jaredsagendorf

bayes-implicit-solvent. experiments with Bayesian calibration of implicit solvent models

blackjax. BlackJAX is a Bayesian Inference library designed for ease of use, speed and modularity.

mdgrad. Pytorch differentiable molecular dynamics

scores. scores: Metrics for the verification, evaluation and optimisation of forecasts, predictions or models.

spyrmsd. 📐 Symmetry-corrected RMSD in Python

jax-md. Differentiable, Hardware Accelerated, Molecular Dynamics

pytorch_MCMC. Lightweight MCMC sampling for PyTorch Models aka My Corona Project

bayespy. Bayesian Python: Bayesian inference tools for Python

torch-kde. A differentiable implementation of kernel density estimation in PyTorch.

sphere-histo. Spherical histogram made simple! The surface colors indicate the density of points lying in the respective direction. Variable bin size. Works with large data sets. Points are read from your .npy files.

MCMCTorch. A library that focuses on Bayesian Markov Chain Monte Carlo (MCMC) sampling methods using PyTorch

hamiltorch. PyTorch-based library for Riemannian Manifold Hamiltonian Monte Carlo (RMHMC) and inference in Bayesian neural networks

openmm-torch. OpenMM plugin to define forces with neural networks

losscape. Jupyter Notebook

kornia. 🐍 Geometric Computer Vision Library for Spatial AI

roma. RoMa: A lightweight library to deal with 3D rotations in PyTorch.

MultiHMCGibbs. A numpyro Gibbs sampler that uses conditioned HMC kernels for each step.

BioEn. BioEn - Bayesian Inference Of ENsembles

pnabind. A python package and collection of scripts for computing protein surface meshes, chemical, electrostatic, geometric features, and building/training graph neural network models of protein-nucleic acid binding

ramachandraw. Ramachandran plotting tool

cpp-dict-pack. RCSB MMCIF Dictionary Suite

py-mmcif. mmCIF Core Access Library

geomloss. Geometric loss functions between point clouds, images and volumes

dcor. Distance correlation and related E-statistics in Python

UQTk. Sandia Uncertainty Quantification Toolkit

dscribe. DScribe is a python package for creating machine learning descriptors for atomistic systems.

multiESS. Multivariate effective sample size (mESS) of Markov chain in Python

ESAC-stats-2014. Material for my lectures at the ESAC statistics conference, Oct 27-31 2014

mzIdentML. Repository for mzIdentML and the corresponding examples

MolProbity. Protein and nucleic acid validation service

IHMCIF. 📖 mmCIF support for hybrid/integrative models

awesome-equivariant-network. Paper list for equivariant neural network

escnn. Equivariant Steerable CNNs Library for Pytorch https://quva-lab.github.io/escnn/

captum. Model interpretability and understanding for PyTorch

pytorch-grad-cam. Advanced AI Explainability for computer vision. Support for CNNs, Vision Transformers, Classification, Object detection, Segmentation, Image similarity and more.

gans-awesome-applications. Curated list of awesome GAN applications and demo

se3cnn. Euclidean Neural Networks

e3nn. A modular framework for neural networks with Euclidean symmetry

se3-transformer-public. code for the SE3 Transformers paper: https://arxiv.org/abs/2006.10503

traveler. Template-based RNA secondary structure visualization

forna. Create force-directed graphs of RNA secondary structures.

R2DT. Visualise RNA secondary structure in consistent, reproducible and recognisable layouts

PyWaffle. 🧇 Make Waffle Charts in Python.

statements. Successful Job Applications and Grants

3D-Zernike-Descriptors. 3D Zernike Descriptors on point clouds, meshes and voxel grids

nanorc. Improved Nano Syntax Highlighting Files

Fast-Quadric-Mesh-Simplification. Mesh triangle reduction using quadrics

lsyncd. Lsyncd (Live Syncing Daemon) synchronizes local directories with remote targets

vedo. A python module for scientific analysis of 3D data based on VTK and Numpy

python-crfsuite. A python binding for crfsuite

libigl-python-bindings. libigl python bindings

pyhks. Simple dependency free Python library for the Heat Kernel Signature on triangle meshes

spectral_descriptors. A collection of spectral descriptors for 3D meshed surfaces

.tmux. Oh my tmux! My self-contained, pretty & versatile tmux configuration made with 💛🩷💙🖤❤️🤍

d3. Bring data to life with SVG, Canvas and HTML. :bar_chart::chart_with_upwards_trend::tada:

deep-pu-learning. Deep Learning with Positive and Unlabeled samples

PyDataset. Instant access to many datasets in Python.

masif. MaSIF- Molecular surface interaction fingerprints. Geometric deep learning to decipher patterns in molecular surfaces.

JabberDock. protein docking using a density-based descriptor for atoms charge and dynamics

PyMesh. Geometry Processing Library for Python

trimesh. Python library for loading and using triangular meshes.

DGM. Direct Graphical Models (DGM) C++ library, a cross-platform Conditional Random Fields library, which is optimized for parallel computing and includes modules for feature extraction, classification and visualization.

pydensecrf. Python wrapper to Philipp Krähenbühl's dense (fully connected) CRFs with gaussian edge potentials.

pystruct. Simple structured learning framework for python

reveal.js. The HTML Presentation Framework

pytorch3d. PyTorch3D is FAIR's library of reusable components for deep learning with 3D data

kaolin. A PyTorch Library for Accelerating 3D Deep Learning Research

ConvCRF. This repository contains the reference implementation for our proposed Convolutional CRFs.

crfasrnn_pytorch. CRF-RNN PyTorch version http://crfasrnn.torr.vision

coma. Convolutional Mesh Autoencoders for Generating 3D Faces

pytorch_geometric. Graph Neural Network Library for PyTorch

SGC. official implementation for the paper "Simplifying Graph Convolutional Networks"

stellargraph. StellarGraph - Machine Learning on Graphs

graph-based-deep-learning-literature. links to conference publications in graph-based deep learning

libigl. Simple MPL-2.0-licensed C++ geometry processing library.

gcn. Implementation of Graph Convolutional Networks in TensorFlow

cnn_graph. Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering

biopython. Official git repository for Biopython (originally converted from CVS)

MeshCNN. Convolutional Neural Network for 3D meshes in PyTorch

big-json-viewer. A JavaScript library that enables efficient working with large JSON data in the browser.