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arXiv

An Agentic Retrobiosynthesis Framework with Learned Frontier Selection

Philippe Meyer, Guillaume Gricourt, Thomas Duigou, Joan Hérisson, Jean-Loup Faulon

Large language models are increasingly used as agents for multistep retrosynthesis, raising the question of how much their search policy contributes independently of the underlying reaction model. We investigate this question in a biological setting through rule-based retrobiosynthesis: a deterministic biochemical engine generates the same validated transitions for every method, searching for routes that terminate in metabolites available to an \emph{Escherichia coli} chassis, while the policy only selects which frontier molecule to expand next. Prompted and LoRA-tuned Qwen2.5-7B policies use a strict choice-only interface. The fine-tuned policy reaches $65\pm1$\% solve rate at 10 expansions on LASER versus 59\% for MCTS, and at 200 expansions reaches $78\pm1$\% versus 75\% on LASER, $88\pm3$\% versus 80\% on the RetroPath RL Golden benchmark, and $63\pm2$\% versus 45\% on the BioNavi-NP benchmark. Fine-tuning also consistently outperforms direct prompting. These results show that route-supervised frontier selection can improve budgeted search without altering biochemical generation, although performance remains dependent on frontier construction and reaction ranking.

arXiv

Beyond the Payload: How User Invocation Shapes Coding Agent Vulnerability to Repository Poisoning

Fukang Zhu, Binbin Zhao, Ruixiao Lin, Ping He, Tianyu Du, Shouling Ji

Coding agents are increasingly used for software engineering tasks, including bootstrapping projects from third-party repositories whose integrity cannot be assumed. Prior work on repository poisoning largely focuses on attacker-controlled injection and disguise, but developers also shape risk through everyday invocation choices: what task to delegate, how to phrase the request, and which skills or rules to supply. We term these user-side choices Prompt-Level Configurations (PLCs) and introduce CIPR (Coding In Poisoned Repos), the first benchmark that systematically varies PLCs in poisoned real-world repositories. CIPR comprises 1,920 instances across 20 repositories, four task types, three social-media-grounded prompt styles, and three skill/rule conditions, and measures attack success rate (ASR) and agent alert rate (AR) using automated runtime and trace-based oracles. Our evaluation reveals two key insights: (1) Vulnerability is highly context-dependent, with task type creating up to a 4.5-fold difference in ASR, with test-execution task forming a silent attack surface (high ASR, low AR). (2) Prompt expression shifts risk indirectly: underspecified prompts reduce ASR by truncating execution depth; noisy prompts exhibit a directional trend toward suppressing alerts by making malicious content less conspicuous. These findings highlight that coding agent vulnerability is not a static property, but a dynamic outcome shaped by everyday user configurations.

arXiv

WildSEEK: Evaluating Language Models for Information-Seeking

Tanise Ceron, Joachim Baumann, Elisa Bassignana, Berat Cabuk, Dirk Hovy, Debora Nozza

Language models are increasingly mediating information access to end users, urging a systematic evaluation of their responses for a fair and reliable information ecosystem. Existing evaluations, however, are often topic-specific or synthetic, limiting their ability to capture the complexity of "in the wild" information-seeking queries and the risks present in model responses. To address this gap, we introduce WildSEEK, a manually annotated dataset of 3k information-seeking queries from real user interactions, and an evaluation framework for LLM-generated responses. WildSEEK includes annotations for risk-sensitive domains (e.g. health and financial information), and distinguishes factoid queries from analytical queries which seek responses beyond facts. We train classifiers on WildSEEK to analyze more than 1.8M realistic user queries. We find that over a third of information-seeking queries are high-risk and more often analytical. Our findings show that LLM responses fail more often in four criteria: sycophantic behavior, overreliance, a default US-centric perspective, and poor handling of vulnerable populations -- with failure rates being mostly higher for analytical queries. By providing methods to monitor the reliability, safety, and fairness of LLM behavior, our dataset and evaluation framework offer an empirical foundation for the broader question of how these systems should behave as they take on a growing role in information access.

