# Performance on Training Set

## Span Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| Acquired Abnormality | 1.000 | 1.000 | 1.000 | 105 |
| Amino Acid Sequence | 0.995 | 0.986 | 0.990 | 207 |
| Amino Acid, Peptide, or Protein | 0.994 | 0.971 | 0.982 | 659 |
| Amphibian | 0.952 | 1.000 | 0.976 | 20 |
| Anatomical Abnormality | 0.993 | 0.951 | 0.971 | 143 |
| Anatomical Structure | 0.952 | 0.952 | 0.952 | 83 |
| Animal | 1.000 | 0.996 | 0.998 | 238 |
| Antibiotic | 0.997 | 0.997 | 0.997 | 364 |
| Bacterium | 0.988 | 0.964 | 0.976 | 1125 |
| Biologic Function | 0.992 | 0.989 | 0.990 | 622 |
| Biologically Active Substance | 0.993 | 0.987 | 0.990 | 5343 |
| Biomedical Occupation or Discipline | 0.996 | 0.985 | 0.990 | 522 |
| Biomedical or Dental Material | 0.995 | 0.994 | 0.995 | 845 |
| Bird | 0.978 | 0.938 | 0.958 | 242 |
| Body Location or Region | 0.993 | 0.986 | 0.989 | 702 |
| Body Part, Organ, or Organ Component | 0.996 | 0.991 | 0.993 | 3887 |
| Body Space or Junction | 0.997 | 0.989 | 0.993 | 356 |
| Body Substance | 0.996 | 0.994 | 0.995 | 774 |
| Body System | 0.977 | 0.973 | 0.975 | 300 |
| Cell | 0.993 | 0.992 | 0.993 | 3312 |
| Cell Component | 0.998 | 0.998 | 0.998 | 929 |
| Cell Function | 0.996 | 0.994 | 0.995 | 1941 |
| Cell or Molecular Dysfunction | 0.994 | 0.997 | 0.996 | 350 |
| Chemical | 0.994 | 0.987 | 0.990 | 156 |
| Chemical Viewed Functionally | 0.994 | 0.994 | 0.994 | 176 |
| Chemical Viewed Structurally | 0.993 | 0.986 | 0.989 | 284 |
| Classification | 0.995 | 0.988 | 0.991 | 738 |
| Clinical Attribute | 0.991 | 0.980 | 0.986 | 1046 |
| Congenital Abnormality | 0.967 | 0.989 | 0.978 | 177 |
| Diagnostic Procedure | 0.995 | 0.987 | 0.991 | 2426 |
| Disease or Syndrome | 0.998 | 0.988 | 0.993 | 6911 |
| Drug Delivery Device | 1.000 | 0.846 | 0.917 | 13 |
| Element, Ion, or Isotope | 0.998 | 0.982 | 0.990 | 934 |
| Embryonic Structure | 1.000 | 1.000 | 1.000 | 174 |
| Enzyme | 0.991 | 0.982 | 0.986 | 2192 |
| Eukaryote | 0.979 | 0.953 | 0.966 | 989 |
| Experimental Model of Disease | 1.000 | 1.000 | 1.000 | 189 |
| Finding | 0.992 | 0.986 | 0.989 | 8218 |
| Fish | 0.974 | 0.955 | 0.964 | 155 |
| Food | 0.995 | 0.972 | 0.983 | 851 |
| Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 1 |
| Fungus | 0.979 | 0.946 | 0.963 | 353 |
| Gene or Genome | 0.993 | 0.988 | 0.991 | 2776 |
| Genetic Function | 0.993 | 0.997 | 0.995 | 2000 |
| Geographic Area | 0.995 | 0.991 | 0.993 | 1712 |
| Hazardous or Poisonous Substance | 0.993 | 0.981 | 0.987 | 702 |
| Health Care Activity | 0.994 | 0.986 | 0.990 | 2858 |
| Health Care Related Organization | 0.995 | 0.988 | 0.992 | 1041 |
| Hormone | 1.000 | 0.992 | 0.996 | 504 |
| Human | 1.000 | 0.998 | 0.999 | 437 |
| Immunologic Factor | 0.996 | 0.992 | 0.994 | 1722 |
| Indicator, Reagent, or Diagnostic Aid | 0.991 | 0.986 | 0.988 | 649 |
