REFLEX: RNA Ensemble Generation via Flexibility-Calibrated Stochastic Bridge

2 días 6 horas ago
arXiv:2610.26261v3 Announce Type: replace Abstract: RNA molecules often function through multiple experimentally observed conformational states. A central challenge is to capture ensemble diversity without sacrificing structural fidelity: samples may collapse toward averaged representative structures or drift into unsupported conformational regions. We introduce REFLEX (RNA Ensemble generation calibrated by FLEXibility), a sequence-conditioned generator for RNA backbone-frame ensembles based on a heteroscedastic stochastic bridge on SE(3). During training, experimental B-factors calibrate residue-wise bridge widths, exposing each observed conformer through local perturbation neighborhoods with residue-specific scales while keeping constrained regions sharper. A learned flexibility condition guides the bridge-field network to recover target conformer-specific frames from these calibrated noisy states. At inference, REFLEX uses only the input sequence, requiring no MSA-subsampling heuristics. On a multi-conformer RNA benchmark, REFLEX achieves the best precision-recall trade-off for ensemble coverage across evaluation thresholds, while recovery-stress ablations indicate gains in target-frame recovery under stronger perturbations.
Wanli Ma, Tianmeng Hu, Ke Li

When Form Changes but Logic Doesn't: Building Logic-invariant LLMs through Logical Structure

2 días 6 horas ago
arXiv:2610.25402v2 Announce Type: replace Abstract: Large language models (LLMs) have achieved strong performance across diverse reasoning tasks, yet it remains unclear whether this performance reflects an understanding of underlying logical structure or a reliance on shallow semantic cues. A key indicator of such understanding is whether models treat logically equivalent inputs consistently, producing the same predictions despite differences in expression. Through systematic evaluation on curated data, we show that even strong LLMs often fail this test: they do not consistently preserve predictions across logically equivalent inputs and generalize poorly to unseen logical forms. To address this limitation, we propose LoGIcal STructure-guided reasoning (LoGIST), a framework that guides LLM reasoning with explicit logical structure. LoGIST maps each input instance to a decision diagram, a directed acyclic graph that captures the underlying logical structure, and encodes this graph into a logical embedding that conditions the LLM's reasoning process. Across multiple training settings, LoGIST reduces inconsistency under logical equivalence and improves generalization to unseen logical forms, suggesting that logical invariance is a useful target for building more robust and generalizable logical reasoning in LLMs.
Xuyuan Liu, Xinshuai Dong, Elynn Chen, Yujun Yan

HybridResearcher: Bridging the Structured-Unstructured Boundary for Deep Research Agents

2 días 6 horas ago
arXiv:2610.24899v2 Announce Type: replace Abstract: While LLM agents are increasingly capable of gathering and synthesizing evidence from a single homogeneous source, such as structured tables or unstructured data, real-world analytical questions frequently span heterogeneous sources. For example, answering one enterprise question may require both a result computed over an internal database and evidence found on the web. Recent evaluations on benchmarks like HybridDeepResearch show that even frontier agents struggle when evidence must cross this boundary. While these benchmarks have exposed the limitation, methodologies to explicitly teach cross-source reasoning remain absent. To address this, we introduce HybridResearcher, a 4B agent trained to bridge evidence across the structured and unstructured boundary. To build it, we synthesize cross-source bridge trajectories by starting with validated single-source tasks-such as existing text-to-SQL or web search queries-and fabricating the missing source around a bridge entity drawn from the seed's own output. We retain a sample only when strict construction gates confirm that neither side alone suffices, ensuring the data requires true cross-source interdependence. Finally, we train on this curated dataset using supervised fine-tuning followed by reinforcement learning. Evaluated on the existing HybridDeepResearch benchmark, HybridResearcher improves over our base model, Qwen3.5-4B, by 30.0 points pass@8 and surpasses the far larger Qwen3.5-397B-A17B by 8.3 points, while also improving over its base model on established, held-out single-source benchmarks (BrowseComp and BrowseComp-Plus), demonstrating that this complex cross-source reasoning can be taught directly to small models without triggering catastrophic forgetting.
Soyoung Yoon, Peiran Xu, Han Wang, Ruofan Wu, Xiaodong Yu, Feng Yan, Mohit Bansal, Debiao Li, Seung-Won Hwang, Yuxiong He, Zhewei Yao

