| { |
| "checkpoints": [ |
| { |
| "auxiliary_files": [ |
| "aux/config.yml", |
| "aux/uspto_filter_model.onnx", |
| "aux/uspto_templates.csv.gz", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "paroutes_reference_route_holdout", |
| "dataset_id": "aizynthfinder_uspto_onnx_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "Default bundled benchmark for the public AiZynthFinder USPTO ONNX policy.", |
| "The benchmark rows are reconstructed from PaRoutes selected_reactions.csv and ref_routes_reaction_hashes.txt so they match the held-out reference-route reactions used as the AiZynthTrain test set." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_model_onnx", |
| "display_name": "uspto_model.onnx", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "Zenodo", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "aizynthfinder", |
| "model_name": "AiZynthFinder", |
| "normalized_checkpoint_id": "uspto_model_onnx", |
| "package_dir": "checkpoints/aizynthfinder/uspto_model_onnx", |
| "remote_url": "https://zenodo.org/records/11430881", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_model_onnx", |
| "model_id": "aizynthfinder" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "aizynthtrain_uspto_selected_reactions_with_paroutes_holdout" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.onnx", |
| "wrapper_class": "syntheseus_wrappers.wrappers.aizynthfinder.AiZynthFinderModel", |
| "wrapper_family": "aizynthfinder_template_policy" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/at_handler.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/opennmt_metadata.pt", |
| "aux/opennmt_opt_summary.json", |
| "aux/safetensors_conversion.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "benchmark_pending", |
| "dataset_id": "askcos_retro_augmented_transformer_pistachio_23q3_benchmark_pending", |
| "dataset_ref": "askcos_pistachio_23q3_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "benchmark_not_available", |
| "native_source_paths": [], |
| "notes": [ |
| "No redistribution-safe native benchmark split for this ASKCOS model archive is staged in this repository.", |
| "The bundle keeps benchmark metadata so downstream tooling can distinguish unavailable benchmarks from accidental omissions." |
| ], |
| "num_examples": 0, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio_23q3", |
| "display_name": "ASKCOS Retro Augmented Transformer pistachio_23Q3", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_augmented_transformer", |
| "model_name": "ASKCOS Retro Augmented Transformer", |
| "normalized_checkpoint_id": "pistachio_23q3", |
| "package_dir": "checkpoints/askcos_retro_augmented_transformer/pistachio_23q3", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/augmented_transformer", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio_23q3", |
| "model_id": "askcos_retro_augmented_transformer" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_pistachio_23q3_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_augmented_transformer.AskcosRetroAugmentedTransformerModel", |
| "wrapper_family": "askcos_augmented_transformer" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/at_handler.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/opennmt_metadata.pt", |
| "aux/opennmt_opt_summary.json", |
| "aux/safetensors_conversion.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_uspto_full_r_smiles_compatibility_view", |
| "dataset_id": "askcos_retro_augmented_transformer_uspto_full_uspto_full_test", |
| "dataset_ref": "uspto_full_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute a native USPTO-FULL benchmark CSV with this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundle uses the public R-SMILES/GLN USPTO-FULL tokenized test split as a redistribution-safe compatibility view.", |
| "benchmarks/default_test.jsonl collapses the contiguous augmentation factor of 5 back to one benchmark case per underlying reaction." |
| ], |
| "num_examples": 96023, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_full", |
| "display_name": "ASKCOS Retro Augmented Transformer USPTO_FULL", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_augmented_transformer", |
| "model_name": "ASKCOS Retro Augmented Transformer", |
| "normalized_checkpoint_id": "uspto_full", |
| "package_dir": "checkpoints/askcos_retro_augmented_transformer/uspto_full", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/augmented_transformer", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_full", |
| "model_id": "askcos_retro_augmented_transformer" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_uspto_full_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_augmented_transformer.AskcosRetroAugmentedTransformerModel", |
| "wrapper_family": "askcos_augmented_transformer" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/checkpoint_metadata.json", |
| "aux/graph2smiles_runtime/models/attention_xl.py", |
| "aux/graph2smiles_runtime/models/dgat.py", |
| "aux/graph2smiles_runtime/models/dgcn.py", |
| "aux/graph2smiles_runtime/models/graph2smiles.py", |
| "aux/graph2smiles_runtime/models/graphfeat.py", |
| "aux/graph2smiles_runtime/models/model_utils.py", |
| "aux/graph2smiles_runtime/models/transformer_decoder.py", |
| "aux/graph2smiles_runtime/predict.py", |
| "aux/graph2smiles_runtime/train.py", |
| "aux/graph2smiles_runtime/utils/c_calculate.so", |
| "aux/graph2smiles_runtime/utils/chem_utils.py", |
| "aux/graph2smiles_runtime/utils/ctypes_calculator.py", |
| "aux/graph2smiles_runtime/utils/data_utils.py", |
| "aux/graph2smiles_runtime/utils/parsing.py", |
| "aux/graph2smiles_runtime/utils/preprocess_utils.py", |
| "aux/graph2smiles_runtime/utils/rxn_graphs.py", |
| "aux/graph2smiles_runtime/utils/train_utils.py", |
| "aux/mar_files/handler.py", |
| "aux/mar_files/models.zip", |
