Trending repositories

101.evo-design / evo

Biological foundation modeling from molecular to genome scale

102.mlmed / torchxrayvision

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning
• transfer-learning
• dataset
• +13 more

103.3dmol / 3Dmol.js

WebGL accelerated JavaScript molecular graphics library

• molecular-graphics
• molecular-modeling
• computational-biology
• computational-chemistry

104.mahmoodlab / UNI

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab
• pathology
• uni
• +11 more

105.RosettaCommons / RoseTTAFold

This package contains deep learning models and related scripts for RoseTTAFold

106.mborgerding / kissfft

a Fast Fourier Transform (FFT) library that tries to Keep it Simple, Stupid

107.MFlowCode / MFC

Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs

• gpu
• exascale
• cfd
• fortran
• hpc
• mpi
• +14 more

108.schachmat / wego

weather app for the terminal

• go
• wego
• forecast
• weather
• terminal
• ascii-art
• +2 more

109.NVIDIAGameWorks / kaolin

A PyTorch Library for Accelerating 3D Deep Learning Research

• pytorch
• 3d-deep-learning
• neural-networks
• differentiable-rendering
• artificial-intelligence
• camera-api
• +7 more

110.PythonOT / POT

POT : Python Optimal Transport

• optimal-transport
• numerical-optimization
• machine-learning
• emd
• ot-mapping-estimation
• wasserstein-barycenter
• +10 more

111.Reference-LAPACK / lapack

LAPACK development repository

• linear-algebra
• lapack
• blas
• lapacke
• linear-equations
• eigenvalues
• +4 more

112.osrf / gazebo_models

Gazebo database of SDF models. This is a predecessor to https://app.gazebosim.org

• gazebo
• simulation
• robot-simulation
• robotics
• gazebosim
• ros
• +4 more

113.precice / precice

A coupling library and ecosystem for partitioned multi-physics and multi-scale simulations, including surface and volume coupling.

• multi-physics
• fluid-structure-interaction
• high-performance-computing
• conjugate-heat-transfer
• coupling
• co-simulation
• +13 more

114.hypre-space / hypre

Parallel solvers for sparse linear systems featuring multigrid methods.

• math-physics
• library
• hpc
• radiuss

115.scverse / squidpy

Spatial Single Cell Analysis in Python

• single-cell-rna-seq
• single-cell-genomics
• spatial-transcriptomics
• spatial-analysis
• image-analysis
• data-visualization
• +2 more

116.fish-quant / big-fish

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish
• spatial-features
• spot-detection

117.guofei9987 / scikit-opt

Genetic Algorithm, Particle Swarm Optimization, Simulated Annealing, Ant Colony Optimization Algorithm,Immune Algorithm, Artificial Fish Swarm Algorithm, Differential Evolution and TSP(Traveling salesman)

• genetic-algorithm
• pso
• particle-swarm-optimization
• tsp
• travelling-salesman-problem
• simulated-annealing
• +7 more

118.apache / incubator-kie

Apache KIE (Knowledge Is Everything) is the home of Drools, OptaPlanner, jBPM, and Kogito.

• rule-engine
• java
• dmn
• hacktoberfest
• apache
• drools
• +3 more

119.FFTW / fftw3

DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)

120.elixir-nx / nx

Multi-dimensional arrays (tensors) and numerical definitions for Elixir

• gpu
• numerical
• elixir
• tensor
• xla
• pytorch
• +1 more

121.stevengj / nlopt

library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization

122.microsoft / DirectXMath

DirectXMath is an all inline SIMD C++ linear algebra library for use in games and graphics apps

• microsoft
• directx
• simd
• neon
• cpp-library
• sse
• +10 more

123.ethz-adrl / control-toolbox

The Control Toolbox - An Open-Source C++ Library for Robotics, Optimal and Model Predictive Control

• optimal-control
• model-predictive-control
• ilqr
• ilqg
• robotics
• trajectory-optimization
• +9 more

124.deepmodeling / Uni-Mol

Official Repository for the Uni-Mol Series Methods

• molecular-modeling
• pre-trained-model
• pretraining
• deep-learning

125.gromacs / gromacs

Public/backup repository of the GROMACS molecular simulation toolkit. Please do not mine the metadata blindly; we use https://gitlab.com/gromacs/gromacs for code review and issue tracking.

