101.dealii / dealii
The development repository for the deal.II finite element library
- finite-elements
- c-plus-plus
- fem
- hpc
- parallel-computing
- scientific-computing
- +1 more
+95 stars
from 1,660 · score 4.56
Trending repositories
Ranked by Attention Score: stars gained over the last 180 complete days
101–200 of 527 by Attention Score · May 9, 2026 – Nov 4, 2026 (UTC)
102.mims-harvard / PrimeKG
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
- dataset
- graph-machine-learning
- +2 more
+95 stars
from 743 · score 4.56
103.brian-team / brian2
Brian is a free, open source simulator for spiking neural networks.
- python
- neuroscience
- science
- differential-equations
- spiking-neural-networks
- biological-simulations
- +5 more
+93 stars
from 1,164 · score 4.54
104.stevengj / nlopt
library for nonlinear optimization, wrapping many algorithms for global and local, constrained or unconstrained, optimization
+87 stars
from 2,201 · score 4.48
105.chaidiscovery / chai-lab
Chai-1, SOTA model for biomolecular structure prediction
+87 stars
from 1,921 · score 4.48
106.deepmodeling / Uni-Mol
Official Repository for the Uni-Mol Series Methods
- molecular-modeling
- pre-trained-model
- pretraining
- deep-learning
+87 stars
from 1,088 · score 4.48
107.MFlowCode / MFC
Exascale multiphase flow solver — 2025 Gordon Bell Prize Finalist | 200T grid points on 43K+ GPUs
+87 stars
from 352 · score 4.48
108.mahmoud / boltons
🔩 Like builtins, but boltons. 250+ constructs, recipes, and snippets which extend (and rely on nothing but) the Python standard library. Nothing like Michael Bolton.
- python
- utilities
- cache
- data-structures
- statistics
- data-science
- +5 more
+86 stars
from 6,858 · score 4.47
109.evo-design / evo
Biological foundation modeling from molecular to genome scale
+86 stars
from 1,501 · score 4.47
110.HIPS / autograd
Efficiently computes derivatives of NumPy code.
- autograd
- automatic-differentiation
- numpy
- python
- deep-learning
- derivative
- +8 more
+85 stars
from 7,467 · score 4.45
+85 stars
from 1,686 · score 4.45
112.PythonOT / POT
POT : Python Optimal Transport
- optimal-transport
- numerical-optimization
- machine-learning
- emd
- ot-mapping-estimation
- wasserstein-barycenter
- +10 more
+80 stars
from 2,780 · score 4.39
113.Reference-LAPACK / lapack
LAPACK development repository
- linear-algebra
- lapack
- blas
- lapacke
- linear-equations
- eigenvalues
- +4 more
+80 stars
from 1,838 · score 4.39
114.flame / blis
BLAS-like Library Instantiation Software Framework
- blis
- blas
- blas-libraries
- linear-algebra
- linear-algebra-library
- matrix-multiplication
- +8 more
+78 stars
from 2,620 · score 4.37
115.instadeepai / nucleotide-transformer
Foundation Models for Genomics & Transcriptomics
- genomics
- deep-learning
- transformer
- dna
- foundation-models
- transcriptomics
- +1 more
+78 stars
from 859 · score 4.37
116.mahmoodlab / UNI
Pathology Foundation Model - Nature Medicine
- foundation
- foundation-model
- histopathology
- mahmoodlab
- pathology
- uni
- +11 more
+78 stars
from 719 · score 4.37
117.koide3 / fast_gicp
A collection of GICP-based fast point cloud registration algorithms
+77 stars
from 1,627 · score 4.36
118.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
+77 stars
from 1,138 · score 4.36
119.FFTW / fftw3
DO NOT CHECK OUT THESE FILES FROM GITHUB UNLESS YOU KNOW WHAT YOU ARE DOING. (See below.)
+72 stars
from 3,040 · score 4.29
120.symengine / symengine
SymEngine is a fast symbolic manipulation library, written in C++
- math
- computer-algebra
- c-plus-plus
+72 stars
from 1,354 · score 4.29
121.3dmol / 3Dmol.js
WebGL accelerated JavaScript molecular graphics library
- molecular-graphics
- molecular-modeling
- computational-biology
- computational-chemistry
+72 stars
from 964 · score 4.29
122.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.
