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版本更新 · v2arXiv:2611.02275

Data-Scarce, Multi-Granular, Multimodal: Benchmark Design for Biosynthetic Gene Clusters

Hanlin Xiao, Eriko Takano, Mauricio A. Álvarez, Rainer Breitling

原文摘要

Biosynthetic gene clusters (BGCs) are co-located genes that encode the biosynthesis of specialized metabolites, an important source of antibiotics, anticancer agents, immunosuppressants, and agricultural bioactives. Deep learning, particularly self-supervised foundation models, has spurred interest in BGC sequence modeling, but evaluation has lagged behind: existing benchmarks often rely on coarse classification over small curated datasets, providing limited discrimination among models and insight into downstream utility. We propose a benchmark-design framework in which an informative benchmark should be discriminative, separating models with statistical confidence, and applicable, spanning scientifically meaningful tasks under different levels of generalization. We instantiate this framework as BGC-Bench, which derives five tasks from MIBiG, ranging from A-domain substrate prediction to BGC-molecule retrieval, evaluates them under genotype- and phenotype-shift splits, includes an active-learning setting for label-scarce discovery, and is easily extensible to new tasks and encoders. BGCs further provide a shared testbed across granularities and modalities: BGC-Bench compares twelve encoders on nucleotide, amino-acid, or Pfam-domain sequences, including compositional baselines for each input type, and combines BGC and chemical encoders for cross-modal retrieval. No single representation dominates: the best granularity depends on the biological scale of the task, and pretrained encoders do not consistently outperform other representations across tasks and splits. Active-learning experiments show that most tasks remain data-limited, encoder rankings change with labeling budget, and acquisition strategies yield modest gains. These results show that BGC model evaluation requires task-diverse, shift-aware benchmarks, and the framework can be generalized to benchmark design beyond BGCs.

cs.AI

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arXiv ↗PDF ↗
版本更新 · v2arXiv:2602.15012

Cold-Start Personalization via Bayesian Adaptive Questioning

Avinandan Bose, Shuyue Stella Li, Faeze Brahman, Pang Wei Koh, Simon Shaolei Du, Yulia Tsvetkov, Maryam Fazel, Lin Xiao 等 9 位作者

原文摘要

Cold-start personalization requires inferring preferences from minimal interaction when no user-specific historical data is available. The space of possible preferences is vast, yet users care about only a sparse subset and rarely articulate them upfront; combined with limited interaction budgets, this makes preference elicitation challenging. Our key insight is that preferences exhibit predictable structure across populations; e.g., users who want detailed explanations often also value worked examples. We propose CAPE (Cold-start Adaptive Preference Elicitation), which learns a structured world model of preference correlations offline from complete profiles, then performs training-free Bayesian inference online to select informative questions and predict complete preference profiles, including dimensions never asked about. Even simple belief model instantiations (e.g., linear regression) substantially outperform end-to-end RL. Across medical, mathematical, social, and commonsense reasoning, CAPE achieves 80.8% alignment with ground-truth user preferences versus 68.5% for RL, requires 2.5x to over 15x fewer interactions, and adapts its questions twice as often as RL. Our contribution is a principled decomposition of cold-start personalization that makes Bayesian preference elicitation practical at scale for LLM systems.

cs.CL · cs.AI · cs.LG

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.12095

From Fluent Text to Ontology-Compatible Definitions: A Quality-Control Agentic Workflow

Kun Feng, Chenchen Chu, Yan Liu, Haojie Sun, Jijun Tang, Chen Tian, Shuolin Xiao, Jianping He 等 9 位作者

原文摘要

Biomedical ontologies are structured knowledge systems that must evolve continuously to represent newly emerging knowledge, but their manual maintenance remains time-consuming and laborintensive. Textual definitions are especially costly because they must be readable to humans and compatible with controlled entities, relations, and logical constraints. Large language models (LLMs) offer a promising way to assist ontology engineering tasks, including definition generation. However, textual plausibility does not guarantee knowledge-system compatibility. A generated definition may be fluent and close to a reference definition, yet still fail to ground its implied entities or violate ontology-level constraints. Directly inserting such definitions into ontology libraries may therefore introduce entity-level hallucinations and logical inconsistencies. To address this problem, we propose two structured-knowledge incompatibility metrics, Entity Error Rate (EER) and Logical Inconsistency Rate (LIR), to quantify entity grounding and logical consistency for LLM-generated ontology definitions. We further develop an agentic quality-control (QC) workflow that treats definition generation as an iterative process rather than a direct decoding step: it generates definitions, extracts axioms, checks entity existence and logical consistency, and uses the resulting diagnostics to drive repair loops. Comprehensive experiments on Disease Ontology, Uberon Ontology, and Uberon-ConstraintStress demonstrate that EER and LIR complement conventional reference-based metrics by evaluating whether generated content can be grounded and checked inside the target ontology. The workflow effectively decreases EER while maintaining strong conventional text-generation performance. LIR further exposes sparse ontology-level logical failures that are invisible to text similarity metrics, although their repair remains limited.

