Alternatives and similar repositories for BiologicalTokenizers

Users that are interested in BiologicalTokenizers are comparing it to the libraries listed below

• jmschrei / ledidi
  Ledidi turns any machine learning model into a biological sequence editor, allowing you to design sequences with desired properties.
  ☆95Updated 5 months ago
• m42-health / biofm-eval
  Library to extract embeddings for DNA sequences using BioFM genomics foundation model
  ☆16Updated 3 months ago
• bowang-lab / Orthrus
  Orthrus is a mature RNA model for RNA property prediction. It uses a mamba encoder backbone, a variant of state-space models specifical…
  ☆82Updated 3 months ago
• konstin / knn-for-homology
  Repository for "Nearest neighbor search on embeddings rapidly identifies distant protein relations"
  ☆13Updated 2 years ago
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆42Updated last year
• TattaBio / OMG
  ☆47Updated last year
• mims-harvard / Phyla
  Phyla: Towards a Foundation Model for Phylogenetic Inference
  ☆24Updated this week
• alrojo / UniLanguage
  Homology reduced UniProt, train-/valid-/testsets for language modeling
  ☆16Updated 3 years ago
• science-machine / biomlbench
  Benchmark agents on BioML tasks
  ☆56Updated 2 months ago
• OATML / EVE
  Official repository for the paper "Large-scale clinical interpretation of genetic variants using evolutionary data and deep learning". Jo…
  ☆65Updated 3 years ago
• Rostlab / goPredSim
  ☆48Updated 11 months ago
• biagent-dev / bia
  BioInformatics Agent (BIA): Unleashing the Power of Large Language Models to Reshape Bioinformatics Workflow
  ☆39Updated last year
• dnbaker / bioseq
  Tokenizers and Machine Learning Models for biological sequence data
  ☆25Updated last year
• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆49Updated last year
• macwiatrak / Bacformer
  Modeling whole bacterial genome as a sequence of proteins.
  ☆78Updated 3 weeks ago
• regev-lab / interpretable-splicing-model
  Interpretable splicing model
  ☆20Updated 2 years ago
• frederikkemarin / BEND
  Benchmarking DNA Language Models on Biologically Meaningful Tasks
  ☆127Updated last year
• johli / scrambler
  Interpretation by Deep Generative Masking for Biological Sequences
  ☆37Updated 3 years ago
• cebel / pyuniprot
  Python package to query and analyse UniProt
  ☆25Updated 5 years ago
• chenkenbio / SpliceBERT
  Primary RNA sequence model
  ☆40Updated last year
• liudan111 / EvoMIL
  Prediction of virus-host association using protein language models and multiple instance learning
  ☆20Updated last year
• krishnanlab / PyGenePlexus
  A network based gene classification library to generate genome wide predictions about genes that are functionally similar to the input ge…
  ☆20Updated this week
• FunctionLab / tapioca
  a framework for predicting global protein-protein interaction networks from dynamic mass spec data
  ☆24Updated last year
• joanaapa / Distillation-DNABERT-Promoter
  Knowledge distillation on DNABERT (DistilBERT and MiniLM techniques) for promoter identification.
  ☆24Updated 3 years ago
• p-koo / evoaug
  Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
  ☆24Updated 5 months ago
• JonnyTran / OpenOmics
  A bioinformatics API to interface with public multi-omics bio databases for wicked fast data integration.
  ☆35Updated last year
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆22Updated last year
• TattaBio / DGEB
  Diverse Genomic Embedding Benchmark
  ☆48Updated 2 months ago
• BiomedSciAI / biomed-multi-omic
  Build foundation model on RNA or DNA data
  ☆31Updated 2 weeks ago
• Future-House / BixBench
  Benchmark for LLM-based Agents in Computational Biology
  ☆62Updated last month