+71 stars
from 903 · score 4.28
123.X-DataInitiative / tick
Module for statistical learning, with a particular emphasis on time-dependent modelling
- machine-learning
- python
- point-process
- optimization
- modelling
- statistics
+69 stars
from 544 · score 4.25
124.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
+67 stars
from 1,168 · score 4.22
125.RainerKuemmerle / g2o
g2o: A General Framework for Graph Optimization
- g2o
- slam
- c-plus-plus
- graph-optimization
- cpp
+65 stars
from 3,413 · score 4.19
126.hjwdzh / QuadriFlow
QuadriFlow: A Scalable and Robust Method for Quadrangulation
- quadriflow
- quad
- remeshing
- quadrangulation
- geometry
+65 stars
from 817 · score 4.19
127.snap-stanford / GEARS
GEARS is a geometric deep learning model that predicts outcomes of novel multi-gene perturbations
+64 stars
from 358 · score 4.17
128.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
+64 stars
from 207 · score 4.17
129.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
+63 stars
from 1,379 · score 4.16
130.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
+63 stars
from 924 · score 4.16
131.simbody / simbody
High-performance C++ multibody dynamics/physics library for simulating articulated biomechanical and mechanical systems like vehicles, robots, and the human skeleton.
- multibody-dynamics
- physics-engine
- physics-simulation
- robotics
- biomechanics
+62 stars
from 2,507 · score 4.14
132.microsoft / DirectXMath
DirectXMath is an all inline SIMD C++ linear algebra library for use in games and graphics apps
+62 stars
from 1,754 · score 4.14
133.DavidArayan / ezy-slice
An open source mesh slicer framework for Unity3D Game Engine. Written in C#.
+61 stars
from 2,220 · score 4.13
+60 stars
from 3,715 · score 4.11
135.OATML-Markslab / ProteinGym
Official repository for the ProteinGym benchmarks
- benchmark
- computational-biology
- protein
- protein-design
- protein-fitness
+60 stars
from 424 · score 4.11
136.brick / math
Arbitrary-precision arithmetic library for PHP
- php
- arbitrary-precision
- biginteger
- bigdecimal
- bigrational
- gmp
- +1 more
+59 stars
from 2,121 · score 4.09
+57 stars
from 1,150 · score 4.06
138.TUDelft-CNS-ATM / bluesky
The open source air traffic simulator
- python
- traffic
- aircraft
- simulation
- air-traffic-control
- air-transport
- +11 more
+56 stars
from 521 · score 4.04
139.NetTopologySuite / NetTopologySuite
A .NET GIS solution that is fast and reliable for the .NET platform.
- topology
- nts
- sfs
- c-sharp
- library
- jts
- +1 more
+55 stars
from 1,673 · score 4.03
+55 stars
from 1,309 · score 4.03
+55 stars
from 618 · score 4.03
142.mlange-42 / ark
Ark -- Archetype-based Entity Component System (ECS) for Go.
- ecs
- entity-component-system
- go
- golang
- agent-based-modeling
- gamedev
- +2 more
+54 stars
from 251 · score 4.01
143.PixarAnimationStudios / OpenSubdiv
An Open-Source subdivision surface library.
+53 stars
from 3,037 · score 3.99
144.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
+52 stars
from 3,718 · score 3.97
145.PyWavelets / pywt
PyWavelets - Wavelet Transforms in Python
- wavelets
- wavelet-transform
- signal-processing
- image-processing
- continuous-wavelet
+52 stars
from 2,360 · score 3.97
146.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
+52 stars
from 1,446 · score 3.97
147.elixir-nx / nx
Multi-dimensional arrays (tensors) and numerical definitions for Elixir
+51 stars
from 2,869 · score 3.95
148.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
+51 stars
from 2,183 · score 3.95
149.unknown-horizons / godot-port
Unknown Horizons Godot Engine Port
- simulation
- strategy
- game-development
- godot
- gdscript
- game
+51 stars
from 860 · score 3.95
150.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
+49 stars
from 1,152 · score 3.91
151.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
+49 stars
from 563 · score 3.91
152.songlab-cal / gpn
Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star
- dna
- language-model
- variant-effect-prediction
- genomics
+49 stars
from 338 · score 3.91
153.DTolm / VkFFT
Vulkan/CUDA/HIP/OpenCL/Level Zero/Metal Fast Fourier Transform library
+48 stars
from 1,739 · score 3.89
154.vqdang / hover_net
Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.
