Hongxuan Liu, Roman Bushuiev, Ivy Lightheart, Mrunali Manjrekar, Anton Bushuiev, Magdalena Lederbauer, Filip Jozefov, Yinkai Wang 等 15 位作者
Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and model evaluation procedures can degrade the trustworthiness of such benchmarks and lead to erroneous conclusions. We conduct a thorough review of model evaluation issues in the recent MS/MS machine learning literature, using the standard MassSpecGym benchmark suite as a case study to illustrate the impact of these issues. We find evaluation issues in at least 17 of 26 papers reporting MassSpecGym benchmark results in the first year of its adoption. We isolate three classes of failures: (i) data leakage, (ii) shortcut learning, and (iii) implementation bugs and metric divergence. Through extensive experimentation and code replication, we quantify the impact of these issues and show how they corrupt the evaluation standards MassSpecGym was designed to enforce. We distill our findings into recommendations generalizable to MS/MS challenges, benchmarks, and custom evaluation setups. We also release MassSpecGym v1.5, an implementation of our recommendations in the MassSpecGym benchmarking suite which addresses the failure modes identified in this audit. MassSpecGym v1.5 is publicly available at https://github.com/pluskal-lab/MassSpecGym.
Yunpeng Gong, Can Yang, Qingyuan Zeng, Dejun Xu, Zhiming Luo, Zhenzhong Wang, Min Jiang
Cross-modal person re-identification (ReID) adversarial attacks face a transferability challenge: existing methods may exhibit source-pair overfitting, where learned perturbations become overly dependent on the feature statistics of the source modality pair, thereby limiting their transferability under heterogeneous domain shifts. We argue that a key challenge is reducing source-pair-specific bias while maintaining attack effectiveness. To address this, we propose Multiform Attack (MA). The framework first learns a universal perturbation via Mahalanobis-guided gradient optimization. Since this perturbation may still retain source-pair-specific bias, the second stage performs sparse refinement through attention-shift-filtered multi-objective evolutionary search, leveraging heterogeneous source distributions in transfer settings. By separating universal perturbation learning from sparse evolutionary refinement, MA aims to reduce reliance on source-pair-specific patterns and improve transferability to unseen domains. Extensive experiments demonstrate strong attack effectiveness on cross-modal ReID benchmarks and improved transferability in the evaluated held-out-domain settings, with additional evaluations across model architectures.
Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor W. Coley
Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. While recent autoregressive and graph diffusion models have shown promise in de novo elucidation, performance remains limited by poor scalability during both training and inference time. In this work, we present FRIGID, a framework with a novel diffusion language model that generates molecular structures conditioned on mass spectra via intermediate fingerprint representations and determined chemical formulae, training at the scale of hundreds of millions of unlabeled structures. We then demonstrate how forward fragmentation models enable inference-time scaling by identifying spectrum-inconsistent fragments and refining them through targeted remasking and denoising. While FRIGID already achieves strong performance with its diffusion base, inference-time scaling significantly improves its accuracy, surpassing 18% Top-1 accuracy on the challenging MassSpecGym benchmark and tripling the Top-1 accuracy of the leading methods on NPLIB1. Further empirical analyses show that FRIGID exhibits log-linear performance scaling with increasing inference-time compute, opening a promising new direction for continued improvements in de novo structural elucidation. FRIGID code is publicly available at https://github.com/coleygroup/FRIGID.
Haozhong Wang, Zhuo Li The Chinese University of Hong Kong, Shenzhen, Yibo Yang Shanghai Jiao Tong University, He Zhao Commonwealth Scientific and Industrial Research Organisation, CSIRO, Hongyuan Zha The Chinese University of Hong Kong, Shenzhen, Dandan Guo
The inherent safety alignment of Large Language Models (LLMs) is prone to erosion during fine-tuning, even when using seemingly innocuous datasets. While existing defenses attempt to mitigate this via data selection, they typically rely on heuristic, instance-level assessments that neglect the global geometry of the data distribution and fail to explicitly repel harmful patterns. To address this, we introduce Safety Optimal Transport (SOT), a novel framework that reframes safe fine-tuning from an instance-level filtering challenge to a distribution-level alignment task grounded in Optimal Transport (OT). At its core is a dual-reference “push-pull” weight-learning mechanism: SOT optimizes sample importance by actively pulling the downstream distribution towards a trusted safe anchor while simultaneously pushing it away from a general harmful reference. This establishes a robust geometric safety boundary that effectively purifies the training data. Extensive experiments across diverse model families and domains demonstrate that SOT significantly enhances model safety while maintaining competitive downstream performance, achieving a superior safety-utility trade-off compared to baselines.
