syntheseus-runtime / checkpoints /forward_runtime_registry.json
Ian-L's picture
Add files using upload-large-folder tool
73fd193 verified
Raw
History Blame Contribute Delete
21.3 kB
{
"checkpoints": [
{
"auxiliary_files": [
"aux/bart_vocab.json",
"aux/bart_vocab_downstream.json",
"aux/ds_config.json",
"aux/hparams.yaml",
"aux/hyper_parameters.json",
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json",
"benchmarks/native/uspto_mixed.pickle"
],
"benchmark_datasets": [
{
"benchmark_semantics": "forward_product_prediction_with_mixed_inputs",
"benchmark_variant": "forward_product_prediction",
"dataset_id": "uspto_mixed_forward_checkpoint_test",
"dataset_ref": "uspto_mixed_chemformer_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "pandas_pickled_dataframe",
"native_source_paths": [
"benchmarks/native/uspto_mixed.pickle"
],
"notes": [
"Native Chemformer forward benchmark source extracted from the public Box release uspto_mixed pickle.",
"benchmarks/default_test.jsonl preserves reactant-side input SMILES plus expected product SMILES from the test partition."
],
"num_examples": 40000,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants"
],
"targets": [
"expected_products"
]
},
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "uspto_mixed_forward_checkpoint",
"display_name": "uspto_mixed forward checkpoint",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": "Forward Chemformer checkpoint fine-tuned on the public USPTO_mixed product-prediction split.",
"fine_tuning_role": "task_finetuned_seed",
"fine_tuning_supported": true,
"hf_model_name": null,
"host": "Box shared folder",
"inference_supported": true,
"input_schema": {
"reactants_field": "reactants_mol",
"reagents_field": null,
"serialization": "dot_joined_smiles",
"source_dataset_member": "data/seq-to-seq_datasets/uspto_mixed.pickle",
"target_field": "products_mol"
},
"larger_than_uspto50k": false,
"model_id": "chemformer_forward",
"model_name": "Chemformer Forward",
"normalized_checkpoint_id": "uspto_mixed_forward_checkpoint",
"package_dir": "checkpoints/chemformer_forward/uspto_mixed_forward_checkpoint",
"remote_url": "https://az.app.box.com/s/7eci3nd9vy0xplqniitpk02rbg9q2zcq/folder/145317555751",
"source_registry_refs": [
{
"checkpoint_id": "uspto_mixed_forward_checkpoint",
"model_id": "chemformer_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"uspto_mixed_chemformer_project_release"
],
"unsupported_reason": null,
"weights_path": "model.safetensors",
"wrapper_class": "syntheseus_wrappers.wrappers.chemformer_forward.ChemformerForwardModel",
"wrapper_family": "chemformer_bart"
},
{
"auxiliary_files": [
"aux/bart_vocab.json",
"aux/bart_vocab_downstream.json",
"aux/ds_config.json",
"aux/hparams.yaml",
"aux/hyper_parameters.json",
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json",
"benchmarks/native/uspto_sep.pickle"
],
"benchmark_datasets": [
{
"benchmark_semantics": "forward_product_prediction_with_separated_reagents",
"benchmark_variant": "forward_product_prediction",
"dataset_id": "uspto_sep_forward_checkpoint_test",
"dataset_ref": "uspto_sep_chemformer_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "pandas_pickled_dataframe",
"native_source_paths": [
"benchmarks/native/uspto_sep.pickle"
],
"notes": [
"Native Chemformer forward benchmark source extracted from the public Box release uspto_sep pickle.",
"benchmarks/default_test.jsonl preserves separated reactants/reagents fields plus expected product SMILES from the test partition."
