AstraZeneca/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).

Language: Jupyter Notebook - Size: 1.93 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 4 - Forks: 1

AstraZeneca/awesome-explainable-graph-reasoning

A collection of research papers and software related to explainability in graph machine learning.

Size: 1.7 MB - Last synced: 4 days ago - Pushed: about 2 years ago - Stars: 1,940 - Forks: 130

AstraZeneca/awesome-shapley-value

Reading list for "The Shapley Value in Machine Learning" (JCAI 2022)

Size: 622 KB - Last synced: 4 days ago - Pushed: almost 2 years ago - Stars: 134 - Forks: 10

AstraZeneca/persist-seq-galaxy-tools-setup

Language: Python - Size: 233 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 0 - Forks: 0

AstraZeneca/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)

Size: 431 KB - Last synced: 4 days ago - Pushed: 9 months ago - Stars: 172 - Forks: 19

AstraZeneca/biomedical-kg-topological-imbalance

Code to accompany the "Implications of Topological Imbalance for Representation Learning on Biomedical Knowledge Graphs" (Briefings in Bioinformatics, 2022)

Language: Jupyter Notebook - Size: 48.1 MB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 14 - Forks: 0

AstraZeneca/kgem-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)

Language: Python - Size: 258 KB - Last synced: 5 days ago - Pushed: 5 days ago - Stars: 29 - Forks: 6

AstraZeneca/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 science

Language: Jupyter Notebook - Size: 4.67 MB - Last synced: 7 days ago - Pushed: 7 days ago - Stars: 1 - Forks: 0

AstraZeneca/runnable

Runnable

Language: Python - Size: 9.07 MB - Last synced: 7 days ago - Pushed: 8 days ago - Stars: 38 - Forks: 4

AstraZeneca/qsuse

R library that provides an import mechanism like python to import local source files. It is not meant to replace library(), or doublecolon:: prefixing

Language: R - Size: 13.7 KB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

AstraZeneca/reactive6

Reactive R6 models for Shiny

Language: R - Size: 7.81 KB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 0 - Forks: 0

AstraZeneca/jazzy

Fast calculation of hydrogen-bond strengths and free energy of hydration of small molecules.

Language: Python - Size: 2.97 MB - Last synced: 19 days ago - Pushed: 20 days ago - Stars: 71 - Forks: 6

AstraZeneca/peptide-tools

Programs to calculate phys-chem properties of synthetic peptides and proteins: isoelectric point and extinction coefficients.

Language: Python - Size: 556 KB - Last synced: 19 days ago - Pushed: 19 days ago - Stars: 15 - Forks: 4

AstraZeneca/KAZU

Fast, world class biomedical NER

Language: Python - Size: 10.4 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 59 - Forks: 4

AstraZeneca/roo

A package and environment manager for R

Language: Python - Size: 354 KB - Last synced: 17 days ago - Pushed: 3 months ago - Stars: 11 - Forks: 1

AstraZeneca/rexmex

A general purpose recommender metrics library for fair evaluation.

Language: Python - Size: 2.68 MB - Last synced: 15 days ago - Pushed: 9 months ago - Stars: 276 - Forks: 25

AstraZeneca/maraca

R package for the creation of "maraca" plots

Language: R - Size: 1.44 MB - Last synced: 6 days ago - Pushed: 2 months ago - Stars: 3 - Forks: 0

AstraZeneca/chemicalx

A PyTorch and TorchDrug based deep learning library for drug pair scoring. (KDD 2022)

Language: Python - Size: 20.4 MB - Last synced: 25 days ago - Pushed: 9 months ago - Stars: 700 - Forks: 88

AstraZeneca/MCPL

ICML 2024 submission - An image is worth multiple words: learning object level concepts using multi-concepts prompts learning.

Language: Python - Size: 46.1 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

AstraZeneca/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.

Language: Jupyter Notebook - Size: 2.17 MB - Last synced: about 1 month ago - Pushed: 7 months ago - Stars: 2 - Forks: 1

AstraZeneca/metabolic_classifier

Language: Jupyter Notebook - Size: 993 KB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 0 - Forks: 0

AstraZeneca/napari-wsi

A plugin to read whole slide images within napari.

Language: Python - Size: 2.86 MB - Last synced: 14 days ago - Pushed: 8 months ago - Stars: 15 - Forks: 1

AstraZeneca/onto_merger

OntoMerger is an ontology alignment library for deduplicating knowledge graph nodes that represent the same domain.

Language: HTML - Size: 32.8 MB - Last synced: 2 months ago - Pushed: 5 months ago - Stars: 90 - Forks: 5

AstraZeneca/SubTab

The official implementation of the paper, "SubTab: Subsetting Features of Tabular Data for Self-Supervised Representation Learning"

Language: Python - Size: 42.6 MB - Last synced: 3 months ago - Pushed: almost 2 years ago - Stars: 134 - Forks: 18

AstraZeneca/awesome-drug-pair-scoring

Readings for "A Unified View of Relational Deep Learning for Drug Pair Scoring." (IJCAI 2022)

Size: 1.47 MB - Last synced: about 1 month ago - Pushed: almost 2 years ago - Stars: 86 - Forks: 14

AstraZeneca/kallisto

Efficiently calculate 3D-features for quantitative structure-activity relationship approaches.

Language: Python - Size: 445 KB - Last synced: 3 months ago - Pushed: 4 months ago - Stars: 55 - Forks: 20

AstraZeneca/SelfPAD

The official implementation of "Improving Antibody Humanness Prediction using Patent Data".

