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Computer Science Computation and Language

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Saturday 31 January

Computation and Language

When Agents "Misremember" Collectively: Exploring the Mandela Effect in LLM-based Multi-Agent Systems

Recent advancements in large language models (LLMs) have significantly enhanced the capabilities of collaborative multi-agent systems, enabling them to address complex challenges. However, within these multi-agent systems, the susceptibility of agents to collective cognitive biases remains an underexplored issue. A compelling example is the Mandela effect, a phenomenon where groups collectively misremember past events as a result of false details reinforced through social influence and internalized misinformation. This vulnerability limits our understanding of memory bias in multi-agent systems and raises ethical concerns about the potential spread of misinformation. In this paper, we conduct a comprehensive study on the Mandela effect in LLM-based multi-agent systems, focusing on its existence, causing factors, and mitigation strategies. We propose MANBENCH, a novel benchmark designed to evaluate agent behaviors across four common task types that are susceptible to the Mandela effect, using five interaction protocols that vary in agent roles and memory timescales. We evaluate agents powered by several LLMs on MANBENCH to quantify the Mandela effect and analyze how different factors affect it. Moreover, we propose strategies to mitigate this effect, including prompt-level defenses (e.g., cognitive anchoring and source scrutiny) and model-level alignment-based defense, achieving an average 74.40% reduction in the Mandela effect compared to the baseline. Our findings provide valuable insights for developing more resilient and ethically aligned collaborative multi-agent systems. Code and dataset are available at https://github.com/bluedream02/Mandela-Effect.
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All authors Naen Xu, Hengyu An, Shuo Shi, Jinghuai Zhang, Chunyi Zhou, Changjiang Li, Tianyu Du, Zhihui Fu, Jun Wang, Shouling Ji

Computation and Language · Cross-listed from cs.LG

LLMs as High-Dimensional Nonlinear Autoregressive Models with Attention: Training, Alignment and Inference

Large language models (LLMs) based on transformer architectures are typically described through collections of architectural components and training procedures, obscuring their underlying computational structure. This review article provides a concise mathematical reference for researchers seeking an explicit, equation-level description of LLM training, alignment, and generation. We formulate LLMs as high-dimensional nonlinear autoregressive models with attention-based dependencies. The framework encompasses pretraining via next-token prediction, alignment methods such as reinforcement learning from human feedback (RLHF), direct preference optimization (DPO), rejection sampling fine-tuning (RSFT), and reinforcement learning from verifiable rewards (RLVR), as well as autoregressive generation during inference. Self-attention emerges naturally as a repeated bilinear–softmax–linear composition, yielding highly expressive sequence models. This formulation enables principled analysis of alignment-induced behaviors (including sycophancy), inference-time phenomena (such as hallucination, in-context learning, chain-of-thought prompting, and retrieval-augmented generation), and extensions like continual learning, while serving as a concise reference for interpretation and further theoretical development.
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Computation and Language

Segment-Level Attribution for Selective Learning of Long Reasoning Traces

Large Reasoning Models (LRMs) achieve strong reasoning performance by generating long chains of thought (CoTs), yet only a small fraction of these traces meaningfully contributes to answer prediction, while the majority contains repetitive or truncated content. Such output redundancy is further propagated after supervised finetuning (SFT), as models learn to imitate verbose but uninformative patterns, which can degrade performance. To this end, we incorporate integrated gradient attribution to quantify each token's influence on final answers and aggregate them into two segment-level metrics: (1) attribution strength measures the overall attribution magnitude; and (2) direction consistency captures whether tokens' attributions within a segment are uniformly positive or negative (high consistency), or a mixture of both (moderate consistency). Based on these two metrics, we propose a segment-level selective learning framework to identify important segments with high attribution strength but moderate consistency that indicate reflective rather than shallow reasoning. The framework then applies selective SFT on these important segments while masking loss for unimportant ones. Experiments across multiple models and datasets show that our approach improves accuracy and output efficiency, enabling more effective learning from long reasoning traces~\footnote{Code and data are available at https://github.com/SiyuanWangw/SegmentSelectiveSFT}.
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Friday 30 January

Computation and Language · Cross-listed from cs.IR

RAG-DIVE: A Dynamic Approach for Multi-Turn Dialogue Evaluation in Retrieval-Augmented Generation