],
"num_examples": 40000,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants",
"reagents"
],
"targets": [
"expected_products"
]
},
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "uspto_sep_forward_checkpoint",
"display_name": "uspto_sep forward checkpoint",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": "Forward Chemformer checkpoint fine-tuned on the public USPTO_sep product-prediction split.",
"fine_tuning_role": "task_finetuned_seed",
"fine_tuning_supported": true,
"hf_model_name": null,
"host": "Box shared folder",
"inference_supported": true,
"input_schema": {
"reactants_field": "reactants_mol",
"reagents_field": "reagents_mol",
"serialization": "dot_joined_smiles",
"source_dataset_member": "data/seq-to-seq_datasets/uspto_sep.pickle",
"target_field": "products_mol"
},
"larger_than_uspto50k": false,
"model_id": "chemformer_forward",
"model_name": "Chemformer Forward",
"normalized_checkpoint_id": "uspto_sep_forward_checkpoint",
"package_dir": "checkpoints/chemformer_forward/uspto_sep_forward_checkpoint",
"remote_url": "https://az.app.box.com/s/7eci3nd9vy0xplqniitpk02rbg9q2zcq/folder/145317555751",
"source_registry_refs": [
{
"checkpoint_id": "uspto_sep_forward_checkpoint",
"model_id": "chemformer_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"uspto_sep_chemformer_project_release"
],
"unsupported_reason": null,
"weights_path": "model.safetensors",
"wrapper_class": "syntheseus_wrappers.wrappers.chemformer_forward.ChemformerForwardModel",
"wrapper_family": "chemformer_bart"
},
{
"auxiliary_files": [
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json",
"benchmarks/native/src-test.txt",
"benchmarks/native/tgt-test.txt"
],
"benchmark_datasets": [
{
"benchmark_semantics": "forward_product_prediction_with_mixed_inputs",
"benchmark_variant": "forward_product_prediction",
"dataset_id": "mit_mixed_augm_model_average_20_pt_test",
"dataset_ref": "uspto_mit_molecular_transformer_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "parallel_tokenized_smiles",
"native_source_paths": [
"benchmarks/native/src-test.txt",
"benchmarks/native/tgt-test.txt"
],
"notes": [
"Native Molecular Transformer benchmark sources are the official tokenized test split files from the public Box release.",
"benchmarks/default_test.jsonl stores detokenized mixed-input reactant strings mapped to expected product SMILES for forward evaluation."
],
"num_examples": 40000,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants"
],
"targets": [
"expected_products"
]
},
"serialized_input_format": "space_tokenized_smiles",
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "mit_mixed_augm_model_average_20_pt",
"display_name": "MIT_mixed_augm_model_average_20.pt",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": null,
"fine_tuning_role": null,
"fine_tuning_supported": false,
"hf_model_name": null,
"host": "IBM Box shared folder",
"inference_supported": true,
"input_schema": {
"benchmark_variant": "forward_product_prediction",
"reactants_field": "reactants_mixed",
"serialized_format": "space_tokenized_smiles",
"target_field": "PRODUCT",
"tokenizer": "smiles_regex_space_tokenizer"
},
"larger_than_uspto50k": true,
"model_id": "molecular_transformer_forward",
"model_name": "Molecular Transformer Forward",
"normalized_checkpoint_id": "mit_mixed_augm_model_average_20_pt",
"package_dir": "checkpoints/molecular_transformer_forward/mit_mixed_augm_model_average_20_pt",
"remote_url": "https://ibm.box.com/v/MolecularTransformerModels",
"source_registry_refs": [
{
"checkpoint_id": "mit_mixed_augm_model_average_20_pt",
"model_id": "molecular_transformer_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"uspto_mit_molecular_transformer_project_release"
],
"unsupported_reason": null,
"weights_path": "model.pt",
"wrapper_class": "syntheseus_wrappers.wrappers.molecular_transformer_forward.MolecularTransformerForwardModel",
"wrapper_family": "opennmt_transformer"
},
{
"auxiliary_files": [
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json",
"benchmarks/native/src-test.txt",
"benchmarks/native/tgt-test.txt"
],
"benchmark_datasets": [
{
"benchmark_semantics": "forward_product_prediction_with_mixed_inputs",
"benchmark_variant": "forward_product_prediction",
"dataset_id": "stereo_mixed_augm_model_average_20_pt_test",
"dataset_ref": "uspto_stereo_molecular_transformer_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "parallel_tokenized_smiles",
"native_source_paths": [
"benchmarks/native/src-test.txt",
"benchmarks/native/tgt-test.txt"
],
"notes": [
"Native Molecular Transformer benchmark sources are the official tokenized test split files from the public Box release.",
"benchmarks/default_test.jsonl stores detokenized mixed-input reactant strings mapped to expected product SMILES for forward evaluation."
