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.
https://arxiv.org/abs/2610.26261
Using an LLM to generate training data for another is among the most general ways to train one, and it remains common practice. Some frontier teams have closed that route for their own models: what comes back is an answer, or a short summary, without the detailed reasoning trace behind it. That is a little ironic: they were themselves built on distilling human knowledge, and distilling an open-source model is still entirely routine; the restriction applies to their own outputs alone. Recent work recovers the hidden reasoning by replaying encrypted blocks across models. It somehow works, but it breaks the providers' terms of service, so it is not something a product can be built on long-term. We built the alternative. We take the context and the teacher's answer as input, and generate the reasoning trace ourselves, in the style of the student's own model family. Training is two-stage, supervised and then adversarial: a generator learns to regenerate the family's own reasoning traces from their context and answer, and a critic learns how real a reasoning trace looks. Applied to a teacher's answer, the generator writes one in the family's style. An independent judge rates how likely traces are to be genuine on a scale from 0 to 1: ours average 0.68, real traces 0.66, and traces selected by the critic from four candidates 0.82. These are authenticity scores, not correctness rates. We test the idea on five benchmarks with everything else held fixed. On general tasks the five training corpora are about the same; on coding, the generated reasoning beats Fable 5's own thinking content. With the same 5,000 questions and the same teacher answers, HumanEval+ improves by 3.7 points and MBPP+ by 7.1 at the final checkpoint, and the MBPP+ lead holds at every checkpoint. We suspect that reasoning written in the student's family style is easier for it to learn from.
https://arxiv.org/abs/2610.29680
How do LLM agents' strategies differ, and how much can instructions to adopt a persona change their behavior over a game? We study these questions with AgentMonopoly, an environment where agents communicate, buy and trade properties, and make decisions that affect later turns. We compare models from four families, each at two sizes, in games with identical models, different sizes of the same family, or different families. We also assign one agent a persona, a description of how it should behave, intended to change a tendency observed in games without that persona. The tested models differ in how often they trade, waive rent, and manage cash and properties. Larger models do not consistently win more games. Persona instructions change the words agents use and some of their actions, but the changes do not always match the role across all decisions. These results show why persona following should be assessed through actions and outcomes as well as language. As our findings are conditional on the tested checkpoints, prompts, and five seeds per configuration, the open-source nature of AgentMonopoly provides the experimental infrastructure for further extending these comparisons. Our code is available at this https URL.
https://arxiv.org/abs/2610.29330
Language models relying on verbalized Chain-of-Thought (CoT) are constrained to token-by-token generation in the language space, where many tokens serve textual coherence rather than core reasoning. This entangles genuine differences in logical trajectories with superficial variations in verbalization. Moving reasoning into a compact, continuous latent space offers a promising alternative for efficiently representing and exploring diverse reasoning trajectories. However, current latent models remain largely deterministic, capturing only a single reasoning trajectory rather than modeling a distribution over multiple valid alternatives. While stochastic approaches parameterize distributions over latent reasoning steps, they frequently suffer from unstable optimization and limited empirical performance. Furthermore, their reliance on autoregressive latent prediction during training precludes effective parallelization, leading to prohibitively long training times. To overcome these bottlenecks, we propose Probabilistic Latent Reasoning Models (PLRM), a parallelizable variational framework for probabilistic latent reasoning. PLRM adopts a JEPA-style objective in which the posterior infers latent distributions in parallel from observed reasoning trajectories, while the prior learns to predict the subsequent latent distribution via teacher forcing. To model heterogeneous reasoning processes, we introduce a discrete strategy variable together with a mixture-based prior, allowing the model to preserve the Gaussian-mixture structure induced by multiple distinct reasoning trajectories rather than collapsing them into a single Gaussian. Across diverse benchmarks, PLRM achieves performance competitive with deterministic latent reasoning models on single-trajectory datasets while enabling efficient training and consistently outperforming competing stochastic baselines on multi-trajectory datasets.