cs.AI

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.09407

ROAM: Retrieval-Augmented Optimization for Feasible Multi-Day Itinerary Planning

Ye Zihao, Lin Xiaoheng

原文摘要

Large language models (LLMs) can draft plausible travel itineraries, but the plans they produce are frequently infeasible: attractions are grouped into days without regard for geography, opening hours are ignored, and a single generation pass cannot reliably organize a multi-day trip. We present ROAM, a retrieval-augmented agentic framework for spontaneous multi-day itinerary planning that couples semantic preference retrieval with explicit spatiotemporal optimization. ROAM embeds the natural-language request, retrieves a compact candidate set from a curated point-of-interest (POI) database, partitions candidates into day groups through maximal-clique analysis and K-means, orders each day with a quality-biased simulated-annealing TSP solver, and repairs hard opening-hour violations with greedy exchange. A spatiotemporal retrieval layer injects weather forecasts, real road distances and POI operating hours into the prompt, after which the LLM renders a structured, map-ready itinerary; an interactive ReAct-style replanning agent then supports natural-language edits while re-checking feasibility. Across four Chinese cities and 510 POIs, ROAM produces 27.5 POIs per three-day plan versus 19.3 for a bare LLM and 17.0 for a retrieval-only baseline (+42% and +62%), while reducing route dispersion from 2,101 to 677 (3.1x). Ablations show that spatial optimization is the dominant driver of route efficiency and that hard time-window repair prevents roughly 30% of attractions from violating operating hours.

cs.AI

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arXiv ↗PDF ↗
新论文 · v1arXiv:2611.06103

SenTrojan: Revealing Analog Hardware Trojan Attacks on Sensors

Kun Wang, Ruochen Zhou, Wenjun Zhu, Shilin Xiao, Kai Wang, Chen Yan, Xiaoyu Ji, Wenyuan Xu

原文摘要

Sensors bridge the physical and digital worlds, making their integrity critical to cyber-physical system security. Existing sensor attacks largely exploit unintended and sensor-specific physical vulnerabilities, limiting their generalizability and motivating a different threat model, i.e., whether an adversary can implant hidden attack surfaces into sensors before deployment. In this paper, we present SenTrojan, an analog hardware Trojan framework for sensors. SenTrojan embeds malicious functionality into analog signal circuitry commonly shared across diverse sensor architectures, and activates the hidden behavior through crafted external physical signals. Once activated, SenTrojan can induce sensor malfunctions ranging from permanent denial-of-service to static or dynamic spoofing. To achieve these effects under different architectural constraints, we introduce two complementary designs. The Logic-Rule-Driven (LRD) Trojan adds lightweight analog monitoring logic to detect trigger features such as frequency and amplitude, enabling reliable activation across various sensor types. The Physical-Effect-Driven (PED) Trojan targets sensors with exploitable native analog effects, e.g., nonlinearity and rectification, and realizes attacks with minimal component insertion. We evaluate SenTrojan on 14 sensors spanning 6 transduction principles and demonstrate its effectiveness across diverse real-world scenarios. Overall, SenTrojan achieves an average successful trigger rate above 95%, maintains over 97% similarity to benign behavior, incurs zero false-trigger rate for LRD designs, and introduces less than 5% average deviation in drift, noise floor, and response time. To our knowledge, this work is the first systematic study of analog sensor Trojans, broadening sensor security from unintended physical vulnerabilities to intentional supply-chain compromise.

cs.CR

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arXiv ↗PDF ↗
版本更新 · v3arXiv:2606.06388

Humans' ALMANAC: A Human Collaboration Dataset of Action-Level Mental Model Annotations for Agent Collaboration

Jiaju Chen, Yuxuan Lu, Jiayi Su, Chaoran Chen, Songlin Xiao, Zheng Zhang, Yun Wang, Yunyao Li 等 13 位作者

原文摘要

Recent advances in LLM agents have enabled complex cognitive capabilities, such as multi-step reasoning, planning, and tool use, that increasingly position these agents as collaborative partners in human workflows. Effective collaboration, however, requires collaborators to continuously maintain and align mental models of their own reasoning, partners' intentions, and shared goals during the collaborative process. Today's agents rarely develop such capabilities since they are primarily optimized for task completion rather than for maintaining the underlying mental models required for collaborative processes. Moreover, the community lacks authentic human collaboration data with action-level mental model annotations that could guide agents toward collaborative competence. To bridge this gap, we present ALMANAC, a dataset of Action-Level Mental model ANnotations for Agent Collaboration built from the Map Task, a classic dyadic routing task from social science. ALMANAC contains 2,987 collaboration actions, each paired with theory-informed mental model annotations that record the participants' self-reasoning, perceived partner intent, and perceived team goal. We benchmark six LLMs on predicting humans' next-turn behavior and mental models. Our results demonstrate ALMANAC's utility in evaluating models' ability to simulate human collaborative behaviors and infer their underlying mental models. The project page is available at https://human-agent-collab.hailab.io/almanac.

