ICML 2026 Papers

International Conference on Machine Learning

Decision breakdown

6,341papers

Counted from the official paper list; may differ slightly from the number the conference announced.

  • Spotlight
    5368.5%
  • Poster
    5,80591.5%

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WorldCache: Accelerating World Models for Free via Heterogeneous Token Caching

Weilun Feng, Guoxin Fan, Haotong Qin, Mingqiang Wu, Yuqi Li, Xiangqi Li, Zhulin An, Libo Huang, Dingrui Wang, Longlong Liao, Michele Magno, Yongjun Xu, Chuanguang Yang

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Diffusion-based world models have shown strong potential for unified world simulation, but the iterative denoising remains too costly for interactive use and long-horizon rollouts. While feature caching can accelerate inference without training, we find that policies designed for single-modal diffusion transfer poorly to world models due to two world-model-specific obstacles: *token heterogeneity* from multi-modal coupling and spatial variation, and *non-uniform temporal dynamics* where a small set of hard tokens drives error growth, making uniform skipping either unstable or overly conservative. We propose **WorldCache**, a caching framework tailored to diffusion world models. We introduce *Curvature-guided Heterogeneous Token Prediction*, which uses a physics-grounded curvature score to estimate token predictability and applies a Hermite-guided damped predictor for chaotic tokens with abrupt direction changes. We also design *Chaotic-prioritized Adaptive Skipping*, which accumulates a curvature-normalized, dimensionless drift signal and recomputes only when bottleneck tokens begin to drift. Experiments on diffusion world models show that WorldCache delivers up to **3.7$\times$** end-to-end speedups while maintaining **98\%** rollout quality, demonstrating the vast advantages and practicality of WorldCache in resource-constrained scenarios.

Poster
Guaranteed Optimal Compositional Explanations for Neurons

Biagio La Rosa, Leilani H. Gilpin

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Compositional explanations are a family of methods that aim to describe the spatial alignment between neurons' receptive field activations and concepts through logical rules, typically computed via a search over all possible concept combinations. Since computing the spatial alignment over the entire state space is computationally infeasible, the literature commonly adopts assumptions related to the structure of the combinations and beam search to restrict the state space. However, beam search cannot provide any theoretical guarantees of optimality, and it remains unclear how close current explanations are to the true optimum. In this theoretical paper, we address this gap by introducing the first framework for computing guaranteed optimal compositional explanations over the entire state space spanned by the adopted assumptions. Specifically, we propose: (i) a decomposition that identifies the factors influencing the spatial alignment, (ii) a heuristic to estimate the alignment at any stage of the search, and (iii) the first algorithm that can compute optimal compositional explanations in a time comparable to exhaustive beam search. Using this framework, we demonstrate that 10-40\% of explanations previously obtained with beam search are suboptimal when overlapping concepts are involved. Finally, we evaluate a beam-search variant guided by our proposed decomposition and heuristic, showing that it matches or improves runtime over prior methods while offering greater flexibility in hyperparameters and computational resources.

Spotlight
SWE-Compass: Towards Unified Evaluation of Agentic Coding Abilities for Large Language Models

Jingxuan Xu, Ken Deng, Weihao Li, Songwei Yu, Haoyang Huang, Xinping Lei, Yifan Yao, Huaixi Tang, Zhiyi Lai, Kepeng Lei, Zizheng Zhan, Yanan Wu, Chenchen Zhang, Wenqiang Zhu, Wen Xiang, Zongxian Feng, Han Li, Junqi Xiong, Dailin Li, Zuchen Gao, Kun Wu, Yuanxing Zhang, Wuxuan Gong, Ziyuan Gao, Guanxiang Wang, Yirong Xue, Mengfei Xie, Xiaojiang Zhang, Jinghui Wang, Wenhao Zhuang, Zheng Lin, Huiming Wang, Zhaoxiang Zhang, Yuqun Zhang, Haotian Zhang, Ming Sun, Chen Bin, Jiaheng Liu

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Evaluating large language models (LLMs) for software engineering has been limited by narrow task coverage, language bias, and insufficient alignment with real-world developer workflows. Existing benchmarks often focus on algorithmic problems or Python-centric bug fixing, leaving critical dimensions of software engineering underexplored. To address these gaps, we introduce SWE-Compass, a comprehensive benchmark that unifies heterogeneous code-related evaluations into a structured and production-aligned framework. SWE-Compass spans 8 task types, 8 programming scenarios, and 10 programming languages, with 2000 high-quality instances curated from authentic GitHub pull requests and refined through systematic filtering and validation. We benchmark ten state-of-the-art LLMs under two agentic frameworks, SWE-Agent and Claude Code, revealing a clear hierarchy of difficulty across task types, languages, and scenarios. Moreover, by aligning evaluation with real-world developer practices, we hope SWE-Compass can provide a rigorous and reproducible foundation for diagnosing and advancing agentic coding capabilities in large language models.