https://arxiv.org/abs/2610.29385
Understanding large, complex, and rapidly evolving code bases remains a core challenge for software engineering at scale, hindering onboarding, maintenance, refactoring, and impact analysis. Providing this information to a Large-Language Model (LLM) is another hurdle, as the LLM must understand not only the required code method but also its associated methods in the grand scheme of the repository. We propose Code Comprehensor, a hybrid retrieval-reasoning framework combining (i) CodeGraph, a code dependency callgraph, (ii) CodeScribe, which uses code-aware LLMs to generate hierarchical documentation across repository call graphs, and (iii) CodeContrast, a CLIP-style dual-encoder model trained on CodeScribe output to learn aligned text-code embeddings. CodeContrast enables fast, semantically precise retrieval of relevant code-context neighborhoods, which serve as grounded evidence for an MCP-based LLM orchestrator answering domain-specific queries. Evaluation on OpenCV and a proprietary 5M-LOC repository shows that CodeScribe-derived supervision significantly improves cross-modal retrieval in text-to-code accuracy over baseline approaches. Richer textual supervision (hierarchical documentation, parent/sibling context, and LLM-generated synthetic questions) consistently enhances performance across both repositories. LLM-as-a-judge evaluation using the popular RAGAS of the Code Comprehensor output yields above 90% faithfulness scores.
https://arxiv.org/abs/2610.30016
Individual patient data are the gold standard for secondary analysis of time-to-event evidence, but they are rarely released, and reconstruction from a published Kaplan-Meier figure could help. Existing methods all claim high fidelity, each judged by whichever agreements it happens to achieve, and each returns a single dataset although the map from figure to data is not bijective. We define fidelity explicitly: a dataset is admissible when it reproduces the risk table exactly, follows the digitized curve to within the image resolution, and respects the printed median, interval and event count. We propose StochIKM, a stochastic algorithm that digitizes the figure with a vision-capable language model and uses the high-fidelity definition as constraints, returning an admissible set of individual patient datasets. A solution is guaranteed to exist whenever the figure has been read correctly, so a failure indicts either the published figure or its digitization. In simulation and in 79 arms from published oncology trials, StochIKM reproduces the published risk tables and medians more closely than LLM-improved IPDfromKM, a high-impact alternative.
https://arxiv.org/abs/2610.29122
Consensus is a fundamental problem in distributed computing and at the core of state machine replication (SMR). Despite decades of active human research, discovering practical low-latency solutions to the problem is still open, as it requires combining protocol knowledge, correctness reasoning, implementation, and experimental evaluation. We report on how AI helped us discover A-greement, a new consensus protocol for geo-replicated state machines that significantly outperforms state-of-the-art solutions. Averaged across six deployments with 5 or 9 replicas, A-greement reduces the mean latency of a geo-distributed key-value store over the fastest baseline by 12.2% and 33.3% on write-heavy and read-heavy workloads, respectively, and matches the fastest baseline on read-only workloads. A-greement combines lease-authorized local reads, direct client learning for leader-ordered writes, and a fast fixed-quorum per-key write path, selected according to network topology and workload. At the heart of our discovery lies AI-greement, an agent harness for the "autonomous" discovery, implementation, experimentation, and verification of candidate protocols. AI-greement integrates (1) a concept-oriented protocol knowledge base, (2) a modular implementation skeleton, and (3) a Lean-based verification framework with reusable safety definitions, reference specifications, and proofs. AI-greement is of independent interest: its Lean formalization uncovers several previously unreported vulnerabilities in existing consensus protocols, and it provides guidelines on how domain-specific harnesses can turn general-purpose coding agents into effective tools for (distributed) computing research. Yet we argue that human consensus experts remain essential before, during, and after the search: agents reshape the researcher's role rather than end consensus research.
https://arxiv.org/abs/2610.30114
Despite recent advances, current AI systems remain highly susceptible to domain shifts, particularly in biomedical imaging, where images are usually acquired under substantially different experimental conditions. Although recent domain adaptation methods have made substantial progress, significant performance gaps under domain shift persist. To measure progress in this regard, we introduce BatchBench, a leaderboard that evaluates and compares the robustness of AI systems on biomedical images from unseen experimental batches and data sources. BatchBench is built on JUMP-CP, one of the largest publicly available biomedical imaging datasets. Generated using the Cell Painting assay, JUMP-CP exhibits pronounced batch effects and domain shifts, making it a challenging testbed for evaluating robustness to distributional changes.