| "aux/mar_files/predict.py", |
| "aux/mar_files/train.py", |
| "aux/mar_files/utils.zip", |
| "aux/mar_files/vocab.txt", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/vocab.txt", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "benchmark_pending", |
| "dataset_id": "askcos_retro_graph2smiles_pistachio_23q3_benchmark_pending", |
| "dataset_ref": "askcos_pistachio_23q3_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "benchmark_not_available", |
| "native_source_paths": [], |
| "notes": [ |
| "No redistribution-safe native benchmark split for this ASKCOS model archive is staged in this repository.", |
| "The bundle keeps benchmark metadata so downstream tooling can distinguish unavailable benchmarks from accidental omissions." |
| ], |
| "num_examples": 0, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio_23q3", |
| "display_name": "ASKCOS Retro Graph2SMILES pistachio_23Q3", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_graph2smiles", |
| "model_name": "ASKCOS Retro Graph2SMILES", |
| "normalized_checkpoint_id": "pistachio_23q3", |
| "package_dir": "checkpoints/askcos_retro_graph2smiles/pistachio_23q3", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/graph2smiles", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio_23q3", |
| "model_id": "askcos_retro_graph2smiles" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_pistachio_23q3_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_graph2smiles.AskcosRetroGraph2SmilesModel", |
| "wrapper_family": "askcos_graph2smiles" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/checkpoint_metadata.json", |
| "aux/graph2smiles_runtime/models/attention_xl.py", |
| "aux/graph2smiles_runtime/models/dgat.py", |
| "aux/graph2smiles_runtime/models/dgcn.py", |
| "aux/graph2smiles_runtime/models/graph2smiles.py", |
| "aux/graph2smiles_runtime/models/graphfeat.py", |
| "aux/graph2smiles_runtime/models/model_utils.py", |
| "aux/graph2smiles_runtime/models/transformer_decoder.py", |
| "aux/graph2smiles_runtime/predict.py", |
| "aux/graph2smiles_runtime/train.py", |
| "aux/graph2smiles_runtime/utils/c_calculate.so", |
| "aux/graph2smiles_runtime/utils/chem_utils.py", |
| "aux/graph2smiles_runtime/utils/ctypes_calculator.py", |
| "aux/graph2smiles_runtime/utils/data_utils.py", |
| "aux/graph2smiles_runtime/utils/parsing.py", |
| "aux/graph2smiles_runtime/utils/preprocess_utils.py", |
| "aux/graph2smiles_runtime/utils/rxn_graphs.py", |
| "aux/graph2smiles_runtime/utils/train_utils.py", |
| "aux/mar_files/handler.py", |
| "aux/mar_files/models.zip", |
| "aux/mar_files/predict.py", |
| "aux/mar_files/train.py", |
| "aux/mar_files/utils.zip", |
| "aux/mar_files/vocab.txt", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/vocab.txt", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_uspto_full_r_smiles_compatibility_view", |
| "dataset_id": "askcos_retro_graph2smiles_uspto_full_uspto_full_test", |
| "dataset_ref": "uspto_full_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute a native USPTO-FULL benchmark CSV with this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundle uses the public R-SMILES/GLN USPTO-FULL tokenized test split as a redistribution-safe compatibility view.", |
| "benchmarks/default_test.jsonl collapses the contiguous augmentation factor of 5 back to one benchmark case per underlying reaction." |
| ], |
| "num_examples": 96023, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_full", |
| "display_name": "ASKCOS Retro Graph2SMILES USPTO_FULL", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_graph2smiles", |
| "model_name": "ASKCOS Retro Graph2SMILES", |
| "normalized_checkpoint_id": "uspto_full", |
| "package_dir": "checkpoints/askcos_retro_graph2smiles/uspto_full", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/graph2smiles", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_full", |
| "model_id": "askcos_retro_graph2smiles" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_uspto_full_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_graph2smiles.AskcosRetroGraph2SmilesModel", |
| "wrapper_family": "askcos_graph2smiles" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_bkms_metabolic_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "bkms_metabolic", |
| "display_name": "bkms_metabolic", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": false, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "bkms_metabolic", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/bkms_metabolic", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "bkms_metabolic", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_bkms_metabolic_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_pistachio_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio", |
| "display_name": "pistachio", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "pistachio", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/pistachio", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_pistachio_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_pistachio_ringbreaker_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio_ringbreaker", |
| "display_name": "pistachio_ringbreaker", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "pistachio_ringbreaker", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/pistachio_ringbreaker", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio_ringbreaker", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_pistachio_ringbreaker_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_reaxys_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "reaxys", |
