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1. Benchmarking-Physics-Informed-vs.-Foundation-Models-for-Cenozoic-Paleobiology Benchmarking-Physics-Informed-vs.-Foundation-Models-for-Cenozoic-Paleobiology Public

   Benchmarks Physics-Informed Neural ODEs vs. Fine-Tuned Foundation Models (Chronos) on Cenozoic fossil data. Includes a Random Forest analysis of the Lilliput Effect to test climate vs. taphonomy dr…

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2. Rice-BRL3-Metabolomics-ML Rice-BRL3-Metabolomics-ML Public

   A complete metabolomics pipeline for rice drought resilience. Features SAITS imputation, PLS-DA for biomarker discovery, and Partial Correlation Networks to identify the Salicylate-driven rewiring …

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3. Thermodynamic-Resistance-TNBC Thermodynamic-Resistance-TNBC Public

   A physics-based framework for reversing TNBC drug resistance. Using Topological Data Analysis on scRNA-seq, we mapped a COL17A1-driven phase transition at pseudotime 0.7. Includes in silico trials …

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4. geometric-tme-thermodynamics geometric-tme-thermodynamics Public

   A geometry-based framework that models spatial transcriptomics as a gene-weighted manifold. Using Ollivier–Ricci curvature, it identifies thermodynamic instability in tumors. Negative curvature pre…

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5. Secretope-Pipeline Secretope-Pipeline Public

   End-to-end computational pipeline for designing Salmonella-based cancer vaccines. Integrates neoantigen mining, T3SS fusion engineering, DeepSecE AI screening, and OpenMM molecular dynamics to vali…

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6. Topological-Genomics-Rice Topological-Genomics-Rice Public

   By modeling 3,000 rice genomes as a high-dimensional manifold, this study uncovers a persistent topological loop connecting Indica and Japonica. Validated by AI and GWAS, this evolutionary "bridge"…

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