Repository Index

pyMOR - Model Order Reduction with Python

• python
• model-reduction
• model-order-reduction
• control-systems

GraphDTA: Predicting drug-target binding affinity with graph neural networks

Source code for "DeepDTA: deep drug-target binding affinity prediction"

• protein-ligand-interactions
• convolutional-neural-networks

Native R and Python sample-deletion robustness for omics: candidate certificates, minimum deletion bounds, Bioconductor model refits and donor-level pseudobulk

• bioinformatics
• exact-optimization
• metabolomics
• paired-data

RNA-seq prediction with deep convolutional neural networks.

MolTrans: Molecular Interaction Transformer for Drug Target Interaction Prediction (Bioinformatics)

:spider_web: Simple mesh generator inspired by distmesh.

• mesh
• finite-elements
• mathematics
• mesh-generation

Cancer Imaging Phenomics Toolkit (CaPTk) is a software platform to perform image analysis and predictive modeling tasks. Documentation: https://cbica.github.io/CaPTk

• cancer-imaging-research
• radiomics
• radiomics-features
• machine-learning

A Network Integration Approach for Drug-Target Interaction Prediction

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

An automatic code generator for nonlinear model predictive control (NMPC) and the continuation/GMRES method (C/GMRES) based numerical solvers for NMPC

• model-predictive-control
• nonlinear-model-predictive-control
• mpc
• nmpc

OpenBioLink is a resource and evaluation framework for evaluating link prediction models on heterogeneous biomedical graph data.

Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.

• disentanglement
• drug-discovery
• genomics
• perturbation

TransformerCPI: Improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments(BIOINFORMATICS 2020) https://doi.org/10.1093/bioinformatics/btaa524

• self-attention
• compound-protein-interaction
• transformercpi
• structure-free-virtual-sreening

Batched NVIDIA MotionBricks: generate the motion of hundreds of characters in one model call.

• character-animation
• crowd-simulation
• motion-generation
• motionbricks

Interpretable bilinear attention network with domain adaptation improves drug-target prediction.

A collection of tasks to probe the effectiveness of protein sequence representations in modeling aspects of protein design

• protein
• protein-sequences
• protein-design
• representation-learning

Easy link prediction tool

• python
• network-analysis
• link-prediction
• research

code to run sei and obtain sei and sequence class predictions

PRnet is a flexible and scalable perturbation-conditioned generative model predicting transcriptional responses to unseen complex perturbations at bulk and single-cell levels.

slick is a simple to use polygon collision library inspired by bump.lua

SIMD powered simple-math numerical operations on arrays for Common Lisp through CFFI [still experimental]

• lisp
• common-lisp
• scientific-computing
• simd

Predicting Cell Health with Morphological Profiles

• carpenter-lab
• morphological-profiling
• crispr
• cell-painting

Generic, zero-alloc, 100%-test covered Quadtree for golang

• golang-library
• quadtree
• data-structures
• generics