The study evaluates whether a portfolio of compact, semantically named descriptor blocks can match the performance of a 2048‑dimensional CheMeleon embedding in low‑data molecular assays. Using a fixed 11‑dimensional physicochemical base and greedily adding provenance‑screened blocks, the portfolio achieves a mean test AUC of 0.762 across nine ADME/Tox assays, comparable to CheMeleon’s 0.764 and better than Mordred’s 0.756. The results meet a predeclared pooled parity threshold but not all per‑assay thresholds, and further analysis confirms the competitiveness of the auditable representation while highlighting unresolved assay‑level differences.
By Yiqi Yao, Miquel Duran-Frigola
arXiv:2608. 05359v1 Announce Type: new Abstract: CASCADE is an agentic framework that predicts downstream transcriptional effects of gene perturbation from precomputed ARACNe regulatory networks, exposed via MCP.
By Jose A. Bird
arXiv:2512. 22240v5 Announce Type: replace-cross Abstract: Machine learning models are primarily judged by predictive performance, especially in applied genomics, where explanations are read as biological findings.
By Chama Bensmail
arXiv:2607. 17671v1 Announce Type: new Abstract: Large-scale single-cell perturbation atlases make it possible to ask an inverse question: given an observed transcriptional response, which annotated targets and compounds in a fixed library are most consistent with that response?
By Kseniia Vaniushkina, Jeongmin Lim, Jinyong Park
The paper introduces PhenoAIR, a reliability‑aware multi‑agent framework for predicting mechanisms of action (MOA) from Cell Painting morphological profiles. It treats retrieved neighbors as uncertain evidence, calibrating their reliability based on source, phenotype stability, and mechanism confusion, and refines predictions through controller‑guided evidence evaluation. PhenoAIR is benchmarked on JUMP Cell Painting data and outperforms both representation‑matching and LLM‑based baselines across controlled, realistic, and open‑world settings.
By Jiayuan Chen, Botao Yu, Tianyu Liu, Thai-Hoang Pham, Meng Wu, Ping Zhang
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:2609.08618v1 Announce Type: new
Abstract: Benchmark scores describe what a checkpoint can do now, but they do not determine how it will respond to the next training episode. We measure this mis...
By Zhongxuan Liu, Sicheng Zhou, Hongzhi Wang
arXiv:2608.00152v3 Announce Type: replace-cross
Abstract: AI evaluation can support the wrong inference when an in-domain benchmark success does not survive distribution shift, or when the benchmark...
By Mehrdad Shoeibi, Niloofar Yousefi
arXiv:2606. 05263v1 Announce Type: new Abstract: Reinforcement learning with verifiable rewards improves reasoning and tool use, yet long-horizon language agents still learn unsupported evidence chains, belief drift, and shortcut actions that satisfy terminal checks.
By Renwei Meng
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
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
The paper investigates how memory systems can answer a current query correctly yet fail to retain distinctions needed for later updates. Using a paired‑history audit, the authors evaluate 24 history pairs across six synthetic mechanisms and two model backends, achieving perfect reveal accuracy on DeepSeek and high accuracy on GLM. Record‑level audits reveal specific failures in structured reveal memories and frontier late‑reference adequacy, and the authors test a label‑equivariant repair that only partially restores correctness.
By Guangzhe Zhang