],
"num_examples": 50258,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants"
],
"targets": [
"expected_products"
]
},
"serialized_input_format": "space_tokenized_smiles",
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "stereo_mixed_augm_model_average_20_pt",
"display_name": "STEREO_mixed_augm_model_average_20.pt",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": null,
"fine_tuning_role": null,
"fine_tuning_supported": false,
"hf_model_name": null,
"host": "IBM Box shared folder",
"inference_supported": true,
"input_schema": {
"benchmark_variant": "forward_product_prediction",
"reactants_field": "reactants_mixed",
"serialized_format": "space_tokenized_smiles",
"target_field": "PRODUCT",
"tokenizer": "smiles_regex_space_tokenizer"
},
"larger_than_uspto50k": true,
"model_id": "molecular_transformer_forward",
"model_name": "Molecular Transformer Forward",
"normalized_checkpoint_id": "stereo_mixed_augm_model_average_20_pt",
"package_dir": "checkpoints/molecular_transformer_forward/stereo_mixed_augm_model_average_20_pt",
"remote_url": "https://ibm.box.com/v/MolecularTransformerModels",
"source_registry_refs": [
{
"checkpoint_id": "stereo_mixed_augm_model_average_20_pt",
"model_id": "molecular_transformer_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"uspto_stereo_molecular_transformer_project_release"
],
"unsupported_reason": null,
"weights_path": "model.pt",
"wrapper_class": "syntheseus_wrappers.wrappers.molecular_transformer_forward.MolecularTransformerForwardModel",
"wrapper_family": "opennmt_transformer"
},
{
"auxiliary_files": [
"aux/.gitattributes",
"aux/README.md",
"aux/UPSTREAM_URL.txt",
"aux/config.json",
"aux/generation_config.json",
"aux/hf_model_info.json",
"aux/provenance/README.txt",
"aux/provenance/ReactionT5v2_source_README.md",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_test.csv",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_train.csv",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_valid.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/test.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/train.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/val.csv",
"aux/provenance/reactiont5v2_forward_split_provenance.json",
"aux/special_tokens_map.json",
"aux/tokenizer.json",
"aux/tokenizer_config.json",
"aux/trainer_state.json",
"aux/training_args.bin",
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json"
],
"benchmark_datasets": [
{
"benchmark_semantics": "ord_trained_forward_checkpoint_evaluated_on_uspto_mit_holdout",
"benchmark_variant": "forward_product_prediction",
"blank_reagent_value": " ",
"dataset_id": "sagawa_reactiont5v2_forward_test",
"dataset_ref": "uspto_mit_forward_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "csv_forward_reaction_rows",
"native_source_paths": [
"aux/provenance/datasets/USPTO_MIT/MIT_separated/test.csv"
],
"notes": [
"Native forward benchmark split for the public USPTO_MIT product-prediction task.",
"The normalized JSONL preserves reactants, reagents, and expected product(s) rather than the backward exact-match schema.",
"This ORD-trained checkpoint is evaluated on the USPTO_MIT holdout documented in the upstream README/model card."
],
"num_examples": 40000,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants",
"reagents"
],
"targets": [
"expected_products"
]
},
"serialized_input_format": "REACTANT:<reactants>REAGENT:<reagents>",
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "sagawa_reactiont5v2_forward",
"display_name": "sagawa/ReactionT5v2-forward",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": "ORD-trained forward-synthesis checkpoint that can serve as a continued-training seed.",
"fine_tuning_role": "task_finetuned_seed",
"fine_tuning_supported": true,
"hf_model_name": "sagawa/ReactionT5v2-forward",
"host": "Hugging Face",
"inference_supported": true,
"input_schema": {
"blank_reagent_value": " ",
"reactants_field": "REACTANT",
"reagents_field": "REAGENT",
"serialized_format": "REACTANT:<reactants>REAGENT:<reagents>",
"target_field": "PRODUCT"
},
"larger_than_uspto50k": true,