| "display_name": "reaxys", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "reaxys", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/reaxys", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "reaxys", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_reaxys_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_reaxys_biocatalysis_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "reaxys_biocatalysis", |
| "display_name": "reaxys_biocatalysis", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "reaxys_biocatalysis", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/reaxys_biocatalysis", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "reaxys_biocatalysis", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_reaxys_biocatalysis_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/MAR-INF/MANIFEST.json", |
| "aux/mar_files/misc.py", |
| "aux/mar_files/models.py", |
| "aux/mar_files/templ_rel_handler.py", |
| "aux/mar_files/templ_rel_parser.py", |
| "aux/mar_files/utils.py", |
| "aux/mar_members.json", |
| "aux/model_args.json", |
| "aux/safetensors_conversion.json", |
| "aux/templates.jsonl", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/ref_routes_reaction_hashes.txt", |
| "benchmarks/native/selected_reactions.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "askcos_paroutes_compatibility_view", |
| "dataset_id": "askcos_retro_template_relevance_uspto_higher_level_paroutes_reference_route_test", |
| "dataset_ref": "paroutes2_reference_route_reactions", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tab_delimited_reactants_reagents_product_rows", |
| "native_source_paths": [ |
| "benchmarks/native/selected_reactions.csv", |
| "benchmarks/native/ref_routes_reaction_hashes.txt" |
| ], |
| "notes": [ |
| "ASKCOS does not redistribute the native train/validation/test split for this TorchServe archive in datasets/modelos_ASKCOS.", |
| "This bundled benchmark is therefore a public PaRoutes one-step retrosynthesis compatibility view, not a claim about the model's original validation split." |
| ], |
| "num_examples": 56657, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_higher_level", |
| "display_name": "uspto_higher_level", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "ASKCOSv2 TorchServe MAR", |
| "inference_supported": true, |
| "input_schema": { |
| "product_field": "smiles", |
| "request_format": { |
| "smiles": [ |
| "product_smiles" |
| ] |
| }, |
| "target_field": "reactants" |
| }, |
| "larger_than_uspto50k": true, |
| "model_id": "askcos_retro_template_relevance", |
| "model_name": "ASKCOS Retro Template Relevance", |
| "normalized_checkpoint_id": "uspto_higher_level", |
| "package_dir": "checkpoints/askcos_retro_template_relevance/uspto_higher_level", |
| "remote_url": "https://gitlab.com/mlpds_mit/askcosv2/retro/template_relevance", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_higher_level", |
| "model_id": "askcos_retro_template_relevance" |
| } |
| ], |
| "task_direction": "retrosynthesis", |
| "training_dataset_refs": [ |
| "askcos_uspto_higher_level_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.core.wrappers.askcos_template_relevance.AskcosRetroTemplateRelevanceModel", |
| "wrapper_family": "askcos_template_relevance" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/bart_vocab.json", |
| "aux/bart_vocab_downstream.json", |
| "aux/ds_config.json", |
| "aux/hparams.yaml", |
| "aux/hyper_parameters.json" |
| ], |
| "checkpoint_id": "combined_large_pre_trained_checkpoint", |
| "display_name": "combined-large pre-trained checkpoint", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "base_pretraining", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Box shared folder", |
| "inference_supported": false, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "chemformer", |
| "model_name": "Chemformer", |
| "normalized_checkpoint_id": "combined_large_pre_trained_checkpoint", |
| "package_dir": "checkpoints/chemformer/combined_large_pre_trained_checkpoint", |
| "remote_url": "https://az.app.box.com/s/7eci3nd9vy0xplqniitpk02rbg9q2zcq/folder/144881806154", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "combined_large_pre_trained_checkpoint", |
| "model_id": "chemformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "zinc15_100m_chemformer_pretraining" |
| ], |
| "unsupported_reason": "pretraining-only Chemformer large bundle; not a retrosynthesis fine-tuned backward reaction checkpoint", |
| "weights_path": "model.safetensors", |
| "wrapper_class": null, |
| "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" |
| ], |
| "checkpoint_id": "combined_pre_trained_base_checkpoint", |
| "display_name": "combined pre-trained base checkpoint", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "base_pretraining", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Box shared folder", |
| "inference_supported": false, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "chemformer", |
| "model_name": "Chemformer", |
| "normalized_checkpoint_id": "combined_pre_trained_base_checkpoint", |
| "package_dir": "checkpoints/chemformer/combined_pre_trained_base_checkpoint", |
| "remote_url": "https://az.app.box.com/s/7eci3nd9vy0xplqniitpk02rbg9q2zcq/folder/144881804954", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "combined_pre_trained_base_checkpoint", |
| "model_id": "chemformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "zinc15_100m_chemformer_pretraining" |
| ], |
| "unsupported_reason": "pretraining-only Chemformer base bundle; not a retrosynthesis fine-tuned backward reaction checkpoint", |
| "weights_path": "model.safetensors", |
| "wrapper_class": null, |
| "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_50.pickle" |
| ], |
| "benchmark_datasets": [ |
| { |
| "dataset_id": "uspto_50_fine_tuned_retrosynthesis_checkpoint_test", |
| "dataset_ref": "uspto_50k_chemformer_project_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "pandas_pickled_dataframe", |
| "native_source_paths": [ |