| Injury or Poisoning | 0.992 | 0.992 | 0.992 | 1062 |
| Inorganic Chemical | 0.995 | 0.996 | 0.995 | 765 |
| Intellectual Product | 0.996 | 0.990 | 0.993 | 5358 |
| Laboratory Procedure | 0.987 | 0.980 | 0.984 | 2761 |
| Laboratory or Test Result | 0.986 | 0.982 | 0.984 | 509 |
| Mammal | 0.996 | 0.987 | 0.992 | 1350 |
| Medical Device | 0.994 | 0.989 | 0.991 | 1157 |
| Mental Process | 0.994 | 0.990 | 0.992 | 1431 |
| Mental or Behavioral Dysfunction | 0.997 | 0.997 | 0.997 | 1099 |
| Molecular Biology Research Technique | 0.991 | 0.986 | 0.989 | 654 |
| Molecular Function | 0.994 | 0.994 | 0.994 | 2007 |
| Molecular Sequence | 0.974 | 0.974 | 0.974 | 39 |
| Neoplastic Process | 0.996 | 0.987 | 0.991 | 2924 |
| Nucleic Acid, Nucleoside, or Nucleotide | 0.998 | 0.992 | 0.995 | 508 |
| Nucleotide Sequence | 0.986 | 0.975 | 0.980 | 360 |
| Organ or Tissue Function | 0.992 | 0.988 | 0.990 | 904 |
| Organic Chemical | 0.994 | 0.988 | 0.991 | 1411 |
| Organism Function | 0.994 | 0.987 | 0.990 | 1639 |
| Organization | 0.983 | 0.992 | 0.988 | 240 |
| Pathologic Function | 0.999 | 0.991 | 0.995 | 2325 |
| Pharmacologic Substance | 0.997 | 0.986 | 0.991 | 4127 |
| Physiologic Function | 0.992 | 0.971 | 0.981 | 758 |
| Plant | 0.982 | 0.969 | 0.975 | 1113 |
| Population Group | 0.998 | 0.990 | 0.994 | 3580 |
| Professional Society | 1.000 | 0.957 | 0.978 | 23 |
| Professional or Occupational Group | 0.998 | 0.991 | 0.995 | 1053 |
| Receptor | 0.993 | 0.990 | 0.992 | 829 |
| Regulation or Law | 1.000 | 0.961 | 0.980 | 51 |
| Reptile | 0.941 | 0.889 | 0.914 | 18 |
| Research Activity | 0.996 | 0.989 | 0.992 | 4787 |
| Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 4 |
| Sign or Symptom | 0.997 | 0.997 | 0.997 | 1131 |
| Spatial Concept | 0.995 | 0.989 | 0.992 | 4126 |
| Therapeutic or Preventive Procedure | 0.994 | 0.986 | 0.990 | 6659 |
| Tissue | 0.991 | 0.983 | 0.987 | 991 |
| Vertebrate | 0.923 | 0.923 | 0.923 | 13 |
| Virus | 0.991 | 0.980 | 0.986 | 702 |
| Vitamin | 1.000 | 0.954 | 0.977 | 262 |
| macro avg | 0.969 | 0.959 | 0.964 | 122183 |
| weighted avg | 0.994 | 0.987 | 0.990 | 122183 |

## Token Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| O | 1.000 | 1.000 | 1.000 | 557052 |
| B-Acquired Abnormality | 1.000 | 1.000 | 1.000 | 105 |
| I-Acquired Abnormality | 1.000 | 1.000 | 1.000 | 138 |
| B-Amino Acid Sequence | 1.000 | 1.000 | 1.000 | 206 |
| I-Amino Acid Sequence | 1.000 | 1.000 | 1.000 | 345 |
| B-Amino Acid, Peptide, or Protein | 0.997 | 0.991 | 0.994 | 649 |
| I-Amino Acid, Peptide, or Protein | 1.000 | 0.997 | 0.998 | 968 |
| B-Amphibian | 1.000 | 1.000 | 1.000 | 20 |
| I-Amphibian | 0.906 | 1.000 | 0.951 | 29 |
| B-Anatomical Abnormality | 1.000 | 0.951 | 0.975 | 143 |
| I-Anatomical Abnormality | 1.000 | 0.985 | 0.992 | 201 |