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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
Zhiwei Zhang The Chinese University of Hong Kong, Fei Zhao Xiaohongshu, Rui Wang, Zezhong Wang, Bin Liang The Chinese University of Hong Kong, Jiakang Wang Kuaishou- 快手科技, Yao Hu Xiaohongshu, Shaosheng Cao 等 9 位作者
Large language models (LLMs) can call tools effectively, yet they remain brittle in multi-turn execution: after a tool-call error, smaller models often fall into repetitive invalid re-invocations instead of interpreting the feedback and recovering. This failure mode persists because current training paradigms do not explicitly teach models how to recover from execution errors. In particular, standard reinforcement learning (RL) collapses rich failure experience into sparse negative rewards, while pre-collected error-correction datasets become mismatched to the policy’s evolving failure modes. To bridge this gap, we propose Fission-GRPO, a framework that converts execution errors into on-policy corrective supervision within the RL training loop. Our core mechanism fissions each failed trajectory into a new training instance by augmenting it with diagnostic feedback from a fine-tuned Error Simulator, then resampling multiple recovery rollouts on-policy. This enables the model to learn from the precise errors it makes during exploration, rather than from static, pre-collected error cases. On BFCL v4 Multi-Turn, Fission-GRPO improves the error recovery rate of Qwen3-8B by 5.7% absolute and overall accuracy by 4.0% (from 42.75% to 46.75%), outperforming both RL baselines and specialized tool-use agents. The method further generalizes to TAU-Bench and TAU2-Bench, achieving leading results across most settings with gains up to +17.4%.
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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
Zhengyi Zhao The Chinese University of Hong Kong, Shubo Zhang, Zezhong Wang, Yuxi Zhang, Huimin Wang Jarvis Research Center, Tencent YouTu Lab, Yutian Zhao, Yefeng Zheng, Binyang Li 等 10 位作者
Retrieval-Augmented Generation (RAG) significantly enhances Large Language Models (LLMs) by providing access to external knowledge. However, current research primarily focuses on retrieval quality, often overlooking the critical ”integration bottleneck”: even when relevant documents are retrieved, LLMs frequently fail to utilize them effectively due to conflicts with their internal parametric knowledge. In this paper, we argue that implicitly resolving this conflict in a single generation pass is suboptimal. We introduce GuarantRAG, a framework that explicitly decouples reasoning from evidence integration. First, we generate an ”Inner-Answer” based solely on parametric knowledge to capture the model’s reasoning flow. Second, to guarantee faithful evidence extraction, we generate a ”Refer-Answer” using a novel Contrastive DPO objective. This objective treats the parametric Inner-Answer as a negative constraint and the retrieved documents as positive ground truth, forcing the model to suppress internal hallucinations in favor of external evidence during this phase. Finally, rather than naive concatenation or using the DPO trained model directly, we propose a joint decoding mechanism that dynamically fuses the logical coherence of the Inner-Answer with the factual precision of the Refer-Answer at the token level. Experiments on five QA benchmarks demonstrate that GuarantRAG improves accuracy by up to 12.1% and reduces hallucinations by 16.3% compared to standard and dynamic RAG baselines.
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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
Bo Zhang Xi’an Research Institute of High Technology, Jiawei Zhang, Cong Gao, Bingxu Han, Minghao Hu, Jun Zhang National University of Defense Technology, Yunbo Cao Information Center, Academy of Military Science, Zhunchen Luo 等 11 位作者
Although large reasoning models (LRMs) exhibit exceptional mathematical reasoning capabilities on clean inputs, their reasoning accuracy drops substantially in the presence of character-level noise such as typographical errors. Critically, their confidence estimates fail to reflect the corresponding decline in reasoning accuracy. While confidence calibration offers a principled solution, existing methods predominantly target clean inputs, leaving noisy scenarios largely unexplored. To address this gap, we propose DisCal (Distribution-aware Calibration), a confidence calibration framework for character-level noisy inputs. DisCal extracts uncertainty signals from both the empirical answer distribution and the model’s predictive distribution, and integrates them via a learned calibrator to produce well-calibrated confidence. Experiments across multiple mathematical reasoning benchmarks demonstrate that DisCal consistently outperforms existing calibration methods under noisy inputs, reducing Expected Calibration Error (ECE) by up to 39.21% and improving Area Under the Receiver Operating Characteristic Curve (AUROC) by up to 31.44%.
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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
Inference providers must maintain availability for many LLMs, including low-volume but essential models, making resource efficiency increasingly important as token prices fall. Analysis of production traces reveals a dynamic bursty-group pattern in which sets of models become active together and shift over time; existing space- and time-sharing approaches lack principled mechanisms to adapt to this variability, forcing trade-offs between SLO adherence and efficiency. We observe that elastic memory allocation can unify spatial and temporal sharing. Based on this insight, we have developed Prism, a memory-centric LLM co-serving framework that applies memory ballooning to reclaim memory across models and support both forms of sharing under a single scheme. Prism's balloon driver, referred to as kvcached, has been open-sourced at https://github.com/ovg-project/kvcached, and deployed in production environments across 10K+ GPUs.
AI 速览：ToolACE提出一种自动化的智能体流水线，用于生成准确、复杂且多样的工具学习数据，以提升大语言模型的函数调用能力。
Function calling significantly extends the application boundary of large language models, where high-quality and diverse training data is critical for unlocking this capability. However, real function-calling data is quite challenging to collect and annotate, while synthetic data generated by existing pipelines tends to lack coverage and accuracy. In this paper, we present ToolACE, an automatic agentic pipeline designed to generate accurate, complex, and diverse tool-learning data. ToolACE leverages a novel self-evolution synthesis process to curate a comprehensive API pool of 26,507 diverse APIs. Dialogs are further generated through the interplay among multiple agents, guided by a formalized thinking process. To ensure data accuracy, we implement a dual-layer verification system combining rule-based and model-based checks. We demonstrate that models trained on our synthesized data, even with only 8B parameters, achieve state-of-the-art performance on the Berkeley Function-Calling Leaderboard, rivaling the latest GPT-4 models. Our model and a subset of the data are publicly available at https://huggingface.co/Team-ACE.