Upload model files
Browse files- config.json +191 -0
- optimizer.pt +3 -0
- pytorch_model.bin +3 -0
- rng_state.pth +3 -0
- scheduler.pt +3 -0
- special_tokens_map.json +7 -0
- tokenizer.json +0 -0
- tokenizer_config.json +16 -0
- trainer_state.json +1808 -0
- training_args.bin +3 -0
- vocab.txt +0 -0
config.json
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{
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"_name_or_path": "dmis-lab/biobert-base-cased-v1.1",
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"architectures": [
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"BertForSpanClassification"
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],
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"attention_probs_dropout_prob": 0.1,
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"classifier_dropout": null,
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"hidden_act": "gelu",
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"hidden_dropout_prob": 0.1,
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"hidden_size": 768,
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"id2label": {
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"0": "O",
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"1": "B-AminoAcidPeptideOrProtein",
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"2": "I-AminoAcidPeptideOrProtein",
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"3": "B-AnatomicalAbnormality",
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"4": "I-AnatomicalAbnormality",
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"5": "B-Bacterium",
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"6": "I-Bacterium",
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"7": "B-BiologicFunction",
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"8": "I-BiologicFunction",
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"9": "B-BiologicallyActiveSubstance",
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"10": "I-BiologicallyActiveSubstance",
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"11": "B-BiomedicalOccupationOrDiscipline",
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"12": "I-BiomedicalOccupationOrDiscipline",
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"13": "B-BodyPartOrganOrOrganComponent",
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"14": "I-BodyPartOrganOrOrganComponent",
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"15": "B-Cell",
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"16": "I-Cell",
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"17": "B-CellComponent",
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"18": "I-CellComponent",
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"19": "B-CellFunction",
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"20": "I-CellFunction",
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"21": "B-CellOrMolecularDysfunction",
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"22": "I-CellOrMolecularDysfunction",
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"23": "B-Chemical",
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"24": "I-Chemical",
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"25": "B-ClinicalAttribute",
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"26": "I-ClinicalAttribute",
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"27": "B-DiseaseOrSyndrome",
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"28": "I-DiseaseOrSyndrome",
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"29": "B-EmbryonicStructure",
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"30": "I-EmbryonicStructure",
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"31": "B-EnvironmentalEffectOfHumans",
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"32": "I-EnvironmentalEffectOfHumans",
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"33": "B-Eukaryote",
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"34": "I-Eukaryote",
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"35": "B-ExperimentalModelOfDisease",
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"36": "I-ExperimentalModelOfDisease",
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"37": "B-Finding",
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"38": "I-Finding",
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"39": "B-GeneOrGenome",
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"40": "I-GeneOrGenome",
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"41": "B-HealthCareActivity",
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"42": "I-HealthCareActivity",
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"43": "B-HealthCareRelatedOrganization",
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"44": "I-HealthCareRelatedOrganization",
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"45": "B-IndividualBehavior",
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"46": "I-IndividualBehavior",
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"47": "B-InjuryOrPoisoning",
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"48": "I-InjuryOrPoisoning",
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"49": "B-MachineActivity",
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"50": "I-MachineActivity",
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"51": "B-ManufacturedObject",
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"52": "I-ManufacturedObject",
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"53": "B-MolecularSequence",
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"54": "I-MolecularSequence",
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"55": "B-NaturalPhenomenonOrProcess",
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"56": "I-NaturalPhenomenonOrProcess",
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"57": "B-NucleicAcidNucleosideOrNucleotide",
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"58": "I-NucleicAcidNucleosideOrNucleotide",
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"59": "B-Organism",
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| 72 |
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"60": "I-Organism",
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"61": "B-OrganismAttribute",
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"62": "I-OrganismAttribute",
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"63": "B-PathologicFunction",
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"64": "I-PathologicFunction",
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"65": "B-PatientOrDisabledGroup",
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"66": "I-PatientOrDisabledGroup",
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"67": "B-PharmacologicSubstance",
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"68": "I-PharmacologicSubstance",
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"69": "B-PopulationGroup",
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"70": "I-PopulationGroup",
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"71": "B-ResearchActivity",
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"72": "I-ResearchActivity",
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"73": "B-SignOrSymptom",
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| 86 |
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"74": "I-SignOrSymptom",
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"75": "B-Substance",
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"76": "I-Substance",
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"77": "B-TemporalConcept",
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"78": "I-TemporalConcept",
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| 91 |
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"79": "B-Virus",
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"80": "I-Virus"
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},
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"initializer_range": 0.02,
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"intermediate_size": 3072,
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| 96 |
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"label2id": {
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| 97 |
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"B-AminoAcidPeptideOrProtein": 1,
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| 98 |
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"B-AnatomicalAbnormality": 3,
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| 99 |
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"B-Bacterium": 5,
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| 100 |