Poster
QHyer: Q-conditioned Hybrid Attention-mamba Transformer for Offline Goal-conditioned RL

Xing Lei, Jincheng Wang, Xuetao Zhang, Donglin Wang

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Offline goal-conditioned RL (GCRL) learns goal-reaching policies from static datasets, but real-world environments are often partially observable, so the collected trajectories are only partly consistent with the Markov assumption while other segments remain history-dependent. History-aware sequence models such as Decision Transformer (DT) are a natural fit for long-term dependency modeling, yet pure attention is inefficient and brittle when handling local Markovian structure and long-range context simultaneously. Although recent hybrid architectures (e.g., LSDT) introduce local extractors, their fixed-window extraction cannot adapt the effective memory to varying dependency lengths, often truncating long-range context instead of compressing it. Moreover, under sparse rewards, return-to-go (RTG) becomes non-discriminative across sub-trajectories, offering little guidance for stitching goal-reaching behaviors from diverse demonstrations. To address these limitations, we propose QHyer (Q-conditioned Hybrid Attention-Mamba Transformer), which replaces RTG with a Normalizing Flows (NFs) parameterized goal-reaching Q-estimator used directly as conditioning tokens, and a gated Hybrid Attention-Mamba backbone whose selective state-space dynamics enable content-adaptive history compression while attention captures global goal-directed dependencies. Extensive experiments on OGBench and D4RL demonstrate that QHyer achieves state-of-the-art performance on both non-Markovian and Markovian datasets, validating its effectiveness for diverse scenarios.

Poster
Facts in Stats: Impacts of Pretraining Diversity on Language Model Generalization

Tina Behnia, Puneesh Deora, Christos Thrampoulidis

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Language models are pretrained on sequences that blend statistical regularities, which make text fluent, with factual associations between specific tokens, which encode knowledge of facts. While recent works suggest that generalization depends critically on the interaction of these two streams, such as the diversity of the contexts in which facts appear, these effects remain difficult to study systematically. This paper introduces a flexible synthetic testbed that combines a statistical stream of generic tokens with an abstract factual stream of source-target token pairs, enabling fine-grained control over their interaction, such as their composition into a sequence (contextual structure) or the level of context diversity carrying the facts at training time. Through controlled experiments, we find that higher contextual diversity delays in-distribution factual learning, while low diversity can harm out-of-distribution generalization in ways that depend on the contextual structure. As a result, the optimal diversity level depends on the training budget. Beyond factual recall failures, we also identify failures in statistical generalization as we study how the interplay between contextual design and diversity level impacts different aspects of generalization. Furthermore, through a series of controlled interventions on the model components, we trace failure in different aspects of generalization to distinct optimization bottlenecks, highlighting the importance of the embedding and unembedding layers. Overall, our synthetic framework allows us to isolate effects that would be confounded in large-scale studies, offering a controlled testbed for future investigations.

Poster
Adaptive Residual-Update Steering for Low-Overhead Hallucination Mitigation in Large Vision-Language Models

Zhengtao Zou, Ya Gao, Jiarui Guan, Bin Li, Pekka Marttinen

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Large Vision-Language Models (LVLMs) typically process visual inputs as a prefix to the language decoder. As the model autoregressively generates text, this initial visual information inevitably undergoes ``dilution'', leading the model to over-rely on language priors and hallucinate objects. Existing interventions attempt to correct this by contrasting logits or iteratively refining outputs, but they incur prohibitive latency costs. We propose **Residual-Update Directed DEcoding Regulation (RUDDER)**, a framework that counters visual dilution by creating a persistent visual anchor. We extract a robust evidence direction (**CARD**) directly from the model's prefill residual updates, and inject it into the decoding process. This injection is modulated by an adaptive gate, the **Beta Gate**, which acts as a trust mechanism and ensures the visual reminder is applied only when necessary. Experiments on LLaVA-1.5 (7B/13B), Idefics2, InstructBLIP, and Qwen2.5-VL demonstrate that RUDDER consistently mitigates hallucination (with greedy decoding, RUDDER reduces CHAIR$_S$ by an average of **24.4\%** and CHAIR$_i$ by **23.6\%** relative) and scales effectively across architectures, all while maintaining **>96.0\%** throughput. The code is available at https://github.com/Akko000/RUDDER-Residual-Update-Directed-DEcoding-Regulation-

