Sep 2026· Journal of Chemical Information and Modeling
Artificial IntelligenceBioinformatics
Abstract
Abstract Building a working mental model of a protein typically requires weeks of reading, cross-referencing crystal and predicted structures, and inspecting ligand complexes, an effort that is slow, unevenly accessible, and often requires specialized computational skills. We introduce Speak to a Protein, a new capability that turns protein analysis into an interactive, multimodal dialogue with an expert coscientist. The AI system retrieves and synthesizes relevant literature, structures, and ligand data; grounds answers in a live 3D scene; and can highlight, annotate, manipulate, and see the visualization. It also generates and runs code when needed, explaining results in both text and graphics. We demonstrate these capabilities on relevant proteins, posing questions about binding pockets, conformational changes, or structure-activity relationships to test ideas in real time. Speak to a Protein reduces the time from question to evidence, lowers the barrier to advanced structural analysis, and enables hypothesis generation by tightly coupling language, code, and 3D structures. Speak to a Protein is freely accessible at https://open.playmolecule.org.
GAOKAO-Bench is introduced, an intuitive benchmark that employs questions from the Chinese GAOKAO examination as test samples, including both subjective and objective questions that contribute a robust evaluation benchmark for future large language models and offers valuable insights into the advantages and limitations...
Xiaotian Zhang, Chun-yan Li, Yi Zong et al.· arXiv.org· 216 citations· ⚡17
This work investigates the possibilities of using LLMs in a resume screening setting via a document retrieval framework that simulates job candidate selection and finds that the MTEs are biased, significantly favoring White-associated names in 85% of cases and female-associated names in only 11.1% of cases.
This paper presents a comprehensive overview of the Ultralytics YOLO family, emphasizing architectural evolution, benchmarking, deployment, and emerging directions from YOLOv5 through YOLO27, and examines detection, segmentation, depth, classification, pose, oriented detection, tracking, export, quantization, and deplo...
This work revisits schema linking when using the latest generation of large language models (LLMs) and finds empirically that newer models are adept at utilizing relevant schema elements during generation even in the presence of large numbers of irrelevant ones.
Karime Maamari, Fadhil Abubaker, Daniel Jaroslawicz et al.· arXiv.org· 109 citations· ⚡19
A novel threat is unveiled in which attackers steer the RAG system's response by injecting malicious passages into its knowledge base, enabling the attacker to steer the response without altering the user input or modifying the RAG weights.
Jiaqi Xue, Meng Zheng, Yebowen Hu et al.· arXiv.org· 109 citations· ⚡8
Empirically, PRISM reduces the end-to-end time for data selection and model tuning to just 30% of conventional pipelines, and achieves this efficiency while simultaneously enhancing performance, surpassing models fine-tuned on the full dataset across eight multimodal and three language understanding benchmarks.
Jinhe Bi, Yifan Wang, Danqi Yan et al.· arXiv.org· 73 citations· ⚡4
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MIT News · Artificial Intelligence· news.mit.eduSep 30, 2026
With $2.1 million funding from Google.org, the open-source Public Transit Intelligence Hub will unify public transit monitoring, operations, and passenger communication.