"model_id": "reactiont5v2_forward",
"model_name": "ReactionT5v2 Forward",
"normalized_checkpoint_id": "sagawa_reactiont5v2_forward",
"package_dir": "checkpoints/reactiont5v2_forward/sagawa_reactiont5v2_forward",
"remote_url": "https://huggingface.co/sagawa/ReactionT5v2-forward",
"source_registry_refs": [
{
"checkpoint_id": "sagawa_reactiont5v2_forward",
"model_id": "reactiont5v2_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"ord_forward_pretraining"
],
"unsupported_reason": null,
"weights_path": "model.safetensors",
"wrapper_class": "syntheseus_wrappers.wrappers.reactiont5v2_forward.ReactionT5v2ForwardModel",
"wrapper_family": "seq2seq_t5"
},
{
"auxiliary_files": [
"aux/.gitattributes",
"aux/README.md",
"aux/UPSTREAM_URL.txt",
"aux/config.json",
"aux/generation_config.json",
"aux/hf_model_info.json",
"aux/provenance/README.txt",
"aux/provenance/ReactionT5v2_source_README.md",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_test.csv",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_train.csv",
"aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_valid.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/test.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/train.csv",
"aux/provenance/datasets/USPTO_MIT/MIT_separated/val.csv",
"aux/provenance/reactiont5v2_forward_split_provenance.json",
"aux/special_tokens_map.json",
"aux/tokenizer.json",
"aux/tokenizer_config.json",
"aux/trainer_state.json",
"aux/training_args.bin",
"benchmarks/default_test.jsonl",
"benchmarks/metadata.json"
],
"benchmark_datasets": [
{
"benchmark_semantics": "benchmark_specific_finetuned_forward_checkpoint",
"benchmark_variant": "forward_product_prediction",
"blank_reagent_value": " ",
"dataset_id": "sagawa_reactiont5v2_forward_uspto_mit_test",
"dataset_ref": "uspto_mit_forward_project_release",
"default": true,
"format": "jsonl",
"metadata_path": "benchmarks/metadata.json",
"native_input_format": "csv_forward_reaction_rows",
"native_source_paths": [
"aux/provenance/datasets/USPTO_MIT/MIT_separated/test.csv"
],
"notes": [
"Native forward benchmark split for the public USPTO_MIT product-prediction task.",
"The normalized JSONL preserves reactants, reagents, and expected product(s) rather than the backward exact-match schema.",
"This is the native USPTO_MIT fine-tuned forward checkpoint benchmark split."
],
"num_examples": 40000,
"path": "benchmarks/default_test.jsonl",
"record_schema": {
"inputs": [
"reactants",
"reagents"
],
"targets": [
"expected_products"
]
},
"serialized_input_format": "REACTANT:<reactants>REAGENT:<reagents>",
"split": "test",
"task_direction": "forward"
}
],
"checkpoint_id": "sagawa_reactiont5v2_forward_uspto_mit",
"display_name": "sagawa/ReactionT5v2-forward-USPTO_MIT",
"embedding_modes": [],
"embedding_supported": false,
"fine_tuning_notes": "USPTO_MIT fine-tuned forward-synthesis checkpoint that can be adapted further.",
"fine_tuning_role": "task_finetuned_seed",
"fine_tuning_supported": true,
"hf_model_name": "sagawa/ReactionT5v2-forward-USPTO_MIT",
"host": "Hugging Face",
"inference_supported": true,
"input_schema": {
"blank_reagent_value": " ",
"reactants_field": "REACTANT",
"reagents_field": "REAGENT",
"serialized_format": "REACTANT:<reactants>REAGENT:<reagents>",
"target_field": "PRODUCT"
},
"larger_than_uspto50k": true,
"model_id": "reactiont5v2_forward",
"model_name": "ReactionT5v2 Forward",
"normalized_checkpoint_id": "sagawa_reactiont5v2_forward_uspto_mit",
"package_dir": "checkpoints/reactiont5v2_forward/sagawa_reactiont5v2_forward_uspto_mit",
"remote_url": "https://huggingface.co/sagawa/ReactionT5v2-forward-USPTO_MIT",
"source_registry_refs": [
{
"checkpoint_id": "sagawa_reactiont5v2_forward_uspto_mit",
"model_id": "reactiont5v2_forward"
}
],
"task_direction": "forward",
"training_dataset_refs": [
"uspto_mit_forward_project_release"
],
"unsupported_reason": null,
"weights_path": "model.safetensors",
"wrapper_class": "syntheseus_wrappers.wrappers.reactiont5v2_forward.ReactionT5v2ForwardModel",
"wrapper_family": "seq2seq_t5"
}
],
"registry_kind": "runtime",
"runtime_registry_version": 1
}