Poster
SafeHarbor: Defining Precise Decision Boundaries via Hierarchical Memory-Augmented Guardrail for LLM Agent Safety

Zhe Liu, Zonghao Ying, Wenxin Zhang, Quanchen Zou, Deyue Zhang, Dongdong Yang, Xiangzheng Zhang, Hao Peng

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Recent advances in foundation models have transformed LLMs from passive conversational systems into autonomous agents capable of reasoning and tool execution. While these capabilities unlock substantial practical value, they also introduce new security risks, as adversaries can manipulate agents into performing harmful actions in real-world environments. Existing defense strategies mitigate such threats but frequently struggle to balance safety and utility, resulting in over-refusal of benign user requests. To mitigate this trade-off, we propose SafeHarbor, a novel framework designed to establish precise decision boundaries for LLM agents. Unlike static guidelines, SafeHarbor extracts context-aware defense rules through enhanced adversarial generation. We design a local hierarchical memory system for dynamic rule injection, offering a training-free, efficient, and plug-and-play solution. Furthermore, we introduce an information entropy-based self-evolution mechanism that continuously optimizes the memory structure through dynamic node splitting and merging. Extensive experiments demonstrate that SafeHarbor achieves state-of-the-art performance on both ambiguous benign tasks and explicit malicious attacks, notably attaining a peak benign utility of 63.6\% on GPT-4o while maintaining a robust refusal rate exceeding 93\% against harmful requests. The source code is publicly available at https://github.com/ljj-cyber/SafeHarbor.

Poster
Linguistic Nepotism: Trading-off Quality for Language Preference in Multilingual RAG

Dayeon Ki, Marine Carpuat, Paul McNamee, Daniel Khashabi, Eugene Yang, Dawn Lawrie, Kevin Duh

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Multilingual Retrieval-Augmented Generation (mRAG) systems enable language models to answer knowledge-intensive queries with citation-supported responses across languages. Despite their growing use, an open questions is whether the mixture of different document languages impacts generation and citation behavior in *unintended* ways. To investigate this, we introduce a controlled methodology using model internals to measure language preference while holding other factors such as document relevance constant. Across eight languages and six open-weight models, we find that models preferentially cite English sources when queries are in English, with this bias amplified for lower-resource languages and for documents positioned mid-context. More crucially, we find that models sometimes trade-off document relevance for language preference, indicating that citation choices are not always driven by informativeness alone. Our findings shed light on how language models leverage multilingual context and influence citation behavior.

Spotlight
Weakly Supervised Cross-Modal Learning for 4D Radar Scene Flow Estimation

Jingyun Fu, Zhiyu Xiang, Na Zhao

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Due to the difficulty of obtaining ground-truth data for 4D radar scene flow estimation, previous methods typically rely on either self-supervised losses or cross-modal supervision using 3D LiDAR data, 2D images, and odometry. However, self-supervised approaches often yield suboptimal results due to radar's inherently low-fidelity measurements, while existing cross-modal supervised methods introduce complex multi-task architecture and require costly LiDAR sensors to generate pseudo radar scene flow labels from pretrained 3D tracking models. To overcome these limitations, we propose a task-specific iterative framework for weakly supervised radar scene flow learning, using only images and odometry for auxiliary supervision during training. Specially, we establish two novel instance-aware self-supervised losses by exploiting off-the-shelf 2D tracking and segmentation algorithms to obtain tracked instance masks, which are back-projected into 3D space to provide instance-level semantic guidance; for static regions, we integrate vehicle odometry with radar's intrinsic motion cues to construct a rigid static loss. Extensive experiments on the real-world View-of-Delft (VoD) dataset demonstrate that our method not only surpasses state-of-the-art cross-modal supervised approaches that rely on 3D multi-object tracking on dense LiDAR point clouds but also outperforms existing fully supervised scene flow estimation methods. The code is open-sourced at \href{https://github.com/FuJingyun/IterFlow}{https://github.com/FuJingyun/IterFlow}.

