OmniVCBench is a figure‑centric, source‑traceable benchmark designed to evaluate the interpretation component of Artificial Intelligence Virtual Cells (AIVCs). It comprises 6,077 curated question–answer pairs drawn from scientific figures and experimental contexts, organized into three scientific reasoning tasks that mirror the AIVC Predict–Explain–Discover agenda. The benchmark also introduces AIVC‑Judge, a task‑conditioned MLLM‑as‑a‑judge framework with reference‑aware rubrics, and a Model‑Derived Hard‑Negative Mining strategy to generate multiple‑choice distractors for efficient evaluation.
By Manyu Li, Xunkai Li, Yongfu Xiong, Yi Liu, Rong-Hua Li, Guoren Wang
CellCanon is an agentic cellular world model that integrates single‑cell expression prediction, evidence‑grounded explanation, and observation‑driven updating. Its predictive core reuses condition‑level biological evidence to generate gene‑specific readouts, while a shared world state links predictions, measurements, and source‑linked claims to support explanation and revision. On 339 held‑out SciPlex3 conditions across three cell lines, CellCanon outperforms baselines in differential‑expression AUPRC, Macro‑F1, and direction Macro‑F1, and its explanation module correctly answers all answerable questions with supporting proofs.
By Zhaokang Liang, Shuyang Zhuang, Xiaoran Jiao, Hao Chen
arXiv:2609.15938v1 Announce Type: new
Abstract: Scientific agents contribute to hypothesis discovery by synthesizing evidence, assessing proposals, and developing new explanations. Recent systems com...
By Jieyuan Liu, Mengzhou Hu, Jefferson Chen, JungHo Kong, Pratibha Jagannatha, Yiming Gao, Dexter Pratt, Hsin-Yuan Lee, Zhiting Hu, Trey Ideker, Wei Wang, Eric P. Xing, Zhen Wang
arXiv:2606. 01042v1 Announce Type: cross Abstract: Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions.
By Xinyu Yuan, Xixian Liu, Jianan Zhao, Yashi Zhang, Hongyu Guo, Jian Tang
arXiv:2607. 18777v1 Announce Type: new Abstract: Evaluating machine learning in scientific domains requires separating correct predictions from correct reasons under realistic distribution shifts.
By Dongkwan Kim, Yiming Gao, Yining Yang, Yang Shen
arXiv:2605. 09366v3 Announce Type: replace Abstract: Transforming neuroimaging data into clinically actionable biomarkers is a knowledge-intensive and labor-intensive process.
By Keqi Han, Songlin Zhao, Yao Su, Xiang Li, Yixuan Yuan, Lifang He, Carl Yang
arXiv:2502. 18864v2 Announce Type: replace Abstract: Scientific discovery is driven by scientists generating novel hypotheses for complex problems that undergo rigorous experimental validation.
By Juraj Gottweis, Wei-Hung Weng, Alexander Daryin, Tao Tu, Petar Sirkovic, Artiom Myaskovsky, Grzegorz Glowaty, Felix Weissenberger, Alessio Orlandi, Dan Popovici, Anil Palepu, Keran Rong, Ryutaro Tanno, Khaled Saab, Fan Zhang, Jacob Blum, Andrew Carroll, Kavita Kulkarni, Nenad Tomasev, Dina Zverinski, Ivor Rendulic, Elahe Vedadi, Florian Hasler, Luka Rimanic, Marina Boia, Ivan Budiselic, Ben Feinstein, Mathias Bellaiche, Tom Sheffer, Jan Freyberg, Jeremy Ratcliff, Ottavia Bertolli, Katherine Chou, Avinatan Hassidim, Burak Gokturk, Amin Vahdat, Yuan Guan, Vikram Dhillon, Eeshit Dhaval Vaishnav, Byron Lee, Tiago R D Costa, Jos\'e R Penad\'es, Gary Peltz, Yossi Matias, James Manyika, Demis Hassabis, Yunhan Xu, Pushmeet Kohli, Annalisa Pawlosky, Alan Karthikesalingam, Vivek Natarajan
arXiv:2610.16975v1 Announce Type: new
Abstract: Drug discovery remains a resource-intensive and time-consuming process, involving billions of dollars and a decade of development to advance a drug to...
By Ye Liu, Reza Averly, Avery Meyer, Frazier N. Baker, Ruoxi Gao, Daniel Adu-Ampratwum, Xia Ning
arXiv:2605. 06177v2 Announce Type: replace Abstract: Reproducing and comparing deep research agents today is hard: the same backbone evaluated on the same benchmark can report different accuracies across papers because the harness and tool registry differ, and integrating a new model into a comparable evaluation surface costs weeks of model-specific engineering.
By Jinge Wu, Hongjian Zhou, Mingde Zeng, Jiayuan Zhu, Junde Wu, Jiazhen Pan, Ayush Noori, Sean Wu, Honghan Wu, Fenglin Liu, David A. Clifton
arXiv:2610.19810v1 Announce Type: cross
Abstract: Large language models are increasingly competent at leveraging scientific knowledge and existing computational tools to execute complex workflows. At...
By Shiv Muthupandiyan, Tolga H. Dur, Mac Walker, Timo Flesch, Mahmoud Ghanem, Steph Suddell, Giles Harper-Donnelly, Sophie Rose, Jasper G\"otting, Coleman Breen, Jake Pencharz
arXiv:2607. 16262v1 Announce Type: cross Abstract: The acceleration of automated scientific discovery has been fundamentally bottlenecked by the epistemic gap between the semantic reasoning of large language models (LLMs) and the deterministic physics of mammalian biology.
By Christopher Baker, Tianyu Ren, Karen Rafferty, Hui Wang, Simon McDade
AgentFold is a multi‑agent framework that treats protein‑folding model design as a closed‑loop search over executable code variants. Starting from the ESMFold codebase, the agents generate hypotheses, modify and debug code, evaluate model variants, and store both successes and failures in structured memory, guided by an MCTS‑style policy that allocates GPU resources. In an engineering‑scale experiment, AgentFold explored about 80 variants using 5,000 GPU‑hours and 170 million LLM tokens, improving the best lDDT score by 7.5% over independent Codex proposals and outperforming a random‑search baseline, while also uncovering empirical design patterns such as the benefits of early, soft, learnable priors.
By Mingquan Liu, Jiangyu Chen, Hanqun Cao, Xujun Zhang, Pengsen Ma, Xiangru Tang, Shuting Jin, Zhuo Yang, Tianfan Fu, Fang Wu, Xiangxiang Zeng