kirjner

GGS

This repository implements Gibbs sampling with Graph-based Smoothing

bepler

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

bio_embeddings

Get protein embeddings from protein sequences

BioSeq-GFN-AL

Code for "Biological Sequence Design with GFlowNets", 2022

clamp-gen-data

Code to load data and oracle for active learning on peptides

ConFit

contact_map

Contact map analysis for biomolecules; based on MDTraj

CPCProt

Parameter-efficient embeddings for proteins, pretrained using a contrastive loss.

design-bench

Benchmarks for Model-Based Optimization

esm

Evolutionary Scale Modeling (esm): Pretrained language models for proteins

GGS-private

lambo-original

Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)

evo

DNA foundation modeling from molecular to genome scale

kickstart.nvim

A launch point for your personal nvim configuration

kirjner.github.io

local-pdf-llama

Yes, it's another chat over documents implementation... but this one is entirely local!

nuclease_design

ML-guided enzyme engineering

stripedhyena

Repository for StripedHyena, a state-of-the-art beyond Transformer architecture

transformer-debugger

TransMEP

Transfer learning for Mutation Effect Prediction

walk-jump

Official repository for discrete Walk-Jump Sampling (dWJS)