Rahi Navelkar, Andrea Cosolo, Iago Maceda Porto, Bogdan Bintu, Yubao Cheng, Vincent Gardeux, Silvia Gutnik, Taihei Fujimori 等 40 位作者
In recent years, multiplexed Fluorescence In Situ Hybridization (FISH) or FISH-omics methods have rapidly expanded, enabling the quantification of chromatin organization in single cells, often in conjunction with measurements of RNAs and proteins. These approaches have deepened our understanding of how 3D chromosome architecture relates to transcriptional activity and cell states in health and disease. Despite these advances, results from Chromatin Tracing FISH-omics experiments remain challenging to share, reuse, and analyze due to the absence of standardized data exchange specifications. Building on the release of microscopy metadata standards, we introduce the FISH Omics Format-Chromatin Tracing (FOF-CT), a community-developed standard for processed results from diverse imaging modalities. We describe the FOF-CT file format and present a curated collection of datasets deposited in the 4D Nucleome Data Portal and the OME Image Data Resource (IDR). We also highlight their potential for reuse, integration, and modeling by outlining example analysis pipelines and illustrating biological insights enabled by standardized, FAIR-compliant Chromatin Tracing datasets. FOF-CT natively represents both ball-and-stick and volumetric Chromatin Tracing data, unifying the two modalities within a single, modular table-based architecture (FOF-bas-CT and FOF-vol-CT, respectively).
Xinying Qian, Ying Zhang, Yu Zhao, Xubo Liu, Baohang Zhou, Jeff Z. Pan
Long-term memory enables Large Language Models (LLMs) to maintain coherent and personalized interactions across extended conversations. However, existing memory systems face two key challenges: (1) Information Entanglement, where heterogeneous information is mixed within coarse-grained memory units; and (2) Organizational Mismatch, where memory structures based primarily on semantic similarity may overlook other associations. To address these challenges, we propose ETAMem, a multi-view memory framework that decouples heterogeneous conversational information and aligns memory representations and organization with its distinct characteristics. Specifically, heterogeneous information parsing extracts atomic memory units and identifies affective information. View-specific memory structuring then organizes these units into three complementary hierarchical views: Event, Affect, and Time. ETAMem incrementally maintains memory structures with adaptively calibrated thresholds. For retrieval, entropy-based retrieval allocates query-specific budgets across views and performs hierarchical search within each view. Experiments on LoCoMo and LongMemEval-S demonstrate that ETAMem outperforms state-of-the-art baselines, achieving relative accuracy improvements of 12.46% and 7.96%, respectively, while maintaining competitive token efficiency. Further analyses demonstrate the complementary benefits of different memory views.
Hyperbolic graph representation learning has emerged as a powerful paradigm for modeling hierarchical data. Unlike Euclidean space, which exhibits polynomial volume growth, hyperbolic space grows exponentially with radius, naturally accommodating tree-like structures without the geometric distortion known as Euclidean crowding. Despite strong empirical performance, the theoretical mechanisms underlying hyperbolic embeddings remain poorly understood. In this work, we provide a geometric quantifcation research for Euclidean crowding, a generalization-theoretic explanation for the superiority of hyperbolic space on hierarchical data, and further develop an adaptive Euclidean-hyperbolic fusion learning framework toward bridging this gap. Specifically, we \textbf{first} establish a geometric quantification of Euclidean crowding by analyzing layer-wise minimum separation in node embeddings, proving that fixed-dimensional Euclidean embeddings of tree-like graphs inevitably exhibit layer-wise crowding that leads to weaker margin-based generalization bounds. \textbf{Second}, we provide a generalization-bound for the superiority of hyperbolic geometry on hierarchical data. \textbf{Third}, we propose EH-Fusion, a geometry-adaptive framework that lifts Euclidean GNN representations into hyperbolic space via exponential mapping and adaptively fuses both geometries based on node-level neighborhood expansion patterns. Extensive experiments validate our theoretical insights and demonstrate the effectiveness of EH-Fusion on benchmark datasets.