arXiv

LCoT-GV: Graph Attention Networks for Verifying Long Reasoning Chains in Large Language Models

Bérénice Jaulmes, Mehwish Alam

Large Reasoning Models produce Long Chains-of-Thought (LCoTs) which involve breaking down the problem into smaller reasoning steps before reaching the conclusion. However, these steps often contain contradictions, unsupported inferences, or irrelevant steps, even when the final answer is correct. We propose Long Chain-of-Thought Graph Verifier (LCoT-GV), a graph-based framework that represents LCoTs as reasoning graphs. Each node in the graph represents a reasoning step and the edges encode semantic and logical relations. A Graph Attention Network is then trained to predict chain-of-thought correctness from the reasoning graph. We construct a new graph-oriented verification dataset from multiple reasoning benchmarks for question answering in various domains. The results show that our method is competitive with the most similar approaches.

arXiv

OCR-MetaReasoning Benchmark: Evaluating the Meta-Reasoning Ability of MLLMs in Text-Rich Image Understanding

Gengxu Li, Yuan Wu, Yi Chang

Text-rich image understanding requires multimodal large language models (MLLMs) to organize OCR (Optical Character Recognition)-grounded evidence across words, layout, fields, charts, and visual correspondences. Existing evaluations often conflate extraction with reasoning and rarely test whether models follow the required reasoning direction: applying visible rules, abstracting hidden regularities, or recovering missing premises. We introduce OCR-MetaReasoning, a controlled single-image benchmark that treats deduction, induction, and abduction as distinct directions and separates final-answer correctness from reasoning-process compliance. The benchmark contains 1,500 verified samples in a balanced \(3\times5\) taxonomy crossing three reasoning types with five OCR-object categories, along with reference reasoning steps, automatic answer scoring, the Meta-Reasoning Macro Score (MRMS), and the Reasoning Process Compliance Score (RPCS). Experiments with representative closed-source and open-source MLLMs show that OCR-grounded meta-reasoning remains far from saturated: models struggle with visible-rule application and layout-sensitive inference, while process-compliant rationales can accompany incorrect final answers under exact-match evaluation. The code is available at https://github.com/gengxuli/OCR-MetaReasoning.

arXiv

MURANO: Design, Run, and Reproduce Mechanistic Interpretability Experiments as Composable Pipelines

Alireza Bayat Makou, Emirhan Böge, Phu Gia Hoang, Federico Tiblias, Jingcheng Niu, Subhabrata Dutta, Richard Eckart de Castilho, Iryna Gurevych

This paper presents Murano, an open source framework for designing, running, and reproducing mechanistic interpretability studies of large language models, intended for researchers across disciplines. These studies often combine loading, recording, attribution, intervention, and evaluation, while existing libraries tend to focus on different parts of this workflow. As a result, researchers using several libraries may need to adapt outputs from one for use by another. To bridge this gap, Murano represents operations from these five areas as composable steps. Steps exchange named result artifacts and declare the inputs they require and the outputs they produce. A pipeline executes its steps in the order supplied, and Murano uses canonical addresses when component identities pass between operations. Murano builds on existing interpretability and machine learning libraries. We demonstrate Murano through two reproductions of established interpretability studies and one illustrative sparse autoencoder case study.

arXiv

SwarmBench: Can Large Language Models Act as Agent Swarm Orchestrators?

Jinshan Gao, Zhuoran Jin, Tianyi Men, Kang Liu, Jun Zhao

Large language model-based multi-agent systems are evolving from fixed interaction topologies toward dynamically orchestrated Agent Swarms. However, existing benchmarks are still largely based on single-agent or general-purpose agent tasks, making it difficult to systematically evaluate key orchestration capabilities. We propose SwarmBench, a benchmark that evaluates model performance from multiple perspectives, including accuracy, efficiency, cost, and process quality. Experimental results show that current models exhibit substantial differences in orchestration capability. These differences are reflected not only in final accuracy, efficiency, and cost, but also in the overall quality of the orchestration process itself. Based on these findings, we further propose SwarmExp, a simple yet effective method based on experience extraction and experience replay, which consistently improves the orchestration performance of large language models.