| "benchmarks/native/uspto_50.pickle" |
| ], |
| "notes": [ |
| "Native Chemformer benchmark source extracted from the public Box release pickle.", |
| "benchmarks/default_test.jsonl stores product/reactant SMILES converted from the pickled RDKit molecule objects in the test partition." |
| ], |
| "num_examples": 5004, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_50_fine_tuned_retrosynthesis_checkpoint", |
| "display_name": "uspto_50 fine-tuned retrosynthesis checkpoint", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Box shared folder", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "chemformer", |
| "model_name": "Chemformer", |
| "normalized_checkpoint_id": "uspto_50_fine_tuned_retrosynthesis_checkpoint", |
| "package_dir": "checkpoints/chemformer/uspto_50_fine_tuned_retrosynthesis_checkpoint", |
| "remote_url": "https://az.app.box.com/s/7eci3nd9vy0xplqniitpk02rbg9q2zcq/folder/145317555751", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_50_fine_tuned_retrosynthesis_checkpoint", |
| "model_id": "chemformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_chemformer_project_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.chemformer.ChemformerModel", |
| "wrapper_family": "chemformer_bart" |
| }, |
| { |
| "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_50k/test.csv", |
| "aux/provenance/datasets/USPTO_50k/train.csv", |
| "aux/provenance/datasets/USPTO_50k/val.csv", |
| "aux/provenance/reactiont5v2_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": [ |
| { |
| "dataset_id": "sagawa_reactiont5v2_retrosynthesis_test", |
| "dataset_ref": "ord_retrosynthesis_pretraining", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "csv_reaction_rows", |
| "native_source_paths": [ |
| "aux/provenance/datasets/ORD/all_ord_reaction_uniq_with_attr20240506_v3_test.csv" |
| ], |
| "notes": [ |
| "Native benchmark split for the public ORD-trained retrosynthesis checkpoint.", |
| "USPTO_50k/test.csv was used upstream for duplicate-removal / leakage control, not as the native training benchmark for this checkpoint." |
| ], |
| "num_examples": 225282, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "sagawa_reactiont5v2_retrosynthesis", |
| "display_name": "sagawa/ReactionT5v2-retrosynthesis", |
| "embedding_modes": [ |
| "product_encoder", |
| "reactant_decoder", |
| "reaction_pair", |
| "token" |
| ], |
| "embedding_supported": true, |
| "fine_tuning_notes": "ORD-trained retrosynthesis checkpoint that can serve as a continued-training seed.", |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": "sagawa/ReactionT5v2-retrosynthesis", |
| "host": "Hugging Face", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "reactiont5v2", |
| "model_name": "ReactionT5v2", |
| "normalized_checkpoint_id": "sagawa_reactiont5v2_retrosynthesis", |
| "package_dir": "checkpoints/reactiont5v2/sagawa_reactiont5v2_retrosynthesis", |
| "remote_url": "https://huggingface.co/sagawa/ReactionT5v2-retrosynthesis", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "sagawa_reactiont5v2_retrosynthesis", |
| "model_id": "reactiont5v2" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "ord_retrosynthesis_pretraining" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.reactiont5v2.ReactionT5v2Model", |
| "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_50k/test.csv", |
| "aux/provenance/datasets/USPTO_50k/train.csv", |
| "aux/provenance/datasets/USPTO_50k/val.csv", |
| "aux/provenance/reactiont5v2_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": [ |
| { |
| "dataset_id": "sagawa_reactiont5v2_retrosynthesis_uspto_50k_test", |
| "dataset_ref": "uspto_50k_project_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "csv_reaction_rows", |
| "native_source_paths": [ |
| "aux/provenance/datasets/USPTO_50k/test.csv" |
| ], |
| "notes": [ |
| "Native benchmark split for the public USPTO-50K fine-tuned retrosynthesis checkpoint." |
| ], |
| "num_examples": 5004, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "sagawa_reactiont5v2_retrosynthesis_uspto_50k", |
| "display_name": "sagawa/ReactionT5v2-retrosynthesis-USPTO_50k", |
| "embedding_modes": [ |
| "product_encoder", |
| "reactant_decoder", |
| "reaction_pair", |
| "token" |
| ], |
| "embedding_supported": true, |
| "fine_tuning_notes": "USPTO-50K fine-tuned retrosynthesis checkpoint that can be adapted further.", |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": "sagawa/ReactionT5v2-retrosynthesis-USPTO_50k", |
| "host": "Hugging Face", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "reactiont5v2", |
| "model_name": "ReactionT5v2", |
| "normalized_checkpoint_id": "sagawa_reactiont5v2_retrosynthesis_uspto_50k", |
| "package_dir": "checkpoints/reactiont5v2/sagawa_reactiont5v2_retrosynthesis_uspto_50k", |
| "remote_url": "https://huggingface.co/sagawa/ReactionT5v2-retrosynthesis-USPTO_50k", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "sagawa_reactiont5v2_retrosynthesis_uspto_50k", |
| "model_id": "reactiont5v2" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_project_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.reactiont5v2.ReactionT5v2Model", |
| "wrapper_family": "seq2seq_t5" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/models.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "smiles_transformer/aux/checkpoint_metadata.json", |
| "smiles_transformer/aux/hyper_parameters.json", |
| "smiles_transformer/aux/vocab.txt", |
| "template_localization/aux/checkpoint_metadata.json", |
| "template_localization/aux/hyper_parameters.json", |
| "template_localization/aux/template_lib.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "benchmark_pending", |
| "dataset_id": "pistachio_test", |
| "dataset_ref": "pistachio_retrochimera_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "benchmark_not_available", |
