Biological models

59 model records in release 2026-09-22-f58a0f1d267f. Showing 25–48; page 2 of 3.

Evaluated configurations, methods and pipelines are listed separately. Names alone do not establish equivalent models or checkpoints.

• GEARS

  Single cell

  GEARS predicts transcriptional responses to single- and multi-gene perturbations from single-cell perturbation screens.

  Record: discovery-model-gears

• Geneformer

  Cells and tissues

  Geneformer represents single-cell transcriptomes as ranked genes and learns contextual gene and cell representations.

• Genie 3

  Protein structure

  Genie 3 generates protein designs through all-atom equivariant diffusion.

• GlycanGT

  Glycomics

  GlycanGT learns glycan representations by treating monosaccharides and linkages as graph tokens.

• METAGENE-1

  Microbes and communities

  METAGENE-1 is an autoregressive DNA/RNA sequence model trained on wastewater metagenomic data.

• MIMIC

  RNA and transcriptomes · Proteins and complexes

  MIMIC represents DNA, RNA, protein and associated molecular measurements in a shared multimodal model.

• mRNA-FM

  RNA and transcriptomes

  mRNA-FM encodes coding RNA with codon-level tokens to produce representations for downstream analysis.

• MSAlign

  Metabolomics

  MSAlign retrieves candidate molecules from tandem mass spectra by aligning pretrained molecular and spectral representations.

• Nucleotide Transformer

  Genomics

  Nucleotide Transformer is a family of DNA encoders pretrained on human or multispecies sequence corpora.

• Nucleotide Transformer v2

  DNA and genomes

  Nucleotide Transformer v2 represents DNA using an encoder pretrained on multiple species.

• OpenFold

  Protein structure

  OpenFold is a trainable PyTorch implementation of AlphaFold 2 and AlphaFold-Multimer workflows.

• Pangolin

  DNA and genomes

  Pangolin predicts splice-site strength and changes caused by genetic variants.

  Record: catalog-model-pangolin

• Pangolin

  Genomics

  Pangolin predicts splice-site strength and changes caused by genetic variants.

  Record: discovery-model-pangolin

• ProkBERT

  Microbes and communities

  ProkBERT is a family of microbial DNA encoders used for sequence representation, promoter prediction and phage identification.

• ProteinMPNN

  Proteins and complexes

  ProteinMPNN designs amino-acid sequences for a supplied protein backbone.

  Record: catalog-model-proteinmpnn

• ProteinMPNN

  Protein structure

  ProteinMPNN designs amino-acid sequences for a supplied protein backbone.

  Record: discovery-model-proteinmpnn

• RFdiffusion

  Protein structure

  RFdiffusion generates protein structures, optionally conditioned on a motif, target or symmetry constraint.

• RhoFold+

  RNA and transcriptomes

  RhoFold+ predicts RNA three-dimensional structures from RNA sequence with alignment information.

• RNA-FM

  RNA and transcriptomes

  RNA-FM learns contextual representations of RNA nucleotides for downstream RNA analyses.

  Record: catalog-model-rna-fm

• RNA-FM

  RNA

  RNA-FM learns contextual representations of RNA nucleotides for downstream RNA analyses.

  Record: discovery-model-rna-fm

• scFoundation

  Cells and tissues

  scFoundation produces contextual cell and gene representations from gene-expression measurements.

• scGPT

  Cells and tissues

  scGPT learns representations of single-cell molecular measurements and supports task-specific adaptation.

  Record: catalog-model-scgpt

• scGPT

  Single cell

  scGPT learns representations of single-cell molecular measurements and supports task-specific adaptation.

  Record: discovery-model-scgpt

• scVI

  Cells and tissues

  scVI models single-cell RNA counts with a probabilistic latent-variable model that accounts for observed covariates.

  Record: catalog-model-scvi

This index reflects a dated catalogue, not an exhaustive census. Source checking does not mean independent reproduction; compare results only under compatible protocols, datasets and metrics.