arXiv Machine Learning By Mengran Li, Bo Li, Chengyang Zhang, Yang Yan, Jinfeng Xu, Zhenchao Tang

Discover, Falsify, Revise: Auditing Input-Use Claims from Source Code to Predictive Contribution in Agent-Discovered Cell Models

Read the original on arXiv Machine Learning →

The paper introduces CELLAUDIT, a method for auditing whether inputs claimed to influence predictive models actually do so. By testing if an input can enter the computation, whether predictions depend on it, and if that dependence improves observed responses, the authors evaluate agent-generated predictors on a morphology‑transcriptomics benchmark (BBBC047). Their findings show that many models claim compound contributions that are not supported by the data, and that falsification‑guided revisions can recover genuine input effects while improving performance.

Machine-generated by The Flow from the publisher's headline and feed description — not written or checked by a human. The full article lives at arXiv Machine Learning.

arXiv Machine Learning
3d ago

Interpretable-by-Design Descriptor Portfolios Match a 2048-Dimensional Foundation Embedding on Low-Data Molecular Assays

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 AI
2d ago

From Retrieval to Reasoning: Agentic Mechanism Prediction from Cell Painting Profiles

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 Computation and Language
Sep 15

HypoEvolve: Genetic Algorithms Enable Multi-Agent LLMs to Discover Scientific Hypotheses

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