linearAI

linearAI's Stars

• westlake-repl/SaProt

  [ICLR'24 spotlight] Saprot: Protein Language Model with Structural Alphabet

  Language:Python27925

• SchubertLab/mvTCR_reproducibility

  Reproducibility Repo for mvTCR paper

  Language:Jupyter Notebook103

• regeneron-mpds/TCRAI

  Language:Jupyter Notebook143

• hammerlab/multi-omic-urothelial-anti-pdl1

  Contribution of systemic and somatic factors to clinical response and resistance in urothelial cancer: an exploratory multi-omic analysis

  Language:Jupyter Notebook2123

• airr-community/airr-standards

  AIRR Community Data Standards

  Language:Python3523

• bhoov/exbert

  A Visual Analysis Tool to Explore Learned Representations in Transformers Models

  Language:Python57751

• statbiophys/pygor3

  pygor3 repository

  Language:Jupyter Notebook94

• wukevin/tcr-bert

  Large language modeling applied to T-cell receptor (TCR) sequences.

  Language:Jupyter Notebook447

• sacdallago/bio_embeddings

  Get protein embeddings from protein sequences

  Language:HTML44764

• yangkky/Machine-learning-for-proteins

  Listing of papers about machine learning for proteins.

  1.4k196

• BenTenmann/setriq

  Fast string distance computation in Python

  Language:Python152

• uio-bmi/immuneML

  immuneML is a platform for machine learning analysis of adaptive immune receptor repertoire data.

  Language:Python5929

• gcorso/NeuroSEED

  Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

  Language:Python6817

• pogorely/ALICE

  Detecting TCR involved in immune responses from single RepSeq datasets

  Language:R2513

• google-deepmind/alphafold

  Open source code for AlphaFold.

  Language:Python12.1k2.2k

• MilesCranmer/symbolic_deep_learning

  Code for "Discovering Symbolic Models from Deep Learning with Inductive Biases"

  Language:Python701132

• gordicaleksa/pytorch-GAT

  My implementation of the original GAT paper (Veličković et al.). I've additionally included the playground.py file for visualizing the Cora dataset, GAT embeddings, an attention mechanism, and entropy histograms. I've supported both Cora (transductive) and PPI (inductive) examples!

  Language:Jupyter Notebook2.4k319

• scverse/scirpy

  A scanpy extension to analyse single-cell TCR and BCR data.

  Language:Python20431

• s175573/iSMART

  Highly specific clustering of T cell receptor CDR3s

  Language:Python4232

• immunoengineer/gliph

  Grouping of Lymphocyte Interactions by Paratope Hotspots

  9028

• gwgundersen/dpcca

  Code for the paper "End-to-end training of deep probabilistic CCA on paired biomedical observations".

  Language:Python245

• SchubertLab/mvTCR

  Language:Jupyter Notebook384

• 1Konny/Beta-VAE

  Pytorch implementation of β-VAE

  Language:Python508125

• haofuml/cyclical_annealing

  Language:OpenEdge ABL17819

• jaanli/variational-autoencoder

  Variational autoencoder implemented in tensorflow and pytorch (including inverse autoregressive flow)

  Language:Python1.1k256

• samsinai/VAE_protein_function

  Protein function prediction using a variational autoencoder

  Language:Jupyter Notebook8825

• matsengrp/vampire-analysis-1

  Data analysis using the vampire models for immune cell receptor distributions

  Language:Jupyter Notebook51

• matsengrp/vampire

  🧛 Deep generative models for TCR sequences 🧛

  Language:Python164

• psipred/protein-vae

  Variational autoencoder for protein sequences - add metal binding sites and generate sequences for novel topologies

  Language:Python7917

• kihyuks/nips2015_cvae

  Language:MATLAB1