support.md

Model support

This file is generated from src/fastplms/models.toml. A listed capability is selectable. Strict-parity exceptions are documented in the checkpoint cards.

Family interfaces

Family	Architecture	Checkpoints	Public input	AutoClasses	Tokenizer class
esm2	ESM2	5	Amino-acid sequences tokenized to residue IDs	AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification	n/a
esm_plusplus	ESMC	3	Amino-acid sequences tokenized to residue IDs	AutoConfig, AutoModel, AutoModelForMaskedLM	n/a
esm3	ESM3	1	Sequence, structure, and function tracks prepared through the multimodal helpers	AutoConfig, AutoModel	n/a
e1	E1	3	Raw amino-acid sequences prepared by the native E1 adapter	AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification	n/a
dplm	DPLM	3	Amino-acid sequences tokenized to masked or partially masked residue IDs	AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification	n/a
dplm2	DPLM2	3	Tokenized amino-acid and structure tracks with explicit modality boundaries	AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSequenceClassification, AutoModelForTokenClassification	fastplms.models.dplm2.tokenization_dplm2.DPLM2Tokenizer
ankh	ANKH	5	Amino-acid sequences tokenized for encoder or sequence-to-sequence use	AutoConfig, AutoModel, AutoModelForMaskedLM, AutoModelForSeq2SeqLM, AutoModelForSequenceClassification, AutoModelForTokenClassification	n/a
boltz2	Boltz2	1	Raw amino-acid sequences through the convenience API, or prepared model features	AutoConfig, AutoModel	n/a
esmfold	ESMFold	1	Raw amino-acid sequences through folding helpers, or prepared residue tensors	AutoConfig, AutoModel	n/a
esmfold2	ESMFold2	4	Raw amino-acid sequences or typed molecular-complex specifications; low-level forward accepts prepared feature tensors	AutoConfig, AutoModel	n/a

AutoClass weight status

pretrained means the advertised head is present in the checkpoint. base weights + untrained task head means the task head must be trained before use. FastPLMs extension is an integration or head that is not an official pretrained ANKH capability.

Family	AutoClass	Weight status
esm2	AutoConfig	FastPLMs extension
esm2	AutoModel	pretrained
esm2	AutoModelForMaskedLM	pretrained
esm2	AutoModelForSequenceClassification	base weights + untrained task head
esm2	AutoModelForTokenClassification	base weights + untrained task head
esm_plusplus	AutoConfig	FastPLMs extension
esm_plusplus	AutoModel	pretrained
esm_plusplus	AutoModelForMaskedLM	pretrained
esm3	AutoConfig	FastPLMs extension
esm3	AutoModel	pretrained
e1	AutoConfig	FastPLMs extension
e1	AutoModel	pretrained
e1	AutoModelForMaskedLM	pretrained
e1	AutoModelForSequenceClassification	base weights + untrained task head
e1	AutoModelForTokenClassification	base weights + untrained task head
dplm	AutoConfig	FastPLMs extension
dplm	AutoModel	pretrained
dplm	AutoModelForMaskedLM	pretrained
dplm	AutoModelForSequenceClassification	base weights + untrained task head
dplm	AutoModelForTokenClassification	base weights + untrained task head
dplm2	AutoConfig	FastPLMs extension
dplm2	AutoModel	pretrained
dplm2	AutoModelForMaskedLM	pretrained
dplm2	AutoModelForSequenceClassification	base weights + untrained task head
dplm2	AutoModelForTokenClassification	base weights + untrained task head
ankh	AutoConfig	FastPLMs extension
ankh	AutoModel	pretrained
ankh	AutoModelForMaskedLM	FastPLMs extension
ankh	AutoModelForSeq2SeqLM	pretrained
ankh	AutoModelForSequenceClassification	base weights + untrained task head
ankh	AutoModelForTokenClassification	base weights + untrained task head
boltz2	AutoConfig	FastPLMs extension
boltz2	AutoModel	pretrained
esmfold	AutoConfig	FastPLMs extension
esmfold	AutoModel	pretrained
esmfold2	AutoConfig	FastPLMs extension
esmfold2	AutoModel	pretrained