126.invesalius / invesalius3

3D medical imaging reconstruction software

• dicom
• dicom-viewer
• magnetic-resonance-imaging
• medical-image-processing
• medical-imaging
• segmentation
• +2 more

127.kinnala / scikit-fem

Simple finite element assemblers

• fem
• python
• pde

128.deeplearning4j / deeplearning4j

Suite of tools for deploying and training deep learning models using the JVM. Highlights include model import for keras, tensorflow, and onnx/pytorch, a modular and tiny c++ library for running math code and a java based math library on top of the core c++ library. Also includes samediff: a pytorch/tensorflow like library for running deep learn...

• java
• gpu
• deeplearning
• neural-nets
• deeplearning4j
• dl4j
• +9 more

129.facebookresearch / esmArchived

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

130.RainerKuemmerle / g2o

g2o: A General Framework for Graph Optimization

• g2o
• slam
• c-plus-plus
• graph-optimization
• cpp

131.symengine / symengine

SymEngine is a fast symbolic manipulation library, written in C++

• math
• computer-algebra
• c-plus-plus

132.weewx / weewx

WeeWX code repository

• weather
• python
• weewx
• raspberry-pi
• vantage-pro
• fine-offset
• +1 more

133.libtom / libtommath

LibTomMath is a free open source portable number theoretic multiple-precision integer library written entirely in C.

• mpi
• libtommath
• c
• math
• multi-precision

134.runmat-org / runmat

Open source math and physics engine that executes MATLAB-syntax code. Features a modern compiler, automatic GPU acceleration for large calculations, and support for math on geometry / FEA calculations.

• matlab
• rust
• jit-compiler
• linear-algebra
• mathematics
• numerical-analysis
• +6 more

135.flame / blis

BLAS-like Library Instantiation Software Framework

• blis
• blas
• blas-libraries
• linear-algebra
• linear-algebra-library
• matrix-multiplication
• +8 more

136.chaidiscovery / chai-lab

Chai-1, SOTA model for biomolecular structure prediction

137.ashvardanian / NumKong

SIMD-accelerated distances, dot products, matrix ops, geospatial & geometric kernels for 16 numeric types — from 6-bit floats to 64-bit complex — across x86, Arm, RISC-V, and WASM, with bindings for Python, Rust, C, C++, Swift, JS, and Go 📐

• arm-neon
• assembly
• metrics
• simd
• information-retrieval
• numpy
• +10 more

138.flexible-collision-library / fcl

Flexible Collision Library

• collision
• collision-detection

139.psi4 / psi4

Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python

• quantum-chemistry
• c-plus-plus
• python
• computational-chemistry
• chemistry
• physics

140.kexinhuang12345 / DeepPurpose

A Deep Learning Toolkit for DTI, Drug Property, PPI, DDI, Protein Function Prediction (Bioinformatics)

• drug-repurposing
• deep-learning
• drug-target-interactions
• toolkit
• covid19
• virtual-screening
• +13 more

141.suyashkumar / dicom

⚡High Performance DICOM Medical Image Parser in Go.

• dicom
• dicom-images
• golang
• golang-library
• golang-package
• parser
• +10 more

142.hjwdzh / QuadriFlow

QuadriFlow: A Scalable and Robust Method for Quadrangulation

• quadriflow
• quad
• remeshing
• quadrangulation
• geometry

143.mims-harvard / PrimeKG

Precision Medicine Knowledge Graph (PrimeKG)

• knowledge-graph
• precision-medicine
• therapeutics
• bioinformatics
• dataset
• graph-machine-learning
• +2 more

144.TUDelft-CNS-ATM / bluesky

The open source air traffic simulator

• python
• traffic
• aircraft
• simulation
• air-traffic-control
• air-transport
• +11 more

145.OATML-Markslab / ProteinGym

Official repository for the ProteinGym benchmarks

• benchmark
• computational-biology
• protein
• protein-design
• protein-fitness

146.brandon-rhodes / python-sgp4

Python version of the SGP4 satellite position library

147.ericstoneking / 42

Simulation for spacecraft attitude control system analysis and design

148.snap-stanford / GEARS

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

149.arrayfire / arrayfire

ArrayFire: a general purpose GPU library.

