Pinned Repositories
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
cheap-proteins
Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1
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
GGS
This repository implements Gibbs sampling with Graph-based Smoothing
kirjner's Repositories
kirjner/GGS
This repository implements Gibbs sampling with Graph-based Smoothing
kirjner/bepler
Source code for "Learning protein sequence embeddings using information from structure" - ICLR 2019
kirjner/bio_embeddings
Get protein embeddings from protein sequences
kirjner/BioSeq-GFN-AL
Code for "Biological Sequence Design with GFlowNets", 2022
kirjner/cheap-proteins
Joint embedding of protein sequence and structure with discrete and continuous compressions of protein folding model latent spaces. https://www.biorxiv.org/content/10.1101/2024.08.06.606920v1
kirjner/clamp-gen-data
Code to load data and oracle for active learning on peptides
kirjner/ConFit
kirjner/contact_map
Contact map analysis for biomolecules; based on MDTraj
kirjner/CPCProt
Parameter-efficient embeddings for proteins, pretrained using a contrastive loss.
kirjner/design-bench
Benchmarks for Model-Based Optimization
kirjner/esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
kirjner/GGS-private
kirjner/lambo-original
Code to reproduce experiments in "Accelerating Bayesian Optimization for Protein Design with Denoising Autoencoders" (Stanton et al 2022)
kirjner/esm3
kirjner/evo
DNA foundation modeling from molecular to genome scale
kirjner/kickstart.nvim
A launch point for your personal nvim configuration
kirjner/kirjner.github.io
kirjner/local-pdf-llama
Yes, it's another chat over documents implementation... but this one is entirely local!
kirjner/nuclease_design
ML-guided enzyme engineering
kirjner/ProteinNPT
Official code repository for the paper "ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers"
kirjner/stripedhyena
Repository for StripedHyena, a state-of-the-art beyond Transformer architecture
kirjner/targettrack
User-friendly graphical interface for annotating 3D recordings of C. elegans and tracking neuronal activity
kirjner/transformer-debugger
kirjner/TransMEP
Transfer learning for Mutation Effect Prediction
kirjner/walk-jump
Official repository for discrete Walk-Jump Sampling (dWJS)