arXiv

Geometry of Divergence: Tracking Hidden-State Trajectories for Adaptive Multi-Turn Reasoning

Jie Liang, Zhengxin Yu, Hamid Nasiri, Peter Garraghan

LLM agents need to sustain goal-consistent reasoning across long multi-turn interactions under strict resource constraints. However, as the multi-turn context accumulates, it can destabilize the underlying LLM's internal representation of task-relevant information from earlier turns, blurring the boundary between constructive reasoning and representation drift. We formulate multi-turn reasoning as a hidden-state trajectory of the underlying LLM that is characterized via two complementary signals: temporal curvature that captures the directional consistency of turn-to-turn updates, and variance slope which measures the expansion or contraction of the exploration space. Across four tasks and three underlying LLMs, we observed that these geometric signals distinguish between correct and incorrect episodes prior to completion. We further decompose each episode into three-action chains formed from four actions (Read, Write, Respond, Transfer) and show that separability is action-dependent, with different signals distinguishing various chain patterns. Our experiments demonstrate that trajectory geometry can identify critical turns in the reasoning process, increasing task success rates on $τ$-Bench from 24.1% to 39.6% while reducing token cost by 11.2%.

arXiv

Where Identity Lives: Localized, Retain-Free Identity Unlearning in Multimodal Large Language Models

Kangwook Ko, Jaehyuk Jang, Wonjun Lee, Hee-Seon Kim, Changick Kim

Removing a specific individual's information from multimodal large language models (MLLMs) is often needed after deployment, but existing methods rely on a retain set, which is hardest to obtain at that point, and rebuilding it recreates the privacy exposure that unlearning aims to remove. Forgetting from the forget set alone instead damages the shared visual-language computation, harming perception. We cast retain-free unlearning as a localization problem: causal tracing, weight transplant, and Fisher overlap all point to early-to-mid decoder MLPs as the layers where identity information is stored and, unlike other module families, can be modified without substantially disrupting vision. We turn this into Pathway-Aware Visual-attribute Anchoring (PAVA), which confines updates to these layers and pairs a forget loss with a visual-attribute anchor that preserves image-grounded behavior by distilling the model's own pre-unlearning answers from the forget images alone. On MLLMU-Bench and ReMem, PAVA gives the strongest forget-retain trade-off among forget-set-only methods and remains competitive with retain-based baselines.

arXiv

What It Costs to Compose, Rebuild, and Correct Precomputed Memory

Asa Shepard

Language models can answer from precomputed memory, a model's saved reading of a body of material, reused across requests instead of read again at each. This paper maps where that practice preserves correctness and the conditions under which it fails. Across experiments on Llama-3.1-8B-Instruct using both saved key-value caches and trained compressions of them, precomputed memory degrades when assembled from separately prepared parts, stays current only through rebuilds costing a large fraction of full preparation in our measurements, and ignores corrections served beside it conditional on phrasing. If precomputed memories can be served alongside one another, be cost-efficiently rebuilt, and be superseded by new information arriving in real-time, they can serve as a way to avoid re-feeding context to a model over repeated queries. The implication of our results for a deployed system that deals with a variety of queries is that precomputed memories are best rebuilt on the cadence at which new information changes what the memory was originally computed from. Both warm-rebuilding trained compressions of key-value caches and serving specifically-phrased updates beside a memory, as pasted text or injected cache state, show particular promise for keeping precomputed memories current, the latter as an interim measure between rebuilds, and we measure the cost and name the remaining questions associated with each.

arXiv

BiG-SURE - Bipartite Graph for Semantic Uncertainty and Reliability Estimation of LLMs