+48 stars
from 708 · score 3.89
155.prov-gigapath / prov-gigapath
Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data
+48 stars
from 597 · score 3.89
156.RosettaCommons / RoseTTAFold
This package contains deep learning models and related scripts for RoseTTAFold
+47 stars
from 2,235 · score 3.87
+47 stars
from 567 · score 3.87
158.nasa / trick
Trick Simulation Environment. Trick provides a common set of simulation capabilities and utilities to build simulations automatically.
+47 stars
from 133 · score 3.87
159.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
+46 stars
from 1,676 · score 3.85
160.mahmoodlab / CONCH
Vision-Language Pathology Foundation Model - Nature Medicine
- bioimage-analysis
- bioimage-informatics
- conch
- foundation-model
- health-informatics
- histopathology
- +9 more
+46 stars
from 494 · score 3.85
161.hypre-space / hypre
Parallel solvers for sparse linear systems featuring multigrid methods.
- math-physics
- library
- hpc
- radiuss
+45 stars
from 830 · score 3.83
162.Teichlab / celltypist
A tool for semi-automatic cell type classification
- python
- single-cell
- machine-learning
- scrna-seq
- cell-type-classification
- label-transfer
+44 stars
from 473 · score 3.81
163.oemof / oemof-solph
A model generator for energy system modelling and optimisation (LP/MILP).
- energy
- energy-system
- modelling
- modelling-framework
+43 stars
from 383 · score 3.78
164.gradientspace / geometry3Sharp
C# library for 2D/3D geometric computation, mesh algorithms, and so on. Boost license.
+42 stars
from 1,862 · score 3.76
165.arrayfire / arrayfire
ArrayFire: a general purpose GPU library.
+41 stars
from 4,867 · score 3.74
+41 stars
from 1,108 · score 3.74
167.jerryji1993 / DNABERT
DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome
- kmer
- dnabert-model
- kmer-format
- gpu
- sequence
- genome
- +4 more
+41 stars
from 742 · score 3.74
168.suyashkumar / dicom
⚡High Performance DICOM Medical Image Parser in Go.
- dicom
- dicom-images
- golang
- golang-library
- golang-package
- parser
- +10 more
+40 stars
from 1,056 · score 3.71
169.samtools / htslib
C library for high-throughput sequencing data formats
- htslib
- bioinformatics
- sam
- bam
- cram
- vcf
- +2 more
+39 stars
from 917 · score 3.69
170.ericstoneking / 42
Simulation for spacecraft attitude control system analysis and design
+39 stars
from 428 · score 3.69
171.ddemidov / amgcl
C++ library for solving large sparse linear systems with algebraic multigrid method
- amg
- c-plus-plus
- sparse-linear-systems
- opencl
- cuda
- gpgpu
- +6 more
+38 stars
from 848 · score 3.66
172.ginkgo-project / ginkgo
Numerical linear algebra software package
- linear-algebra
- hpc
- gpu-computing
- cuda
- krylov-methods
- preconditioning
- +6 more
+38 stars
from 592 · score 3.66
173.arneschneuing / DiffSBDD
A Euclidean diffusion model for structure-based drug design.
