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awesome-explainable-graph-reasoning
A collection of research papers and software related to explainability in graph machine learning.chemicalx
A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)rexmex
A general purpose recommender metrics library for fair evaluation.awesome-drug-discovery-knowledge-graphs
A collection of research papers, datasets and software related to knowledge graphs for drug discovery. Accompanies the paper "A review of biomedical datasets relating to drug discovery: a knowledge graph perspective" (Briefings in Bioinformatics, 2022)SubTab
The official implementation of the paper, "SubTab: Subsetting Features of Tabular Data for Self-Supervised Representation Learning"awesome-shapley-value
Reading list for "The Shapley Value in Machine Learning" (JCAI 2022)onto_merger
OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.awesome-drug-pair-scoring
Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)biology-for-ai
learning biology syllabus, geared for machine learning folksKAZU
Fast, world class biomedical NERjazzy
Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.judgyprophet
Forecasting for knowable future events using Bayesian informative priors (forecasting with judgmental-adjustment).kallisto
Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.skywalkR
code for Gogleva et al manuscriptrunnable
Runnablekgem-in-drug-discovery
Code to accompany the "Understanding the Performance of Knowledge Graph Embeddings in Drug Discovery" manuscript (Artificial Intelligence in the Life Sciences, 2022)StarGazer
StarGazer is a tool designed for rapidly assessing drug repositioning opportunities. It combines multi-source, multi-omics data with a novel target prioritization scoring system in an interactive Python-based Streamlit dashboard. StarGazer displays target prioritization scores for genes associated with 1844 phenotypic traits.Omicsfold
Multi-omics data normalisation, model fitting and visualisation.VecNER
A library of tools for dictionary-based Named Entity Recognition (NER), based on word vector representations to expand dictionary terms.peptide-tools
Programs to calculate phys-chem properties of synthetic peptides and proteins: isoelectric point and extinction coefficients.data-science-python-course
napari-wsi
A plugin to read whole slide images within napari.biomedical-kg-topological-imbalance
Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022)ibd-interpret
We trained high performing open source models on image scans of tissue biopsies to predict endoscopic categories in inflammatory bowel disease. These predictive models can help us better understand the disease pathology and represent a step towards automated clinical recruitment strategies.roo
A package and environment manager for RNESS
Official implementation of "NESS: Node Embeddings from Static Subgraphs"detectIS
A pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing dataskywalkR-graph-features
Example notebooks that illustrate how to generate knowledge-based features. Features can be used in a variety of ML models, including recommender systems.multimodal-python-course
The purpose of the code is to facilitate a comprehensive understanding of multimodal data science applications within medical domain. The code serves to support the delivery of a cutting-edge workshop designed to introduce researchers to the rapidly evolving field of multimodal data scienceUnlockingHeart
This repository accompanies our paper Unlocking the Heart Using Adaptive Locked Agnostic Networks and enables replication of the key results.Tendril
This repository contains R package code for calculating tendril plots.CTELC-Patient-Attrition-Model
Clinical Trial Enrollment Life Cycle (CTELC) modeling project aims to leverage "industry-wide" data to understand key drivers and build predictive models. Patient attrition, also referred to as dropout or patient withdrawal, occurs when patients enrolled in a clinical trial either withdraw or are lost to follow-up by the clinical site and trial sponsor.MVDA_exploration_tools
Multivariate data analysis (MVDA) exploration tool is a Python library utilizing the scikit-learn library for partial least squares (PLS) and principal components analysis (PCA).Siamese-Regression-Pairing
Siamese Neural Networks for Regression: Similarity-Based Pairing and Uncertainty QuantificationConvCaps-DR
Tensorflow-Keras implementation of deep Convolutional Capsule Networks with Dynamic Routing algorithmhsqc_structure_elucidation
Implementation of the SGNN graph neural network for 1H and 13C NMR prediction and a tool for distinguishing different molecules based on HSQC simulationsMultimodal_NSCLC
multi-omics data integration helps improving patient survival prediction. We provide a pipeline allowing for early integration of multiple omics plus clinical modalities in order to predict patient survival for NSCLC. The pipeline utilizes autoencoders, and helps identify main driving factor in survival predictionmagnus-extensions
Extensions packages for magnusfragler
maraca
R package for the creation of "maraca" plotsPatientSafetyKG
SelfPAD
The official implementation of "Improving Antibody Humanness Prediction using Patent Data".MCPL
ICML 2024 submission - An image is worth multiple words: learning object level concepts using multi-concepts prompts learning.qscheck
An R library to perform assertions and decision on input arguments.molecular-complexity
Python implementation of the molecular complexity metric described by Proudfoot 2017 (http://dx.doi.org/10.1016/j.bmcl.2017.03.008).Machine-Learning-for-Predicting-Targeted-Protein-Degradation
The code was developed for training diverse ML and DL models to predict PROTACs degradation. Data cleaning for two public datasets, PROTAC-DB and PROTACpedia, are also included. PROTACs are of high interest for all disease areas of AZ and thus predicting their degradation is of general interest.OSPred
The OSPred tool offers interactive visualization of clinical trial end point correlations with reference to a large pool of historical NSCLC studies. Its focused capability has the potential to digitally transform and accelerate data-driven decision making as part of the drug development process. OSPred enables data scientists to rapidly visualize, analyze and validate the endpoint (PFS, ORR, OS) correlation hypothesis and to predict HR OS, which potentially could lead to faster and cost-effective NSCLC clinical trials. OSPred - A Digital Health Aid for Rapid Analysis of Early Endpoints (PFS, ORR) In clinical trials that assess novel therapeutic agents in patients with non-small-cell lung cancer (NSCLC), early endpoints (e.g. progression-free survival [PFS] and objective response rate) are often evaluated as indicators of biological drug activity, and are used as surrogate endpoints for overall survival (OS). A data set was compiled to investigate ascertain correlation trends between early endpoints (e.g. odds ratio [OR] for PFS at 6 months) and late endpoints (e.g. hazard ratio [HR] OS). The dataset was curated from multiple source databases, including ClinicalTrials.gov, PubMed and Citeline(TrialTrove). We applied a random-effects method for meta-analysis of prior RCT data to correlate a variety of estimates with the hazard ratio (HR) for OS and PFS. We performed meta-regression analyses across different data-strata, stratified by the mechanism of action as PD1/PDL1, EGFR, VEGFR, DNA and evaluated the correlation of trial-level, treatment effects between early (e.g. PFS) and late (e.g. OS) endpoints in NSCLC oncology trials.dpp_imp
Improved clinical data imputation via classical and quantum determinantal point processessurvextrap-excesshazards
Demonstration of excess hazard and excess hazard cure models for survival extrapolationadhce
trim21-bioprotac
Bioinformatics data analyses - Fletcher A. et al., Nature Communications 2023, doi: 10.1038/s41467-023-42546-2OCT_publication
This repository contains the source code for the image analysis of optical coherence tomography images, as stated in the publication of Volumetric wound healing by machine learning and optical coherence tomography in type 2 diabetes.lung-tumour-mice-mri
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