| "native_source_paths": [], |
| "notes": [ |
| "Benchmark companion for the end-to-end RetroChimera hybrid checkpoint on Pistachio.", |
| "These RetroChimera packages bundle both released ensemble components together and are intended for the upstream combined inference API.", |
| "No public benchmark split is bundled yet for this checkpoint; benchmarks/default_test.jsonl is intentionally empty for now.", |
| "The public RetroChimera checkpoint release documents Pistachio-trained checkpoints, but this repository does not yet bundle a public Pistachio evaluation split." |
| ], |
| "num_examples": 0, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio", |
| "display_name": "pistachio", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_hybrid", |
| "model_name": "RetroChimera Hybrid", |
| "normalized_checkpoint_id": "pistachio", |
| "package_dir": "checkpoints/retrochimera_hybrid/pistachio", |
| "remote_url": "https://figshare.com/ndownloader/files/59468882", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio", |
| "model_id": "retrochimera_hybrid" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "pistachio_retrochimera_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "template_localization/model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_hybrid.RetroChimeraHybridModel", |
| "wrapper_family": "retrochimera_hybrid" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/models.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt", |
| "smiles_transformer/aux/checkpoint_metadata.json", |
| "smiles_transformer/aux/hyper_parameters.json", |
| "smiles_transformer/aux/vocab.txt", |
| "template_localization/aux/checkpoint_metadata.json", |
| "template_localization/aux/hyper_parameters.json", |
| "template_localization/aux/template_lib.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_hybrid_gln_compatibility_view", |
| "dataset_id": "uspto_50k_test", |
| "dataset_ref": "uspto_50k_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for the end-to-end RetroChimera hybrid checkpoint on USPTO-50K via GLN/Coley split compatibility view.", |
| "These RetroChimera packages bundle both released ensemble components together and are intended for the upstream combined inference API.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 20; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera cites Dai et al./GLN preprocessing for USPTO-50K; GLN in turn follows the Coley/RetroSim 80/10/10 split family." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_50k", |
| "display_name": "uspto_50k", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "retrochimera_hybrid", |
| "model_name": "RetroChimera Hybrid", |
| "normalized_checkpoint_id": "uspto_50k", |
| "package_dir": "checkpoints/retrochimera_hybrid/uspto_50k", |
| "remote_url": "https://figshare.com/ndownloader/files/59511926", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_50k", |
| "model_id": "retrochimera_hybrid" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "template_localization/model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_hybrid.RetroChimeraHybridModel", |
| "wrapper_family": "retrochimera_hybrid" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/models.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt", |
| "smiles_transformer/aux/checkpoint_metadata.json", |
| "smiles_transformer/aux/hyper_parameters.json", |
| "smiles_transformer/aux/vocab.txt", |
| "template_localization/aux/checkpoint_metadata.json", |
| "template_localization/aux/hyper_parameters.json", |
| "template_localization/aux/template_lib.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_hybrid_r_smiles_selected_full_view", |
| "dataset_id": "uspto_full_test", |
| "dataset_ref": "uspto_full_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for the end-to-end RetroChimera hybrid checkpoint on USPTO-FULL via RetroChimera\u2192R-SMILES\u2192GLN compatibility view.", |
| "These RetroChimera packages bundle both released ensemble components together and are intended for the upstream combined inference API.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 5; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera notes that multiple USPTO-FULL variants exist and selects the R-SMILES/Zhong et al. version for fair comparison; the R-SMILES release points that data lineage back to GLN." |
| ], |
| "num_examples": 96023, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_full", |
| "display_name": "uspto_full", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": null, |
| "fine_tuning_supported": false, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_hybrid", |
| "model_name": "RetroChimera Hybrid", |
| "normalized_checkpoint_id": "uspto_full", |
| "package_dir": "checkpoints/retrochimera_hybrid/uspto_full", |
| "remote_url": "https://figshare.com/ndownloader/files/59494598", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_full", |
| "model_id": "retrochimera_hybrid" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_full_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "template_localization/model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_hybrid.RetroChimeraHybridModel", |
| "wrapper_family": "retrochimera_hybrid" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/template_lib.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "benchmark_pending", |
| "dataset_id": "pistachio_test", |
| "dataset_ref": "pistachio_retrochimera_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "benchmark_not_available", |
| "native_source_paths": [], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on Pistachio.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "No public benchmark split is bundled yet for this checkpoint; benchmarks/default_test.jsonl is intentionally empty for now.", |
