8 papers
ResearchClawBench: A Benchmark for End-to-End Autonomous Scientific Research
Wanghan Xu, Shuo Li, Tianlin Ye +48
AI coding agents are increasingly used for scientific work, but their end-to-end autonomous research capability remains difficult to verify. We present ResearchClawBench, a benchma…
Structure-guided taxonomic placement of divergent RNA viruses with ViraClass
Sheng Xu, Wenxuan Huang, Shutong Yue +8
Metatranscriptomic sequencing has expanded our knowledge of the RNA virosphere far more rapidly than novel viruses can be taxonomically classified. Taxonomic assignment above the f…
ViraHinter: a dual-modal artificial intelligence framework for predicting virus-host interactions
Weiqiang Bai, Fei Wang, Jialin Wang +10
Protein-protein interactions (PPIs) between a virus and its host govern infection, replication, and pathogenesis. While high-throughput mapping has identified thousands of virus-ho…
Accurate de novo sequencing of the modified proteome with OmniNovo
Yuhan Chen, Shang Qu, Zhiqiang Gao +13
Post-translational modifications (PTMs) serve as a dynamic chemical language regulating protein function, yet current proteomic methods remain blind to a vast portion of the modifi…
Bidirectional Representations Augmented Autoregressive Biological Sequence Generation
Xiang Zhang, Jiaqi Wei, Zijie Qiu +5
Autoregressive (AR) models, common in sequence generation, are limited in many biological tasks such as de novo peptide sequencing and protein modeling by their unidirectional natu…
Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning
Yuhao Zhou, Yiheng Wang, Xuming He +26
Scientific discoveries increasingly rely on complex multimodal reasoning based on information-intensive scientific data and domain-specific expertise. Empowered by expert-level sci…