Evaluating Retrieval-Augmented Generation (RAG) systems using static multi-turn datasets fails to capture the dynamic nature of real-world dialogues. Existing evaluation methods rely on predefined datasets, which restrict them to static, one-directional queries and limit their ability to capture the adaptive, context-dependent performance of RAG systems in interactive, multi-turn settings. Thus, we introduce the RAG-DIVE, a Dynamic Interactive Validation and Evaluation approach, that simulates user interactions with RAG systems. RAG-DIVE leverages an LLM to generate multi-turn conversations dynamically and is organized into three components. The dialogue generation stage consists of the (1) Conversation Generator, which simulates a user by creating multi-turn queries, and the (2) Conversation Validator, which filters and corrects invalid or low-quality outputs to ensure coherent conversations. The evaluation stage is handled by the (3) Conversation Evaluator, which assesses the RAG system's performance across the entire dialogue and generates both per-turn and multi-turn metrics that provide an aggregated view of system behavior. We validated RAG-DIVE through two experimental setups. First, we tested a sample RAG system, including human evaluation of dialogue quality, repeated trials to assess consistency, and an ablation study showing that RAG-DIVE detects performance changes caused by system modifications. Second, we compared RAG-DIVE with a traditional static dataset evaluation on an industrial RAG system under different configurations to verify whether both approaches reveal similar performance trends. Our findings demonstrate that RAG-DIVE facilitates dynamic, interaction-driven evaluation for multi-turn conversations, thereby advancing the assessment of RAG systems.
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All authors Lorenz Brehme, Benedikt Dornauer, Jan-Henrik Böttcher, Klaus Schmid, Mircea-Cristian Racasan, Ruth Breu

Computation and Language

Applied Sociolinguistic AI for Community Development (ASA-CD): A New Scientific Paradigm for Linguistically-Grounded Social Intervention

This paper establishes Applied Sociolinguistic AI for Community Development (ASA-CD) as a novel scientific paradigm for addressing community challenges through linguistically grounded, AI-enabled intervention. ASA-CD introduces three key contributions: (1) linguistic biomarkers as computational indicators of discursive fragmentation; (2) development-aligned natural language processing (NLP), an AI optimisation paradigm prioritising collective outcomes; and (3) a standardised five-phase protocol for discursive intervention. A proof-of-concept study, incorporating real-world and synthetic corpora, demonstrates systematic associations between exclusionary language and negative sentiment and simulates intervention-based improvements. ASA-CD provides a unified methodological, ethical and empirical framework for scalable, value-aligned AI in the service of community empowerment.
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Computation and Language

EQ-5D Classification Using Biomedical Entity-Enriched Pre-trained Language Models and Multiple Instance Learning

The EQ-5D (EuroQol 5-Dimensions) is a standardized instrument for the evaluation of health-related quality of life. In health economics, systematic literature reviews (SLRs) depend on the correct identification of publications that use the EQ-5D, but manual screening of large volumes of scientific literature is time-consuming, error-prone, and inconsistent. In this study, we investigate fine-tuning of general-purpose (BERT) and domain-specific (SciBERT, BioBERT) pre-trained language models (PLMs), enriched with biomedical entity information extracted through scispaCy models for each statement, to improve EQ-5D detection from abstracts. We conduct nine experimental setups, including combining three scispaCy models with three PLMs, and evaluate their performance at both the sentence and study levels. Furthermore, we explore a Multiple Instance Learning (MIL) approach with attention pooling to aggregate sentence-level information into study-level predictions, where each abstract is represented as a bag of enriched sentences (by scispaCy). The findings indicate consistent improvements in F1-scores (reaching 0.82) and nearly perfect recall at the study-level, significantly exceeding classical bag-of-words baselines and recently reported PLM baselines. These results show that entity enrichment significantly improves domain adaptation and model generalization, enabling more accurate automated screening in systematic reviews.
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Computation and Language

Inference-time Alignment via Sparse Junction Steering

Token-level steering has emerged as a pivotal approach for inference-time alignment, enabling fine grained control over large language models by modulating their output distributions without parameter updates. While effective, existing methods rely on dense intervention at every decoding step. This persistent manipulation not only incurs substantial computational overhead but also risks compromising generation quality by excessively drifting from the model's intrinsic distribution. In this work, we show that dense intervention is unnecessary and propose Sparse Inference time Alignment (SIA), which performs sparse junction steering by intervening only at critical decision points along the generation trajectory. Our key insight is that high entropy junctions mark pivotal decision points in the generation trajectory and are particularly susceptible to misalignment, indicating the need to introduce alignment related reward signals at these points. Extensive experiments across different model families and alignment objectives show that steering only 20% to 80% of tokens achieves superior alignment-efficiency trade offs. For strong base models such as Qwen3, intervening on as few as 20% of tokens matches or even surpasses heavily post-trained instruct models. This sparsity enables stronger guidance while better preserving the model's native distribution, integrates seamlessly with search based methods such as Best-of-N, and reduces computational cost by up to 6x.
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All authors Runyi Hu, Jie Zhang, Shiqian Zhao, Jiale Meng, Jiwei Li, Jason Zeng, Ming Wu, Michael Heinrich, Yonggang Wen, Tianwei Zhang