cs.AI · cs.CL

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arXiv ↗PDF ↗
首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.1156ACL Anthology · ACL 2026

Collision to Cognition: Hash-Driven Graph Construction for Efficient RAG

Chuang Zhou, Zheng Yuan Hong Kong Polytechnic University, Linhao Luo, Zhaozhuo Xu Workato and Stevens Institute of Technology, Yilin Xiao, Junnan Dong, Siyu An, di Yin Tencent Youtu 等 10 位作者

原文摘要

Retrieval-Augmented Generation (RAG) has long been a promising paradigm for enhancing large language models (LLMs) with external knowledge. Traditional embedding-based methods for graph construction can capture semantic similarity but struggle to establish fine-grained, interpretable logical relationships. Recently, Graph-enhanced RAG (GraphRAG) has gained increasing popularity for its capability in modeling logical relationships. However, graph construction requires extensive token consumption for triple extraction and summarization, making it costly and slow. Accordingly, we propose MeshRAG, a novel framework for mining efficient structures via hashing to enhance RAG. We adopt an inductive paradigm in which global graph structure emerges from local hash collisions rather than explicit symbolic extraction. By replacing neural embedding search with lightweight and bitwise operations, MeshRAG automates a simple and rapid graph construction process. Furthermore, the hash collision mechanism provides transparent evidence for logical connections and retrieval decisions. Experimental results show that MeshRAG outperforms existing baselines, while its graph construction requires no GPU resources or token budget and can structure over ten thousand chunks in a few minutes.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.252ACL Anthology · ACL 2026

LogicPoison: Logical Attacks on Graph Retrieval-Augmented Generation

Yilin Xiao, Jin Chen, Qinggang Zhang Jilin University, Yujing Zhang, Chuang Zhou, Longhao Yang Southwest University of Finance and Economics, Lingfei Ren, Xin Yang Southwestern University of Finance and Economics 等 9 位作者

原文摘要

Graph-based Retrieval-Augmented Generation (GraphRAG) enhances the reasoning capabilities of Large Language Models (LLMs) by grounding their responses in structured knowledge graphs. Leveraging community detection and relation filtering techniques, GraphRAG systems demonstrate inherent resistance to traditional RAG attacks, such as text poisoning and prompt injection. However, in this paper, we find that the security of GraphRAG systems fundamentally relies on the topological integrity of the underlying graph, which can be undermined by implicitly corrupting the logical connections, without altering surface-level text semantics. To exploit this vulnerability, we propose LogicPoison, a novel attack framework that targets logical reasoning rather than injecting false contents. Specifically, LogicPoison employs a type-preserving entity swapping mechanism to perturb both global logic hubs for disrupting overall graph connectivity and query-specific reasoning bridges for severing essential multi-hop inference paths. This approach effectively reroutes valid reasoning into dead ends while maintaining surface-level textual plausibility. Comprehensive experiments across multiple benchmarks demonstrate that LogicPoison successfully bypasses GraphRAG’s defenses, significantly degrading performance and outperforming state-of-the-art baselines in both effectiveness and stealth. Our code is available at https://github.com/Jord8061/logicPoison.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表

首次观测 · 记录 #1ACL Anthology · ACL 2026:acl:2026.acl-long.986ACL Anthology · ACL 2026

Query-Aware Knowledge Retrieval via Hyperbolic Structuring

Chuang Zhou, Junnan Dong, Yilin Xiao, Shengyuan Chen, Su Dong, di Yin Tencent Youtu, Xing Sun Tencent YouTu Lab, Zhaozhuo Xu Workato and Stevens Institute of Technology 等 9 位作者

原文摘要

Retrieval-Augmented Generation (RAG) has demonstrated significant potential in enhancing large language models (LLMs) by supplementing external knowledge. However, existing approaches focus primarily on retrieving isolated factual knowledge entities while neglecting the critical reasoning relationships. To address this limitation, Graph-Augmented Generation (GraphRAG) has emerged as an effective solution, which explicitly integrates structured knowledge graphs to support complex reasoning tasks. Although diverse graph construction methods have been explored, they typically rely on static, query-agnostic graphs constructed via fixed heuristics. We are thereby motivated to propose a query-centric retrieval framework that adaptively constructs a graph tailored to each query. However, it is challenging to accurately identify these latent relationships from queries to the corpus. Moreover, unifying multiple local-perspective connections into a globally coherent structured corpus introduces additional complexity. To this end, we introduce HyperRAG, a novel framework in the Hyperbolic space that captures both explicit entity-based links and implicit query-aware connections. Extensive experiments on three benchmark datasets demonstrate that HyperRAG consistently outperforms existing baselines.

cs.CL

Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表