Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

  PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 7 claims · 6 setups

  Has reproduction · 77

  SurvConvMixer reformats KEGG Pathways-in-Cancer gene expression values into pathway-level 2D gene expression images and applies a ConvMixer-based model for overall survival prediction

  luad lung bulk gene machine

• Artificial Intelligence Approach in Machine Learning-Based Modeling and Networking of the Coronavirus Pathogenesis Pathway.

  PMID 40699865 · PMC12191508 · Current issues in molecular biology · 2025 · 8 claims · 8 setups

  Has reproduction

  The coronavirus pathogenesis pathway is activated in SARS-CoV-2-infected iPSC-derived cardiac cells and in SARS-CoV/SARS-CoV-2-infected LUAD cells

  ace2-transfected calu-3 luad ipsc-derived ipa sequencing convolutional

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 7 claims · 8 setups

  Has reproduction

  Tabular ML classifiers (TabNet, XGBoost, LightGBM) trained on tumor-only-derived features achieve state-of-the-art somatic vs germline classification, with AUC>94% on TCGA holdout and AUC>85% on metastatic melanoma.

  tcga metastatic tumor-only whole-exome wes copy-number

• Graph Random Forest: A Graph Embedded Algorithm for Identifying Highly Connected Important Features.

  PMID 37509188 · PMC10377046 · Biomolecules · 2023 · 8 claims · 3 setups

  Has reproduction · 89

  Graph Random Forest (GRF) embeds graph/network information directly into the decision-tree building process by splitting on features in the k-hop neighborhood of a data-driven head-splitting node.

  scale-free non-small embryonic simulation rna-seq