Poster
Profiling the Irrational Agent: Cognitive Modeling of LLM Behaviors in Sequential Jailbreaks

Xikang Yang, biyu zhou, Xuehai Tang, Jizhong Han, Songlin Hu

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Large language models (LLMs) are increasingly deployed in high-stakes settings, yet they remain vulnerable to sequential jailbreaks that exploit multi-turn interaction to circumvent safety mechanisms. Current safety evaluations are largely outcome-based, offering little insight into the latent decision processes that lead to unsafe compliance. We propose an interpretable cognitive modeling framework that couples a controlled elicitation paradigm, the Contextual Iowa Gambling Task (C-IGT), with a Generalized Rescorla--Wagner (GRW) architecture to decompose behavior into measurable mechanisms. Across a diverse set of mainstream LLMs, we find that sequential vulnerability is not explained by scale alone but emerges from interactions among cognitive factors, including optimism-biased learning, perceptual reward amplification, and choice inertia. Moreover, counterfactual feedback and psychologically framed rewards (e.g., regret, authority, threat) substantially accelerate the transition from refusal to compliance. These results yield principled cognitive profiles of LLM "irrationality" and provide insights for interdisciplinary research on LLM agents at the intersection of machine learning and human behavioral science.

Poster
When Distance Distracts: Representation Distance Bias in BT-Loss for Reward Models

Tong Xie, Andrew Bai, Yuanhao Ban, Yunqi Hong, Haoyu Li, Cho-Jui Hsieh

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Reward models are central to Large Language Model (LLM) alignment within the framework of RLHF. The standard objective used in reward modeling is the Bradley-Terry (BT) loss, which learns from pairwise data consisting of chosen and rejected responses. In this work, we analyze the per-sample gradient of BT-loss and show spurious learning signals due to representation distance. In particular, BT gradient norm scales with two distinct components: (1) **prediction error**, reflected by the difference in predicted rewards between chosen and rejected responses, and critically, (2) **representation distance** between the pair measured in the output space of the final layer. While the first term captures the intended training signal, the second term can significantly impact the update magnitude and misalign learning. Specifically, pairs with small representation distance often receive vanishingly weak updates, even when misranked, while pairs with large distance receive disproportionately strong updates. This leads to gradients from large-distance pairs overshadowing those from small-distance pairs, where fine-grained distinctions are especially important. To overcome this limitation, we propose NormBT, an adaptive pair-wise normalization scheme that rescales update to balance representation-driven effects and focuses learning signals on prediction error. NormBT is a lightweight, drop-in modification to BT loss with negligible overhead. Across various LLM backbones and datasets, NormBT improves reward model performance consistently, with notable gains of over 5% on the Reasoning category of RewardBench, which contains numerous fine-grained pairs.

Poster
On the Theoretical Limitations of Embedding-based Link Prediction

Samy Badreddine, Emile van Krieken, Luciano Serafini

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Neural networks often map low-dimensional embeddings to high-dimensional output spaces. Usually, the output layer is linear, which can create a *rank bottleneck* that limits the functions a model can represent. Such bottlenecks are ubiquitous in link prediction models, such as knowledge graph embeddings (KGEs), as the output space of entities can be orders of magnitude larger than the embedding dimension. We investigate how rank bottlenecks limit model expressivity for fitting the training data. While previous work focused on sufficient bounds on the embedding dimension required for specific KGEs, we show necessary bounds for *all* KGEs with a linear output layer, which grow with graph size and connectivity. We also consider a non-linear output layer using mixtures to break the bottleneck without significant parameter overhead. Empirically, we show that models using this non-linear layer improve in ranking performance and probabilistic fit for large and dense datasets at a low parameter cost, as predicted by our theory. Our work reveals how linear output layers limit KGEs and motivates non-linear alternatives for scaling to large and dense graphs.

Poster
Welfare-Optimal Classification with Accuracy Auctions

Bana Sadi, Eden Saig, Nir Rosenfeld

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Prediction algorithms are increasingly used to inform decisions about humans, but maximizing accuracy—the standard learning objective—is not necessarily optimal for this purpose. Instead, we propose optimizing social welfare, defined as the average gain users receive from correct predictions. Welfare enables to express, and therefore account for, heterogeneity in how much users benefit from accuracy. But since these valuations are private and users can benefit from overreporting them, learning must simultaneously elicit truthful values and optimize welfare with respect to them. To this end, we propose a novel learning algorithm that incorporates a truthful auction. We show how to compute allocations and prices efficiently, and bound the number of paying users—which surprisingly is independent of the sample size. We conclude with experiments on real and synthetic data that demonstrate our algorithm and explore the connections between welfare and accuracy.