https://arxiv.org/abs/2610.30104
Reinforcement Learning with Human Feedback (RLHF) has become a central paradigm for aligning Large Language Models with human values. However, the reliance on sensitive preference data necessitates rigorous differential privacy (DP) guarantees to prevent user information leakage. Existing private alignment methods typically assume dense reward parameterizations, resulting in estimation error bounds that scale polynomially with the ambient {model size $d$}. Such dependence is prohibitive in modern {overparameterized models} where $d$ is vast. In this work, we study \emph{Private Sparse RLHF} problem to address this limitation, assuming that human preferences (reward model) are governed by a subset of $s^* \ll d$ relevant features. We provide the first comprehensive theoretical framework for differentially private sparse reward estimation from pairwise preference feedback under the Bradley-Terry-Luce model, and introduce efficient algorithms for both Sample-DP and Label-DP settings. Theoretically, under the squared $\ell_2$ parameter estimation error, we establish upper bounds of $\widetilde{O}(s^*/n + {s^*}^2/n^2\varepsilon^2)$ for $(\varepsilon,\delta)$-Sample-DP and $\widetilde{O}(s^*/n + s^*/n\varepsilon^2)$ for $\varepsilon$-Label-DP based on randomized response, where $n$ is the training data size. For the lower bounds, we show that the Sample-DP rate is nearly optimal, and that the guarantee for our Label-DP method cannot be further improved within the randomized-response framework. We also provide a general lower bound for the problem with Label-DP. Empirically, our framework demonstrates superior efficacy over dense baselines across sentiment generation and safety alignment benchmarks, offering a significantly more favorable privacy-utility trade-off.
https://arxiv.org/abs/2610.30099
Parallel AI agents can produce useful local edits yet degrade a shared solution when their edits are combined. We model this coordination problem as discrete block optimization with an exactly evaluable objective and a known dependency graph. Independent sets certify compatible edits whose verified gains, measured against the same current solution, add exactly. A coordinator constructs a safe compatible candidate and can also evaluate interacting edits to capture favorable interactions. We prove that an optimal fractional coloring yields a merger that preserves a $1/\chi_f(G)$ fraction of the total verified local improvement, where $\chi_f(G)$ is the graph's fractional chromatic number. This guarantee is tight among mergers that select a subset of the same proposals. Under conditional local-improvement guarantees and a block error-bound condition, repeated collaboration converges geometrically in the objective gap. The rate separates task structure, agent allocation, and computation cost, yielding a linear program for agent assignment and an explicit time-cost trade-off. Code-repair experiments show that verified merging resolves conflicts between individually useful edits that cause naive merging to fail. On larger conflict-free tasks, parallel agents reduce modeled completion time at higher input-token-equivalent cost. On three public road networks, fractional integration retains 922 units of verified graph-cut improvement across 90 paired runs. For route-search agents sharing exclusive access to vehicle routes, fractional scheduling reduces measured wall time by a median of 15% across twelve paired runs, with route-cost changes varying across runs.
https://arxiv.org/abs/2610.30074
Data agents built on ReAct-style loops now execute complex analytical workflows over structured data, yet their intermediate reasoning still runs almost entirely through text. Human analysts instead move between numbers, tables, and charts, reading visual evidence to expose trends and anomalies that text summaries drop. We ask whether charts can serve as internal epistemic actions inside a data agent's reasoning loop, and how to teach an agent to use them. We first build \probe{}, a suite of 200 controlled tasks under four matched interface conditions, and find a persistent gap between what agents can read and what they choose to use. Agents score as well from self-generated charts as from numeric output, yet plotting access alone does not translate into consistent use. Task slices show that charts lead on temporal, pattern, and anomaly reasoning, while text leads on precise reading and conditional verification. We then propose \method{}, which distils two families of experience from conditioned trajectory rollouts. One family records how to select and verify analytical operations, and the other records when to invoke text, charts, or both. A trajectory judge scores outcomes and labels intermediate steps, and a validation gate admits only experience that improves held-out performance. On three held-out benchmarks with four LLM backbones, \method{} raises analytical accuracy and visual evidence quality over matched baselines, and backbones that never drew charts begin using them, all without touching model parameters.
https://arxiv.org/abs/2610.30072
Tabular studies are a common way to compare independent and centralized multi-agent learners, because they avoid function approximation. A natural expectation is that centralized learning, which learns joint actions, helps agents coordinate, especially when their bodies make solo success hard. Earlier work tests this only in parts: it measures coordination for one learning method, compares methods with the agents' bodies fixed, or varies speed but reports only how well the team did. We test it in a predator-prey environment, where teammates cooperatively hunt together while two teams compete. We compare independent Q-learning (IQL) with central Q-learning (CQL) in all four predator and prey pairings, under limits on speed and stamina, on a 5x5 and an 8x8 grid trained for 200,000 episodes each, and check that the agents learn on both. We measure coordination directly, with predictions for the main measurement fixed in advance. In this task, where one predator can capture prey alone, we find three things. First, CQL costs its agents in both roles on both grids, and its predators coordinate no more than IQL's. Second, its one benefit comes from acting on the best joint action: this cut capture time by 42% on the small grid with faster prey and unlimited stamina, but helped nowhere on the larger grid, where the best joint action had mostly never been tried. Third, on the larger grid a tie-breaking default decided which method won, even though the agents had passed a learning check. A tabular comparison can therefore be trusted only if it also checks how much of the state space the agents covered and implements the methods alike. We propose simple checks for both.