World of SWECraft: Agent Collaboration at Scale via Simulated Software Worlds

2 días 6 horas ago
arXiv:2610.24061v2 Announce Type: replace Abstract: As teams of AI agents take on larger projects and long-standing open problems, agent collaboration offers another dimension for scaling inference-time compute. To understand what makes such collaboration effective and scalable, we develop Software World, a framework for simulating multi-agent coworking in realistic software ecosystems. It comes with a pipeline to create environments of real, interdependent Python packages of different topics, sizes, and dependency structures, which we call software worlds. In a simulation, agents maintain packages in the world with a high-level goal of improving software efficiency, and they are free to discover tasks to work on and collaborate with others. We evaluate agents' work in a world collectively by measuring speedup in hidden dependent packages. The framework allows us to study different elements of collaboration by varying communication, ownership, and resource allocation. We run simulations in three different worlds, totaling more than 10,000 hours of agent work across eight models. Overall, performance improvement scales with inference-time compute, with the best model improving downstream efficiency by up to 31%. We show that most agents can find meaningful tasks via collaboration, but some frontier models can prematurely stop looking for improvements and make little progress. We release the simulation framework and traces to support future studies of agent collaboration at https://szj.io/sw.
Shannon Zejiang Shen, Yapei Chang, Qiyao Liang, Benjamin Newman, Jenny Liang, Rulin Shao, Ziqiao Ma, Junjie Oscar Yin, Yung-Sung Chuang, Weijia Shi, Yejin Choi, Luke Zettlemoyer, Pang Wei Koh, Mohit Iyyer, Tongshuang Wu, David Sontag

OwlSight: A Panoramic Monitor for Chain-of-Thought Reasoning

2 días 6 horas ago
arXiv:2610.23670v2 Announce Type: replace Abstract: Chain-of-Thought (CoT) monitoring offers actionable evidence for oversight AI systems, with the potential to enable early detection and intervention. However, existing approaches are focused on specific tasks, whereas the regulation of AI, particularly reasoning models, requires monitoring a broader range of tasks. We introduce Factor for CoT monitoring, a strategy that supports customizing monitoring requirements in the prompt, which enables a single monitor to cover different tasks by relying on different factors. Furthermore, we introduce two types of factors, fine-grained and coarse-grained (e.g., monitoring whether a specific email address has been leaked versus monitoring privacy leakage), to accommodate diverse user monitoring needs. Based on this, we develop a CoT monitor named OwlSight that relies solely on factor to monitor behaviors related to multiple dimensions, including capability, safety, and trustworthiness. Experiments across 15,971 reasoning trajectories show that OwlSight surpasses general-purpose LLMs by 1.32-30.57 and 11.71-27.81 points at fine and coarse granularity, respectively, and achieves state-of-the-art results on OpenAI's CoT monitorability benchmark. It also generalizes to unseen models' CoTs and remains robust to Factor rephrasings, CoT compression, and obfuscation, offering a promising paradigm for CoT monitoring that can contribute to the oversight of frontier AI.
Lewen Yan, Yanxu Zhu, Jie Zhang, Jing Shao

LOADBench: A Large Open Analog Dataset and Benchmark for Machine Learning in IC Design