| B-Anatomical Structure | 0.976 | 0.976 | 0.976 | 83 |
| I-Anatomical Structure | 1.000 | 0.972 | 0.986 | 71 |
| B-Animal | 1.000 | 0.996 | 0.998 | 238 |
| I-Animal | 1.000 | 1.000 | 1.000 | 95 |
| B-Antibiotic | 0.997 | 1.000 | 0.999 | 363 |
| I-Antibiotic | 1.000 | 1.000 | 1.000 | 294 |
| B-Bacterium | 1.000 | 1.000 | 1.000 | 1111 |
| I-Bacterium | 1.000 | 1.000 | 1.000 | 2449 |
| B-Biologic Function | 0.995 | 0.997 | 0.996 | 619 |
| I-Biologic Function | 0.997 | 0.997 | 0.997 | 305 |
| B-Biologically Active Substance | 0.999 | 0.998 | 0.998 | 5337 |
| I-Biologically Active Substance | 0.999 | 1.000 | 0.999 | 6779 |
| B-Biomedical Occupation or Discipline | 1.000 | 0.990 | 0.995 | 518 |
| I-Biomedical Occupation or Discipline | 0.990 | 1.000 | 0.995 | 393 |
| B-Biomedical or Dental Material | 0.995 | 0.998 | 0.996 | 842 |
| I-Biomedical or Dental Material | 1.000 | 1.000 | 1.000 | 1080 |
| B-Bird | 0.987 | 1.000 | 0.994 | 232 |
| I-Bird | 0.997 | 1.000 | 0.999 | 338 |
| B-Body Location or Region | 0.999 | 0.997 | 0.998 | 697 |
| I-Body Location or Region | 0.997 | 1.000 | 0.998 | 643 |
| B-Body Part, Organ, or Organ Component | 0.999 | 0.999 | 0.999 | 3868 |
| I-Body Part, Organ, or Organ Component | 1.000 | 1.000 | 1.000 | 3015 |
| B-Body Space or Junction | 0.997 | 0.997 | 0.997 | 353 |
| I-Body Space or Junction | 1.000 | 1.000 | 1.000 | 425 |
| B-Body Substance | 0.996 | 0.999 | 0.997 | 770 |
| I-Body Substance | 1.000 | 1.000 | 1.000 | 378 |
| B-Body System | 0.997 | 0.997 | 0.997 | 298 |
| I-Body System | 0.993 | 0.997 | 0.995 | 297 |
| B-Cell | 0.998 | 0.999 | 0.999 | 3301 |
| I-Cell | 0.999 | 1.000 | 0.999 | 3622 |
| B-Cell Component | 0.999 | 0.999 | 0.999 | 929 |
| I-Cell Component | 1.000 | 0.999 | 0.999 | 825 |
| B-Cell Function | 0.996 | 0.996 | 0.996 | 1937 |
| I-Cell Function | 0.999 | 0.999 | 0.999 | 1716 |
| B-Cell or Molecular Dysfunction | 0.997 | 1.000 | 0.999 | 350 |
| I-Cell or Molecular Dysfunction | 1.000 | 0.998 | 0.999 | 423 |
| B-Chemical | 0.994 | 1.000 | 0.997 | 154 |
| I-Chemical | 1.000 | 1.000 | 1.000 | 22 |
| B-Chemical Viewed Functionally | 0.994 | 0.994 | 0.994 | 176 |
| I-Chemical Viewed Functionally | 1.000 | 1.000 | 1.000 | 98 |
| B-Chemical Viewed Structurally | 0.996 | 1.000 | 0.998 | 281 |
| I-Chemical Viewed Structurally | 0.996 | 1.000 | 0.998 | 282 |
| B-Classification | 0.997 | 0.995 | 0.996 | 736 |
| I-Classification | 0.998 | 1.000 | 0.999 | 447 |
| B-Clinical Attribute | 0.996 | 0.999 | 0.998 | 1030 |
| I-Clinical Attribute | 0.995 | 0.999 | 0.997 | 854 |
| B-Congenital Abnormality | 0.967 | 1.000 | 0.983 | 177 |
| I-Congenital Abnormality | 0.988 | 1.000 | 0.994 | 331 |
| B-Diagnostic Procedure | 0.999 | 0.997 | 0.998 | 2412 |
| I-Diagnostic Procedure | 0.998 | 1.000 | 0.999 | 3191 |
