Repository Index

🎯 A comprehensive gradient-free optimization framework written in Python

• metaheuristics
• optimization
• optimization-algorithms
• python

A pure JavaScript medical research image viewer.

Molecular Processing Made Easy.

• python
• molecule
• rdkit
• drug-discovery

Generative biopolymer design with rich conditioning.

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

A Euclidean diffusion model for structure-based drug design.

• ddpm
• drug-design
• equivariance
• generative-model

U-Net Brain Tumor Segmentation

• tensorflow
• tensorlayer
• unet
• medical-imaging

Dicoogle - Open Source PACS

• dicoogle
• dicom
• pacs
• medical-imaging

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

[ICLR 2024] DNABERT-2: Efficient Foundation Model and Benchmark for Multi-Species Genome

• dataset
• dna
• dna-processing
• dna-training

C library for reading virtual slide images

• pathology
• whole-slide-imaging
• c

A Python native dynamical system simulation framework in the block diagram paradigm.

• blockdiagram
• control-systems
• hierarchical-modeling
• nonlinear-dynamics

Large collection of number systems providing custom arithmetic for mixed-precision algorithm development and optimization for AI, Machine Learning, Computer Vision, Signal Processing, CAE, EDA, control, optimization, estimation, and approximation.

• arithmetic
• integer-arithmetic
• fixed-point-arithmetic
• rational-arithmetic

open source software for bidimensional and tridimensional remeshing

• mesh
• mesh-adaptation
• anisotropic-mesh-adaptation
• isotropic-mesh-adaptation

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

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

Sequential regulatory activity predictions with deep convolutional neural networks.

Advanced date, time and interval library for Java with sun/moon-astronomy and calendars like Chinese, Coptic, Ethiopian, French Republican, Hebrew, Hijri, Historic Christian, Indian National, Japanese, Julian, Korean, Minguo, Persian, Thai, Vietnamese

• java
• time4j
• calendar
• interval

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

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

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

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

• gpu
• exascale
• cfd
• fortran

PyKEP is a scientific library providing basic tools for research in interplanetary trajectory design.

• interplanetary
• mission-analysis
• astrodynamics
• aerospace

Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models

• trajectory-optimization
• differential-dynamic-programming
• theano
• dynamics-models

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