| "The public RetroChimera checkpoint release documents Pistachio-trained checkpoints, but this repository does not yet bundle a public Pistachio evaluation split." |
| ], |
| "num_examples": 0, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio", |
| "display_name": "pistachio", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_template", |
| "model_name": "RetroChimera Template Localization", |
| "normalized_checkpoint_id": "pistachio", |
| "package_dir": "checkpoints/retrochimera_template/pistachio", |
| "remote_url": "https://figshare.com/ndownloader/files/59468882", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio", |
| "model_id": "retrochimera_template" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "pistachio_retrochimera_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_template.RetroChimeraTemplateModel", |
| "wrapper_family": "retrochimera_template_localization" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/template_lib.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_component_gln_compatibility_view", |
| "dataset_id": "uspto_50k_test", |
| "dataset_ref": "uspto_50k_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on USPTO-50K via GLN/Coley split compatibility view.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 20; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera cites Dai et al./GLN preprocessing for USPTO-50K; GLN in turn follows the Coley/RetroSim 80/10/10 split family." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_50k", |
| "display_name": "uspto_50k", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "retrochimera_template", |
| "model_name": "RetroChimera Template Localization", |
| "normalized_checkpoint_id": "uspto_50k", |
| "package_dir": "checkpoints/retrochimera_template/uspto_50k", |
| "remote_url": "https://figshare.com/ndownloader/files/59511926", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_50k", |
| "model_id": "retrochimera_template" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_template.RetroChimeraTemplateModel", |
| "wrapper_family": "retrochimera_template_localization" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/template_lib.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_component_r_smiles_selected_full_view", |
| "dataset_id": "uspto_full_test", |
| "dataset_ref": "uspto_full_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on USPTO-FULL via RetroChimera\u2192R-SMILES\u2192GLN compatibility view.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 5; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera notes that multiple USPTO-FULL variants exist and selects the R-SMILES/Zhong et al. version for fair comparison; the R-SMILES release points that data lineage back to GLN." |
| ], |
| "num_examples": 96023, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_full", |
| "display_name": "uspto_full", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_template", |
| "model_name": "RetroChimera Template Localization", |
| "normalized_checkpoint_id": "uspto_full", |
| "package_dir": "checkpoints/retrochimera_template/uspto_full", |
| "remote_url": "https://figshare.com/ndownloader/files/59494598", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_full", |
| "model_id": "retrochimera_template" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_full_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_template.RetroChimeraTemplateModel", |
| "wrapper_family": "retrochimera_template_localization" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/vocab.txt", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "benchmark_pending", |
| "dataset_id": "pistachio_test", |
| "dataset_ref": "pistachio_retrochimera_release", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "benchmark_not_available", |
| "native_source_paths": [], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on Pistachio.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "No public benchmark split is bundled yet for this checkpoint; benchmarks/default_test.jsonl is intentionally empty for now.", |
| "The public RetroChimera checkpoint release documents Pistachio-trained checkpoints, but this repository does not yet bundle a public Pistachio evaluation split." |
| ], |
| "num_examples": 0, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "pistachio", |
| "display_name": "pistachio", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_transformer", |
| "model_name": "RetroChimera Smiles Transformer", |
| "normalized_checkpoint_id": "pistachio", |
| "package_dir": "checkpoints/retrochimera_transformer/pistachio", |
| "remote_url": "https://figshare.com/ndownloader/files/59468882", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "pistachio", |
| "model_id": "retrochimera_transformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "pistachio_retrochimera_release" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_transformer.RetroChimeraTransformerModel", |
| "wrapper_family": "retrochimera_smiles_transformer" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/vocab.txt", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_component_gln_compatibility_view", |
| "dataset_id": "uspto_50k_test", |
| "dataset_ref": "uspto_50k_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on USPTO-50K via GLN/Coley split compatibility view.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 20; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera cites Dai et al./GLN preprocessing for USPTO-50K; GLN in turn follows the Coley/RetroSim 80/10/10 split family." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_50k", |
| "display_name": "uspto_50k", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "retrochimera_transformer", |
| "model_name": "RetroChimera Smiles Transformer", |
| "normalized_checkpoint_id": "uspto_50k", |