Computation and Language

Prompt Optimization Via Diffusion Language Models

We propose a diffusion-based framework for prompt optimization that leverages Diffusion Language Models (DLMs) to iteratively refine system prompts through masked denoising. By conditioning on interaction traces, including user queries, model responses, and optional feedback, our method enables flexible, span-level prompt updates without requiring gradient access or modifying the downstream language model. Across diverse benchmarks (e.g., $\tau$-bench, SST-2, SST-5), DLM-optimized prompts consistently improve the performance of a frozen target LLM (e.g., GPT-4o-mini). We further show that moderate diffusion step counts provide the best balance between refinement quality and stability. These results highlight diffusion-based prompt optimization as a general, model-agnostic, and scalable approach for enhancing LLM performance through iterative prompt refinement.
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All authors Shiyu Wang, Haolin Chen, Liangwei Yang, Jielin Qiu, Rithesh Murthy, Ming Zhu, Zixiang Chen, Silvio Savarese, Caiming Xiong, Shelby Heinecke, Huan Wang

Computation and Language · Cross-listed from cs.AI

Retrieval Augmented (Knowledge Graph), and Large Language Model-Driven Design Structure Matrix (DSM) Generation of Cyber-Physical Systems

We explore the potential of Large Language Models (LLMs), Retrieval-Augmented Generation (RAG), and Graph-based RAG (GraphRAG) for generating Design Structure Matrices (DSMs). We test these methods on two distinct use cases–a power screwdriver and a CubeSat with known architectural references–evaluating their performance on two key tasks: determining relationships between predefined components, and the more complex challenge of identifying components and their subsequent relationships. We measure the performance by assessing each element of the DSM and overall architecture. Despite design and computational challenges, we identify opportunities for automated DSM generation, with all code publicly available for reproducibility and further feedback from the domain experts.
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Computation and Language · Cross-listed from cs.CV

Brazilian Portuguese Image Captioning with Transformers: A Study on Cross-Native-Translated Dataset

Image captioning (IC) refers to the automatic generation of natural language descriptions for images, with applications ranging from social media content generation to assisting individuals with visual impairments. While most research has been focused on English-based models, low-resource languages such as Brazilian Portuguese face significant challenges due to the lack of specialized datasets and models. Several studies create datasets by automatically translating existing ones to mitigate resource scarcity. This work addresses this gap by proposing a cross-native-translated evaluation of Transformer-based vision and language models for Brazilian Portuguese IC. We use a version of Flickr30K comprised of captions manually created by native Brazilian Portuguese speakers and compare it to a version with captions automatically translated from English to Portuguese. The experiments include a cross-context approach, where models trained on one dataset are tested on the other to assess the translation impact. Additionally, we incorporate attention maps for model inference interpretation and use the CLIP-Score metric to evaluate the image-description alignment. Our findings show that Swin-DistilBERTimbau consistently outperforms other models, demonstrating strong generalization across datasets. ViTucano, a Brazilian Portuguese pre-trained VLM, surpasses larger multilingual models (GPT-4o, LLaMa 3.2 Vision) in traditional text-based evaluation metrics, while GPT-4 models achieve the highest CLIP-Score, highlighting improved image-text alignment. Attention analysis reveals systematic biases, including gender misclassification, object enumeration errors, and spatial inconsistencies. The datasets and the models generated and analyzed during the current study are available in: https://github.com/laicsiifes/transformer-caption-ptbr.
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All authors Gabriel Bromonschenkel, Alessandro L. Koerich, Thiago M. Paixão, Hilário Tomaz Alves de Oliveira

Computation and Language

Clause-Internal or Clause-External? Testing Turkish Reflexive Binding in Adapted versus Chain of Thought Large Language Models

This study evaluates whether state-of-the-art large language models capture the binding relations of Turkish reflexive pronouns. We construct a balanced evaluation set of 100 Turkish sentences that systematically pit local against non-local antecedents for the reflexives kendi and kendisi. We compare two contrasting systems: an OpenAI chain-of-thought model optimized for multi-step reasoning and Trendyol-LLM-7B-base-v0.1, a LLaMA 2 derived model extensively fine-tuned on Turkish data. Antecedent choice is assessed using a combined paradigm that integrates sentence-level perplexity with a forced-choice comparison between minimally differing continuations. Overall, Trendyol-LLM favors local bindings in approximately 70 percent of trials, exhibiting a robust locality bias consistent with a preference for structurally proximate antecedents. By contrast, the OpenAI model (o1 Mini) distributes its choices nearly evenly between local and long-distance readings, suggesting weaker or less consistent sensitivity to locality in this binding configuration. Taken together, these results reveal a marked contrast in binding behavior across the two systems and motivate closer analysis of how model architecture, training data, and inference-time reasoning strategies shape the representation of Turkish anaphoric dependencies.
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Computation and Language

