Feature | Description |
---|---|
Name | BiomedNLP-PubMedBERT-ProteinStructure-NER-2.1_onnx |
Default Pipeline | transformer , ner |
Components | transformer , ner |
Vectors | 0 keys, 0 unique vectors (0 dimensions) |
Sources | n/a |
License | n/a |
Author | Melanie Vollmar |
Label Scheme
View label scheme (20 labels for 1 components)
Component | Labels |
---|---|
ner |
"bond_interaction", "chemical", "complex_assembly", "evidence", "experimental_method", "gene", "mutant", "oligomeric_state", "protein", "protein_state", "protein_type", "ptm", "residue_name", "residue_name_number", "residue_number", "residue_range", "site", "species", "structure_element", "taxonomy_domain" |
Scores for entity types
entity type | precision | recall | F1 | sample number |
---|---|---|---|---|
"bond_interaction" | 0.94 | 0.92 | 0.93 | 41 |
"chemical" | 0.86 | 0.92 | 0.89 | 589 |
"complex_assembly" | 0.85 | 0.89 | 0.87 | 185 |
"evidence" | 0.83 | 0.89 | 0.86 | 392 |
"experimental_method" | 0.86 | 0.85 | 0.86 | 310 |
"gene" | 0.73 | 0.86 | 0.79 | 26 |
"mutant" | 0.88 | 0.94 | 0.91 | 216 |
"oligomeric_state" | 0.92 | 0.96 | 0.94 | 116 |
"protein" | 0.91 | 0.95 | 0.93 | 755 |
"protein_state" | 0.78 | 0.88 | 0.82 | 577 |
"protein_type" | 0.87 | 0.85 | 0.86 | 265 |
"ptm" | 0.67 | 0.69 | 0.68 | 33 |
"residue_name" | 0.88 | 0.95 | 0.91 | 76 |
"residue_name_number" | 0.94 | 0.96 | 0.95 | 262 |
"residue_number" | 0.62 | 0.88 | 0.73 | 45 |
"residue_range" | 0.87 | 0.79 | 0.83 | 31 |
"site" | 0.88 | 0.90 | 0.89 | 245 |
"species" | 0.95 | 0.97 | 0.96 | 76 |
"structure_element" | 0.90 | 0.93 | 0.92 | 751 |
"taxonomy_domain" | 0.99 | 0.99 | 0.99 | 83 |
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Evaluation results
- NER Precisionself-reported0.900
- NER Recallself-reported0.930
- NER F Scoreself-reported0.910