• arrayfire
• c-plus-plus
• gpu
• cuda
• opencl
• gpgpu
• +5 more

150.mathnet / mathnet-numerics

Math.NET Numerics

• math
• numerics
• linear-algebra
• fsharp
• matrix
• random
• +8 more

151.markrogoyski / math-php

Powerful modern math library for PHP: Features descriptive statistics and regressions; Continuous and discrete probability distributions; Linear algebra with matrices and vectors, Numerical analysis; special mathematical functions; Algebra

• math
• mathematics
• linear-algebra
• statistics
• matrix
• probability
• +11 more

152.fo-dicom / fo-dicom

Fellow Oak DICOM for .NET, .NET Core, Universal Windows, Android, iOS, Mono and Unity

• dicom
• netcore
• medical
• medical-imaging
• dot-net
• c-sharp
• +4 more

153.prov-gigapath / prov-gigapath

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

154.wildmeshing / fTetWild

Fast Tetrahedral Meshing in the Wild

155.Teichlab / celltypist

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq
• cell-type-classification
• label-transfer

156.auto-differentiation / xad

The fastest automatic differentiation library for C++, with Python bindings. Forward, adjoint and higher-order derivatives, checkpointing, Eigen support and JIT. Reproducible benchmarks against CppAD, Adept and autodiff.

• automatic-differentiation
• aad
• algorithmic-differentiation
• autodiff
• adjoint
• cpp
• +13 more

157.hms-dbmi / viv

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

• hubmap
• imaging
• openmicroscopy
• ome-tiff
• zarr
• viv
• +1 more

158.dpilger26 / NumCpp

C++ implementation of the Python Numpy library

• python
• numpy
• c-plus-plus
• numerical-analysis
• scientific-computing
• algorithms
• +3 more

159.DavidArayan / ezy-slice

An open source mesh slicer framework for Unity3D Game Engine. Written in C#.

160.ahmedfgad / GeneticAlgorithmPython

Source code of PyGAD, a Python 3 library for building the genetic algorithm and training machine learning algorithms (Keras & PyTorch).

• python
• genetic-algorithm
• optimization
• numpy
• pygad
• pygad-documentation
• +4 more

161.DTolm / VkFFT

Vulkan/CUDA/HIP/OpenCL/Level Zero/Metal Fast Fourier Transform library

• vulkan
• fft
• convolution
• r2c
• c2r
• hpc
• +7 more

162.NetTopologySuite / NetTopologySuite

A .NET GIS solution that is fast and reliable for the .NET platform.

• topology
• nts
• sfs
• c-sharp
• library
• jts
• +1 more

163.trilinos / Trilinos

Primary repository for the Trilinos Project

• snl-science-libs
• sandia-national-laboratories
• hpsf
• scientific-computing
• high-performance-computing
• c-plus-plus
• +2 more

164.datenwolf / linmath.h

a lean linear math library, aimed at graphics programming. Supports vec3, vec4, mat4x4 and quaternions

165.Mariewelt / OpenChem

OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research

• computational-chemistry
• computational-biology
• deep-learning
• deep-neural-networks
• graph-convolutional-networks
• drug-discovery
• +5 more

166.vqdang / hover_net

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

167.chainer / chainer-chemistry

Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry

• deep-learning
• chemistry
• neural-network
• biology
• chainer
• python
• +1 more

168.DLR-SC / tigl

The TiGL Geometry Library to process aircraft geometries in pre-design.

• opencascade
• aircraft
• c-plus-plus
• geometry
• b-spline
• cpacs
• +1 more

169.CSOgroup / cellcharter

A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.

170.kreshuklab / panseg

A tool for cell instance aware segmentation in densely packed 3D volumetric images

• segmentation
• deep-learning
• bioinformatics
• neural-network
• bioimage-analysis
• image-segmentation
• +1 more

171.xtensor-stack / xtensor

C++ tensors with broadcasting and lazy computing

• c-plus-plus-14
• numpy
• multidimensional-arrays
• tensors
• c-plus-plus-17
• c-plus-plus-20
• +1 more

172.PyWavelets / pywt

PyWavelets - Wavelet Transforms in Python

• wavelets
• wavelet-transform
• signal-processing
• image-processing
• continuous-wavelet

173.Aceinna / gnss-ins-sim

Open-source GNSS + inertial navigation, sensor fusion simulator. Motion trajectory generator, sensor models, and navigation