2 días 6 horas ago
arXiv:2610.21591v2 Announce Type: replace Abstract: Machine learning (ML) for analog IC design is constrained by limited open data and the absence of standardized evaluation: results reported in different papers are typically obtained on bespoke, often closed, datasets and with ad-hoc metrics, leaving comparisons across methods unreliable. We address both gaps with a large opensource dataset and a suite of standardized benchmarks. The dataset contains more than 100 operational amplifier (opamp) topologies (1-, 2-, and 3-stage) in the SkyWater130 PDK, each shipped with structural and functional annotations, topology-specific sizing constraints (symmetry and sizing rules), an Ngspice testbench, and a multi-objective NSGA-II sizing run producing around 103 Pareto-optimal and 106 intermediate sizing-performance pairs per topology. On top of this data we define six benchmark tasks with precise protocols: inverse sizing, topology selection, sub-circuit classification, structural circuit generation, Pareto-membership prediction, and multi-objective optimization. Thus, the data presented here constitutes the most comprehensive dataset for ML development in over four decades of analog IC design automation. The dataset, ground-truth annotations, and reference implementations of the metric-defining routines are released under an open license, enabling reproducible and directly comparable evaluation across heterogeneous analog design automation methods.
M. Leibl, F. Azevedo, S. Uhlich, A. Bonetti, A. Venkitaraman, C. Hsieh, P. Pham, L. Servadei, H. Graeb, R. Martins

Incentivizing Tool-Use Reinforcement Learning for Post-Arrival Emergency Care Prediction

2 días 6 horas ago
arXiv:2610.21449v2 Announce Type: replace Abstract: Large language models (LLMs) can reason over both structured measurements and free-text records, which makes them attractive for emergency department (ED) prediction. However, most existing LLMs still fall short of conventional ML methods like trees on EHR-based prediction tasks. Our controlled analysis traces this gap to two weaknesses: LLMs do not select informative features, and they misjudge what numerical values imply for risk even when given the right features. We propose TIR-EC, a tool-integrated reinforcement learning framework that addresses both. TIR-EC exposes EHR feature groups as tools the LLM can call. It trains the LLM with rewards from a gradient-boosted tree teacher, which provides a reference set of informative tools and a graded risk target. TIR-EC also distills task-specific clinical skills into the model weights through a reverse curriculum that gradually removes the skills from the prompt during RL process. Evaluation on three clinical prediction tasks shows that our 4B agent achieves the highest macro F1 of all compared models, outperforms conventional ML baselines, and is competitive with much larger frontier LLMs. Further analysis shows that TIR-EC selects more useful evidence with fewer tool calls and combines measurements more effectively.
Pengfei Hu, Chenwei Wu, Qiao Jin, Jun Deng, Zhiyong Lu, Liyue Shen, Yue Ning

SkillNEO: Non-Elitist Evolutionary Optimization of Agent Skills

2 días 6 horas ago
arXiv:2610.20926v2 Announce Type: replace Abstract: Agent skills turn procedural knowledge into reusable artifacts, allowing LLM agents to accumulate and refine expertise through experience. Building on this, skill evolution iteratively improves skills using execution feedback. However, improvement may require several interdependent edits, so low-reward versions can still be worth developing. Requiring immediate reward gains can discard useful partial repairs before their benefits emerge. Non-elitist evolution allows new versions to receive further edits despite scoring below earlier ones. For agent skills, this calls for evidence of what to preserve and repair next. We introduce SkillNEO (Non-Elitist Evolutionary Optimization for Agent Skills), which separately selects a version to use and versions to keep improving. Comparing how related versions perform the same task reveals working steps to preserve and remaining failures to fix. It can also revisit and revise earlier versions using later evidence. Across 86 SkillsBench tasks in eight domains, including software engineering and office work, SkillNEO raises GPT-5.4 Mini's average reward from 49.1% to 66.4%, within GPT-5.5 and GPT-5.6 Luna's original-skill range. Mini executes tasks, proposes revisions, and edits skills; final evaluation uses the same task instances. Gains span all eight domains. The same skills improve stronger models without further editing. On the 41 tasks with modified skills, reuse improves Luna by 10.5 percentage points and places GPT-5.5 10.6 points above its published original-skill reference. Execution records show these skills can benefit stronger models even when Mini still fails some task requirements. Search histories also show lower-scoring versions leading to skills ultimately selected for use. Together, these findings show that skill evolution can turn a weaker model's partial progress into reusable procedural knowledge for improving more capable agents.
Enze Ma, Chunyu Miao, Yankai Chen, Jie Yang, Liancheng Fang, Kening Zheng, Hanrong Zhang, Muyao Xu, Xinle Yu, Chengze Li, Wei-Chieh Huang, Ziwei Ren, Yunhao Du, Zhixiang Shen, Xue Liu, Philip S. Yu, Zhen Wang