| "package_dir": "checkpoints/retrochimera_transformer/uspto_50k", |
| "remote_url": "https://figshare.com/ndownloader/files/59511926", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_50k", |
| "model_id": "retrochimera_transformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_transformer.RetroChimeraTransformerModel", |
| "wrapper_family": "retrochimera_smiles_transformer" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/checkpoint_metadata.json", |
| "aux/hyper_parameters.json", |
| "aux/models.json", |
| "aux/vocab.txt", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "retrochimera_component_r_smiles_selected_full_view", |
| "dataset_id": "uspto_full_test", |
| "dataset_ref": "uspto_full_gln", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "tokenized_parallel_txt", |
| "native_source_paths": [ |
| "benchmarks/native/src-test.txt", |
| "benchmarks/native/tgt-test.txt" |
| ], |
| "notes": [ |
| "Benchmark companion for RetroChimera component checkpoint on USPTO-FULL via RetroChimera\u2192R-SMILES\u2192GLN compatibility view.", |
| "These RetroChimera packages contain component checkpoints rather than the full end-to-end ensemble, so the bundled benchmark is best interpreted as a dataset compatibility view.", |
| "The underlying test split is preserved from the local R-SMILES/GLN-compatible tokenized benchmark files already tracked by this repository.", |
| "The source files preserve rooted augmentation with factor 5; benchmarks/default_test.jsonl collapses each contiguous augmentation block back to one benchmark case per underlying reaction.", |
| "The native source files are tokenized parallel text; benchmarks/default_test.jsonl stores the corresponding de-tokenized product/reactant pairs.", |
| "RetroChimera notes that multiple USPTO-FULL variants exist and selects the R-SMILES/Zhong et al. version for fair comparison; the R-SMILES release points that data lineage back to GLN." |
| ], |
| "num_examples": 96023, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "uspto_full", |
| "display_name": "uspto_full", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Figshare file", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "retrochimera_transformer", |
| "model_name": "RetroChimera Smiles Transformer", |
| "normalized_checkpoint_id": "uspto_full", |
| "package_dir": "checkpoints/retrochimera_transformer/uspto_full", |
| "remote_url": "https://figshare.com/ndownloader/files/59494598", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "uspto_full", |
| "model_id": "retrochimera_transformer" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_full_gln" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.retrochimera_transformer.RetroChimeraTransformerModel", |
| "wrapper_family": "retrochimera_smiles_transformer" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/configs/base.yml", |
| "aux/configs/rxngpt_llama1B.json", |
| "aux/deepspeed.yaml", |
| "aux/tokenizer/special_tokens_map.json", |
| "aux/tokenizer/tokenizer.json", |
| "aux/tokenizer/tokenizer_config.json", |
| "aux/vocab.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/USPTO-50k_test_tidy.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "class_unknown_test_aug_best_effort_underlying_test_examples", |
| "dataset_id": "finetune_50k_aug20_pth_test", |
| "dataset_ref": "uspto_50k_rsgpt", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "reaction_smiles_txt", |
| "native_source_paths": [ |
| "benchmarks/native/USPTO-50k_test_tidy.txt" |
| ], |
| "notes": [ |
| "The exact upstream test-time augmentation prefix file test_50k_prefixs20.txt is not present in the local manual artifacts or pinned source snapshot.", |
| "This bundle therefore preserves the underlying standard USPTO-50K test reactions as the normalized benchmark truth set, while the checkpoint metadata still records the intended aug20 evaluation variant." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "finetune_50k_aug20_pth", |
| "display_name": "finetune_50k_aug20.pth", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Zenodo Sandbox", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "rsgpt", |
| "model_name": "RSGPT", |
| "normalized_checkpoint_id": "finetune_50k_aug20_pth", |
| "package_dir": "checkpoints/rsgpt/finetune_50k_aug20_pth", |
| "remote_url": "https://sandbox.zenodo.org/records/203391", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "finetune_50k_aug20_pth", |
| "model_id": "rsgpt" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_rsgpt", |
| "synthetic_10b_rsgpt" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.rsgpt.RSGPTModel", |
| "wrapper_family": "rsgpt_llama_decoder" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/configs/base.yml", |
| "aux/configs/rxngpt_llama1B.json", |
| "aux/deepspeed.yaml", |
| "aux/tokenizer/special_tokens_map.json", |
| "aux/tokenizer/tokenizer.json", |
| "aux/tokenizer/tokenizer_config.json", |
| "aux/vocab.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/USPTO-50k_test_tidy_class1.csv" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "class_known", |
| "dataset_id": "finetune_50k_pth_test", |
| "dataset_ref": "uspto_50k_rsgpt", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "class_csv_reaction_smiles", |
| "native_source_paths": [ |
| "benchmarks/native/USPTO-50k_test_tidy_class1.csv" |
| ], |
| "notes": [ |
| "This is the class-labeled USPTO-50K benchmark companion file corresponding to the best-effort class-known mapping for finetune_50k_pth." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "finetune_50k_pth", |
| "display_name": "finetune_50k.pth", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Zenodo Sandbox", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "rsgpt", |
| "model_name": "RSGPT", |
