samgoldman97 Goto Github PK

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

brenda-parser

A repository designated to parsing entries from the BRENDA database

codon-optimization

A neural based approach to the task of genetic codon optimization

cookiecutter-data-science

A logical, reasonably standardized, but flexible project structure for doing and sharing data science work.

dlkcat

Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction

enz-pred

enzyme-datasets

Enzyme datasets used to benchmark enzyme-substrate promiscuity models

hgraph2graph

Hierarchical Generation of Molecular Graphs using Structural Motifs

icml18-jtnn

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)

kinase-cpi-reanalysis

Reanalysis of Hie et al. using uncertainty paper

markdown-cheatsheet

Markdown Cheatsheet for Github Readme.md

mist

Encoding MS/MS spectra using formula transformers for inferring molecular properties

mist-cf

Predicting MS1 precursor chemical formula from MS/MS data

ms-pred

Predicting tandem mass spectra from molecules

msnovelist

namedtensor

Proof of concept for a dynamic named tensor for pytorch

nist-parser

Script to parse NIST mass spec library

protein-sequence-embedding-iclr2019

Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019

prottrans

ProtTrans is providing state of the art pre-trained models for proteins. ProtTrans was trained on thousands of GPUs from Summit and hundreds of Google TPUs using Transformers Models.

pyfingerprint

Python tool for generate fingerprints of a molecule

pytorch-made

MADE (Masked Autoencoder Density Estimation) implementation in PyTorch

resonant-learning

samgoldman97.github.io

spec2vec

Word2Vec based similarity measure of mass spectrometry data.

tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

tide-reformatter

Python scripts to reformat NOAA tide data to an ICS file for calendar import

trrosetta

A package to predict protein inter-residue geometries from sequence data

uncertainty

Learning with uncertainty for biological discovery and design

vimconfig

Vim config file