Alternatives and similar repositories for genomic-FM:

Users that are interested in genomic-FM are comparing it to the libraries listed below

• Genentech / regLM
  Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
  ☆39Updated 7 months ago
• kundajelab / DART-Eval
  ☆34Updated last week
• microsoft / zero-shot-scfoundation
  ☆62Updated 8 months ago
• rahuldhodapkar / cell2sentence
  Create cell sentences from sequencing data
  ☆22Updated 8 months ago
• jkobject / geneformer
  ☆64Updated last year
• 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…
  ☆62Updated 3 months ago
• sjgosai / boda2
  Computational Optimization of DNA Activity (CODA)
  ☆57Updated last month
• Genentech / iterative-perturb-seq
  Sequential Optimal Experimental Design of Perturbation Screens Guided by Multimodal Priors
  ☆40Updated 11 months ago
• amberT15 / LLM_eval
  Code repository for study ''Evaluating the representational power of pre-trained DNA language models for regulatory genomics"
  ☆18Updated 10 months ago
• snap-stanford / KGWAS
  KGWAS: novel genetics discovery enabled by massive functional genomics knowledge graph
  ☆68Updated 2 months ago
• aristoteleo / awesome-bioagent-papers
  Agent self-driven repository on bio-agent papers, i.e. papers on LLM-based agents in biology and medicine.
  ☆36Updated this week
• jimmylihui / GenBench
  ☆21Updated 2 months ago
• czi-ai / transcriptformer
  ☆35Updated this week
• aaronwtr / PertEval
  Evaluation suite for transcriptomic perturbation effect prediction models. Includes support for single-cell foundation models.
  ☆25Updated last month
• bowang-lab / BIONIC
  Biological Network Integration using Convolutions
  ☆62Updated last year
• bowang-lab / IntegrAO
  Integrate Any Omics: Towards genome-wide data integration for patient stratification
  ☆50Updated last month
• dohlee / chromoformer
  The official code implementation for Chromoformer in PyTorch. (Lee et al., Nature Communications. 2022)
  ☆35Updated last year
• Genentech / polygraph
  Polygraph evaluates and compares groups of nucleic acid sequences based on their sequence and functional content for effective design of …
  ☆29Updated last month
• epigen / KPNN
  Knowledge-primed neural networks
  ☆36Updated 2 years ago
• mims-harvard / COMPASS
  Generalizable AI predicts immunotherapy outcomes across cancers and treatments
  ☆19Updated this week
• clinicalml / sc-foundation-eval
  Code for evaluating single cell foundation models scBERT and scGPT
  ☆43Updated 8 months ago
• HakimBenkirane / CustOmics
  A deep-learning framework for multi-omics integration
  ☆26Updated last year
• carpenter-singh-lab / 2022_Haghighi_NatureMethods
  High-Dimensional Gene Expression and Morphology Profiles of Cells across 28,000 Genetic and Chemical Perturbations
  ☆48Updated 3 months ago
• p-koo / evoaug
  Evolution-inspired data augmentations for PyTorch-based models for regulatory genomics
  ☆21Updated last year
• OmicsML / CellPLM
  Official repo for CellPLM: Pre-training of Cell Language Model Beyond Single Cells.
  ☆84Updated last year
• TencentAILabHealthcare / DNAGPT
  ☆39Updated last year
• OmicsML / scDiff
  scDiff: A General Single-Cell Analysis Framework via Conditional Diffusion Generative Models
  ☆28Updated 8 months ago
• johahi / borzoi-pytorch
  Pytorch implementation of the Borzoi model from Calico, and Flashzoi, a 3x faster Borzoi enhancement.
  ☆48Updated 2 weeks ago
• Genentech / pascient
  ☆15Updated last week
• BoevaLab / CancerFoundation
  CancerFoundation: A single-cell RNA sequencing foundation model to decipher drug resistance in cancer
  ☆17Updated 2 weeks ago