Debarpan Bhattacharya, Malay Phadke, Sriram Ganapathy

Reliable uncertainty estimation is a crucial requirement for deploying large language models (LLMs) and vision-language models (VLMs) in safety-critical settings, especially when the model parameters are not accessible (black-box). We propose BiG-SURE, an uncertainty estimator based on cross-temperature semantic agreement. The method samples low-temperature responses as stable semantic anchors and high-temperature responses as probes under meaning-preserving input transformations. It then constructs an anchor-probe Bipartite Graph (BiG) using NLI-based entailment scores and defines confidence through the normalized squared spectral energy of this matrix, with uncertainty given by its complement. This bipartite graph-based Semantic Uncertainty and Reliability Estimation (SURE) score measures whether high-temperature probes remain semantically aligned with the model's stable low-temperature belief or not. We evaluate BiG-SURE on text QA, multilingual QA, and multimodal QA tasks across multiple model families. In these experiments, BiG-SURE improves average abstention AUROC over prior black-box uncertainty estimators, while remaining simple, unsupervised, and applicable to black-box model settings.

arXiv

GMTS: Gradient Magnitude-based Token Selection Improves RLVR Training for LLM Reasoning

Outongyi Lv, Yuanwei Zhang, Xiaoqun Zhang

Reinforcement learning (RL), particularly RL with Verifiable Rewards (RLVR), has recently emerged as a central paradigm for enhancing large language models' (LLMs) reasoning abilities, demonstrating remarkable effectiveness across reasoning tasks. Recent studies suggest that high-entropy tokens play an exceptionally important role in model training, since training with only the highest 20% entropy tokens yields significant performance gains. However, why such high-entropy tokens are beneficial remains insufficiently understood. In this work, we find that although high-entropy tokens within one answer tend to correlate with large gradient magnitude, entropy alone fails to consistently reflect token importance across different answers, considering the variations in the answer-level reward signals. Based on this observation, we introduce the Gradient Magnitude-based Token Selection (GMTS) method to quantify token importance, which leverages the entropy-gradient connection to approximate gradient-magnitude rankings for token selection. We find that training on the top 20% tokens ranked by GMTS consistently outperforms entropy-based token selection across three reasoning domains and various model sizes, suggesting that GMTS provides a more fine-grained estimate of token contribution for RLVR training.

arXiv

REER-PT: Reverse-Engineered Reasoning for Perplexity-Guided Pre-training Data Augmentation

Haoran Que, Jiajun Shi, Ting Huang, Renming Pang, Jiaheng Liu, Ge Zhang, Wenhao Huang, Shen Yan, Wei Ye, Shikun Zhang

As language-model compute continues to scale, high-quality training data is becoming an increasingly important bottleneck. Conventional next-token prediction supervises what follows a context but leaves the intermediate reasoning behind that continuation implicit. We introduce \textbf{REER-PT}, a scalable framework that extends Reverse-Engineered Reasoning (REER) to raw pre-training data. REER-PT identifies continuations that are difficult to predict but can still be inferred from the preceding context, and inserts concise reasoning annotations that reconstruct the missing connection between context and continuation. Candidate annotations are generated and refined offline, with perplexity serving as the optimization signal. Constraints on length and target leakage filter out unhelpful or trivial annotations. This sparse transformation preserves the source text and remains compatible with standard next-token prediction, avoiding online reasoning rollouts during pre-training. We apply REER-PT to transform a source pre-training corpus into an augmented one. Across augmented-data, original-token, and selected-continuation comparisons, perplexity reductions range from 0.42 to 7.29, and only about 0.05\% of annotation 13-grams appear verbatim in the source text. We then train two 680M-parameter models with the same architecture and training configuration on the source and augmented corpora, respectively. The augmented-data model gains up to 2.07 percentage points on several knowledge and reasoning benchmarks. Together, the perplexity analysis indicates improved continuation predictability, while the controlled pre-training experiments suggest that this augmentation can improve model performance without changing the standard pre-training objective.

arXiv

Hidden Threat in Synthetic Data: Covert Targeted Bias Injection through Benign Text

Minkyung Cho, Jihyo Kim, SeungWoo Song, Junghun Yuk, Minjoon Kee, Hoyun Song, KyungTae Lim

