This work introduces CryoAtlas, a rigorously curated dataset and unified benchmark for density-guided atomic model building of protein chains, and constructs a 618-target benchmark with a shared evaluation protocol that jointly assesses structural accuracy, model-to-map fit, and stereochemical validity.
Ming-Rui Li, Min-Zhang Li, Wei-Chen Qin et al.· 0 citations
Recent advances in single-cell technologies have enabled the profiling of multiple molecular modalities, including transcriptomics, proteomics, and chromatin accessibility, providing a more comprehensive understanding of cellular states. However, integrating heterogeneous modalities and predicting missing molecular inf...
Zhaoqi Song, Ye Du, Yusuke Iwasawa et al.· 0 citations
Computer-use agents act through graphical interfaces, command lines, APIs, scripts, and Model Context Protocol servers. A policy decision can be interface-invariant while its executable authorization is not: another route can bypass mediation, alter a security-relevant default, or commit after the authorized state has...
Evidence-grounded NLP systems often verify nested text regions sequentially, so verifying one region constrains others. We formalize this as Online Evidence-Containment Prediction (OECP): each candidate is predicted before exact verification and queried at most once. Span containment is exactly a triangular 2D product...
Xiang Liu, Haochen Ding· 0 citations
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Parallel LLM agents tackle complex tasks by exploring multiple trajectories, yet useful discoveries remain isolated in individual execution histories. Existing sharing methods often select or summarize information before other agents' needs become clear, potentially overlooking details that become important later. We p...
Haofu Yang, Hongyang Yin, Ran Bi et al.· 0 citations
BULLPEN (Behavioral Understanding of Large Language models via Profile ENcodings), a framework that extends EmbedLLM in three ways and is the first framework to read a model's own answer text jointly with its correctness and the question text, is introduced.
Russell Ro, Qi-Ming Cui, Reza Abbasi-Asl· 0 citations
This work introduces RECITE (Revising Eligibility Criteria Incorporating Textual Evidence), a framework for automated discovery, extraction, and implementation of evidence-based eligibility criteria revisions and suggests that existing clinical knowledge can be operationalized into actionable trial design recommendatio...
Russell Ro, R. Abbasi-Asl· Knowledge Discovery and Data...· 0 citations
Length-aware scheduling reduces request latency in LLM serving by prioritizing shorter requests. However, despite their large model sizes, length predictors can suffer degraded ranking performance under domain and task shifts, and adapting them can require costly retraining. Their prediction overhead can further offset...
Existing visual preference evaluation relies on costly human annotations or preference reward models, whereas online marketplace transaction prices are readily available and reflect real purchasing behavior, offering potential low-cost supervision. However, transaction prices conflate visual preferences with non-visual...
Fengxian Ji, Jingpu Yang, Fan Zhang et al.· 0 citations
Language-model agents now carry out long scientific work in biology, but their judgements about conventions, skills, errors, evidence and stopping are made inside the reasoning that does the work, where they cannot be measured, replaced or improved on their own. Here we present Operon-S1, a fast decision system, a Syst...
Genoria AI Team, Yuejie Hou, Yueyuxiao Yang et al.· 0 citations
Large language models increasingly generate structured outputs consumed by programs and downstream systems, where semantic correctness alone does not guarantee reliable execution. We introduce SERIAL-7, a Korean-English benchmark built around an executable verification framework for machine-verifiable generation across...
Youngkyung Seo, MiHyeon Kim, Jisoo Lee et al.· 0 citations
Subliminal learning, the transfer of a model's trait through data with no semantic trace of it, has been shown for students trained on a teacher's text. Post-training relies on group relative policy optimization with a language-model judge, where the student learns only from its own outputs and one judge's scores. We s...