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neuralbioinfo
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model-registry

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basemodels · 11 rows

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train · 11 rows

name stringlengths 4 18	hf_name stringlengths 10 44	hf_prefix stringclasses 5 values	hf_path stringlengths 22 56	model_complexity int64 25 7k	max_token_scaling float64 0.2 1	tokenizer_class_name stringclasses 2 values	train_tokenizer_function stringclasses 4 values	tokenization stringclasses 3 values	tokenization_kmer int64 1 6 ⌀	tokenization_shift int64 1 6 ⌀	tokenizer_short_name stringclasses 7 values	model_id stringlengths 4 18
prokbert-mini	prokbert-mini	neuralbioinfo	neuralbioinfo/prokbert-mini	25	1	LCATokenizer	tokenize_function_prokbert	LCA	6	1	mini	prokbert-mini
prokbert-mini-long	prokbert-mini-long	neuralbioinfo	neuralbioinfo/prokbert-mini-long	25	0.5	AutoTokenizer	tokenize_function_prokbert	LCA	6	2	minil	prokbert-mini-long
prokbert-mini-c	prokbert-mini-c	neuralbioinfo	neuralbioinfo/prokbert-mini-c	25	1	AutoTokenizer	tokenize_function_prokbert	LCA	1	1	minic	prokbert-mini-c
dnabert2	DNABERT-2-117M	zhihan1996	zhihan1996/DNABERT-2-117M	117	0.3333	AutoTokenizer	tokenize_function_DNABERT	SenPiece	null	null	dnabert2	dnabert2
nt2.5b	nucleotide-transformer-2.5b-multi-species	InstaDeepAI	InstaDeepAI/nucleotide-transformer-2.5b-multi-species	2,500	0.2	AutoTokenizer	tokenize_function_NT	LCA	6	6	nt	nt2.5b
nt500	nucleotide-transformer-v2-500m-multi-species	InstaDeepAI	InstaDeepAI/nucleotide-transformer-v2-500m-multi-species	500	0.2	AutoTokenizer	tokenize_function_NT	LCA	6	6	nt	nt500
nt100	nucleotide-transformer-v2-100m-multi-species	InstaDeepAI	InstaDeepAI/nucleotide-transformer-v2-100m-multi-species	100	0.2	AutoTokenizer	tokenize_function_NT	LCA	6	6	nt	nt100
nt50	nucleotide-transformer-v2-50m-multi-species	InstaDeepAI	InstaDeepAI/nucleotide-transformer-v2-50m-multi-species	50	0.2	AutoTokenizer	tokenize_function_NT	LCA	6	6	nt	nt50
nt250	nucleotide-transformer-v2-250m-multi-species	InstaDeepAI	InstaDeepAI/nucleotide-transformer-v2-250m-multi-species	250	0.2	AutoTokenizer	tokenize_function_NT	LCA	6	6	nt	nt250
metagene1	METAGENE-1	metagene-ai	metagene-ai/METAGENE-1	7,000	0.3333	AutoTokenizer	tokenize_function_evo_metagene	BPE	null	null	mg1	metagene1
evo1-8k	evo-1-8k-base	togethercomputer	togethercomputer/evo-1-8k-base	7,000	1	AutoTokenizer	tokenize_function_evo_metagene	LCA	1	1	evo1	evo1-8k

ProkBERT Training Registry

JSON-backed training registry for ProkBERT and related nucleotide foundation models.

Files:

basemodels.json: model metadata and tokenizer dispatch.
default_training_parameters.json: default finetuning parameters by model and sequence-length range.
finetuning_task.json: placeholder task mapping from the workbook.
task.json: empty sheet placeholder preserved from the workbook.
manifest.json: simple schema and file manifest.

Conventions:

model_id is the canonical short internal model identifier.
basemodel is preserved from the original workbook.
seq_length_min / seq_length_max are raw sequence-length ranges.
max_token_length is the model-facing token-length cap used by training defaults.

This dataset is intended to be consumed directly from the Hugging Face Hub by the ProkBERT helper utilities.

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