| B-Disease or Syndrome | 0.999 | 0.999 | 0.999 | 6843 |
| I-Disease or Syndrome | 0.999 | 1.000 | 1.000 | 7295 |
| B-Drug Delivery Device | 1.000 | 1.000 | 1.000 | 11 |
| I-Drug Delivery Device | 1.000 | 1.000 | 1.000 | 3 |
| B-Element, Ion, or Isotope | 1.000 | 0.995 | 0.997 | 924 |
| I-Element, Ion, or Isotope | 0.999 | 1.000 | 0.999 | 922 |
| B-Embryonic Structure | 1.000 | 1.000 | 1.000 | 174 |
| I-Embryonic Structure | 1.000 | 1.000 | 1.000 | 73 |
| B-Enzyme | 0.998 | 1.000 | 0.999 | 2182 |
| I-Enzyme | 1.000 | 1.000 | 1.000 | 3095 |
| B-Eukaryote | 1.000 | 0.998 | 0.999 | 985 |
| I-Eukaryote | 1.000 | 1.000 | 1.000 | 2332 |
| B-Experimental Model of Disease | 1.000 | 1.000 | 1.000 | 189 |
| I-Experimental Model of Disease | 1.000 | 1.000 | 1.000 | 213 |
| B-Finding | 0.997 | 0.998 | 0.997 | 8158 |
| I-Finding | 0.996 | 0.999 | 0.998 | 7036 |
| B-Fish | 0.994 | 1.000 | 0.997 | 154 |
| I-Fish | 1.000 | 1.000 | 1.000 | 364 |
| B-Food | 0.999 | 0.998 | 0.998 | 832 |
| I-Food | 0.997 | 0.999 | 0.998 | 705 |
| B-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 1 |
| I-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 0 |
| B-Fungus | 1.000 | 1.000 | 1.000 | 348 |
| I-Fungus | 1.000 | 1.000 | 1.000 | 748 |
| B-Gene or Genome | 0.998 | 0.999 | 0.998 | 2768 |
| I-Gene or Genome | 1.000 | 1.000 | 1.000 | 4238 |
| B-Genetic Function | 0.995 | 0.999 | 0.997 | 1999 |
| I-Genetic Function | 0.999 | 1.000 | 1.000 | 1245 |
| B-Geographic Area | 0.998 | 1.000 | 0.999 | 1702 |
| I-Geographic Area | 0.996 | 0.998 | 0.997 | 1370 |
| B-Hazardous or Poisonous Substance | 0.997 | 0.997 | 0.997 | 697 |
| I-Hazardous or Poisonous Substance | 0.999 | 1.000 | 0.999 | 882 |
| B-Health Care Activity | 0.997 | 0.997 | 0.997 | 2833 |
| I-Health Care Activity | 0.998 | 0.999 | 0.999 | 2092 |
| B-Health Care Related Organization | 0.998 | 0.999 | 0.999 | 1031 |
| I-Health Care Related Organization | 0.999 | 1.000 | 0.999 | 1447 |
| B-Hormone | 1.000 | 1.000 | 1.000 | 500 |
| I-Hormone | 1.000 | 1.000 | 1.000 | 454 |
| B-Human | 1.000 | 1.000 | 1.000 | 436 |
| I-Human | 1.000 | 1.000 | 1.000 | 75 |
| B-Idea or Concept | 0.000 | 0.000 | 0.000 | 0 |
| I-Idea or Concept | 0.000 | 0.000 | 0.000 | 0 |
| B-Immunologic Factor | 0.997 | 0.998 | 0.997 | 1714 |
| I-Immunologic Factor | 1.000 | 1.000 | 1.000 | 2675 |
| B-Indicator, Reagent, or Diagnostic Aid | 0.995 | 0.998 | 0.997 | 644 |
| I-Indicator, Reagent, or Diagnostic Aid | 1.000 | 1.000 | 1.000 | 952 |
| B-Injury or Poisoning | 0.994 | 1.000 | 0.997 | 1056 |
| I-Injury or Poisoning | 0.998 | 1.000 | 0.999 | 1028 |
| B-Inorganic Chemical | 0.996 | 1.000 | 0.998 | 763 |
| I-Inorganic Chemical | 0.998 | 1.000 | 0.999 | 588 |
| B-Intellectual Product | 0.998 | 0.997 | 0.998 | 5336 |
| I-Intellectual Product | 0.999 | 0.999 | 0.999 | 6776 |
