model-registry / basemodels.json
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{
"schema_version": "1.0.0",
"source_workbook": "Modelling.xlsx",
"source_sheet": "Basemodels",
"generated_at": "2026-03-25",
"records": [
{
"name": "prokbert-mini",
"hf_name": "prokbert-mini",
"hf_prefix": "neuralbioinfo",
"hf_path": "neuralbioinfo/prokbert-mini",
"model_complexity": 25,
"max_token_scaling": 1,
"tokenizer_class_name": "LCATokenizer",
"train_tokenizer_function": "tokenize_function_prokbert",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 1,
"tokenizer_short_name": "mini",
"model_id": "prokbert-mini"
},
{
"name": "prokbert-mini-long",
"hf_name": "prokbert-mini-long",
"hf_prefix": "neuralbioinfo",
"hf_path": "neuralbioinfo/prokbert-mini-long",
"model_complexity": 25,
"max_token_scaling": 0.5,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_prokbert",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 2,
"tokenizer_short_name": "minil",
"model_id": "prokbert-mini-long"
},
{
"name": "prokbert-mini-c",
"hf_name": "prokbert-mini-c",
"hf_prefix": "neuralbioinfo",
"hf_path": "neuralbioinfo/prokbert-mini-c",
"model_complexity": 25,
"max_token_scaling": 1,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_prokbert",
"tokenization": "LCA",
"tokenization_kmer": 1,
"tokenization_shift": 1,
"tokenizer_short_name": "minic",
"model_id": "prokbert-mini-c"
},
{
"name": "dnabert2",
"hf_name": "DNABERT-2-117M",
"hf_prefix": "zhihan1996",
"hf_path": "zhihan1996/DNABERT-2-117M",
"model_complexity": 117,
"max_token_scaling": 0.3333,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_DNABERT",
"tokenization": "SenPiece",
"tokenization_kmer": null,
"tokenization_shift": null,
"tokenizer_short_name": "dnabert2",
"model_id": "dnabert2"
},
{
"name": "nt2.5b",
"hf_name": "nucleotide-transformer-2.5b-multi-species",
"hf_prefix": "InstaDeepAI",
"hf_path": "InstaDeepAI/nucleotide-transformer-2.5b-multi-species",
"model_complexity": 2500,
"max_token_scaling": 0.2,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_NT",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 6,
"tokenizer_short_name": "nt",
"model_id": "nt2.5b"
},
{
"name": "nt500",
"hf_name": "nucleotide-transformer-v2-500m-multi-species",
"hf_prefix": "InstaDeepAI",
"hf_path": "InstaDeepAI/nucleotide-transformer-v2-500m-multi-species",
"model_complexity": 500,
"max_token_scaling": 0.2,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_NT",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 6,
"tokenizer_short_name": "nt",
"model_id": "nt500"
},
{
"name": "nt100",
"hf_name": "nucleotide-transformer-v2-100m-multi-species",
"hf_prefix": "InstaDeepAI",
"hf_path": "InstaDeepAI/nucleotide-transformer-v2-100m-multi-species",
"model_complexity": 100,
"max_token_scaling": 0.2,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_NT",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 6,
"tokenizer_short_name": "nt",
"model_id": "nt100"
},
{
"name": "nt50",
"hf_name": "nucleotide-transformer-v2-50m-multi-species",
"hf_prefix": "InstaDeepAI",
"hf_path": "InstaDeepAI/nucleotide-transformer-v2-50m-multi-species",
"model_complexity": 50,
"max_token_scaling": 0.2,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_NT",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 6,
"tokenizer_short_name": "nt",
"model_id": "nt50"
},
{
"name": "nt250",
"hf_name": "nucleotide-transformer-v2-250m-multi-species",
"hf_prefix": "InstaDeepAI",
"hf_path": "InstaDeepAI/nucleotide-transformer-v2-250m-multi-species",
"model_complexity": 250,
"max_token_scaling": 0.2,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_NT",
"tokenization": "LCA",
"tokenization_kmer": 6,
"tokenization_shift": 6,
"tokenizer_short_name": "nt",
"model_id": "nt250"
},
{
"name": "metagene1",
"hf_name": "METAGENE-1",
"hf_prefix": "metagene-ai",
"hf_path": "metagene-ai/METAGENE-1",
"model_complexity": 7000,
"max_token_scaling": 0.3333,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_evo_metagene",
"tokenization": "BPE",
"tokenization_kmer": null,
"tokenization_shift": null,
"tokenizer_short_name": "mg1",
"model_id": "metagene1"
},
{
"name": "evo1-8k",
"hf_name": "evo-1-8k-base",
"hf_prefix": "togethercomputer",
"hf_path": "togethercomputer/evo-1-8k-base",
"model_complexity": 7000,
"max_token_scaling": 1,
"tokenizer_class_name": "AutoTokenizer",
"train_tokenizer_function": "tokenize_function_evo_metagene",
"tokenization": "LCA",
"tokenization_kmer": 1,
"tokenization_shift": 1,
"tokenizer_short_name": "evo1",
"model_id": "evo1-8k"
}
]
}