DecompressionLM: Deterministic, Diagnostic, and Zero-Shot Concept Graph Extraction from Language Models

Existing knowledge probing methods rely on pre-defined queries, limiting extraction to known concepts. We introduce DecompressionLM, a stateless framework for zero-shot concept graph extraction that discovers what language models encode without pre-specified queries or shared cross-sequence state. Our method targets three limitations of common decoding-based probing approaches: (i) cross-sequence coupling that concentrates probability mass on high-frequency prefixes, (ii) competitive decoding effects that suppress long-tail concepts, and (iii) scalability constraints arising from sequential exploration. Using Van der Corput low-discrepancy sequences with arithmetic decoding, DecompressionLM enables deterministic, embarrassingly parallel generation without shared state across sequences. Across two model families and five quantization variants, we find that activation-aware quantization (AWQ-4bit) expands concept coverage by 30-170%, while uniform quantization (GPTQ-Int4) induces 71-86% coverage collapse - divergent behaviors not reliably reflected by explanation-level perplexity. Corpus-based verification further reveals a 19.6-point hallucination gap between top- and bottom-ranked MMLU-Pro Law models. DecompressionLM establishes concept coverage as a complementary evaluation dimension for assessing knowledge breadth and factual grounding in compressed models intended for deployment. Code is available at https://github.com/ulab-uiuc/decompressionlm.
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Computation and Language · Cross-listed from cs.LG

Post-Training Probability Manifold Correction via Structured SVD Pruning and Self-Referential Distillation

Large language models are expensive to deploy. We introduce Sparse Knowledge Distillation (SparseKD), a post-training method that compresses transformer models by combining structured SVD pruning with self-referential knowledge distillation. The key insight is simple: instead of using an external teacher, the model teaches itself by matching its own probability distribution from before compression. This self-referential setup enables surprisingly strong quality recovery after aggressive pruning. Our experiments reveal an unexpected finding: self-referential distillation alone, applied post-training under an identical objective and fixed calibration dataset, improves model quality by 39% relative to the original converged checkpoint. When combined with structured pruning, SparseKD achieves 15-65% parameter reduction with acceptable quality trade-offs. Kernel profiling shows that speedups arise entirely from reduced dense matrix multiplication in feed-forward layers while attention remains unchanged, making this approach complementary to attention optimizations. We validate across two model families (0.6B and 3.8B parameters) with multi-seed experiments confirming high reproducibility. SparseKD requires no external super-teacher, no architectural changes, and no custom inference kernels, making it immediately deployable with existing infrastructure.
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Computation and Language

DETOUR: An Interactive Benchmark for Dual-Agent Search and Reasoning

When recalling information in conversation, people often arrive at the recollection after multiple turns. However, existing benchmarks for evaluating agent capabilities in such tip-of-the-tongue search processes are restricted to single-turn settings. To more realistically simulate tip-of-the-tongue search, we introduce Dual-agent based Evaluation Through Obscure Under-specified Retrieval (DETOUR), a dual-agent evaluation benchmark containing 1,011 prompts. The benchmark design involves a Primary Agent, which is the subject of evaluation, tasked with identifying the recollected entity through querying a Memory Agent that is held consistent across evaluations. Our results indicate that current state-of-the-art models still struggle with our benchmark, only achieving 36% accuracy when evaluated on all modalities (text, image, audio, and video), highlighting the importance of enhancing capabilities in underspecified scenarios.
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All authors Li Siyan, Darshan Deshpande, Anand Kannappan, Rebecca Qian

Computation and Language · Cross-listed from cs.CV

When RAG Hurts: Diagnosing and Mitigating Attention Distraction in Retrieval-Augmented LVLMs

