Repository Index

Code for the ProteinMPNN paper

Python implementation of CMA-ES

Notebooks for financial economics. Keywords: Jupyter notebook pandas Federal Reserve FRED Ferbus GDP CPI PCE inflation unemployment wage income debt Case-Shiller housing asset portfolio equities SPX bonds TIPS rates currency FX euro EUR USD JPY yen XAU gold Brent WTI oil Holt-Winters time-series forecasting statistics econometrics

• jupyter-notebook
• pandas
• federal-reserve
• gdp

WebGL accelerated JavaScript molecular graphics library

• molecular-graphics
• molecular-modeling
• computational-biology
• computational-chemistry

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

Wrapper for RDKit's RunReactants to improve stereochemistry handling

A python Two Source Energy Balance model for estimation of evapotranspiration with remote sensing data

• source-energy-balance
• canopy
• soil
• radiometric-temperatures

🏃 The go-to single-cell Foundation Model

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

GeneCompass

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

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

• cell-annotation
• multiplexed-imaging
• mpif

Classification and Gradient-based Localization of Chest Radiographs using PyTorch.

• fine-tuning
• vgg16
• resnet18
• densenet121

UV-first benchmark for protein-ligand docking with reproducible annotation, pocket similarity, and HPC workflows.

• benchmark
• bioinformatics
• cheminformatics
• computational-chemistry