Repository Index

Deep Reinforcement Learning for de-novo Drug Design

• deeplearning
• reinforcement-learning
• cheminformatics
• molecular-modeling

Fusing Histology and Genomics via Deep Learning - IEEE TMI

• pathomic
• fusion
• multimodal
• pathology

TranslatedLLM teaching material for high school students: based on Karpathy's microgpt, for Google Colab

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

Pan-Cancer Integrative Histology-Genomic Analysis via Multimodal Deep Learning - Cancer Cell

• histology
• wsi-images
• pan-cancer-analysis
• genomics

Usiigaci: stain-free cell tracking in phase contrast microscopy enabled by supervised machine learning

• tensorflow
• python3
• keras
• resnet-101

An enhanced interactive Shell for Common Lisp (based on the Jupyter protocol)

This repository is a collection of TTS Models in TFLite

Wrapper for RDKit's RunReactants to improve stereochemistry handling

scPerturb: A resource and a python/R tool for single-cell perturbation data

• cite-seq
• database
• perturbation
• scatac-seq

🏃 The go-to single-cell Foundation Model

• batch-correction
• cell-biology
• celltype-annotation
• denoising

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

• disentanglement
• drug-discovery
• genomics
• perturbation

Tools for pen plotting in Python

⬛ Python Individual Conditional Expectation Plot Toolbox

• machine-learning
• interpretability

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

Integrated pipeline for multiplexed image analysis

• multiplexed-imaging
• python

REVISE: A Tool for Measuring and Mitigating Bias in Visual Datasets --- https://arxiv.org/abs/2004.07999

tutorials made for biologists to learn deep learning

• biologists
• keras
• deeplearning
• deep-learning

Cyber Defence Monitoring Course Suite :: Suricata, Arkime (and others in the past)

• moloch
• suricata
• monitoring
• nsm

a nose plugin for finding and running IPython notebooks as nose tests

Code repository for The Automation Ahead series, showcasing practical examples for GenAI-driven automation in investments. Each installment dives into specific tools, techniques, and use cases to help professionals assess and apply GenAI effectively.

• data-science
• deep-learning
• finance
• financial-data

Peax is a tool for interactive visual pattern search and exploration in epigenomic data based on unsupervised representation learning with autoencoders

• epigenomics
• pattern-search
• data-visualization
• interactive-machine-learning

Machine learning for Analysis of Proteomics in Spatial biology - Nature Communications

• cell-annotation
• multiplexed-imaging
• mpif

High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations