Repository Index

Main yt repository

• data
• visualization
• analysis
• python

A Python platform to perform parallel computations of optimisation tasks (global and local) via the asynchronous generalized island model.

• optimization
• optimization-algorithms
• optimization-methods
• optimization-problem

A Euclidean diffusion model for structure-based drug design.

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

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

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

a numpy-like fast vector module for micropython, circuitpython, and their derivatives

• micropython-ulab
• numpy
• micropython
• module

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

• bioinformatics
• taxonomy
• cross-platform
• lineage

Sequential regulatory activity predictions with deep convolutional neural networks.

Python-centric Cookiecutter for Molecular Computational Chemistry Packages

• cookiecutter
• python-packages
• molecular-sciences
• conda-environment

A dependency-free cross-platform swiss army knife for PDB files.

• python
• protein
• pdb
• bioinformatics

A thin layer of graphic data types

• graphics-library
• vector
• transformations
• matrix

A High-Level Abstraction Framework for Quantum Algorithms

Multi-Omics Factor Analysis

• multi-omics
• factor-analysis
• mofa

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

• interplanetary
• mission-analysis
• astrodynamics
• aerospace

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

Iterative Linear Quadratic Regulator with auto-differentiatiable dynamics models

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

A simple script for fracturing polygons. Also adds nice helper functions for polygons like calculateArea, triangulate, getRandomPointsInPolygon, getBoundingRect)

• gdscript
• polygon2d-fracture
• godot-engine
• godot

Reference mapping for single-cell genomics

• single-cell
• deep-learning
• rna-seq-analysis
• data-integration

V library to develop Artificial Intelligence and High-Performance Scientific Computations

• v
• hacktoberfest
• linear-algebra
• optimization

Python library for multilinear algebra and tensor factorizations

JavaScript helper functions for manipulating GeoJSON

Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

• dna
• language-model
• variant-effect-prediction
• genomics