Repository Index

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

• histology
• pathology
• wsi-images
• histopathology

Simple RDKit molecule editor GUI using PySide

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.

LLM for Drug Editing, ICLR 2024

• chatgpt
• conversation
• drug
• drug-discovery

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

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

Chemical 2D structure editor application/applet based on the Chemistry Development Kit

• blueobelisk
• java
• chemistry

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.

TypeDB Bio: Biomedical Knowledge Graph

• bioinformatics
• knowledge-graph
• knowledge-base
• drug-discovery

Predicting Cell Health with Morphological Profiles

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

DE-9IM spatial predicate library implemented in Javascript.

• de-9im
• spatial
• predicates
• javascript

PyTorch implementation of "TGSA: Protein-Protein Association-Based Twin Graph Neural Networks for Drug Response Prediction with Similarity Augmentation"

Nova DSO Tracker is an open-source Flask application for astrophotographers, providing real-time tracking of deep-sky objects' altitude, observability prediction, and integration with Stellarium and SIMBAD databases.

• astrophotography
• astronomy
• ephem
• flask

Satellite prediction library for crystal using the sgp4 model

• sgp4
• crystal
• satellite
• satellite-prediction

Realtime Weather and Earthquake alerts in Neovim

• editor
• neovim
• neovim-plugin
• plugin

mrQA: tools for quality assurance in medical imaging datasets, including protocol compliance

• qa
• mri
• neuroimaging
• niqc

DeepAEG: A model for predicting cancer drug response based on data enhancement and edge-collaborative update strategies

Functions for the input/output and visualization of medical imaging data that follow either the ANALYZE, NIfTI or AFNI formats.

• nifti
• afni
• analyze

Interpretable drug response prediction with graph neural networks over drugs, cell lines, and genes.