AssetForge: Asset-Augmented Task Synthesis for Business Automation Agents

2 días 6 horas ago
arXiv:2610.18330v2 Announce Type: replace Abstract: Training business automation agents requires executable tasks that connect a natural-language request to an application state and a verifiable end state. Traditional Rubrics requires Authors to recreate application interfaces, initial records, policy evidence, and outcome checks for each task, entangling business logic with repeated infrastructure work. We introduce AssetForge, an asset-augmented task-construction pipeline that pairs a reusable construction-asset library with task-specific Rubrics. The assets provide application interfaces, world-state components, policy/evidence carriers, and native assertion definitions; the Rubric directs their instantiation for a particular business task. Executable checks and an additional model-based review validate each candidate, return targeted feedback, and support bounded repair before acceptance. On AutomationBench v1.0.6 public-600, fine-tuning Qwen3.6-35B-A3B on 6,000 AssetForge examples yields 41.17% on the official strict pass@1 metric, 4.4 times the 9.33% base score (+31.83 points). With the same backbone and GLM-5.3 supervision, AssetForge reaches 41.17% versus 30.33% for traditional Rubrics, a 10.84-point gain (35.7% relative) at the same accepted-example scale (6,000 versus 6,000 examples). Both DeepSeek- and GLM-supervised AssetForge models improve AppWorld completion over the base model on Test-Normal and Test-Challenge. These results establish the advantage of AssetForge's complete construction pipeline on AutomationBench public: the coupled asset-Rubric interface directs Authors toward business logic, while executable checks and model-based review validate their tasks.
Xiangrui Liu, Shuo Tang, Siheng Chen

SFT Leaves a Reproducible Signature in Activation Geometry: Calibrating Post-Training Interpretability Against Run-to-Run Noise

2 días 6 horas ago
arXiv:2610.17093v2 Announce Type: replace Abstract: A model diff credits post-training with whatever separates a base checkpoint from one post-trained descendant, presuming a rerun would land close by. On the sparse co-activation graph of Qwen3-1.7B it does not: two LoRA-SFT reruns sit over half as far apart as either sits from the base. We score each base-to-post contrast against the run-to-run band of its own recipe, and show that $k$ runs certify no better than $p=1/(k+1)$ under run exchangeability, however large the effect, so the band $z$-score is a descriptive scale. SFT leaves a large, reproducible signature: base $\to$ SFT displaces the graph by 17.8 pairwise-distance SDs beyond the mean distance between four independent LoRA-SFT runs, and the pre-registered estimator replicates on Llama-3.1-8B with Llama-Scope. At 29 steps each, four SFT and four DPO runs occupy disjoint displacement ranges, a gap $5.0\times$ and $5.6\times$ the spreads of the two arms, without any band. All bands use graphs built on one GPU architecture. Three other readings stop short of a verdict: DPO band counts (3/4, 1/4, 3/4 contrasts outside at 12, 29, 60 steps) show no consistent dose ordering while its displacement stays flat; light GRPO is a secondary non-detection, not an absence, and we run no equivalence test; and the graph concentration read as an RL signature is already in the zero-RL base. A pre-registered causal sweep at three edge budgets on 4,816 held-out prompts found the displaced sources load-bearing ($12\times$ a matched random control in mean, $3.5\times$ in median at 10,000 edges), but their stage-specificity interaction reversed at two budgets and the third failed its faithfulness gate, so we claim calibrated structural displacement, not a changed mechanism. Scope: one backbone, one SFT recipe and general-text probe states for the full protocol.
Xupeng Chen, Chenqian Le, Jiayi Cheng, Runhao Li, Michael Yue