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"B-BiologicFunction": 7,
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| 101 |
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"B-BiologicallyActiveSubstance": 9,
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| 102 |
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"B-BiomedicalOccupationOrDiscipline": 11,
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| 103 |
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"B-BodyPartOrganOrOrganComponent": 13,
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| 104 |
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"B-Cell": 15,
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| 105 |
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"B-CellComponent": 17,
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| 106 |
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"B-CellFunction": 19,
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| 107 |
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"B-CellOrMolecularDysfunction": 21,
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| 108 |
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"B-Chemical": 23,
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| 109 |
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"B-ClinicalAttribute": 25,
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| 110 |
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"B-DiseaseOrSyndrome": 27,
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| 111 |
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"B-EmbryonicStructure": 29,
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| 112 |
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"B-EnvironmentalEffectOfHumans": 31,
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| 113 |
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"B-Eukaryote": 33,
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| 114 |
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"B-ExperimentalModelOfDisease": 35,
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| 115 |
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"B-Finding": 37,
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| 116 |
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"B-GeneOrGenome": 39,
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| 117 |
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"B-HealthCareActivity": 41,
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| 118 |
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"B-HealthCareRelatedOrganization": 43,
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| 119 |
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"B-IndividualBehavior": 45,
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| 120 |
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"B-InjuryOrPoisoning": 47,
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| 121 |
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"B-MachineActivity": 49,
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| 122 |
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"B-ManufacturedObject": 51,
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| 123 |
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"B-MolecularSequence": 53,
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| 124 |
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"B-NaturalPhenomenonOrProcess": 55,
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| 125 |
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"B-NucleicAcidNucleosideOrNucleotide": 57,
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| 126 |
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"B-Organism": 59,
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| 127 |
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"B-OrganismAttribute": 61,
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| 128 |
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"B-PathologicFunction": 63,
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| 129 |
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"B-PatientOrDisabledGroup": 65,
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| 130 |
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"B-PharmacologicSubstance": 67,
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| 131 |
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"B-PopulationGroup": 69,
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| 132 |
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"B-ResearchActivity": 71,
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| 133 |
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"B-SignOrSymptom": 73,
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| 134 |
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"B-Substance": 75,
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| 135 |
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"B-TemporalConcept": 77,
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| 136 |
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"B-Virus": 79,
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| 137 |
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"I-AminoAcidPeptideOrProtein": 2,
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| 138 |
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"I-AnatomicalAbnormality": 4,
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| 139 |
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"I-Bacterium": 6,
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| 140 |
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"I-BiologicFunction": 8,
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| 141 |
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"I-BiologicallyActiveSubstance": 10,
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| 142 |
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"I-BiomedicalOccupationOrDiscipline": 12,
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| 143 |
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"I-BodyPartOrganOrOrganComponent": 14,
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| 144 |
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"I-Cell": 16,
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| 145 |
+
"I-CellComponent": 18,
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| 146 |
+
"I-CellFunction": 20,
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| 147 |
+
"I-CellOrMolecularDysfunction": 22,
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| 148 |
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"I-Chemical": 24,
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| 149 |
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"I-ClinicalAttribute": 26,
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| 150 |
+
"I-DiseaseOrSyndrome": 28,
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| 151 |
+
"I-EmbryonicStructure": 30,
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| 152 |
+
"I-EnvironmentalEffectOfHumans": 32,
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| 153 |
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"I-Eukaryote": 34,
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| 154 |
+
"I-ExperimentalModelOfDisease": 36,
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| 155 |
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"I-Finding": 38,
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| 156 |
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"I-GeneOrGenome": 40,
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| 157 |
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"I-HealthCareActivity": 42,
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| 158 |
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"I-HealthCareRelatedOrganization": 44,
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| 159 |
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"I-IndividualBehavior": 46,
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| 160 |
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"I-InjuryOrPoisoning": 48,
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| 161 |
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"I-MachineActivity": 50,
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| 162 |
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"I-ManufacturedObject": 52,
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| 163 |
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"I-MolecularSequence": 54,
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| 164 |
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"I-NaturalPhenomenonOrProcess": 56,
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| 165 |