Language: Python - Size: 425 KB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 3 - Forks: 0

AstraZeneca/mcpl.github.io

Language: HTML - Size: 52.4 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

AstraZeneca/CKD_molecular_stratification

Language: R - Size: 3.24 MB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

AstraZeneca/adhce

Language: R - Size: 16.6 KB - Last synced: 4 months ago - Pushed: 4 months ago - Stars: 0 - Forks: 0

AstraZeneca/Tendril

This repository contains R package code for calculating tendril plots.

Language: R - Size: 2.61 MB - Last synced: 6 days ago - Pushed: about 2 years ago - Stars: 6 - Forks: 1

AstraZeneca/NESS

Official implementation of "NESS: Node Embeddings from Static Subgraphs"

Language: Python - Size: 762 KB - Last synced: 5 months ago - Pushed: 12 months ago - Stars: 8 - Forks: 0

AstraZeneca/arrayedCRISPRscreener

The goal of arrayedCRISPRscreener is to simulate arrayed CRISPR screening data for the purpose of benchmarking data analysis tools as well as power calculation.

Language: R - Size: 227 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 0 - Forks: 0

AstraZeneca/dpp_imp

Improved clinical data imputation via classical and quantum determinantal point processes

Language: Python - Size: 15.6 KB - Last synced: 6 months ago - Pushed: 6 months ago - Stars: 1 - Forks: 0

AstraZeneca/trim21-bioprotac

Bioinformatics data analyses - Fletcher A. et al., Nature Communications 2023, doi: 10.1038/s41467-023-42546-2

Size: 61.5 KB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

AstraZeneca/detectIS

A pipeline to rapidly detect exogenous DNA integration sites using DNA or RNA paired-end sequencing data

Language: Perl - Size: 1.59 MB - Last synced: 7 months ago - Pushed: about 1 year ago - Stars: 10 - Forks: 6

AstraZeneca/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.

Language: Python - Size: 7.43 MB - Last synced: 7 months ago - Pushed: 10 months ago - Stars: 27 - Forks: 10

AstraZeneca/hsqc_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 simulations

Language: Jupyter Notebook - Size: 54 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 0 - Forks: 0

AstraZeneca/skywalkR

code for Gogleva et al manuscript

Language: R - Size: 1.03 MB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 42 - Forks: 12

AstraZeneca/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.

Language: R - Size: 380 KB - Last synced: 10 months ago - Pushed: over 3 years ago - Stars: 6 - Forks: 0

AstraZeneca/Siamese-Regression-Pairing

Siamese Neural Networks for Regression: Similarity-Based Pairing and Uncertainty Quantification

Language: Python - Size: 3.91 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

AstraZeneca/data-science-python-course

Language: Jupyter Notebook - Size: 26 MB - Last synced: 8 months ago - Pushed: 8 months ago - Stars: 16 - Forks: 12

AstraZeneca/survextrap-excesshazards

Demonstration of excess hazard and excess hazard cure models for survival extrapolation

Language: R - Size: 17.6 KB - Last synced: 10 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

AstraZeneca/AdaptedGraphDTA

Language: Python - Size: 16.7 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

AstraZeneca/Omicsfold

Multi-omics data normalisation, model fitting and visualisation.

Language: R - Size: 490 KB - Last synced: 10 months ago - Pushed: about 1 year ago - Stars: 21 - Forks: 6

AstraZeneca/magnus-extensions

Extensions packages for magnus

Language: Python - Size: 2.74 MB - Last synced: 9 months ago - Pushed: 9 months ago - Stars: 3 - Forks: 1

AstraZeneca/judgyprophet

Forecasting for knowable future events using Bayesian informative priors (forecasting with judgmental-adjustment).

Language: Python - Size: 1.84 MB - Last synced: 23 days ago - Pushed: about 2 years ago - Stars: 56 - Forks: 2

AstraZeneca/gonogo

Implement Go/No-Go policies using multiple endpoints, and simulate the outcome under different scenarios.

Language: R - Size: 135 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

AstraZeneca/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.

Language: Python - Size: 2.2 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 6 - Forks: 1

AstraZeneca/biology-for-ai

learning biology syllabus, geared for machine learning folks

Size: 27.3 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 45 - Forks: 6

AstraZeneca/VecNER

A library of tools for dictionary-based Named Entity Recognition (NER), based on word vector representations to expand dictionary terms.

Language: Python - Size: 340 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 13 - Forks: 0

AstraZeneca/skywalkR-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.

Language: Jupyter Notebook - Size: 89.8 KB - Last synced: about 1 month ago - Pushed: over 2 years ago - Stars: 8 - Forks: 5

AstraZeneca/ConvCaps-DR

Tensorflow-Keras implementation of deep Convolutional Capsule Networks with Dynamic Routing algorithm

Language: Python - Size: 2.02 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 3 - Forks: 0

AstraZeneca/Multimodal_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 prediction

Language: R - Size: 61.5 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 1 - Forks: 0

AstraZeneca/PatientSafetyKG

Language: Python - Size: 729 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 2

AstraZeneca/OCT_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.

Language: MATLAB - Size: 1.88 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 0

AstraZeneca/fragler

Language: Python - Size: 19.5 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 1 - Forks: 1

AstraZeneca/multitask_impute

Supplementary code for 'Deep Learning Imputation for Multi Task Learning'

Language: Python - Size: 1.78 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0

AstraZeneca/INSPECTumours

This is a shiny tool to classify and analyse pre-clinical tumour data automatically.

Language: R - Size: 982 KB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 0 - Forks: 1

AstraZeneca/qscheck

An R library to perform assertions and decision on input arguments.

Language: R - Size: 363 KB - Last synced: 2 months ago - Pushed: 7 months ago - Stars: 0 - Forks: 0

AstraZeneca/GIM

gene interaction matrices, a novel approach to using ConvNets on gene expression data

Language: Jupyter Notebook - Size: 95.7 KB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 0 - Forks: 0