Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
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ADAM is a genomics analysis platform with specialized file formats built using Apache Avro, Apache Spark, and Apache Parquet. Apache 2 licensed.
Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models
- machine-learning
- generative-models
- drug-discovery
- benchmark
A lightweight high performance tensor algebra framework for modern C++
- tensors
- tensor-contraction
- multidimensional-arrays
- simd
Precision Medicine Knowledge Graph (PrimeKG)
- knowledge-graph
- precision-medicine
- therapeutics
- bioinformatics
OpenMDAO repository.
- nasa
- open-source
- framework
- openmdao
An axiom-free formalization of category theory in Coq for personal study and practical work
- category-theory
- coq
- monad
- profunctor
Python package for graph neural networks in chemistry and biology
- deep-learning
- graph-neural-networks
- dgl
- cheminformatics
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)
- deep-learning
- pytorch
- deep-chemistry
- graph-neural-network
Throw in the towel.
- dotnet
- towel
- csharp
- library
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
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
A flexible framework for solving PDEs with modern spectral methods.
- spectral-methods
- fluid-dynamics
- pde-solver
Chainer Chemistry: A Library for Deep Learning in Biology and Chemistry
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
DiffSharp: Differentiable Functional Programming
- machine-learning
- tensor
- dotnet
- autodiff
A Swift micro library for generating Sunrise and Sunset times on device, requiring no network access.
- swift
- sunrise
- sunset
- ios
ACADO Toolkit is a software environment and algorithm collection for automatic control and dynamic optimization. It provides a general framework for using a great variety of algorithms for direct optimal control, including model predictive control, state and parameter estimation and robust optimization.
🎯 A comprehensive gradient-free optimization framework written in Python
- metaheuristics
- optimization
- optimization-algorithms
- python
Benchmarks for generative chemistry
A Euclidean diffusion model for structure-based drug design.
- ddpm
- drug-design
- equivariance
- generative-model
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 Python native dynamical system simulation framework in the block diagram paradigm.
- blockdiagram
- control-systems
- hierarchical-modeling
- nonlinear-dynamics