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@Bitbol-Lab

Bitbol-Lab

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  1. ProtMamba-ssm ProtMamba-ssm Public

    ProtMamba: a homology-aware but alignment-free protein state space model

    Jupyter Notebook 52 7

  2. Iterative_masking Iterative_masking Public

    Iterative masking algorithm on MSA Transformer to generate synthetic sequences

    Jupyter Notebook 23 7

  3. DiffPALM DiffPALM Public

    Differentiable Pairing using Alignment-based Language Models

    Jupyter Notebook 17 3

  4. Phylogeny-MSA-Transformer Phylogeny-MSA-Transformer Public

    Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s41467-022-34032-y)

    Jupyter Notebook 16 1

  5. DiffPaSS DiffPaSS Public

    Differentiable Pairing using Soft Scores

    Jupyter Notebook 3 1

  6. Phylogeny-Partners Phylogeny-Partners Public

    Jupyter Notebook 1

Repositories

Showing 10 of 20 repositories
  • partial_sampling_spatially_structured_population Public

    Repository for my lab immersion on spatially structured populations with partial updates.

    Bitbol-Lab/partial_sampling_spatially_structured_population’s past year of commit activity
    Jupyter Notebook 1 0 0 0 Updated Dec 12, 2024
  • Phylogeny-MSA-Transformer Public

    Supporting repository for "Protein language models trained on multiple sequence alignments learn phylogenetic relationships" (https://www.nature.com/articles/s41467-022-34032-y)

    Bitbol-Lab/Phylogeny-MSA-Transformer’s past year of commit activity
    Jupyter Notebook 16 MIT 1 0 0 Updated Dec 11, 2024
  • ProtMamba-ssm Public

    ProtMamba: a homology-aware but alignment-free protein state space model

    Bitbol-Lab/ProtMamba-ssm’s past year of commit activity
    Jupyter Notebook 52 Apache-2.0 7 2 0 Updated Oct 28, 2024
  • fitness-landscapes Public
    Bitbol-Lab/fitness-landscapes’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Oct 14, 2024
  • DrugRes_StructPop Public

    Repository for "Spatial structure facilitates evolutionary rescue by cost-free drug resistance" (2024) by C. Fruet, E. L. Müller, C. Loverdo, and A.-F. Bitbol.

    Bitbol-Lab/DrugRes_StructPop’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Sep 2, 2024
  • Phylogeny-ESM2 Public

    Monte-Carlo generation of synthetic multiple sequence alignments along phylogenetic trees using a protein language model

    Bitbol-Lab/Phylogeny-ESM2’s past year of commit activity
    Python 0 0 1 0 Updated Jun 29, 2024
  • ProtMamba-frozen-nips Public
    Bitbol-Lab/ProtMamba-frozen-nips’s past year of commit activity
    Python 0 Apache-2.0 0 0 0 Updated May 22, 2024
  • DiffPaSS Public

    Differentiable Pairing using Soft Scores

    Bitbol-Lab/DiffPaSS’s past year of commit activity
    Jupyter Notebook 3 Apache-2.0 1 2 0 Updated May 20, 2024
  • Phylogeny-sector-inference Public
    Bitbol-Lab/Phylogeny-sector-inference’s past year of commit activity
    Python 0 MIT 0 0 0 Updated Apr 19, 2024
  • Structured_pop Public

    This repository provides the python code used to generate Figures in articles "Frequent asymmetric migrations suppress natural selection in spatially structured populations" , and "Mutant fate in spatially structured populations on graphs: connecting models to experiments" by A. Abbara, L. Pagani, C. García-Pareja, and A.-F. Bitbol.

    Bitbol-Lab/Structured_pop’s past year of commit activity
    Jupyter Notebook 0 MIT 1 0 0 Updated Feb 6, 2024
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