Family execution

Family	Attention	Precision	BF16 execution	Extra	Reference
esm2	eager, sdpa, flex_attention, flash_attention_2, flash_attention_3	default	fp32_parameters_autocast	core	reference-esm2
esm_plusplus	eager, sdpa, flex_attention, flash_attention_2, flash_attention_3	default, fp8 (experimental)	static_parameters	core	reference-biohub-esm
esm3	eager, sdpa, flex_attention	default	fp32_parameters_autocast	core	reference-biohub-esm
e1	sdpa, flex_attention	default	static_parameters	core	reference-e1
dplm	eager, sdpa, flex_attention, flash_attention_3	default	fp32_parameters_autocast	core	reference-dplm
dplm2	sdpa	default	fp32_parameters_autocast	core	reference-dplm
ankh	eager, sdpa	default	static_parameters	core	reference-ankh
boltz2	eager	default	fp32_parameters_autocast	structure	reference-boltz2
esmfold	eager, sdpa, flex_attention	default	fp32_parameters_autocast	structure	reference-esmfold
esmfold2	eager, sdpa, flex_attention	auto, fp32, bf16, fp8 (experimental)	fp32_parameters_autocast	structure	reference-esmfold2

Family release contracts

Family	Checkpoint terms	Hub license	Weight publication	Tiers
esm2	MIT	mit	manifest policy	check, compliance, feature, artifact, benchmark
esm_plusplus	MIT	mit	manifest policy	check, compliance, feature, artifact, benchmark
esm3	MIT	mit	manifest policy	check, compliance, feature, artifact, benchmark
e1	Profluent-E1-Agreement	other (Profluent-E1 Clickthrough License Agreement)	manifest policy	check, compliance, feature, artifact, benchmark
dplm	Apache-2.0	apache-2.0	manifest policy	check, compliance, feature, artifact, benchmark
dplm2	Apache-2.0	apache-2.0	manifest policy	check, compliance, feature, artifact, benchmark
ankh	CC-BY-NC-SA-4.0	cc-by-nc-sa-4.0	manifest policy	check, compliance, feature, artifact, benchmark
boltz2	MIT	mit	manifest policy	structure, artifact, benchmark
esmfold	MIT	mit	manifest policy	check, compliance, structure, feature, artifact, benchmark
esmfold2	MIT	mit	manifest policy	check, compliance, structure, feature, artifact, benchmark

Runtime assets

ID	Family	Repository	Path	SHA-256	Size	License	Trust boundary	Offline behavior
esmfold2_ccd	esmfold2	biohub/ESMFold2	ccd.pkl	9ff44b1927c6b9198e38ffe0928706827a09a350c15530beeeabebfa88038fc5	417306584	MIT	hash_pinned_pickle	requires_cached_verified_file

