Repository Index

Theano was a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. It is being continued as PyTensor: www.github.com/pymc-devs/pytensor

A library for scientific machine learning and physics-informed learning

• neural-network
• deep-learning
• scientific-machine-learning
• pinn

NSGA2, NSGA3, R-NSGA3, MOEAD, Genetic Algorithms (GA), Differential Evolution (DE), CMAES, PSO

• optimization
• multi-objective-optimization
• nsga2
• nsga3

Infrastructure for evolutionary AI systems. GPU-accelerated, PyTorch-based optimization with an ecosystem of algorithm libraries, benchmarks, and tools.

• evolutionary-algorithms
• neuroevolution
• gpu-acceleration
• multi-objective-optimization

Large Language-and-Vision Assistant for Biomedicine, built towards multimodal GPT-4 level capabilities.

A library for generative social simulation

• agent-based-simulation
• generative-agents
• multi-agent
• social-simulation

Generation of protein sequences and evolutionary alignments via discrete diffusion models

• discrete-diffusion
• generative-model
• multiple-sequence-alignment
• protein-sequences

Algebraic Multigrid Solvers in Python

• amg
• solver
• python
• multigrid

A Free and Open Source Python Library for Multiobjective Optimization

• optimization
• multiobjective
• evolutionary
• algorithm

Graph-linked unified embedding for single-cell multi-omics data integration

• bioinformatics
• deep-learning
• single-cell
• single-cell-multiomics

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

Multibody dynamics tool kit.

• python
• dynamics
• physics
• simulation

Python library for multilinear algebra and tensor factorizations

MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.

An automatic code generator for nonlinear model predictive control (NMPC) and the continuation/GMRES method (C/GMRES) based numerical solvers for NMPC

• model-predictive-control
• nonlinear-model-predictive-control
• mpc
• nmpc

Automated 3D brain registration with support for multiple species and atlases.

• registration
• atlases
• brain
• neuroscience

CASSIA: A Multi-Agent LLM-Based Single-Cell Cell Type Annotation Framework

• ai4science
• llm
• multiagent-systems
• prompt-engineering

PyTorch implementation of the MIDAS algorithm for single-cell multimodal data integration (Nature Biotechnology 2024).

• deep-generative-model
• deep-learning
• single-cell-data-integration
• single-cell-multiomics

Multi-stage Riemannian flow matching for physically valid molecular docking, with GNINA scoring, PoseBusters filtering, CLI inference, and benchmarks.

• alphafold3
• docking
• drug-design
• drug-discovery

Multigrate: multiomic data integration for single-cell genomics

Official implementation of JAMIE, Joint variational Autoencoders for Multimodal Imputation and Embedding

• autoencoder
• imputation
• integration
• multimodal

scPair: Boosting single cell multimodal analysis by leveraging single cell atlases and implicit feature selection