While Retrieval-Augmented Generation (RAG) is one of the dominant paradigms for enhancing Large Vision-Language Models (LVLMs) on knowledge-based VQA tasks, recent work attributes RAG failures to insufficient attention towards the retrieved context, proposing to reduce the attention allocated to image tokens. In this work, we identify a distinct failure mode that previous study overlooked: Attention Distraction (AD). When the retrieved context is sufficient (highly relevant or including the correct answer), the retrieved text suppresses the visual attention globally, and the attention on image tokens shifts away from question-relevant regions. This leads to failures on questions the model could originally answer correctly without the retrieved text. To mitigate this issue, we propose MAD-RAG, a training-free intervention that decouples visual grounding from context integration through a dual-question formulation, combined with attention mixing to preserve image-conditioned evidence. Extensive experiments on OK-VQA, E-VQA, and InfoSeek demonstrate that MAD-RAG consistently outperforms existing baselines across different model families, yielding absolute gains of up to 4.76%, 9.20%, and 6.18% over the vanilla RAG baseline. Notably, MAD-RAG rectifies up to 74.68% of failure cases with negligible computational overhead.
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All authors Beidi Zhao, Wenlong Deng, Xinting Liao, Yushu Li, Nazim Shaikh, Yao Nie, Xiaoxiao Li

Computation and Language

Detecting AI-Generated Content in Academic Peer Reviews

The growing availability of large language models (LLMs) has raised questions about their role in academic peer review. This study examines the temporal emergence of AI-generated content in peer reviews by applying a detection model trained on historical reviews to later review cycles at International Conference on Learning Representations (ICLR) and Nature Communications (NC). We observe minimal detection of AI-generated content before 2022, followed by a substantial increase through 2025, with approximately 20% of ICLR reviews and 12% of Nature Communications reviews classified as AI-generated in 2025. The most pronounced growth of AI-generated reviews in NC occurs between the third and fourth quarter of 2024. Together, these findings provide suggestive evidence of a rapidly increasing presence of AI-assisted content in peer review and highlight the need for further study of its implications for scholarly evaluation.
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Computation and Language

MiNER: A Two-Stage Pipeline for Metadata Extraction from Municipal Meeting Minutes

Municipal meeting minutes are official documents of local governance, exhibiting heterogeneous formats and writing styles. Effective information retrieval (IR) requires identifying metadata such as meeting number, date, location, participants, and start/end times, elements that are rarely standardized or easy to extract automatically. Existing named entity recognition (NER) models are ill-suited to this task, as they are not adapted to such domain-specific categories. In this paper, we propose a two-stage pipeline for metadata extraction from municipal minutes. First, a question answering (QA) model identifies the opening and closing text segments containing metadata. Transformer-based models (BERTimbau and XLM-RoBERTa with and without a CRF layer) are then applied for fine-grained entity extraction and enhanced through deslexicalization. To evaluate our proposed pipeline, we benchmark both open-weight (Phi) and closed-weight (Gemini) LLMs, assessing predictive performance, inference cost, and carbon footprint. Our results demonstrate strong in-domain performance, better than larger general-purpose LLMs. However, cross-municipality evaluation reveals reduced generalization reflecting the variability and linguistic complexity of municipal records. This work establishes the first benchmark for metadata extraction from municipal meeting minutes, providing a solid foundation for future research in this domain.
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All authors Rodrigo Batista, Luís Filipe Cunha, Purificação Silvano, Nuno Guimarães, Alípio Jorge, Evelin Amorim, Ricardo Campos

Computation and Language

Faithful-Patchscopes: Understanding and Mitigating Model Bias in Hidden Representations Explanation of Large Language Models

Large Language Models (LLMs) have demonstrated strong capabilities for hidden representation interpretation through Patchscopes, a framework that uses LLMs themselves to generate human-readable explanations by decoding from internal hidden representations. However, our work shows that LLMs tend to rely on inherent linguistic patterns, which can override contextual information encoded in the hidden representations during decoding. For example, even when a hidden representation encodes the contextual attribute "purple" for "broccoli", LLMs still generate "green" in their explanations, reflecting a strong prior association. This behavior reveals a systematic unfaithfulness in Patchscopes. To systematically study this issue, we first designed a dataset to evaluate the faithfulness of Patchscopes under biased cases, and our results show that there is an 18.84% faithfulness decrease on average. We then propose Bias Alignment through Logit Recalibration (BALOR), which treats the output logits from an unpatched prompt as capturing model bias and contrasts them with logits obtained under patched contextual information. By recalibrating the logit distribution through this contrast, BALOR suppresses model bias and amplifies contextual information during generation. Experiments across multiple LLMs demonstrate that BALOR consistently outperforms existing baselines, achieving up to 33% relative performance improvement.
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All authors Xilin Gong, Shu Yang, Zehua Cao, Lynne Billard, Di Wang

Computation and Language

Semantic Calibration Prevails Where Token Confidence Fails: Benchmarking Long-Form Scientific QA