Spotlight
LazyAttention: Efficient Retrieval-Augmented Generation with Deferred Positional Encoding

Haocheng Xia, Mihir Pamnani, Hanxi Fang, Supawit Chockchowwat, Yongjoo Park

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Key-value (KV) caching accelerates inference of large language models (LLMs) by reusing past computations for generated tokens. Its importance becomes even greater in long-context applications such as retrieval-augmented generation (RAG) and in-context learning (ICL). However, conventional KV caching embeds positional information directly into the cache, limiting its reusability. Existing solutions either restrict reuse to prefixes or require expensive memory materialization for positional re-encoding. We introduce LazyAttention, a novel attention mechanism that kernelizes deferred positional encoding to enable zero-copy, position-agnostic KV reuse. By adjusting positional encoding within attention kernels on-the-fly, LazyAttention resolves the materialization bottleneck, allowing a single physical KV copy to serve multiple logical requests at arbitrary positions. Leveraging attention kernels tailored for prefilling and decoding, our system achieves significant efficiency improvements: under skewed document distributions, it reduces time-to-first-token (TTFT) by 1.37× and increases inference throughput by 1.40× compared to the state-of-the-art Block-Attention, while maintaining comparable output quality.

Poster
Online Fair Division with Additional Information

Tzeh Yuan Neoh, Jannik Peters, Nicholas Teh

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We study the problem of fairly allocating indivisible goods to agents in an online setting, where goods arrive sequentially and must be allocated irrevocably. Focusing on the popular fairness notions of envy-freeness, proportionality, and maximin share fairness (and their approximate variants), we investigate how access to future information changes what guarantees are achievable. Without any information, we prove strong impossibility results even for approximate fairness. With normalization information (agents' total values), we provide an algorithm that achieves stronger fairness guarantees than previously known results, and show matching impossibilities for stronger notions. With frequency predictions (value multisets without order), we design a meta-algorithm that lifts a broad class of offline “share-based” guarantees to the online setting, matching the best-known offline bounds. Finally, we provide learning-augmented variants of both models: under noisy totals or noisy frequency predictions, our guarantees are robust and degrade gracefully with the error parameters.

Poster
Detecting and Filtering Unsafe Training Data via Data Attribution with Denoised Representation

Yijun Pan, Taiwei Shi, Jieyu Zhao, Jiaqi W. Ma

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Large language models (LLMs) are highly sensitive to even small amounts of unsafe training data, making effective detection and filtering essential for trustworthy model development. Current state-of-the-art (SOTA) detection approaches primarily rely on moderation classifiers, which require significant computation overhead for training and are limited to predefined taxonomies. In this work, we explore data attribution approaches that measure the similarity between individual training samples and a small set of unsafe target examples, based on data representations such as hidden states or gradients. We identify a key limitation in existing methods: unsafe target texts contain both critical tokens that make them unsafe and neutral tokens (e.g., stop words or benign facts) that are necessary to form fluent language, and the latter of which makes the overall representations noisy for the purpose of detecting unsafe training data. To address this challenge, we propose Denoised Representation Attribution (DRA), a novel representation-based data attribution approach that denoises training and target representations for unsafe data detection. Across tasks of filtering jailbreaks and detecting gender bias, the proposed approach leads to significant improvement for data attribution methods, outperforming SOTA methods that are mostly based on moderation classifiers.

Poster
Triadic Dynamics Aware Diffusion Posterior Sampling for Inverse Problems: Optimizing Guidance and Stochasticity Schedules

Junseo Bang, Dong Ju Mun, Hoigi Seo, Seongmin Hong, Se Young Chun

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Generative posterior sampling using diffusion models has emerged as a dominant paradigm for solving inverse problems in imaging, which usually consists of three main components: data consistency (DC) guidance, classifier-free guidance (CFG) and stochasticity. While prior arts have focused on how to develop each or all components, less attention has given to how to schedule them, leading to heuristically fixed or partially adjusted suboptimal schedules. In this work, we argue that the interactions among all three components in terms of scheduling are crucial for significantly improved performance in solving inverse problems in imaging. Our analysis shows that aggressive CFG early in sampling conflict with DC guidance, while stochasticity brings the trajectory back to higher-probability regions. Based on these findings, we propose Triadic Dynamics Aware Posterior Sampling (TriPS), which reformulates posterior sampling as a time-varying control problem and optimizes schedules following a triadic trend of decreasing DC and stochasticity scales alongside increasing CFG scale. TriPS achieves this through two strategies: template-based search over functional priors for reliable baseline schedules, and Group Relative Policy Optimization (GRPO)-based reinforcement learning for more flexible temporal curves. Experiments demonstrate TriPS outperforms state-of-the-art baselines in data fidelity and perceptual realism.