- ddpm
- drug-design
- equivariance
- generative-model
- graph-neural-networks
- machine-learning
+38 stars
from 499 · score 3.66
174.MAGICS-LAB / DNABERT_2
[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome
- dataset
- dna
- dna-processing
- dna-training
- genome
- genome-analysis
- +10 more
+38 stars
from 481 · score 3.66
175.pmp-library / pmp-library
The Polygon Mesh Processing Library
- mesh-processing
- geometry-processing
- polygon-mesh
- triangle-mesh
- c-plus-plus
- surface-mesh
- +9 more
+37 stars
from 1,473 · score 3.64
176.NVIDIA / MatX
An efficient C++20 GPU numerical computing library with Python-like syntax
+37 stars
from 1,414 · score 3.64
+37 stars
from 394 · score 3.64
178.MikeMcl / bignumber.js
A JavaScript library for arbitrary-precision decimal and non-decimal arithmetic
- bignumber
- javascript
- arbitrary-precision
- decimal-places
- bigdecimal
+36 stars
from 6,977 · score 3.61
179.autodiff / autodiff
automatic differentiation made easier for C++
- automatic-differentiation
- auto-differentiation
- autodiff
- autodifferentiation
- differentiation
- derivatives
- +1 more
+36 stars
from 1,927 · score 3.61
180.DedalusProject / dedalus
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
+35 stars
from 678 · score 3.58
181.firedrakeproject / firedrake
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
+35 stars
from 646 · score 3.58
182.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
+34 stars
from 2,241 · score 3.56
183.invesalius / invesalius3
3D medical imaging reconstruction software
- dicom
- dicom-viewer
- magnetic-resonance-imaging
- medical-image-processing
- medical-imaging
- segmentation
- +2 more
+34 stars
from 781 · score 3.56
184.molecularsets / moses
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
- machine-learning
- generative-models
- drug-discovery
- benchmark
+33 stars
from 963 · score 3.53
185.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
+33 stars
from 613 · score 3.53
186.cdk / cdk
The Chemistry Development Kit
- code4lib
- chemistry
- java
- cheminformatics
- bioinformatics
- blueobelisk
+33 stars
from 579 · score 3.53
187.dpilger26 / NumCpp
C++ implementation of the Python Numpy library
- python
- numpy
- c-plus-plus
- numerical-analysis
- scientific-computing
- algorithms
- +3 more
+32 stars
from 3,936 · score 3.50
188.hail-is / hail
Cloud-native genomic dataframes and batch computing
- genetics
- vcf
- genomics
- gwas
- bioinformatics
- python
- +2 more
+32 stars
from 1,050 · score 3.50
+32 stars
from 568 · score 3.50
190.dan2097 / opsin
Open Parser for Systematic IUPAC Nomenclature. Chemical name to structure conversion
+32 stars
from 213 · score 3.50
191.CSOgroup / cellcharter
A Python package for the identification, characterization and comparison of spatial clusters from spatial -omics data.
+32 stars
from 172 · score 3.50
192.owlbarn / owl
Owl - OCaml Scientific Computing @ https://ocaml.xyz
- matrix
- linear-algebra
- ndarray
- statistical-functions
- topic-modeling
- regression
- +14 more
+31 stars
from 1,327 · score 3.47
193.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
+31 stars
from 782 · score 3.47
194.JCash / voronoi
A C implementation for creating 2D Voronoi/Delauney diagrams
+31 stars
from 707 · score 3.47
195.chris-mcginnis-ucsf / DoubletFinder
R package for detecting doublets in single-cell RNA sequencing data
+31 stars
from 543 · score 3.47
196.aurora-opensource / au
A C++14-compatible physical units library with no dependencies and a single-file delivery option. Emphasis on safety, accessibility, performance, and developer experience.
- cpp
- cpp14
- cpp14-library
- dimensional-analysis
- physical-quantities
- quantity
- +11 more
+31 stars
from 418 · score 3.47
197.calico / borzoi
RNA-seq prediction with deep convolutional neural networks.
+31 stars
from 238 · score 3.47
198.biolink / biolink-model
Schema and generated objects for biolink data model and upper ontology
- biolink
- monarchinitiative
- gene-ontology
- datamodel
- standard
- specification
- +11 more
+31 stars
from 237 · score 3.47
199.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
+30 stars
from 1,190 · score 3.43
200.mdtraj / mdtraj
An open library for the analysis of molecular dynamics trajectories
- molecular-dynamics
- python
- mdtraj
- rmsd
- dihedral-angles
- pdb
- +2 more
+30 stars
from 713 · score 3.43