Repository Index

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

DNABERT: pre-trained Bidirectional Encoder Representations from Transformers model for DNA-language in genome

• kmer
• dnabert-model
• kmer-format
• gpu

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

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

• deep-learning
• protein-sequences
• protein-structure
• semi-supervised-learning

Robust Tetrahedral Meshing in the Wild.

• geometry-processing
• tetrahedral-meshing
• surface-repair
• 3d-triangulation

VexCL is a C++ vector expression template library for OpenCL/CUDA/OpenMP

• opencl
• cuda
• c-plus-plus
• gpgpu

RBDL is a C++ library that contains some essential and efficient rigid body dynamics algorithms such as the Articulated Body Algorithm (ABA) for forward dynamics, Recursive Newton-Euler Algorithm (RNEA) for inverse dynamics, the Composite Rigid Body Algorithm (CRBA) for the efficient computation of the joint space inertia matrix and is also able to compute forward dynamics with external contact constraints and collision impulses. Furthermore it has some basic support for forward and inverse kinematics.

• articulated-body-algorithm
• inverse-dynamics
• forward-dynamics
• multi-body-dynamics

:1234: Bits, bytes and general-purpose calculator

• storage
• storage-unit-converter
• command-line
• standalone

Simple finite element assemblers

• fem
• python
• pde

The Point Processing Toolkit (pptk) is a Python package for visualizing and processing 2-d/3-d point clouds.

• pointclouds
• 3-d
• visualization
• lidar

A Swift micro library for generating Sunrise and Sunset times on device, requiring no network access.

• swift
• sunrise
• sunset
• ios

Module for statistical learning, with a particular emphasis on time-dependent modelling

• machine-learning
• python
• point-process
• optimization

Molecular Processing Made Easy.

• python
• molecule
• rdkit
• drug-discovery

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

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

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

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

Official repository for the ProteinGym benchmarks

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

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

Ruby/Numo::NArray - New NArray class library

• numo
• narray
• ruby
• ruby-numo

Tools for computational pathology

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

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