Ying Zhang, Ruoqi Guo, Yi Liu, Gelei Deng, Yuekang Li, Yepang Liu, Leo Zhang
Large language model (LLM) services process massive volumes of user requests, resulting in substantial inference costs. To reduce both cost and latency, providers have introduced prompt caching. However, correctly integrating prompt caching is non-trivial due to heterogeneous provider-specific APIs and continuously evolving caching semantics. To understand prompt-caching mis-integration in downstream applications, we conduct the first empirical study of 120 prompt-caching-related pull requests from 10 popular open-source agent systems. Our findings show that prompt-caching mis-integrations arise in both request-side misconfiguration and read-side usage miscount. More importantly, most mis-integrations fail silently without causing observable runtime failures. Motivated by these findings, we design CACHELINT, which models a prompt-caching mis-integration as an invocation site together with the preconditions required for correct cache integration. CACHELINT locates caching invocation sites with CodeQL and discharges each precondition either against a dated provider capability oracle or with an LLM guard check. CACHELINT achieves 0.71 precision and 0.78 recall in identifying the 120 labeled mis-integrations across the 10 studied agent systems. Our evaluation further demonstrates the effectiveness of CACHELINT in real-world settings, identifying 32 mis-integrations across 571 agent projects with 0.86 precision. These findings have received 21 developer confirmations and led to 18 upstream fixes, including one in Anthropic's official SDK.
Microkernels provide good features such as high security, safety, and flexibility, but their reliance on hardware-based isolation leads to heavy performance overhead, limiting their widespread adoption. Although constructing single-address-space microkernels based on safe language-based isolation is a promising approach to addressing the performance issue, this approach still faces challenges in maintaining the principle of minimality and enforcing capability-based, fine-grained access control over system resources. We propose safeL4, an approach to constructing microkernels based on safe languages. It guarantees minimality through low-level abstractions for unsafe operations, and implements a capability system based on the safe language's object capabilities to achieve fine-grained access control over all operations on system resources. We implement a prototype system in Rust, and our evaluation results show that the primitives provided by safeL4 are, on average, 1.9$\times$ faster than those of seL4.
Yuting Zhang University of New South Wales, Kai Wang Shanghai Jiao Tong University, Wei Ni Edith Cowan University and University of Technology Sydney, Ying Zhang University of Technology Sydney (UTS), Wenjie Zhang the university of new south wales
Recent studies have demonstrated the ability of Large Language Models (LLMs) in processing various graph problems. Substructure counting remains challenging in both scalability and accuracy. Incorporating sensitive edge information into the input prompts also introduces significant privacy risks of exposing the private information of user connections in real-world applications. This paper, for the first time, studies substructure counting for LLMs under edge local differential privacy (LDP) in a multi-agent framework. Unlike the Naive approach whose estimation relies entirely on overly dense noisy graphs, the proposed PSC framework decomposes substructure counting into node-level tasks distributed among node agents, and embeds the knowledge of distributed algorithms and DP frameworks in the curator agent and privacy controller, respectively. Thus, we can leverage the local neighboring information and reasoning capabilities of node agents to improve the estimation accuracy. Extensive experiments on 6 real-world datasets validate the effectiveness of PSC framework for substructure counting tasks under \varepsilon-edge LDP. Moreover, the non-DP version of PSC also demonstrated superior performance over a single LLM on standard substructure counting tasks.