Synthetic data is increasingly used to train large language models (LLMs), yet its security implications remain poorly understood. Prior work on subliminal learning suggests that models can inherit behavioral traits from seemingly unrelated training data. In this work, we investigate whether such mechanisms can be exploited to inject targeted social biases into aligned models through semantically benign synthetic data. We construct a pipeline in which a misaligned teacher model generates filtered synthetic datasets across domains such as creative writing and code generation, which are then used to fine-tune aligned student models. Our experiments show that benign-looking synthetic data can act as a covert channel for transmitting targeted biases while largely preserving the student model's general task capabilities. These results reveal a previously underexplored security risk in synthetic data-driven LLM training pipelines and highlight the need for improved safeguards. As one possible step toward this goal, we suggest that log-linearity-based scoring may provide a useful signal for screening seemingly benign synthetic data.

arXiv

TaxCE : A Framework for Automated Taxonomy Construction and Evaluation at Scale

Sandeep Sricharan Mukku, Albert Aristotle Nanda, Rohit Pyati

Organizing unstructured feedback text into hierarchical taxonomy is a fundamental challenge in NLP, particularly in domains where feedback arrives at massive scale in varied forms such as reviews, transcripts, and surveys. Existing approaches either produce shallow hierarchies, neglect long-tail topics, or lack rigorous evaluation frameworks. We present TaxCE, a fully automated framework that constructs multi-level hierarchical taxonomies from raw text through progressive condensation of corpus content into actionable segments, deduplicated semantic units, and granular topics with definitions, which are then organized bottom-up into a hierarchy with corpus-groundedness. We also introduce three corpus-grounded evaluation metrics, Exclusivity, Exhaustivity, and Granularity (EEG), and integrate them into a metrics-in-the-loop iterative refinement mechanism that diagnoses deficiencies and applies targeted corrections until convergence. Extensive experiments demonstrate that TaxCE consistently outperforms existing baselines spanning classical topic models, neural methods, and LLM-based approaches, with average improvements of 11.8, 20.5, and 15.7 percentage points in exclusivity, exhaustivity, and granularity respectively over the strongest baseline. Human evaluation further confirms superior taxonomy quality, actionability, and navigability.

arXiv

Reading the News: Adapting Large Language Models to Swedish Journalism Through Continued Pre-Training

Lukas Borggren, Jenny Kunz, Marco Kuhlmann

Large language models are increasingly capable in general, but their utility can remain modest in niche or understudied areas. One approach to address this limitation is to specialise existing models through additional training on target-domain corpora. In this work, we investigate such continued pre-training for adapting large language models to Swedish journalism, using a high-quality dataset that we curate from millions of news articles. To evaluate the adaptation efficacy, we also construct a novel domain-specific benchmark that covers six editorial tasks. Through full and parameter-efficient fine-tuning across two model sizes, we find that continued pre-training yields benefits in the target domain, but only when paired with experience replay to mitigate forgetting. We observe consistent enhancements in the models' generation quality and factual knowledge, but not their proficiency in discriminative tasks. Exploring a training-free method to facilitate instruction following, we see further improvements, but exclusively for models trained with low-rank adaptation. Crucially, we demonstrate the importance of targeted evaluation in the adaptation process, as an existing Swedish benchmark largely fails to capture the models' in-domain performance gains.

arXiv

PLC-DPO: Posterior Label Correction in Noisy and Ambiguous Preference Optimization

Boryeong Cho, Sumyeong Ahn, Se-Young Yun

Direct Preference Optimization (DPO) simplifies alignment through pairwise comparisons but assumes all observed preferences are reliable. Real data often violates this assumption, leading to reversed, weak, or ambiguous labels that cause harmful policy updates. To address this, we propose Posterior Label Correction DPO (PLC-DPO) to robustly optimize preferences by routing each pair's training signal as a clean, flip, or tie case. The key idea is to use the calibrated policy-reference margin as online evidence to take appropriate correction actions. This reframes noisy preference learning as actively correcting supervision direction and strength rather than merely filtering suspicious examples. Across 57 dataset-model-benchmark cells, PLC-DPO obtains the best mean win rate against DPO (60.5 vs. 55.5 for the next-best method). Injected-noise and tie stress tests, human disagreement analysis, and self-confirmation diagnostics further show that the routing remains stable and distinguishes flipped from weakly directional pairs.