| "normalized_checkpoint_id": "finetune_50k_pth", |
| "package_dir": "checkpoints/rsgpt/finetune_50k_pth", |
| "remote_url": "https://sandbox.zenodo.org/records/203391", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "finetune_50k_pth", |
| "model_id": "rsgpt" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_rsgpt", |
| "synthetic_10b_rsgpt" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.rsgpt.RSGPTModel", |
| "wrapper_family": "rsgpt_llama_decoder" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/configs/base.yml", |
| "aux/configs/rxngpt_llama1B.json", |
| "aux/deepspeed.yaml", |
| "aux/tokenizer/special_tokens_map.json", |
| "aux/tokenizer/tokenizer.json", |
| "aux/tokenizer/tokenizer_config.json", |
| "aux/vocab.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/USPTO-FULL_test_tidy.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "dataset_id": "finetune_full_pth_test", |
| "dataset_ref": "uspto_full_rsgpt", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "reaction_smiles_txt", |
| "native_source_paths": [ |
| "benchmarks/native/USPTO-FULL_test_tidy.txt" |
| ], |
| "notes": [ |
| "Native RSGPT benchmark source extracted from USPTO_data/USPTO-FULL_test_tidy.txt." |
| ], |
| "num_examples": 95389, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "finetune_full_pth", |
| "display_name": "finetune_full.pth", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Zenodo Sandbox", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "rsgpt", |
| "model_name": "RSGPT", |
| "normalized_checkpoint_id": "finetune_full_pth", |
| "package_dir": "checkpoints/rsgpt/finetune_full_pth", |
| "remote_url": "https://sandbox.zenodo.org/records/203391", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "finetune_full_pth", |
| "model_id": "rsgpt" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_full_rsgpt", |
| "synthetic_10b_rsgpt" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.rsgpt.RSGPTModel", |
| "wrapper_family": "rsgpt_llama_decoder" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/configs/base.yml", |
| "aux/configs/rxngpt_llama1B.json", |
| "aux/deepspeed.yaml", |
| "aux/tokenizer/special_tokens_map.json", |
| "aux/tokenizer/tokenizer.json", |
| "aux/tokenizer/tokenizer_config.json", |
| "aux/vocab.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/USPTO-MIT_test_tidy.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "dataset_id": "finetune_mit_pth_test", |
| "dataset_ref": "uspto_mit_rsgpt", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "reaction_smiles_txt", |
| "native_source_paths": [ |
| "benchmarks/native/USPTO-MIT_test_tidy.txt" |
| ], |
| "notes": [ |
| "Native RSGPT benchmark source extracted from USPTO_data/USPTO-MIT_test_tidy.txt." |
| ], |
| "num_examples": 40000, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "finetune_mit_pth", |
| "display_name": "finetune_mit.pth", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": null, |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Zenodo Sandbox", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": true, |
| "model_id": "rsgpt", |
| "model_name": "RSGPT", |
| "normalized_checkpoint_id": "finetune_mit_pth", |
| "package_dir": "checkpoints/rsgpt/finetune_mit_pth", |
| "remote_url": "https://sandbox.zenodo.org/records/203391", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "finetune_mit_pth", |
| "model_id": "rsgpt" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_mit_rsgpt", |
| "synthetic_10b_rsgpt" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.rsgpt.RSGPTModel", |
| "wrapper_family": "rsgpt_llama_decoder" |
| }, |
| { |
| "auxiliary_files": [ |
| "aux/configs/base.yml", |
| "aux/configs/rxngpt_llama1B.json", |
| "aux/deepspeed.yaml", |
| "aux/tokenizer/special_tokens_map.json", |
| "aux/tokenizer/tokenizer.json", |
| "aux/tokenizer/tokenizer_config.json", |
| "aux/vocab.json", |
| "benchmarks/default_test.jsonl", |
| "benchmarks/metadata.json", |
| "benchmarks/native/USPTO-50k_test_tidy.txt" |
| ], |
| "benchmark_datasets": [ |
| { |
| "benchmark_variant": "class_unknown_no_pretraining_ablation", |
| "dataset_id": "nopretrain_50k_pth_test", |
| "dataset_ref": "uspto_50k_rsgpt", |
| "default": true, |
| "format": "jsonl", |
| "metadata_path": "benchmarks/metadata.json", |
| "native_input_format": "reaction_smiles_txt", |
| "native_source_paths": [ |
| "benchmarks/native/USPTO-50k_test_tidy.txt" |
| ], |
| "notes": [ |
| "Native RSGPT benchmark source extracted from USPTO_data/USPTO-50k_test_tidy.txt." |
| ], |
| "num_examples": 5007, |
| "path": "benchmarks/default_test.jsonl", |
| "split": "test" |
| } |
| ], |
| "checkpoint_id": "nopretrain_50k_pth", |
| "display_name": "nopretrain_50k.pth", |
| "embedding_modes": [], |
| "embedding_supported": false, |
| "fine_tuning_notes": "Task-specific 50K ablation checkpoint without the synthetic pretraining stage.", |
| "fine_tuning_role": "task_finetuned_seed", |
| "fine_tuning_supported": true, |
| "hf_model_name": null, |
| "host": "Zenodo Sandbox", |
| "inference_supported": true, |
| "input_schema": null, |
| "larger_than_uspto50k": false, |
| "model_id": "rsgpt", |
| "model_name": "RSGPT", |
| "normalized_checkpoint_id": "nopretrain_50k_pth", |
| "package_dir": "checkpoints/rsgpt/nopretrain_50k_pth", |
| "remote_url": "https://sandbox.zenodo.org/records/203391", |
| "source_registry_refs": [ |
| { |
| "checkpoint_id": "nopretrain_50k_pth", |
| "model_id": "rsgpt" |
| } |
| ], |
| "task_direction": null, |
| "training_dataset_refs": [ |
| "uspto_50k_rsgpt" |
| ], |
| "unsupported_reason": null, |
| "weights_path": "model.safetensors", |
| "wrapper_class": "syntheseus_wrappers.wrappers.rsgpt.RSGPTModel", |
| "wrapper_family": "rsgpt_llama_decoder" |
| } |
| ], |
| "registry_kind": "runtime", |
| "runtime_registry_version": 1 |
| } |
|
|