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cs.CL · cs.MA
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Bosi Wen, Yilin Niu, Cunxiang Wang, Xiaoying Ling, Ying Zhang, Pei Ke University of Electronic Science and Technology of China, Hongning Wang Tsinghua University, Minlie Huang
Instruction-following is a foundational capability of large language models (LLMs), with its improvement hinging on scalable and accurate feedback from judge models. However, the reliability of current judge models in instruction-following remains underexplored due to several deficiencies of existing meta-evaluation benchmarks, such as their insufficient data coverage and oversimplified pairwise evaluation paradigms that misalign with model optimization scenarios. To this end, we propose IF-RewardBench, a comprehensive meta-evaluation benchmark for instruction-following that covers diverse instruction and constraint types. For each instruction, we construct a preference graph containing all pairwise preferences among multiple responses based on instruction-following quality. This design enables a listwise evaluation paradigm that assesses the capabilities of judge models to rank multiple responses, which is essential in guiding model alignment. Extensive experiments on IF-RewardBench reveal significant deficiencies in current judge models and demonstrate that our benchmark achieves a stronger positive correlation with downstream task performance compared to existing benchmarks. Our codes and data are available at https://github.com/thu-coai/IF-RewardBench.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Jiaying Zhang, Lei Shi Meituan, Jiguo Li, Jun Xu Meituan, Jiuchong Gao, Jinghua Hao, Renqing He
Reinforcement Learning with Verifiable Rewards (RLVR) is a key paradigm for improving large-scale reasoning models. Unlike supervised fine-tuning (SFT), RLVR exhibits distinct optimization dynamics and are sensitive to the preservation of pre-trained geometric structures. However, existing parameter-efficient methods face key limitations in this regime. Low-rank adaptation methods, such as PiSSA, are primarily designed for Supervised Fine-Tuning (SFT) and do not account for the distinct optimization dynamics and geometric structures of RLVR. Conversely, directly fine-tuning the unstructured sparse parameter subspace favored by RLVR encounters efficiency bottlenecks on modern hardware. To address these challenges, we propose GeoRA (Geometry-Aware Low-Rank Adaptation), a low-rank adaptation method tailored for RLVR. Specifically, GeoRA exploits the anisotropic and compressible structure of RL update subspace, and extracts its principal directions via Singular Value Decomposition (SVD) to initialize low-rank adapters, while freezing residual components as a structural anchor during training. This design preserves the pre-trained structure and enables efficient dense computation. Experiments on Qwen and Llama models from 1.5B to 32B parameters show that GeoRA consistently outperforms strong low-rank baselines across RLVR settings in mathematics, medicine, and coding, while showing stronger generalization and less forgetting on out-of-domain tasks.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Bosi Wen, Yilin Niu, Cunxiang Wang, Pei Ke University of Electronic Science and Technology of China, Xiaoying Ling, Ying Zhang, Aohan Zeng Tsinghua University, Tsinghua University, Hongning Wang Tsinghua University 等 9 位作者
Instruction-following is a fundamental ability of Large Language Models (LLMs), requiring their generated outputs to follow multiple constraints imposed in input instructions. Numerous studies have attempted to enhance this ability through preference optimization or reinforcement learning based on reward signals from LLM-as-a-Judge. However, existing evaluation models for instruction-following still possess many deficiencies, such as substantial costs and unreliable assessments. To this end, we propose IF-CRITIC, an LLM critic for fine-grained, efficient, and reliable instruction-following evaluation. We first develop a checklist generator to decompose instructions and generate constraint checklists. With the assistance of the checklists, we collect high-quality critique training data through a multi-stage critique filtering mechanism and employ a constraint-level preference optimization method to train IF-CRITIC. Extensive experiments show that the evaluation performance of IF-CRITIC can beat strong LLM-as-a-Judge baselines, including o4-mini and Gemini-3-Pro. With the reward signals provided by IF-CRITIC, LLMs can achieve substantial performance gains in instruction-following optimization under lowercomputational overhead compared to strong LLM critic baselines. Our code and model are available at https://github.com/thu-coai/IF-CRITIC.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Xiangxu Zhang Renmin University of China, Lei Li, Yanyun Zhou Renmin University of China, Xiao Zhou Renmin University of China, Yingying Zhang Tencent, Xian Wu Tencent