Checkpoints

ID	Family	Size	FastPLMs checkpoint	Official checkpoint	Artifact source	State transform	Generation contract	MSA conditioning	Unresolved files
esm2_8m	esm2	small	Synthyra/ESM2-8M	facebook/esm2_t6_8M_UR50D	fast	esm2_hf_to_fastplms_v1	not_applicable	not applicable	0
esm2_35m	esm2	small	Synthyra/ESM2-35M	facebook/esm2_t12_35M_UR50D	fast	esm2_hf_to_fastplms_v1	not_applicable	not applicable	0
esm2_150m	esm2	medium	Synthyra/ESM2-150M	facebook/esm2_t30_150M_UR50D	fast	esm2_hf_to_fastplms_v1	not_applicable	not applicable	0
esm2_650m	esm2	large	Synthyra/ESM2-650M	facebook/esm2_t33_650M_UR50D	fast	esm2_hf_to_fastplms_v1	not_applicable	not applicable	0
esm2_3b	esm2	xlarge	Synthyra/ESM2-3B	facebook/esm2_t36_3B_UR50D	fast	esm2_hf_to_fastplms_v1	not_applicable	not applicable	0
esmc_small	esm_plusplus	medium	Synthyra/ESMplusplus_small	biohub/ESMC-300M	fast	esmc_to_fastplms_v1	not_applicable	not applicable	0
esmc_large	esm_plusplus	large	Synthyra/ESMplusplus_large	biohub/ESMC-600M	fast	esmc_to_fastplms_v1	not_applicable	not applicable	0
esmc_6b	esm_plusplus	xlarge	Synthyra/ESMplusplus_6B	biohub/ESMC-6B	fast	esmc_to_fastplms_v1	not_applicable	not applicable	0
esm3_small	esm3	large	Synthyra/ESM3_small	biohub/esm3-sm-open-v1	fast	esm3_to_fastplms_v1	not_applicable	not applicable	0
e1_150m	e1	small	Synthyra/Profluent-E1-150M	Profluent-Bio/E1-150m	fast	e1_to_fastplms_v1	not_applicable	not applicable	0
e1_300m	e1	medium	Synthyra/Profluent-E1-300M	Profluent-Bio/E1-300m	fast	e1_to_fastplms_v1	not_applicable	not applicable	0
e1_600m	e1	large	Synthyra/Profluent-E1-600M	Profluent-Bio/E1-600m	fast	e1_to_fastplms_v1	not_applicable	not applicable	0
dplm_150m	dplm	small	Synthyra/DPLM-150M	airkingbd/dplm_150m	fast	dplm_to_fastplms_v1	required	not applicable	0
dplm_650m	dplm	large	Synthyra/DPLM-650M	airkingbd/dplm_650m	fast	dplm_to_fastplms_v1	required	not applicable	0
dplm_3b	dplm	xlarge	Synthyra/DPLM-3B	airkingbd/dplm_3b	fast	dplm_to_fastplms_v1	required	not applicable	0
dplm2_150m	dplm2	small	Synthyra/DPLM2-150M	airkingbd/dplm2_150m	official	dplm2_to_fastplms_v1	required	not applicable	0
dplm2_650m	dplm2	large	Synthyra/DPLM2-650M	airkingbd/dplm2_650m	official	dplm2_to_fastplms_v1	required	not applicable	0
dplm2_3b	dplm2	xlarge	Synthyra/DPLM2-3B	airkingbd/dplm2_3b	official	dplm2_to_fastplms_v1	official_unavailable	not applicable	0
ankh_base	ankh	medium	Synthyra/ANKH_base	ElnaggarLab/ankh-base	official	ankh_t5_to_fastplms_v1	required	not applicable	0
ankh_large	ankh	large	Synthyra/ANKH_large	ElnaggarLab/ankh-large	official	ankh_t5_to_fastplms_v1	required	not applicable	0
ankh2_large	ankh	large	Synthyra/ANKH2_large	ElnaggarLab/ankh2-ext2	official	ankh_t5_to_fastplms_v1	required	not applicable	0
ankh3_large	ankh	large	Synthyra/ANKH3_large	ElnaggarLab/ankh3-large	official	ankh_t5_to_fastplms_v1	required	not applicable	0
ankh3_xl	ankh	xlarge	Synthyra/ANKH3_xl	ElnaggarLab/ankh3-xl	official	ankh_t5_to_fastplms_v1	required	not applicable	0
boltz2	boltz2	structure	Synthyra/Boltz2	boltz-community/boltz-2	fast	boltz2_inference_core_v1	not_applicable	not applicable	0
esmfold	esmfold	structure	Synthyra/FastESMFold	facebook/esmfold_v1	fast	esmfold_meta_to_fastplms_v1	not_applicable	not applicable	0
esmfold2	esmfold2	structure	Synthyra/ESMFold2	biohub/ESMFold2	fast	identity	not_applicable	optional (full checkpoint)	0
esmfold2_fast	esmfold2	structure	Synthyra/ESMFold2-Fast	biohub/ESMFold2-Fast	fast	identity	not_applicable	none (Fast; MSA inputs rejected)	0
esmfold2_experimental_cutoff2025	esmfold2	structure	Synthyra/ESMFold2-Experimental-Cutoff2025	biohub/ESMFold2-Experimental-Cutoff2025	fast	identity	not_applicable	optional (full checkpoint)	0
esmfold2_experimental_fast_cutoff2025	esmfold2	structure	Synthyra/ESMFold2-Experimental-Fast-Cutoff2025	biohub/ESMFold2-Experimental-Fast-Cutoff2025	fast	identity	not_applicable	none (Fast; MSA inputs rejected)	0

A nonzero unresolved-file count blocks release. It is not permission to omit that file from checkpoint, tokenizer, artifact, or compliance checks.