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"I-NucleicAcidNucleosideOrNucleotide": 58,
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| 166 |
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"I-Organism": 60,
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| 167 |
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"I-OrganismAttribute": 62,
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| 168 |
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"I-PathologicFunction": 64,
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| 169 |
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"I-PatientOrDisabledGroup": 66,
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| 170 |
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"I-PharmacologicSubstance": 68,
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| 171 |
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"I-PopulationGroup": 70,
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| 172 |
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"I-ResearchActivity": 72,
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| 173 |
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"I-SignOrSymptom": 74,
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| 174 |
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"I-Substance": 76,
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| 175 |
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"I-TemporalConcept": 78,
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| 176 |
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"I-Virus": 80,
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| 177 |
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"O": 0
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| 178 |
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},
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| 179 |
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"layer_norm_eps": 1e-12,
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| 180 |
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"max_position_embeddings": 512,
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| 181 |
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"model_type": "bert",
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| 182 |
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"num_attention_heads": 12,
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| 183 |
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"num_hidden_layers": 12,
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| 184 |
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"pad_token_id": 0,
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| 185 |
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"position_embedding_type": "absolute",
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| 186 |
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"torch_dtype": "float32",
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| 187 |
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"transformers_version": "4.26.1",
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| 188 |
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"type_vocab_size": 2,
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| 189 |
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"use_cache": true,
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| 190 |
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"vocab_size": 28996
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| 191 |
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}
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optimizer.pt
ADDED
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version https://git-lfs.github.com/spec/v1
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oid sha256:464c1ee428c9cca22e1ed2b4d517f16eaed3d0815665236b7b8b818d541a0e49
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size 862372485
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pytorch_model.bin
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version https://git-lfs.github.com/spec/v1
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oid sha256:9b727ad2df536f52706d689bedc0202e2e081886471bcb235324ebc2126818b3
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size 431200045
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rng_state.pth
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version https://git-lfs.github.com/spec/v1
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oid sha256:c6dd44b93811c5c56d9724cf97be53efd519d663fe5d8bad6343c786b0c0b53b
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size 14575
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scheduler.pt
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version https://git-lfs.github.com/spec/v1
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oid sha256:ab60a5192be98f62c0476693c5fad1177e4700834bb77976e43d293b4de750ba
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size 627
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special_tokens_map.json
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{
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"cls_token": "[CLS]",
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"mask_token": "[MASK]",
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"pad_token": "[PAD]",
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"sep_token": "[SEP]",
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"unk_token": "[UNK]"
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}
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tokenizer.json
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tokenizer_config.json
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{
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"cls_token": "[CLS]",
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"do_basic_tokenize": true,
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"do_lower_case": true,
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"mask_token": "[MASK]",
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"model_max_length": 1000000000000000019884624838656,
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"name_or_path": "dmis-lab/biobert-base-cased-v1.1",
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| 8 |
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"never_split": null,
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"pad_token": "[PAD]",
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"sep_token": "[SEP]",
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"special_tokens_map_file": null,
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"strip_accents": null,
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"tokenize_chinese_chars": true,
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"tokenizer_class": "BertTokenizer",
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"unk_token": "[UNK]"
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}
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trainer_state.json
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|
| 1 |
+
{
|
| 2 |
+
"best_metric": 0.512032280706096,
|
| 3 |
+
"best_model_checkpoint": "modelPaper2_args/checkpoint-2128",
|
| 4 |
+
"epoch": 20.0,
|
| 5 |
+
"global_step": 2240,
|
| 6 |
+
"is_hyper_param_search": false,
|
| 7 |
+
"is_local_process_zero": true,
|
| 8 |
+
"is_world_process_zero": true,
|
| 9 |
+
"log_history": [
|
| 10 |
+
{
|
| 11 |
+
"epoch": 1.0,
|
| 12 |
+
"eval_f1_B-AminoAcidPeptideOrProtein": 0,
|
| 13 |
+
"eval_f1_B-AnatomicalAbnormality": 0,
|
| 14 |
+
"eval_f1_B-Bacterium": 0,
|
| 15 |
+
"eval_f1_B-BiologicFunction": 0,
|
| 16 |
+
"eval_f1_B-BiologicallyActiveSubstance": 0,
|
| 17 |
+
"eval_f1_B-BiomedicalOccupationOrDiscipline": 0,
|
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| 1792 |
+
"eval_f1_I-Substance": 0.8130081300813008,
|
| 1793 |
+
"eval_f1_I-TemporalConcept": 0.7466666666666668,
|
| 1794 |
+
"eval_f1_I-Virus": 0.8373590982286635,
|
| 1795 |
+
"eval_loss": 0.0012418286642059684,
|
| 1796 |
+
"eval_macro_f1": 0.5094370945271087,
|
| 1797 |
+
"eval_runtime": 61.4875,
|
| 1798 |
+
"eval_samples_per_second": 12.929,
|
| 1799 |
+
"eval_steps_per_second": 0.26,
|
| 1800 |
+
"step": 2240
|
| 1801 |
+
}
|
| 1802 |
+
],
|
| 1803 |
+
"max_steps": 3360,
|
| 1804 |
+
"num_train_epochs": 30,
|
| 1805 |
+
"total_flos": 2.917108629762048e+16,
|
| 1806 |
+
"trial_name": null,
|
| 1807 |
+
"trial_params": null
|
| 1808 |
+
}
|
training_args.bin
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:1a613c7a10febb5cbb3f55b96dc5fb8dfe2ce87ce77a82530d655775b3617e22
|
| 3 |
+
size 3515
|
vocab.txt
ADDED
|
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|
|
|