Medical diagnostics is a high-stakes and complex domain that is critical to patient care. However, current evaluations of large language models (LLMs) remain limited in capturing key challenges of clinical diagnostic scenarios. Most rely on benchmarks derived from public exams, raising contamination bias that can inflate performance, and they overlook the confounded nature of real consultations beyond textbook cases. Recent dynamic evaluations offer a promising alternative, but often remain insufficient for diagnosis-oriented benchmarking, with limited coverage of clinically grounded confounders and trustworthiness beyond accuracy. To address these gaps, we propose DyReMe, a dynamic benchmark for medical diagnostics that provides a controlled and scalable stress test of diagnostic robustness. Unlike static exam-style questions, DyReMe generates fresh, consultation-style cases that incorporate clinically grounded confounders, such as differential diagnoses and common misdiagnosis factors. It also varies expression styles to capture heterogeneous patient-style descriptions. Beyond accuracy, DyReMe evaluates LLMs on three additional clinically relevant dimensions: veracity, helpfulness, and consistency. Our experiments show that this dynamic approach yields more challenging assessments and exposes substantial weaknesses of stateof-the-art LLMs under clinically confounded diagnostic settings. These findings highlight the urgent need for evaluation frameworks that better assess trustworthy medical diagnostics under clinically grounded confounders.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Xinying Qian, Ying Zhang Nankai University, Xuhui Sui, Yu Zhao Nankai University, Baohang Zhou Tiangong University, Jeff Z. Pan University of Edinburgh, University of Edinburgh
Temporal reasoning remains a critical challenge for large language models (LLMs), particularly when it requires encompassing relational dependencies and numerical constraints. Yet, existing benchmarks largely overlook the joint consideration of these two dimensions and primarily rely on single-task evaluation paradigms, making it difficult to assess whether correct answers reflect grounded reasoning or arise from superficial statistical recall. To address these gaps, we introduce TNR, a benchmark designed to evaluate both Temporal Numerical and Relational reasoning. We propose a bi-directional evaluation framework consisting of forward generation via Question Answering (QA) and backward verification via Fact Verification (FV). By measuring the alignment between QA and FV, we introduce a Consistency Rate to quantify the robustness of reasoning across these two directions. Experiments on a range of LLMs reveal notable discrepancies between QA and FV performance, particularly in numerical and interval-based tasks. Moreover, our bi-directional error analysis demonstrates that these inconsistencies often stem from heuristic shortcuts and statistical co-occurrences rather than grounded logical deduction, flaws that are frequently masked in standard single-task evaluations.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Chenxu Liu Peking University, Yingjie Fu Peking University, Wei Yang University of Texas, Dallas, Ying Zhang Peking University, Tao Xie Beijing Tongming Lake Information Technology Application Innovation Center, Fudan University Institute of Systems for Advanced Computing, Shanghai Institute of Systems for Open Computing and Key Lab of HCST (PKU), MOE; SCS, Peking University
Web applications (web apps) have become a key arena for large language models (LLMs) to demonstrate their code generation capabilities and commercial potential. However, building a benchmark for LLM-generated web apps remains challenging due to the need for real-world user requirements, generalizable evaluation metrics without relying on ground-truth implementations or test cases, and interpretable evaluation results. To address these challenges, we introduce WebCoderBench, the first real-world-collected, generalizable, and interpretable benchmark for web app generation. WebCoderBench comprises 1,572 user requirements, covering diverse modalities and expression styles that reflect realistic user intentions. WebCoderBench provides 24 fine-grained evaluation metrics across 9 perspectives, combining the rule-based and LLM-as-a-judge paradigms for fully automated, objective, and general evaluation. Moreover, WebCoderBench adopts human-preference-aligned weights over metrics to yield interpretable overall scores. Experiments across 12 representative LLMs and 2 LLM-based agents show that there exists no dominant model across all evaluation metrics, offering an opportunity for LLM developers to optimize their models in a targeted manner for a more powerful version.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表
Mengshi Chen, Yuxiang Sun, Tengchao Li Shanghai Jiaotong University, Jianwei Wang University of New South Wales, Kai Wang Shanghai Jiao Tong University, Xuemin Lin Shanghai Jiaotong University, Ying Zhang University of Technology Sydney (UTS), Wenjie Zhang the university of new south wales
Data preparation is a critical step in enhancing the usability of tabular data and thus boosts downstream data-driven tasks. Traditional methods often face challenges in capturing the intricate relationships within tables and adapting to the tasks involved. Recent advances in Language Models (LMs), especially in Large Language Models (LLMs), offer new opportunities to automate and support tabular data preparation. However, why LMs suit tabular data preparation (i.e., how their capabilities match task demands) and how to use them effectively across phases still remain to be systematically explored. In this survey, we systematically analyze the role of LMs in enhancing tabular data preparation processes, focusing on four core phases: data acquisition, integration, cleaning, and transformation. For each phase, we present an integrated analysis of how LMs can be combined with other components for different preparation tasks, highlight key advancements, and outline prospective pipelines.
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cs.CL
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 1: Long Papers) · 2026 · 正式发表