Reliable uncertainty quantification (UQ) is essential for safe deployment of large language models (LLMs) in scientific question answering, where long-form outputs exceed practical human verification at scale. We introduce the first large-scale benchmark for UQ calibration in long-form, reasoning-demanding scientific QA, evaluating four UQ methods on 685,000 responses across up to 20 LLMs and seven datasets, supported by an extensible open-source framework whose shared-generation design enables reproducible cross-method comparisons. Instruction tuning is shown to associate with systematic token probability polarization, collapsing confidence distributions and undermining the reliability of token-level uncertainty signals. Reasoning model families diverge: some reproduce this polarization while others actively mitigate it, a pattern that clusters by provider and suggests training pipeline design as a key differentiating factor. Verbalized and token-aggregation sequence-level methods fail systematically. Only semantic consistency, as measured by consistency of the final answer, yields well-calibrated outputs, providing the first large-scale evidence that semantic calibration persists in multi-step, dependency-rich reasoning settings.
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All authors Philip Müller, Nicholas Popovič, Michael Färber, Peter Steinbach

Computation and Language · Cross-listed from cs.LG

TABES: Trajectory-Aware Backward-on-Entropy Steering for Masked Diffusion Models

Masked Diffusion Models (MDMs) have emerged as a promising non-autoregressive paradigm for generative tasks, offering parallel decoding and bidirectional context utilization. However, current sampling methods rely on simple confidence-based heuristics that ignore the long-term impact of local decisions, leading to trajectory lock-in where early hallucinations cascade into global incoherence. While search-based methods mitigate this, they incur prohibitive computational costs ($O(K)$ forward passes per step). In this work, we propose Backward-on-Entropy (BoE) Steering, a gradient-guided inference framework that approximates infinite-horizon lookahead via a single backward pass. We formally derive the Token Influence Score (TIS) from a first-order expansion of the trajectory cost functional, proving that the gradient of future entropy with respect to input embeddings serves as an optimal control signal for minimizing uncertainty. To ensure scalability, we introduce ActiveQueryAttention, a sparse adjoint primitive that exploits the structure of the masking objective to reduce backward pass complexity. BoE achieves a superior Pareto frontier for inference-time scaling compared to existing unmasking methods, demonstrating that gradient-guided steering offers a mathematically principled and efficient path to robust non-autoregressive generation. We will release the code.
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All authors Shreshth Saini, Avinab Saha, Balu Adsumilli, Neil Birkbeck, Yilin Wang, Alan C. Bovik

Computation and Language

DIVERGE: Diversity-Enhanced RAG for Open-Ended Information Seeking

Existing retrieval-augmented generation (RAG) systems often assume that each query has a single correct answer. This assumption overlooks open-ended information-seeking scenarios where multiple plausible answers are valuable, and where diversity is important for creativity, fairness, and inclusive access to information. We show that standard RAG systems fail to fully use diverse retrieved contexts: simply increasing retrieval diversity does not necessarily lead to diverse generations. To address this limitation, we propose Diverge, a plug-and-play agentic RAG framework that improves the diversity–quality trade-off through iterative, reflection-guided exploration of diverse viewpoints and diversity-aware retrieval support. We further introduce evaluation metrics for characterizing the diversity-quality trade-off in open-ended question answering. Experiments across multiple real-world datasets and backbone LLMs show that Diverge achieves the best trade-off among competitive baselines, increasing diversity by $\sim2\times$ without noticeable quality degradation. These results reveal a systematic limitation of current RAGs and show the value of explicit diversity modeling.
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Computation and Language · Cross-listed from q-bio.QM

Rank-and-Reason: Multi-Agent Collaboration Accelerates Zero-Shot Protein Mutation Prediction

Zero-shot mutation prediction is vital for low-resource protein engineering, yet existing protein language models (PLMs) often yield statistically confident results that ignore fundamental biophysical constraints. Currently, selecting candidates for wet-lab validation relies on manual expert auditing of PLM outputs, a process that is inefficient, subjective, and highly dependent on domain expertise. To address this, we propose Rank-and-Reason (VenusRAR), a two-stage agentic framework to automate this workflow and maximize expected wet-lab fitness. In the Rank-Stage, a Computational Expert and Virtual Biologist aggregate a context-aware multi-modal ensemble, establishing a new Spearman correlation record of 0.551 (vs. 0.518) on ProteinGym. In the Reason-Stage, an agentic Expert Panel employs chain-of-thought reasoning to audit candidates against geometric and structural constraints, improving the Top-5 Hit Rate by up to 367% on ProteinGym-DMS99. The wet-lab validation on Cas12i3 nuclease further confirms the framework's efficacy, achieving a 46.7% positive rate and identifying two novel mutants with 4.23-fold and 5.05-fold activity improvements. Code and datasets are released on GitHub (https://github.com/ai4protein/VenusRAR/).
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All authors Yang Tan, Yuanxi Yu, Can Wu, Bozitao Zhong, Mingchen Li, Guisheng Fan, Jiankang Zhu, Yafeng Liang, Nanqing Dong, Liang Hong