• inertial-navigation-systems
• gnss
• gps
• imu
• integrated-navigation

174.GENIVI / CANdevStudio

Development tool for CAN bus simulation

• automotive
• can
• can-bus
• genivi

175.molecularsets / moses

Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models

• machine-learning
• generative-models
• drug-discovery
• benchmark

176.nschloe / pygmsh

:spider_web: Gmsh for Python

• python
• pypi
• mesh-generation
• engineering
• mathematics
• meshing

177.mdtraj / mdtraj

An open library for the analysis of molecular dynamics trajectories

• molecular-dynamics
• python
• mdtraj
• rmsd
• dihedral-angles
• pdb
• +2 more

178.pyamg / pyamg

Algebraic Multigrid Solvers in Python

• amg
• solver
• python
• multigrid
• sparse-matrix
• pyamg
• +2 more

179.ginkgo-project / ginkgo

Numerical linear algebra software package

• linear-algebra
• hpc
• gpu-computing
• cuda
• krylov-methods
• preconditioning
• +6 more

180.cdk / cdk

The Chemistry Development Kit

• code4lib
• chemistry
• java
• cheminformatics
• bioinformatics
• blueobelisk

181.mahmoodlab / CONCH

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model
• health-informatics
• histopathology
• +9 more

182.bioFAM / MOFA2

Multi-Omics Factor Analysis

• multi-omics
• factor-analysis
• mofa

183.epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools

• indigo
• bingo
• cheminformatics
• chemistry
• python
• dotnet
• +9 more

184.snap-stanford / UCE

UCE is a zero-shot foundation model for single-cell gene expression data

185.CEED / libCEED

CEED Library: Code for Efficient Extensible Discretizations

• ceed
• high-order
• exascale-computing
• api
• ecp
• high-performance-computing
• +5 more

186.dcjones / proseg

Probabilistic cell segmentation for in situ spatial transcriptomics

187.GeomScale / volesti

Practical volume computation and sampling in high dimensions

• geometry
• statistics
• polyhedral-computations
• random-walk
• sampling
• volume
• +6 more

188.zcang / COMMOT

The repository host gives no description.

189.MikeMcl / bignumber.js

A JavaScript library for arbitrary-precision decimal and non-decimal arithmetic

• bignumber
• javascript
• arbitrary-precision
• decimal-places
• bigdecimal

190.marcomusy / vedo

A python module for scientific analysis of 3D data based on VTK and Numpy

• 3d-graphics
• vtk
• 3d
• mesh
• simulations
• scientific-visualization
• +5 more

191.brick / math

Arbitrary-precision arithmetic library for PHP

• php
• arbitrary-precision
• biginteger
• bigdecimal
• bigrational
• gmp
• +1 more

192.ljvmiranda921 / pyswarms

A research toolkit for particle swarm optimization in Python

• particle-swarm-optimization
• optimization-tools
• pso
• global-optimization
• swarm-intelligence
• machine-learning
• +5 more

193.CMA-ES / pycma

Python implementation of CMA-ES

194.UniMath / UniMath

This rocq library aims to formalize a substantial body of mathematics using the univalent point of view.

• coq
• mathematics
• unimath
• coq-library
• foundations
• rocq
• +1 more

195.sgorsten / linalg

linalg.h is a single header, public domain, short vector math library for C++

196.jwiegley / category-theory

An axiom-free formalization of category theory in Coq for personal study and practical work

• category-theory
• coq
• monad
• profunctor
• comonads
• monoid
• +7 more

197.jarun / bcal

:1234: Bits, bytes and general-purpose calculator

• storage
• storage-unit-converter
• command-line
• standalone
• terminal
• calculator
• +6 more

198.softwareQinc / qpp

Modern C++ quantum computing library

• quantum-computing
• c-plus-plus
• cpp
• cpp11
• quantum
• simulator
• +2 more

199.usnistgov / fipy

FiPy is a Finite Volume PDE solver written in Python

• scientific-computing
• scientific-computing-with-python
• phase-field
• materials-science
• partial-differential-equations
• shared-memory-parallel
• +2 more

200.CATIA-Systems / FMPy

Simulate Functional Mock-up Units (FMUs) in Python

• fmi
• python
• fmi-standard