Song Lab @ Cal

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1. tape tape Public

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

   Python 745 134

2. gpn gpn Public

   Genomic Pretrained Network - GPN, GPN-MSA, PhyloGPN, GPN-Star

   Jupyter Notebook 374 50

3. TraitGym TraitGym Public

   Jupyter Notebook 21 3

4. CherryML CherryML Public

   Scalable Maximum Likelihood Estimation of Phylogenetic Models

   C++ 29 4

5. factored-attention factored-attention Public

   This repository contains code for reproducing results in our paper Interpreting Potts and Transformer Protein Models Through the Lens of Simplified Attention

   Jupyter Notebook 59 9

6. rna-sieve rna-sieve Public

   A library for the deconvolution of bulk cell samples using single-cell RNA expression data.

   Mathematica 23 3