Computation and Language · Cross-listed from cs.LG

FOCUS: DLLMs Know How to Tame Their Compute Bound

Diffusion Large Language Models (DLLMs) offer a compelling alternative to Auto-Regressive models, but their deployment is constrained by high decoding cost. In this work, we identify a key inefficiency in DLLM decoding: while computation is parallelized over token blocks, only a small subset of tokens is decodable at each diffusion step, causing most compute to be wasted on non-decodable tokens. We further observe a strong correlation between attention-derived token importance and token-wise decoding probability. Based on this insight, we propose FOCUS, an inference system designed for DLLMs. By dynamically focusing computation on decodable tokens and evicting non-decodable ones on-the-fly, FOCUS increases the effective batch size, alleviating compute limitations and enabling scalable throughput. Empirical evaluations demonstrate that FOCUS achieves up to 3.52$\times$ throughput improvement over the production-grade engine LMDeploy in large-batch settings, while preserving or improving generation quality across multiple benchmarks.
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All authors Kaihua Liang, Xin Tan, An Zhong, Hong Xu, Marco Canini

Computation and Language

UPA: Unsupervised Prompt Agent via Tree-Based Search and Selection

Prompt agents have recently emerged as a promising paradigm for automated prompt optimization, framing prompt discovery as a sequential decision-making problem over a structured prompt space. While this formulation enables the use of advanced planning algorithms, these methods typically assume access to supervised reward signals, which are often unavailable in practical scenarios. In this work, we propose UPA, an Unsupervised Prompt Agent that realizes structured search and selection without relying on ground-truth (GT) rewards. Specifically, during search, UPA iteratively constructs an evolving tree structure to navigate the prompt space, guided by fine-grained and position-debiased pairwise comparisons from Large Language Models (LLMs). Crucially, as these local comparisons do not inherently yield a consistent global scale, we decouple systematic prompt exploration from final selection, introducing a two-stage framework grounded in the Bradley-Terry-Luce (BTL) model. This framework first performs path-wise Bayesian aggregation of local comparisons to filter candidates under uncertainty, followed by global tournament-style comparisons to infer latent prompt quality and identify the optimal prompt. Experiments across multiple tasks demonstrate that UPA consistently outperforms existing prompt optimization methods, showing that agent-style optimization can remain highly effective even in unsupervised settings.
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All authors Siran Peng, Weisong Zhao, Tianyu Fu, Chenxu Zhao, Tianshuo Zhang, Haoyuan Zhang, Xiangyu Zhu, Minghui Wu, Zhen Lei

Computation and Language

PaperBanana: Automating Academic Illustration for AI Scientists

Despite rapid advances in autonomous AI scientists powered by language models, generating publication-ready illustrations remains a labor-intensive bottleneck in the research workflow. To lift this burden, we introduce PaperBanana, an agentic framework for automated generation of publication-ready academic illustrations. Powered by state-of-the-art VLMs and image generation models, PaperBanana orchestrates specialized agents to retrieve references, plan content and style, render images, and iteratively refine via self-critique. To rigorously evaluate our framework, we introduce PaperBananaBench, comprising 292 test cases for methodology diagrams curated from NeurIPS 2025 publications, covering diverse research domains and illustration styles. Comprehensive experiments demonstrate that PaperBanana consistently outperforms leading baselines in faithfulness, conciseness, readability, and aesthetics. We further show that our method effectively extends to the generation of high-quality statistical plots. Collectively, PaperBanana paves the way for the automated generation of publication-ready illustrations.
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All authors Dawei Zhu, Rui Meng, Yale Song, Xiyu Wei, Sujian Li, Tomas Pfister, Jinsung Yoon

Computation and Language · Cross-listed from cs.LG

Agnostic Language Identification and Generation

Recent works on language identification and generation have established tight statistical rates at which these tasks can be achieved. These works typically operate under a strong realizability assumption: that the input data is drawn from an unknown distribution necessarily supported on some language in a given collection. In this work, we relax this assumption of realizability entirely, and impose no restrictions on the distribution of the input data. We propose objectives to study both language identification and generation in this more general "agnostic" setup. Across both problems, we obtain novel interesting characterizations and nearly tight rates.
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Computation and Language