https://arxiv.org/abs/2601.17454
Coding agents are typically evaluated using one-shot, well-formulated prompts. Benchmarks such as SWE-bench use existing GitHub issues as input for a coding agent and evaluate whether the agent successfully solves the task. However, in real-world use cases, prompts are often not as well-formulated or structured as existing GitHub issues. Additionally, a coding agent session is not limited to a single prompt; it typically involves a multi-turn interaction in which the user iteratively adds new tasks and requirements that the agent must fulfill. To benchmark these abilities, we developed SWE-DIVE, a dynamic, interactive validation and evaluation framework for benchmarking coding agents in a multi-turn environment. To achieve this, we introduce a user simulator that can simulate different behavioral patterns and communicate with the coding agent. We also introduce a conversation validator that evaluates the user simulator's outputs to determine whether they fulfill the initial requirements and guide the agent toward successfully solving the task. The entire framework is embedded in a Harbor environment, which orchestrates the coding agent, user simulator, and conversation validator, and executes the test environment to determine whether the agent successfully solves the task. Our results and source code are available in our GitHub repository (this https URL).
https://arxiv.org/abs/2610.30047
Decision models map stated rules and observed states to discrete answers. Aggregate accuracy leaves unresolved which rule and information changes guide those answers. We connect controlled input changes to transfer, joint reliability, and directed information use through executable arithmetic rules. Semantic rule separation and crossed rule and state tests make transfer and joint success separately measurable. We compare equivalent wordings, calibrate joint correctness through marginal-preserving reassociation, and alter tables to define alternative answer targets. Adaptation gains increase with nearest-source answer agreement; fully conflicting quartets yield small pooled gains and different gain signs across source splits. Equivalent rewrites have opposing task-level effects, linking transfer gains to rule presentation. Joint-score departures depend on which rule and state associations the reference preserves. A decision service changes answers more across equivalent wordings than across identical-text repeats and usually follows the answer targets implied by altered table values or mappings.
https://arxiv.org/abs/2610.30045
Harness optimization, which improves an agent's prompts, tools, and workflows, is an increasingly effective way to enhance agents built on frozen or closed-source LLMs. Leading approaches such as the Darwin--Godel Machine and the Huxley--Godel Machine (HGM) rely on recursive self-improvement and were developed mainly for coding, where the competence needed to improve the agent coincides with the competence being improved. Planning tasks, in which an agent must produce a sequence of tool calls that jointly satisfies interacting constraints, break this alignment. There, open-ended self-modification repeatedly explores ineffective changes and consumes substantial evaluation budgets. We introduce HGM-Dual, a diagnostic-guided framework for budget-efficient harness evolution for planning agents. First, HGM-Dual represents agent evolution as lineage-aware context. This context records what each ancestor changed, which behaviors improved or regressed, and which modifications were ineffective, giving the editor explicit edit-outcome attribution instead of an unstructured archive of past agents. Second, HGM-Dual introduces error-conditioned dual-path child generation. For each selected parent, it generates a general child that preserves open-ended exploration and specialized children that target the harness components most likely responsible for the parent's highest-ranked constraint violations. HGM-Dual outperforms the strongest baseline by up to 14.45% relative improvement in case accuracy while matching HGM variants' final performance with 2x-4x fewer evaluation budget.
https://arxiv.org/abs/2610.30042
Text skills can extend the capabilities of tool-using agents, but long skill descriptions increase computational costs. Soft prompts provide a compact alternative, yet learning from entire successful trajectories may also introduce unnecessary behavioral changes. We find that the useful effect of a text skill is highly concentrated in a small subset of trajectory positions. Based on this observation, we propose Behavioral Localization, which compares the frozen agent with and without the text skill to identify positions where the skill both increases the likelihood of successful tokens and meaningfully changes the next token distribution. We use these localized positions to supervise a short soft prompt. Experiments on SpreadsheetBench with a frozen Qwen3.6-35B-A3B agent show that the top 10\% of trajectory positions capture 96.12\% of the total positive skill gain. In the shared prompt setting, selective supervision improves success from 30.36\% with full trajectory to 36.79\%. Under task-specific conditions, using the top 10\% localized positions achieves 57.38\%, outperforming both the full text skill and the on-policy OPCD baseline. These results show that a small set of behaviorally relevant trajectory positions can provide effective supervision of soft skills.
