arXiv Machine Learning

Position: Genomic Model Research Must Move Beyond Anecdotal Evaluation of Interpretability Methods

arXiv:2606. 07607v1 Announce Type: new Abstract: Advances in machine learning and computational power have unlocked the predictive potential of the human genome, yet biologists now demand that these models also elucidate the underlying biological mechanisms.

arXiv AI

Jul 23

Causal dictionary learning reveals and validates transcription-factor binding features in genomic language models

arXiv:2607. 19618v1 Announce Type: cross Abstract: Genomic language models achieve strong performance across regulatory-genomics tasks, yet what these models internally represent remains opaque, and the field lacks a principled procedure for verifying that an apparent ``concept'' inside a model is real rather than an artifact of sequence composition.

By Sarwan Ali

llms nlp safety

arXiv Machine Learning

Jul 2

Explainable AI for Cancer Drug Response Prediction: Beyond Univariate Feature Attributions

arXiv:2607. 00931v1 Announce Type: new Abstract: Predicting cancer drug response from transcriptomic profiles is a cornerstone of precision oncology, yet the scientific value of machine learning models hinges not solely on predictive accuracy, but also on their capacity to generate reliable biological insights.

By Martino Ciaperoni, Margherita Lalli, Simone Piaggesi, Martina Varisco, Francesco Carli, Riccardo Guidotti, Dino Pedreschi, Francesco Raimondi, Fosca Giannotti

arXiv AI

Jul 7

EvoXplain: When Machine Learning Models Agree on Predictions but Disagree on Why -- Measuring Mechanistic Multiplicity Across Training Runs

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

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arXiv AI

Jun 2

Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

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

llms

arXiv AI

Jun 18

SciHorizon-GENE: Benchmarking LLM for Life Sciences Inference from Gene Knowledge to Functional Understanding

arXiv:2601. 12805v4 Announce Type: replace-cross Abstract: Large language models (LLMs) have shown growing promise in biomedical research, particularly for knowledge-driven interpretation tasks.

By Xiaohan Huang, Meng Xiao, Chuan Qin, Qingqing Long, Jinmiao Chen, Yuanchun Zhou, Hengshu Zhu

llms benchmarks safety

arXiv AI

Aug 7

CASCADE: An Agentic Regulatory Network Framework for Patient-Data-Validated Downstream Perturbation Prediction

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

llms agents benchmarks

arXiv Machine Learning

Jun 5

Symb-xMIL: Symbolic Explanations for Multiple Instance Learning in Digital Pathology

arXiv:2606. 06224v1 Announce Type: cross Abstract: Explanations of multiple instance learning (MIL) models are widely used for validation and discovery in digital histopathology.

By Yanqing Luo (Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Machine Learning Group, Technische Universit\"at Berlin, Berlin, Germany), Julius Hense (Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Machine Learning Group, Technische Universit\"at Berlin, Berlin, Germany), Niklas Preni{\ss}l (Institute of Pathology, Charit\'e Universit\"atsmedizin, Berlin, Germany, Berlin Institute of Health at Charit\'e -- Universit\"atsmedizin Berlin, BIH Biomedical Innovation Academy, BIH Charit\'e Digital Clinician Scientist Program, Berlin, Germany), Andreas Mock (Institute of Pathology, Ludwig Maximilian University of Munich, Munich, Germany, Division of Translational Medical Oncology, DKFZ, Heidelberg, Germany, NCT Heidelberg, Heidelberg, Germany, German Cancer Consortium), Klaus-Robert M\"uller (Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Machine Learning Group, Technische Universit\"at Berlin, Berlin, Germany, Department of Artificial Intelligence, Korea University, Seoul, Korea, Max-Planck Institute for Informatics, Saarbr\"ucken, Germany), Thomas Schnake (Department of Chemistry, Chemical Physics Theory Group, University of Toronto, Canada, Vector Institute for Artificial Intelligence, Toronto, Canada, Acceleration Consortium, University of Toronto, Canada), Mina Jamshidi Idaji (Berlin Institute for the Foundations of Learning and Data, Berlin, Germany, Machine Learning Group, Technische Universit\"at Berlin, Berlin, Germany)

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arXiv AI

Jun 2

Perspective on Bias in Biomedical AI: Preventing Downstream Healthcare Disparities

arXiv:2604. 14514v2 Announce Type: replace Abstract: Healthcare disparities persist across socioeconomic boundaries, often attributed to unequal access to screening, diagnostics, and therapeutics.

By Michal Rosen-Zvi, Yoav Kan-Tor, Michael Danziger, Agata Ferretti, Javier Aula-Blasco, Julia Falcao, Ron Shamir, Mira Marcus-Kalish, Mordechai Muszkat

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arXiv Machine Learning

Jul 7

Biologically Informed Deep Neural Networks for Multi-Omic Integration, Pathway Activity Inference and Risk Stratification in Cancer

arXiv:2607. 05306v1 Announce Type: new Abstract: Integrating complex, multi-omics data presents significant challenges.

By Pedro Henrique da Costa Avelar, Le Ou-Yang, Min Wu, Sophia Tsoka

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arXiv Machine Learning

Jun 9

Biological Reasoning-Informed Regression for Interpretable Regulatory DNA Activity Prediction

arXiv:2606. 08147v1 Announce Type: cross Abstract: DNA cis-regulatory elements (CREs) such as enhancers control gene expression levels.

By Yi Duan, Zhao Yang, Jiwei Zhu, Ying Ba, Chuan Cao, Bing Su

llms reinforcement-learning benchmarks safety

arXiv Machine Learning

Jun 10

TRAPS: Therapeutic Response Analysis via Pathway-informed Stratification

arXiv:2606. 09898v1 Announce Type: new Abstract: Cancer treatment planning requires decisions across multiple clinical dimensions at once.

By Sujoy Banik, Sayantan Chakraborty, Boishakhi Das Toma, Zainab Ghafoor, Ushashi Bhattacharjee, Koushik Howlader, Tirtho Roy

benchmarks

arXiv Machine Learning

23h ago

Conformal Prediction for Molecular Properties under Label Shift

arXiv:2608. 17678v1 Announce Type: new Abstract: Drug discovery and development underpins healthcare but remains costly and failure-prone.

By Hyeonsu Lee, Juyeon Kim, Erkhembayar Jadamba, Seungjin Choi, Hyunjin Shin

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