Poster
Semantic Tube Prediction: Beating LLM Data Efficiency with JEPA

Hai Huang, Yann LeCun, Randall Balestriero

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Large Language Models (LLMs) obey consistent scaling laws---empirical power-law fits that predict how loss decreases with compute, data, and parameters. While predictive, these laws are descriptive rather than prescriptive: they characterize typical training, not optimal training. Surprisingly few works have successfully challenged the data-efficiency bounds implied by these laws---which is our primary focus. To that end, we introduce the Geodesic Hypothesis, positing that token sequences trace geodesics on a smooth semantic manifold and are therefore locally linear. Building on this principle, we propose a novel Semantic Tube Prediction (STP) task, a JEPA-style regularizer that confines hidden-state trajectories to a tubular neighborhood of the geodesic. STP generalizes JEPA to language without requiring explicit multi-view augmentations. We show this constraint improves signal-to-noise ratio, and consequently preserves diversity by preventing trajectory collisions during inference. Empirically, STP allows LLMs to match baseline accuracy with 16$\times$ less training data, directly violating the data term of fine-tuning scaling laws and demonstrating that principled geometric priors can surpass brute-force scaling. Code: \url{https://github.com/galilai-group/llm-jepa#stp}

Poster
OnePO: Direct One-stage Policy Optimization for SFT-free Domain Adaptation

Junying Chen, Xinyuan Xie, Ziniu Li, Benyou Wang

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Domain adaptation typically follows a two-stage pipeline: Supervised Fine-Tuning (SFT) then Reinforcement Learning (RL). However, *does RL necessarily require a pre-SFT phase for domain adaptation?* SFT confines the model to an imitation distribution, limiting RL exploration, while the two-stage transition causes capability regression and extra engineering. We propose **One-stage Policy Optimization (OnePO)**, an SFT-free paradigm that adapts pretrained LLMs to target domains in a single RL stage. OnePO uses teacher outputs as transient guidance to overcome the slow convergence of pure RL, while avoiding two failures of naive teacher-output integration: gradient starvation for low-probability teacher tokens and distribution anchoring from persistent teacher signals. It introduces two mechanisms: (1) *Adaptive Objective Evolution*, reshaping the RL objective for rapid absorption of teacher-provided knowledge; and (2) *Teacher Retirement*, automatically discarding teacher outputs once the model surpasses them. On medical adaptation, OnePO achieves 67.2 on HealthBench with only 20K training samples, outperforming SFT+RL by +2.7 and pure RL by +7.4 points. Scaling the same recipe produces *HuatuoGPT-3*, an open-source medical LLM series whose 32B variant reaches 70.3 on HealthBench. Additional writing and legal-domain experiments show that OnePO extends beyond medicine. Models and code are available at https://github.com/FreedomIntelligence/HuatuoGPT-3.

Poster
Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents

Jacopo Teneggi, SM Bargeen Alam Turzo, Tanya Marwah, Alberto Bietti, P. Douglas Renfrew, Vikram Khipple Mulligan, Siavash Golkar

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Large language models (LLMs) are capable of emulating reasoning and using tools, creating opportunities for autonomous agents that execute complex scientific tasks. Protein design provides a natural testbed: although machine learning (ML) methods achieve strong results, these are largely restricted to canonical amino acids and narrow objectives, leaving unfilled need for a generalist tool for broad design pipelines. We introduce Agent Rosetta, an LLM agent paired with a structured environment for operating Rosetta, the leading physics-based heteropolymer design software, capable of modeling non-canonical building blocks and geometries. Agent Rosetta iteratively refines designs to achieve user-defined objectives, combining LLM reasoning with Rosetta's generality. We evaluate Agent Rosetta on design with canonical amino acids, matching specialized models and expert baselines, and with non-canonical residues---where ML approaches fail---achieving comparable performance. Critically, prompt engineering alone often fails to generate Rosetta actions, demonstrating that environment design is essential for integrating LLM agents with specialized software. Our results show that properly designed environments enable LLM agents to make scientific software accessible while matching specialized tools and human experts.

Poster