs. edges, and the form of the final scoring network that integrates neural representations of the graphs. Our extensive experiments reveal that judicious and hitherto-unexplored combinations of choices in this space lead to large performance benefits. Beyond better performance, our study uncovers valuable insights and establishes general design principles for neural graph representation and interaction, which may be of wider interest.

Poster
Asynchronous Federated Reinforcement Learning with Policy Gradient Updates: Algorithm Design and Convergence Analysis

Guangchen Lan, Dong-Jun Han, Abolfazl Hashemi, Vaneet Aggarwal, Christopher Brinton

展开摘要

To improve the efficiency of reinforcement learning (RL), we propose a novel asynchronous federated reinforcement learning (FedRL) framework termed AFedPG, which constructs a global model through collaboration among $N$ agents using policy gradient (PG) updates. To address the challenge of lagged policies in asynchronous settings, we design a delay-adaptive lookahead technique *specifically for FedRL* that can effectively handle heterogeneous arrival times of policy gradients. We analyze the theoretical global convergence bound of AFedPG, and characterize the advantage of the proposed algorithm in terms of both the sample complexity and time complexity. Specifically, our AFedPG method achieves $\mathcal{O}(\frac{{\epsilon}^{-2.5}}{N})$ sample complexity for global convergence at each agent on average. Compared to the single agent setting with $\mathcal{O}(\epsilon^{-2.5})$ sample complexity, it enjoys a linear speedup with respect to the number of agents. Moreover, compared to synchronous FedPG, AFedPG improves the time complexity from $\mathcal{O}(\frac{t_{\max}}{N})$ to $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$, where $t_{i}$ denotes the time consumption in each iteration at agent $i$, and $t_{\max}$ is the largest one. The latter complexity $\mathcal{O}({\sum_{i=1}^{N} \frac{1}{t_{i}}})^{-1}$ is always smaller than the former one, and this improvement becomes significant in large-scale federated settings with heterogeneous computing powers ($t_{\max}\gg t_{\min}$). Finally, we empirically verify the improved performance of AFedPG in four widely used MuJoCo environments with varying numbers of agents. We also demonstrate the advantages of AFedPG in various computing heterogeneity scenarios.

Poster
Beyond Squared Error: Exploring Loss Design for Enhanced Training of Generative Flow Networks

Rui Hu, Yifan Zhang, Zhuoran Li, Longbo Huang

展开摘要

Generative Flow Networks (GFlowNets) are a novel class of generative models designed to sample from unnormalized distributions and have found applications in various important tasks, attracting great research interest in their training algorithms. In general, GFlowNets are trained by fitting the forward flow to the backward flow on sampled training objects. Prior work focused on the choice of training objects, parameterizations, sampling and resampling strategies, and backward policies, aiming to enhance credit assignment, exploration, or exploitation of the training process. However, the choice of regression loss, which can highly influence the exploration and exploitation behavior of the under-training policy, has been overlooked. Due to the lack of theoretical understanding for choosing an appropriate regression loss, most existing algorithms train the flow network by minimizing the squared error of the forward and backward flows in log-space, i.e., using the quadratic regression loss. In this work, we rigorously prove that distinct regression losses correspond to specific divergence measures, enabling us to design and analyze regression losses according to the desired properties of the corresponding divergence measures. Specifically, we examine two key properties: zero-forcing and zero-avoiding, where the former promotes exploitation and higher rewards, and the latter encourages exploration and enhances diversity. Based on our theoretical framework, we propose three novel regression losses, namely, Shifted-Cosh, Linex(1/2), and Linex(1). We evaluate them across three benchmarks: hyper-grid, bit-sequence generation, and molecule generation. Our proposed losses are compatible with most existing training algorithms, and significantly improve the performances of the algorithms concerning convergence speed, sample diversity, and robustness.