arXiv

Language Proficiency Assessment from Eye Movements in Naturalistic Passage Reading

Shachar Frenkel, Ido Falah, Omer Shubi, Yevgeni Berzak

Standard language proficiency tests rely on linguistic tasks such as vocabulary, grammar and reading comprehension quizzes. An alternative, cognitively motivated approach, introduced in Berzak et al. (2018), proposed instead to predict language proficiency from behavioral traces of eye movements in reading. In this work, we validate and extend this approach from single sentences to more naturalistic reading of contextualized passages in English as a second language, new proficiency measures, prediction models, and reading in an information seeking regime. We find that the approach is effective in all these evaluations. We further address two key open questions on eye movement based proficiency testing: (1) potential scoring biases that reflect the proximity of the reader's native language to English, which may undermine validity, and (2) its reliability. We find that eye movement based proficiency scores are indeed biased towards L1s that are linguistically closer to English. We propose a score debiasing method which effectively remedies this issue. The reliability analyses suggest that eye movement proficiency scores are more reliable than standard language proficiency scores. Overall, our results strengthen and broaden the empirical foundations for future eye movement based language assessment technologies.

arXiv

Seeing the Unseen: Visual Similarity for Pixel Language Model Adaptation

Ran Zhang, Miryam de Lhoneux, Wessel Poelman

Pixel-based language models (LMs) replace traditional tokenizers by processing rendered images of text, making cross-lingual transfer heavily dependent on the visual and structural properties of writing systems. However, the dynamics of adapting these models to low-resource languages with complex morphology and written in unique scripts are not yet explored. Using Tibetan as a case study, we analyze how continued pre-training of pixel-based LMs is influenced by data scale, initial script exposure, and cross-lingual transfer from languages written in other Brahmic scripts. We introduce four rendering-level metrics to quantify visual script similarity. We evaluate downstream performance across three tasks. Our results show that higher orthographic proximity enhances semantic transfer, even under severe data constraints. Additionally, we find a performance asymmetry based on the pre-training starting point: while multilingual pre-training PIXEL-M4 has stronger initial performance, its capacity for subsequent adaptation seems to be constrained, whereas adapting a monolingual model PIXEL with mixed scripts yields more gains on sentence-level tasks. Our metrics and case study offer empirical observations that could help inform data selection and script adaptation choices when working with pixel-based models in similar low-resource settings.

arXiv

WebWorld: The Browser as a World Model for Self-Improving Web Code

Jiajun Wu, Jian Yang, Yaxin Du, Wei Zhang, Haowen Wang, Junhang Cheng, Yuxuan Zhang, Tuney Zheng, Xianglong Liu, Ming Zhou

VLM-driven self-improvement of web code has a structural flaw: the model that proposes the repair is the model that judges it, and visual plausibility under that judge is a poor proxy for whether the page actually works. What the loop is missing is a counterparty the VLM cannot fool, and the browser already is that counterparty: a deterministic, executable simulator of how an HTML artifact behaves under user actions, and in everything but name a world model for web code. We present WebWorld, the interface that lets a VLM prior interact with this browser-as-world-model autonomously and decides which interactions become supervision. Each round, the VLM emits a critique that the planner compiles into a typed interaction contract; the browser re-executes the candidate and issues an acceptance certificate only when both target progress and preservation of every previously verified capability hold; certified transitions accumulate as a quality ratchet that is the only thing the SFT export ever sees. Under matched training, WebWorld-27B improves Raw-27B by 5.3 points on HTMLBench-400 and 14.9 points on MiniAppBench-Val, and reaches the level of strong frontier systems such as Kimi-K2.6 and GPT-5.4 on interactive HTML generation. Equal-size ablations show that browser-backed admission carries the gain: without the certificate, the matched 9B lift nearly disappears.

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