arXiv AI

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.

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)

safety

arXiv AI

Jun 4

You Only Train Once: Differentiable Subset Selection for Omics Data

arXiv:2512. 17678v2 Announce Type: replace-cross Abstract: Selecting compact and informative gene subsets from single-cell transcriptomic data is essential for biomarker discovery, improving interpretability, and cost-effective profiling.

By Daphn\'e Chopard, Jorge da Silva Gon\c{c}alves, Irene Cannistraci, Thomas M. Sutter, Julia E. Vogt

efficiency benchmarks safety

arXiv Machine Learning

2d ago

Learning Auditable Classifier Models: Source-Disjoint Tree Ensembles

arXiv:2608. 15725v1 Announce Type: new Abstract: Predictive models in clinical and regulated settings must be accurate and fully auditable.

By Srikumar Krishnamoorthy

benchmarks

arXiv Machine Learning

Jul 17

Cross-Cluster Weighted Forests

arXiv:2105. 07610v5 Announce Type: replace-cross Abstract: Building trustworthy machine learning algorithms for biological applications requires adapting to data heterogeneity from different sources, batches, distributions, or studies.

By Maya Ramchandran, Rajarshi Mukherjee, Giovanni Parmigiani

safety

arXiv Machine Learning

Jul 24

Evaluation and Prognostic Validation of Deep Regression Models for WSI-Based Gene-Expression Prediction

arXiv:2410. 00945v2 Announce Type: replace-cross Abstract: Gene-expression profiling is widely used in research and central to many areas of precision oncology, but remains costly and not universally accessible.

By Fredrik K. Gustafsson, Constance Boissin, Johan Vallon-Christersson, Mattias Rantalainen

arXiv Machine Learning

Jun 2

OncoReason: Structuring Clinical Reasoning in LLMs for Robust and Interpretable Survival Prediction

arXiv:2510. 17532v2 Announce Type: replace-cross Abstract: Predicting cancer treatment outcomes requires models that are both accurate and interpretable, particularly in the presence of heterogeneous clinical data.

By Raghu Vamshi Hemadri, Geetha Krishna Guruju, Kristi Topollai, Anna Ewa Choromanska

llms nlp reinforcement-learning fine-tuning benchmarks safety

arXiv AI

Jul 21

Benchmarking Machine Learning Models for Multi-Omics-Based Breast Cancer Prediction

arXiv:2607. 16250v1 Announce Type: cross Abstract: Estrogen Receptor (ER) status is a critical biomarker in breast cancer diagnosis, prognosis, and treatment selection.

By Priyanka Paudel, Madan Baduwal

efficiency benchmarks

arXiv AI

Jun 4

Learning to Evaluate: Cost-Effective Model Evaluation on Unlabeled Data with Meta-Learning

arXiv:2605. 23595v2 Announce Type: replace-cross Abstract: The rapid advancement of machine learning has led to an unprecedented expansion of model ecosystems, making it increasingly difficult to assess the reliability of newly released models on unseen and unlabeled data.

By Trinh Pham, Viet Huynh, Hongzhi Yin, Quoc Viet Hung Nguyen, Thanh Tam Nguyen

fine-tuning benchmarks

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 AI

Jun 30

Data-Efficient Multimodal Alignment for Histopathology-based Molecular Prediction

arXiv:2606. 29949v1 Announce Type: cross Abstract: H&E-stained whole-slide images offer cohort-scale availability and rich spatial context but lack molecular specificity, whereas bulk RNA-seq provides transcriptome-wide resolution at high cost with limited archival availability.

By Dominik Winter, Dominik Vonficht, Lo\"ic Le Bescond, Christian Gebbe, Marco Rosati, Richard J. Chen, Markus Schick, Ross Stewart, Nicolas Brieu

llms fine-tuning multimodal safety

arXiv Machine Learning

Jun 2

RobustModelMaker: Coupling Bootstrap Stability Selection with Leakage-Safe Nested Cross-Validation for Scientific Machine Learning

arXiv:2606. 01566v1 Announce Type: new Abstract: Small-to-medium scientific datasets place machine learning pipelines under two compounding pressures.

By Amanda S Barnard

arXiv Machine Learning

1d ago

Pathology Transport: Optimal-Transport Explanations for Clinical Data, and When Their Heatmaps (Fail to) Localize Disease

arXiv:2608. 17370v1 Announce Type: new Abstract: Generative models promise a route to explainable clinical AI: rather than probe a classifier, model the distributions of healthy and diseased patients and read explanations off the geometry between them.

By Lalit Kumar

benchmarks safety

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