Code used to run the data analysis in the hdWGCNA manuscript (Morabito et al 2022)

Qwen-Image-Layered: Layered Decomposition for Inherent Editablity

GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations

[NeurIPS 2025] 4KAgent: Agentic Any Image to 4K Super-Resolution. An intelligent computer vision agent that can magically restore any image to perfect-4K!

Intelligent automation and multi-agent orchestration for Claude Code

🪐 🔧 Model Context Protocol (MCP) Server for Jupyter.

A collection of MCP servers.

This is MCP server for Claude that gives it terminal control, file system search and diff file editing capabilities

State is a machine learning model that predicts cellular perturbation response across diverse contexts

Deep generative modeling for single-cell omics data

Single-cell Graph-based Regulatory Element Analysis Toolkit

Task-based gene regulatory network inference using single-cell or bulk gene expression data conditioned on a prior network.

Granger recurrent autoencoders to network gene expression regulations

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Open Overleaf/ShareLaTex projects in vscode, with full collaboration support.

First metabolite-centric knowledge graph.

Galvatron is an automatic distributed training system designed for Transformer models, including Large Language Models (LLMs).

Github of the FaceForensics dataset

[TMLR 2025] Latte: Latent Diffusion Transformer for Video Generation.

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.