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Starred repositories
A scikit-learn-compatible library for estimating prediction intervals and controlling risks, based on conformal predictions.
Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.
PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).
LLM agents for working with the SRA and associated bioinformatics databases.
CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
A Co-evolving Agentic AI System for Medical Imaging Analysis
[ICML 2025] Code for SUICA: Learning Super-high Dimensional Sparse Implicit Neural Representations for Spatial Transcriptomics.
A Python package for identification Differential Spatial Expression Pattern (DESP) gene by interpretable deep learning from multi-slice spatial omics data.
Learning cell communication from spatial graphs of cells
[AI4Mat-ICLR2025] PriM: Principle-Inspired Material Discovery through Multi-Agent Collaboration
BioDiscoveryAgent is an LLM-based AI agent for closed-loop design of genetic perturbation experiments
Official code for paper: Chain of Ideas: Revolutionizing Research via Novel Idea Development with LLM Agents
This is the official repository for HypoGeniC (Hypothesis Generation in Context) and HypoRefine, which are automated, data-driven tools that leverage large language models to generate hypothesis fo…
Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology
DeepSpot: Leveraging Spatial Context for Enhanced Spatial Transcriptomics Prediction from H&E Images
Decima is a Python library to train sequence models on single-cell RNA-seq data.
GENERator: A Long-Context Generative Genomic Foundation Model
A modular framework for multimodal cross-cell-type transcriptional regulation models
SIMBA: SIngle-cell eMBedding Along with features
LIANA+: an all-in-one framework for cell-cell communication