https://arxiv.org/abs/2610.30041
Empirical exchange-correlation functionals are fitted on fixed orbitals but used self-consistently, so better energies often come with worse densities. We show that the Brillouin residual of a trained functional on the Kohn-Sham orbitals of an accurate density controls, to first order, both the self-consistent density shift and the gap between fitted and self-consistent energies. Penalizing it requires no self-consistent-field solution during training. Trained on 6 energies and 11 CCSD densities, a neural meta-GGA surpasses SCAN in both atomization energies and densities of unseen molecules.
https://arxiv.org/abs/2610.30022
This study introduces GuideEvolve, a self-evolving agent framework incorporating expert guidance and three autonomous regulatory mechanisms, collectively termed the 3Ts: Think Fast and Slow, Throwback, and Termination by choice. The framework addresses critical limitations in extant self-evolving agent paradigms through dual innovations: (1) a task-specific expert-evaluation-driven evolutionary pipeline, and (2) the integration of 3Ts mechanisms to facilitate cognitive optimization, performance recovery via temporal rollback, and adaptive termination protocols. Empirical validation across the MGSM and MMLU benchmarks demonstrates that GuideEvolve attains performance metrics comparable to current state-of-the-art models (89.8% accuracy versus Gödel Agent's 90.6% on MGSM; 89.1% versus 87.9% on MMLU), while exhibiting notably reduced variance (25-59%) and enhanced robustness. Furthermore, the framework achieves a 100% evolution success rate, superior to the baseline's 82%, diminishes required optimization iterations by approximately 50% (from 30 iterations in baseline to 15.1 and 13.4 across tasks), and provides improved stability for production deployment.
https://arxiv.org/abs/2610.30017
Alarm root-cause analysis is studied on data that cannot be shared. Operator logs are confidential, so what the field publishes is a causal graph between alarm types rather than per-incident causes, a fixed scenario set, gated, or never released. Two recent benchmarks carry per-incident root causes at scale; neither states a download location or a licence. We give a generator rather than a dataset. It runs on real backbone topologies from the Internet Topology Zoo and records the exact root cause and the propagation path of every alarm -- a by-product of generation, not a labelling pass. Every emitted field binds to a term in NORIA-O, RFC 8632, RFC 8345 or TMF642, and an unknown term fails the run. We ship fixed configurations, splits, a scorer and nine baselines. A one-line rule -- rank the device that raised the earliest critical alarm -- takes top-1 at 0.650 against 0.575 for our own temporal method, and wins 13 of 15 runs over three backbones and five seeds. An LLM given the same view reaches 0.600, the same model allowed to query the graph 0.625, and the rule wins on real operator alarms too, at 0.773: a property of alarm streams, not of our generator. One fault class separates the table: when a site loses power its PoP reports nothing, so every method that ranks alarmed devices scores 0.000 or near it, while the two that walk the topology to a silent candidate take 1.000 and 0.833.
https://arxiv.org/abs/2610.30004
Benchmark performance is the dominant standard for comparing large language models (LLMs), typically summarized by a single aggregate score, such as accuracy, pass rate, or rubric score. This aggregate score provides limited information about a model's underlying capabilities, yet understanding these capabilities is crucial for model development and evaluation. To this end, we propose Tree-Induced Diagnostic Evaluation (TIDE), which recasts diagnostic evaluation as behavior-driven decision-tree induction to perform fine-grained capability diagnosis. TIDE recursively builds a hierarchical capability tree from benchmark samples and model scores: at each node, an LLM judge proposes candidate splits and performs sample-to-group classification, and behavior-based information gain selects among them. We apply TIDE to five models across four benchmarks to demonstrate its effectiveness, and find fine-grained capability contrasts invisible at the aggregate level: Claude Opus 4.6 achieves 100% on microeconomic market reasoning where GPT-5.4 scores 83.3%, but trails GPT-5.4 on contract law reasoning with 77.8% versus 88.9%. We hope TIDE can be extended to past and future benchmarks so that the rich behavioral signal in evaluation results is fully leveraged for understanding model capabilities.
https://arxiv.org/abs/2610.29985