arXiv Machine Learning

ROOFS: RObust biOmarker Feature Selection

arXiv:2601. 05151v3 Announce Type: replace-cross Abstract: Feature selection (FS) is essential for biomarker discovery and clinical predictive modeling.

arXiv Machine Learning
Jul 24

Multimodality Stacking with Blockwise missing values and application to the PIONeeR biomarkers study for prediction of resistance to immunotherapy

arXiv:2605. 25050v2 Announce Type: replace-cross Abstract: Integrating multimodal datasets in clinical oncology is frequently hindered by high dimensionality and blockwise missingness, where entire data sources are unavailable for specific patient subsets.

By Mohamed Boussena, Florence Monville, Jacques Fieschi-Meric, Frederic Vely, Pierre Milpied, Julien Mazieres, Maurice Perol, Eric Vivier, Laurent Greillier, Fabrice Barlesi, Sebastien Benzekry
arXiv Machine Learning
Aug 31

Advancing Interaction-Sensitive Feature Selection: Novel Relief-Based Algorithms, Expanded Comparisons, and Recommendations for Biomedical Data Mining

The paper refactors and expands the scikit-rebate Python package, adding new Relief‑Based Algorithm (RBA) variants such as SWRF*, mu‑Relief, and five novel methods that use alternative neighbor selection and feature scoring strategies. Benchmarking across diverse genomic simulations shows that most RBAs, except mu‑Relief, effectively detect 2‑way interactions in noisy data, with far‑scoring variants like MultiSWRFDB* excelling at interaction detection but being less sensitive to main effects. The refactored package achieves 10‑ to 35‑fold runtime reductions, and the new RBAs maintain strong performance for both main effects and 2‑way epistatic interactions, preserving predictive signals for downstream modeling.

By Kia Kazemi-Nia, Harsh Bandhey, Philip J. Freda, Ryan J. Urbanowicz
arXiv Machine Learning
Jul 2

Foundation Models vs. Radiomics for Lung Computed Tomography: A Benchmark of Feature Extractors, Classification Heads, and Segmentation Choices

arXiv:2607. 01001v1 Announce Type: cross Abstract: Radiomics is the established approach for CT-based lung cancer phenotyping, yet comparisons with foundation models rarely isolate contributions of feature extractor, classification head, and segmentation choice, or test cross-cohort robustness.

By Nils Neukirch, Martin Maurer, Nils Strodthoff
arXiv Machine Learning
Jun 10

OncoTraj: a public benchmark for longitudinal resistance prediction in EGFR-mutant non-small-cell lung cancer on osimertinib

arXiv:2606. 11144v1 Announce Type: new Abstract: Resistance to first-line osimertinib in EGFR-mutant non-small-cell lung cancer (NSCLC) is the canonical example of predictable clonal evolution under therapeutic pressure, yet no public benchmark exists for training or evaluating computational models on the corresponding longitudinal patient trajectories.

By Abhijoy Sarkar, Aarchi Singh Thakur
arXiv Machine Learning
Sep 25

Feature Space Selection and Heterogeneous Effect Estimation for Blood-Brain Barrier Permeability: A Random Forest to the Generalized Random Forest Pipeline

The study evaluates how different molecular feature spaces—Morgan fingerprints, RDKit physicochemical descriptors, and SMILES bigrams—affect the prediction of blood‑brain barrier permeability using various learning algorithms. Dynamic Random Forests with combined features achieved the best performance (mean AUC 0.970). When applying Generalized Random Forests to estimate heterogeneous effects of LogP on BBB permeability, orthogonalization revealed that apparent heterogeneity largely vanished after accounting for confounding, shifting importance toward residual SMILES bigram information.

By Tshemollo Rapolai, Seite Makgai, Mohammad Arashi