Now You Hear Me: Audio Narrative Attacks Against Large Audio-Language Models

Large audio-language models increasingly operate on raw speech inputs, enabling more seamless integration across domains such as voice assistants, education, and clinical triage. This transition, however, introduces a distinct class of vulnerabilities that remain largely uncharacterized. We examine the security implications of this modality shift by designing a text-to-audio jailbreak that embeds disallowed directives within a narrative-style audio stream. The attack leverages an advanced instruction-following text-to-speech (TTS) model to exploit structural and acoustic properties, thereby circumventing safety mechanisms primarily calibrated for text. When delivered through synthetic speech, the narrative format elicits restricted outputs from state-of-the-art models, including Gemini 2.0 Flash, achieving a 98.26% success rate that substantially exceeds text-only baselines. These results highlight the need for safety frameworks that jointly reason over linguistic and paralinguistic representations, particularly as speech-based interfaces become more prevalent.
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All authors Ye Yu, Haibo Jin, Yaoning Yu, Jun Zhuang, Haohan Wang

Computation and Language · Cross-listed from cs.AI

Scaling Multiagent Systems with Process Rewards

While multiagent systems have shown promise for tackling complex tasks via specialization, finetuning multiple agents simultaneously faces two key challenges: (1) credit assignment across agents, and (2) sample efficiency of expensive multiagent rollouts. In this work, we propose finetuning multiagent systems with per-action process rewards from AI feedback (MAPPA) to address both. Through assigning credit to individual agent actions rather than only at task completion, MAPPA enables fine-grained supervision without ground truth labels while extracting maximal training signal from each rollout. We demonstrate our approach on competition math problems and tool-augmented data analysis tasks. On unseen math problems, MAPPA achieves +5.0–17.5pp on AIME and +7.8–17.2pp on AMC. For data analysis tasks, our method improves success rate by +16.7pp while quality metrics improve by up to 47%, validating that per-action supervision can lead to improvements across different multiagent systems on various domains. By addressing these challenges, our work takes a first step toward scaling multiagent systems for complex, long-horizon tasks with minimal human supervision.
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Computation and Language

Are you going to finish that? A Practical Study of the Partial Token Problem

Language models (LMs) are trained over sequences of tokens, whereas users interact with LMs via text. This mismatch gives rise to the partial token problem, which occurs when a user ends their prompt in the middle of the expected next-token, leading to distorted next-token predictions. Although this issue has been studied using arbitrary character prefixes, its prevalence and severity in realistic prompts respecting word boundaries remains underexplored. In this work, we identify three domains where token and "word" boundaries often do not line up: languages that do not use whitespace, highly compounding languages, and code. In Chinese, for example, up to 25% of word boundaries do not line up with token boundaries, making even natural, word-complete prompts susceptible to this problem. We systematically construct semantically natural prompts ending with a partial tokens; in experiments, we find that they comprise a serious failure mode: frontier LMs consistently place three orders of magnitude less probability on the correct continuation compared to when the prompt is "backed-off" to be token-aligned. This degradation does not diminish with scale and often worsens for larger models. Finally, we evaluate inference-time mitigations to the partial token problem and validate the effectiveness of recent exact solutions. Overall, we demonstrate the scale and severity of probability distortion caused by tokenization in realistic use cases, and provide practical recommentions for model inference providers.
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All authors Hao Xu, Alisa Liu, Jonathan Hayase, Yejin Choi, Noah A. Smith

Computation and Language

Deep Search with Hierarchical Meta-Cognitive Monitoring Inspired by Cognitive Neuroscience

Deep search agents powered by large language models have demonstrated strong capabilities in multi-step retrieval, reasoning, and long-horizon task execution. However, their practical failures often stem from the lack of mechanisms to monitor and regulate reasoning and retrieval states as tasks evolve under uncertainty. Insights from cognitive neuroscience suggest that human metacognition is hierarchically organized, integrating fast anomaly detection with selectively triggered, experience-driven reflection. In this work, we propose Deep Search with Meta-Cognitive Monitoring (DS-MCM), a deep search framework augmented with an explicit hierarchical metacognitive monitoring mechanism. DS-MCM integrates a Fast Consistency Monitor, which performs lightweight checks on the alignment between external evidence and internal reasoning confidence, and a Slow Experience-Driven Monitor, which is selectively activated to guide corrective intervention based on experience memory from historical agent trajectories. By embedding monitoring directly into the reasoning-retrieval loop, DS-MCM determines both when intervention is warranted and how corrective actions should be informed by prior experience. Experiments across multiple deep search benchmarks and backbone models demonstrate that DS-MCM consistently improves performance and robustness.
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All authors Zhongxiang Sun, Qipeng Wang, Weijie Yu, Jingxuan Yang, Haolang Lu, Jun Xu