Official implementation for HyenaDNA, a long-range genomic foundation model built with Hyena
- foundation-models
- genomics
- language-models
Repository Index
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MySQL Spatial Data Extension integration with Laravel.
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
Throw in the towel.
- dotnet
- towel
- csharp
- library
OpenChem: Deep Learning toolkit for Computational Chemistry and Drug Design Research
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
A Go package for engineering organisms.
- synthetic-biology
- synbio
- genetic-engineering
- molecular-biology
A C implementation for creating 2D Voronoi/Delauney diagrams
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
Cosette is an automated SQL solver.
A Python package to visualise neuroanatomical data in atlas space
- neuroscience
- python
- anatomy
- visualization
Firedrake is an automated system for the portable solution of partial differential equations using the finite element method (FEM)
Interactive network visualization in Python and Dash, powered by Cytoscape.js
- plotly-dash
- plotly
- dash
- cytoscape
Fast, sensitive and accurate integration of single-cell data with Harmony
Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data
The Point Processing Toolkit (pptk) is a Python package for visualizing and processing 2-d/3-d point clouds.
- pointclouds
- 3-d
- visualization
- lidar
Module for statistical learning, with a particular emphasis on time-dependent modelling
- machine-learning
- python
- point-process
- optimization
Spatial Single Cell Analysis in Python
- single-cell-rna-seq
- single-cell-genomics
- spatial-transcriptomics
- spatial-analysis
Lightweight, super fast C/C++ (& Python) library for sequence alignment using edit (Levenshtein) distance.
- sequence-alignment
- edit-distance
- levehnstein-distance
- library
Simulate Functional Mock-up Units (FMUs) in Python
- fmi
- python
- fmi-standard
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.