high-performance JAX implementation of Control Barrier Functions (CBFs) for safety-critical control

Fit compact primitive assemblies (SuperFrusta, cuboids, superquadrics) to 3D shapes via residual fitting. CVPR 2026.

Implementation of Alphafold 3 from Google Deepmind in Pytorch

Positron, a next-generation data science IDE

Simple and exhaustive solution for applications network activity controlling and monitoring.

Fort Firewall for Windows

Python implementation of Langevin inference methods from time series.

MapAnything: Universal Feed-Forward Metric 3D Reconstruction

ShapeEmbedLite: a lightweight self-supervised representation learning model for 2D shape analysis

Notebooks to follow along with "Deep Learning for Biology" Chapters 2 to 6.

MicroLive: An Image Processing Toolkit for Quantifying Live-cell Single-Molecule Microscopy.

Cell tracking and segmentation software

A growing collection of bioinformatics tutorials, project guides, tools, and articles I’ve developed to make bioinformatics more accessible.

MONAI Tutorials

https://www.sc-best-practices.org

Antibody structure prediction

12 weeks, 26 lessons, 52 quizzes, classic Machine Learning for all

Multi-agent LLM driven cell type annotation for single-cell RNA-Seq data

State arrays for single particle tracking

Open-source mechanistic model for ion exchange chromatography

Open-Source package for segmentation and analysis of gel electrophoresis images using machine learning. Both a python framework for training/running models and a QuPath GUI extension are available.

This repository contains demos I made with the Transformers library by HuggingFace.

A DIY Guide To Single-Cell RNA-Sequencing Analysis

Rapid and efficient image preprocessing pipeline for multiplexed spatial proteomics. Code to compare several techniques to denoise Imaging Mass cytometry

Python code to model the syncytial development of a cricket in 3D. Additional Mathematica Code for rendering mesh2 objects in povray.