JNapoli

Joe Napoli's starred repositories

alphafold

Open source code for AlphaFold.

Language:PythonApache-2.01218000

Explain, analyze, and visualize NLP language models. Ecco creates interactive visualizations directly in Jupyter notebooks explaining the behavior of Transformer-based language models (like GPT2, BERT, RoBERTA, T5, and T0).

Language:Jupyter NotebookBSD-3-Clause194700

selfies

Robust representation of semantically constrained graphs, in particular for molecules in chemistry

Language:PythonApache-2.063900

roc_comparison

The fast version of DeLong's method for computing the covariance of unadjusted AUC.

Language:PythonMIT13700

comparing_classifiers

Some ideas on methods for comparing classification models

Language:Jupyter NotebookMIT900

SAME

Code for the papers: "Graph Representation Learning for Multi-Task Settings: a Meta-Learning Approach", "A Meta-Learning Approach for Graph Representation Learning in Multi-Task Settings"

Language:PythonNOASSERTION1500

assessing_mol_prediction_confidence

https://arxiv.org/abs/2102.11439

Apache-2.01900

The-NLP-Pandect

A comprehensive reference for all topics related to Natural Language Processing

Language:PythonCC0-1.0200300

miniforge

A conda-forge distribution.

Language:ShellNOASSERTION590700

openforcefield-forcebalance

Optimization of OpenFF parameters using ForceBalance and QCArchive

Language:Python1100

openmmforcefields

CHARMM and AMBER forcefields for OpenMM (with small molecule support)

Language:PythonNOASSERTION23300

graphein

Protein Graph Library

Language:Jupyter NotebookMIT100700

pyro

Deep universal probabilistic programming with Python and PyTorch

Language:PythonApache-2.0845800

pytorch3d

PyTorch3D is FAIR's library of reusable components for deep learning with 3D data

Language:PythonNOASSERTION855000

yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.

Language:PythonMIT17600

biobert

Bioinformatics'2020: BioBERT: a pre-trained biomedical language representation model for biomedical text mining

Language:PythonNOASSERTION189800

stoned-selfies

This repository contains code for the paper: Beyond Generative Models: Superfast Traversal, Optimization, Novelty, Exploration and Discovery (STONED) Algorithm for Molecules using SELFIES

Language:Jupyter Notebook11400