Biological models

320 model records in release 2026-11-02-a7f03c9e55a5 (release manifest, gzip). Showing 25–48; page 2 of 14.

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

• CARP

  Proteins and complexes

  Convolutional protein language model pretrained by masked language modelling on protein sequences, scored in ProteinGym as a zero-shot single-sequence substitution baseline.

• CellPLM

  Single-cell omics · Spatial omics

  Cell-level transformer foundation model pretrained on scRNA-seq and spatial transcriptomics.

• Chai-1

  Proteins and complexes · Molecular interactions

  Chai-1 predicts the structures of biomolecular complexes containing proteins, nucleic acids and small molecules.

• ChemBERTa

  Metabolomics

  ChemBERTa molecular language model.

• ChemFormer

  Metabolomics

  ChemFormer molecular language model.

• ChemLLM-7B

  Protein function

  ChemLLM-7B chemistry large language model, prompted for protein property questions.

• Chroma

  Protein structure

  Diffusion-based protein backbone generation method evaluated in Scaffold-Lab (released 2023-11).

• ChromBPNet

  DNA and genomes

  ChromBPNet predicts base-resolution chromatin accessibility while modeling assay-specific enzyme bias separately.

• CI-SpliceAI

  DNA and genomes

  SpliceAI reimplementation retrained on a collapsed isoform set of manually curated GENCODE HAVANA splice sites from all chromosomes.

• Claude 3 Haiku

  Cells and tissues

  Large multimodal model with vision capabilities, the fastest and least expensive of Anthropic's Claude 3 family.

• Claude 3 Opus

  Cells and tissues

  Large multimodal model with vision capabilities, the most capable of Anthropic's Claude 3 family.

• Claude 3 Sonnet

  Cells and tissues

  Large multimodal model with vision capabilities in Anthropic's Claude 3 family, positioned between Opus and Haiku in skills and speed.

• Claude 3.5 Sonnet

  Cells and tissues

  Large multimodal model from Anthropic, an evolution of the Claude 3 family with improved coding and visual processing.

• Claude Haiku 4.5

  Cells and tissues

  Anthropic's hosted large language model Claude Haiku 4.5.

• Claude Opus 4.8

  Cells and tissues

  Anthropic's hosted large language model Claude Opus 4.8.

• Claude Sonnet 4

  Molecular interactions · Protein function · Single-cell omics

  Anthropic language model, used as the LLM backend for Biomni in BioML-bench.

• Claude Sonnet 4.6

  Cells and tissues

  Anthropic's hosted large language model Claude Sonnet 4.6.

• Claude v1

  Cells and tissues

  Anthropic's original Claude AI assistant model, offered through a chat interface and an API for conversational and text-processing tasks.

• CNN

  Protein function

  Convolutional neural network over the one-hot encoded sequence.

• CNN-RNN

  Protein function

  Convolutional network followed by a recurrent layer over the sequence.

• CodonBERT

  DNA and genomes

  BERT-style language model of mRNA coding sequences at codon resolution.

• CPA

  Cells and tissues · Single-cell omics

  Perturbation-response model the authors benchmarked against (main text paragraph 2); the authors say it was not designed to predict the effects of unseen perturbations (main text paragraphs 16 and 20).

• DeCodon

  DNA and genomes

  Decoder-only codon language model.

• Deep Prot-T5

  Protein function

  DeepProt-T5: Prot-T5-XL fine-tuned per task, introduced by the DeepProtein authors.

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.