Spotlight
Revisiting a Design Choice in Gradient Temporal Difference Learning

Xiaochi Qian, Shangtong Zhang

展开摘要

Off-policy learning enables a reinforcement learning (RL) agent to reason counterfactually about policies that are not executed and is one of the most important ideas in RL. It, however, can lead to instability when combined with function approximation and bootstrapping, two arguably indispensable ingredients for large-scale reinforcement learning. This is the notorious deadly triad. The seminal work Sutton et al. (2008) pioneers Gradient Temporal Difference learning (GTD) as the first solution to the deadly triad, which has enjoyed massive success thereafter. During the derivation of GTD, some intermediate algorithm, called $A^\top$TD, was invented but soon deemed inferior. In this paper, we revisit this $A^\top$TD and prove that a variant of $A^\top$TD, called $A_t^\top$TD, is also an effective solution to the deadly triad. Furthermore, this $A_t^\top$TD only needs one set of parameters and one learning rate. By contrast, GTD has two sets of parameters and two learning rates, making it hard to tune in practice. We provide asymptotic analysis for $A^\top_t$TD and finite sample analysis for a variant of $A^\top_t$TD that additionally involves a projection operator. The convergence rate of this variant is on par with the canonical on-policy temporal difference learning.

Poster
DICE: Data Influence Cascade in Decentralized Learning

Tongtian Zhu, Wenhao Li, Can Wang, Fengxiang He

展开摘要

Decentralized learning offers a promising approach to crowdsource data consumptions and computational workloads across geographically distributed compute interconnected through peer-to-peer networks, accommodating the exponentially increasing demands. However, proper incentives are still in absence, considerably discouraging participation. Our vision is that a fair incentive mechanism relies on fair attribution of contributions to participating nodes, which faces non-trivial challenges arising from the localized connections making influence ``cascade'' in a decentralized network. To overcome this, we design the first method to estimate Data Influence CascadE (DICE) in a decentralized environment. Theoretically, the framework derives tractable approximations of influence cascade over arbitrary neighbor hops, suggesting the influence cascade is determined by an interplay of data, communication topology, and the curvature of loss landscape.DICE also lays the foundations for applications including selecting suitable collaborators and identifying malicious behaviors. Project page is available at https://raiden-zhu.github.io/blog/2025/DICE.

Poster
Fast Uncovering of Protein Sequence Diversity from Structure

luca alessandro silva, Barthelemy Meynard-Piganeau, Carlo Lucibello, Christoph Feinauer

展开摘要

We present InvMSAFold, an inverse folding method for generating protein sequences optimized for diversity and speed. For a given structure, InvMSAFold generates the parameters of a pairwise probability distribution over the space of sequences, capturing the amino acid covariances observed in Multiple Sequence Alignments (MSA) of homologous proteins. This allows for the efficient generation of highly diverse protein sequences while preserving structural and functional integrity. We demonstrate that this increased diversity in sampled sequences translates into greater variability in biochemical properties, highlighting the exciting potential of our method for applications such as protein design. The orders of magnitude improvement in sampling speed compared to existing methods unlocks new possibilities for high-throughput in virtual screening.

Spotlight
ORSO: Accelerating Reward Design via Online Reward Selection and Policy Optimization

Chen Bo Calvin Zhang, Zhang-Wei Hong, Aldo Pacchiano, Pulkit Agrawal

展开摘要

Reward shaping is critical in reinforcement learning (RL), particularly for complex tasks where sparse rewards can hinder learning. However, choosing effective shaping rewards from a set of reward functions in a computationally efficient manner remains an open challenge. We propose Online Reward Selection and Policy Optimization (ORSO), a novel approach that frames the selection of shaping reward function as an online model selection problem. ORSO automatically identifies performant shaping reward functions without human intervention with provable regret guarantees. We demonstrate ORSO's effectiveness across various continuous control tasks. Compared to prior approaches, ORSO significantly reduces the amount of data required to evaluate a shaping reward function, resulting in superior data efficiency and a significant reduction in computational time (up to 8×). ORSO consistently identifies high-quality reward functions outperforming prior methods by more than 50% and on average identifies policies as performant as the ones learned using manually engineered reward functions by domain experts.

Poster