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    31 repositories

    • Persona_Paradox

      Public
      This is the official repository for 'The Persona Paradox: Medical Personas as Behavioral Priors in Clinical Language Models.' This project investigates how distinct medical personas influence LLM behavior and safety alignment across complex clinical scenarios.
      0•0•0•0•Updated Jan 7, 2026Jan 7, 2026

    • pyaging

      Public
      A Python-based compendium of GPU-optimized aging clocks.
      clocktorchagingbiomarkers
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •3•115•1•0•Updated Dec 28, 2025Dec 28, 2025

    • DRIFT

      Public
      Diffusion-based Representation Integration for Foundation models in spatial Transcriptomics
      Jupyter Notebook
      •0•2•0•0•Updated Dec 23, 2025Dec 23, 2025

    • TimeFlies

      Public
      Machine learning framework for aging analysis in Drosophila single-cell RNA-seq data. Deep learning models with SHAP interpretability, batch correction, and comprehensive research workflows.
      pythonmachine-learningbioinformaticsdeep-learningtensorflowcnnmlpdrosophilaagingsingle-cell-rna-seq
      Python
      •
      Other
      •0•1•0•0•Updated Oct 16, 2025Oct 16, 2025

    • scContrast

      Public
      A contrastive learning based approach to learn universal cell representation
      Jupyter Notebook
      •0•2•0•0•Updated Aug 18, 2025Aug 18, 2025

    • STING

      Public
      Spatial Transcriptomics cluster Inference with Nested GNNs
      Python
      •1•0•0•0•Updated Aug 7, 2025Aug 7, 2025

    • scMultiNODE

      Public
      scMultiNODE: Temporal Single-Cell Data Integration across Unaligned Modalities
      Python
      •
      MIT License
      •0•3•0•0•Updated Aug 3, 2025Aug 3, 2025

    • CoRNN

      Public
      Compartment prediction using Recurrent Neural Network
      Python
      •1•2•1•0•Updated Jul 25, 2025Jul 25, 2025

    • PiCME

      Public
      Pipeline for Contrastive Modality Evaluation and Encoding in the MIMIC Dataset
      Python
      •0•4•0•0•Updated Jul 8, 2025Jul 8, 2025

    • K-Paths

      Public
      Official Implementation of K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction.
      knowledge-graphreasoninggraph-neural-networkslarge-language-models
      Python
      •3•19•0•0•Updated Jul 8, 2025Jul 8, 2025

    • gnn_microscopy_segment

      Public
      Memory Efficient Semantic Segmentation of Large Microscopy Images Using Graph-based Neural Networks
      Python
      •0•7•0•0•Updated Jul 3, 2025Jul 3, 2025

    • pixels_vs_priors

      Public
      Jupyter Notebook
      •1•7•0•0•Updated Jun 11, 2025Jun 11, 2025

    • ML_epigenetic_features_glioblastoma

      Public
      Gene expression (RNA-seq) prediction from an initial glioblastoma stem cell epigenetic measurement dataset (H3K27Ac, CTCF, ATAC-seq, and RNAPII) to another.
      machine-learningdeep-learningcomputational-biologyglioblastoma
      Python
      •
      MIT License
      •1•1•0•0•Updated Jun 1, 2025Jun 1, 2025

    • AltumAge

      Public
      Jupyter Notebook
      •
      MIT License
      •10•38•1•0•Updated May 27, 2025May 27, 2025

    • QZERO

      Public
      Retrieval Augmented Zero-Shot Text Classification
      Python
      •0•7•0•0•Updated Apr 24, 2025Apr 24, 2025

    • Shape-Blind

      Public
      Jupyter Notebook
      •0•9•1•0•Updated Mar 4, 2025Mar 4, 2025

    • HistoneClocks

      Public
      This repository contains the code and data to reproduce the results of our paper entitled "Histone mark age of human tissues and cells".
      Jupyter Notebook
      •
      MIT License
      •0•2•0•0•Updated Jan 3, 2025Jan 3, 2025

    • scNODE

      Public
      scNODE: Generative Model for Temporal Single Cell Transcriptomic Data Prediction
      Jupyter Notebook
      •
      MIT License
      •6•28•3•0•Updated Oct 11, 2024Oct 11, 2024

    • OvO

      Public
      Jupyter Notebook
      •
      MIT License
      •1•11•1•0•Updated Sep 30, 2024Sep 30, 2024

    • GC-MERGE

      Public
      This is the repository for the long-range interaction GCNN for predicting gene expression for the Singh Lab.
      Python
      •
      MIT License
      •1•5•3•0•Updated Sep 11, 2024Sep 11, 2024

    • scGrapHiC

      Public
      A graph deconvolution approach to predict Hi-C contact map from pseudo-bulk scRNA-seq.
      Python
      •0•7•1•0•Updated Aug 24, 2024Aug 24, 2024

    • SCOT

      Public
      Gromov-Wasserstein based optimal transport for aligning single-cell multi-omics data
      Jupyter Notebook
      •
      MIT License
      •18•77•6•1•Updated Jan 25, 2024Jan 25, 2024

    • scRNAseq_Coexpression_Benchmark

      Public
      A benchmark of existing gene co-expression estimator on scRNA-seq data.
      HTML
      •
      MIT License
      •0•2•1•0•Updated Oct 11, 2023Oct 11, 2023

    • CliniqIR

      Public
      Code for the paper: Unsupervised Diagnostic Decision Support via Information Retrieval
      Python
      •1•2•0•0•Updated Oct 9, 2023Oct 9, 2023

    • GrapHiC

      Public
      A graph neural network based approach to impute missing Hi-C reads.
      deep-learningpytorch
      Python
      •0•11•1•0•Updated Jul 28, 2023Jul 28, 2023

    • SCOOTR

      Public
      Single-cell CO-Optimal TRansport for jointly aligning cells and genomic features of single-cell multi-omic datasets
      Python
      •1•3•1•0•Updated Jul 13, 2023Jul 13, 2023

    • Hi-CY

      Public
      Python
      •0•0•0•0•Updated May 1, 2023May 1, 2023

    • MADDi

      Public
      This repository is for the Multimodal Alzheimer’s Disease Diagnosis framework (MADDi).
      Jupyter Notebook
      •
      MIT License
      •22•115•3•0•Updated Apr 26, 2023Apr 26, 2023

    • GNN-Tumor-Seg

      Public
      Using Graph Neural Networks to Segment MRIs of Brain Tumors
      Python
      •7•29•0•0•Updated Aug 13, 2022Aug 13, 2022

    • ChromAge

      Public
      Private repository for the chromatin age prediction project developed by Lucas and Haider.
      Python
      •0•1•0•0•Updated Apr 27, 2022Apr 27, 2022