| B-Laboratory Procedure | 0.996 | 0.993 | 0.995 | 2745 |
| I-Laboratory Procedure | 0.999 | 1.000 | 0.999 | 4182 |
| B-Laboratory or Test Result | 0.994 | 0.992 | 0.993 | 505 |
| I-Laboratory or Test Result | 0.997 | 0.999 | 0.998 | 684 |
| B-Mammal | 0.999 | 0.999 | 0.999 | 1338 |
| I-Mammal | 0.999 | 0.999 | 0.999 | 1075 |
| B-Medical Device | 1.000 | 0.997 | 0.998 | 1152 |
| I-Medical Device | 0.999 | 1.000 | 0.999 | 1599 |
| B-Mental Process | 0.994 | 0.996 | 0.995 | 1423 |
| I-Mental Process | 1.000 | 0.997 | 0.999 | 749 |
| B-Mental or Behavioral Dysfunction | 0.997 | 1.000 | 0.999 | 1096 |
| I-Mental or Behavioral Dysfunction | 1.000 | 1.000 | 1.000 | 867 |
| B-Molecular Biology Research Technique | 0.994 | 0.992 | 0.993 | 651 |
| I-Molecular Biology Research Technique | 0.998 | 0.998 | 0.998 | 1121 |
| B-Molecular Function | 0.997 | 0.997 | 0.997 | 2004 |
| I-Molecular Function | 0.998 | 1.000 | 0.999 | 2015 |
| B-Molecular Sequence | 0.974 | 0.974 | 0.974 | 39 |
| I-Molecular Sequence | 1.000 | 1.000 | 1.000 | 42 |
| B-Neoplastic Process | 0.999 | 1.000 | 0.999 | 2900 |
| I-Neoplastic Process | 0.999 | 0.999 | 0.999 | 2938 |
| B-Nucleic Acid, Nucleoside, or Nucleotide | 1.000 | 0.992 | 0.996 | 508 |
| I-Nucleic Acid, Nucleoside, or Nucleotide | 0.997 | 1.000 | 0.998 | 609 |
| B-Nucleotide Sequence | 0.997 | 0.994 | 0.996 | 360 |
| I-Nucleotide Sequence | 0.998 | 0.998 | 0.998 | 641 |
| B-Organ or Tissue Function | 0.996 | 0.993 | 0.994 | 901 |
| I-Organ or Tissue Function | 0.996 | 0.995 | 0.996 | 845 |
| B-Organic Chemical | 0.999 | 0.999 | 0.999 | 1404 |
| I-Organic Chemical | 0.999 | 1.000 | 1.000 | 2838 |
| B-Organism Function | 0.995 | 0.996 | 0.996 | 1626 |
| I-Organism Function | 0.999 | 0.996 | 0.997 | 944 |
| B-Organization | 0.983 | 1.000 | 0.992 | 238 |
| I-Organization | 0.996 | 1.000 | 0.998 | 260 |
| B-Pathologic Function | 1.000 | 0.998 | 0.999 | 2309 |
| I-Pathologic Function | 0.999 | 1.000 | 0.999 | 1677 |
| B-Pharmacologic Substance | 0.999 | 1.000 | 0.999 | 4080 |
| I-Pharmacologic Substance | 0.999 | 1.000 | 1.000 | 6760 |
| B-Physiologic Function | 0.997 | 0.989 | 0.993 | 746 |
| I-Physiologic Function | 0.996 | 1.000 | 0.998 | 507 |
| B-Plant | 0.995 | 0.998 | 0.996 | 1104 |
| I-Plant | 0.998 | 0.999 | 0.999 | 1821 |
| B-Population Group | 0.999 | 0.999 | 0.999 | 3547 |
| I-Population Group | 0.997 | 0.999 | 0.998 | 1310 |
| B-Professional Society | 1.000 | 0.957 | 0.978 | 23 |
| I-Professional Society | 1.000 | 1.000 | 1.000 | 55 |
| B-Professional or Occupational Group | 0.998 | 0.999 | 0.999 | 1045 |
| I-Professional or Occupational Group | 1.000 | 1.000 | 1.000 | 700 |
| B-Receptor | 0.994 | 0.998 | 0.996 | 824 |
| I-Receptor | 0.998 | 0.998 | 0.998 | 1291 |
| B-Regulation or Law | 1.000 | 0.961 | 0.980 | 51 |
| I-Regulation or Law | 1.000 | 1.000 | 1.000 | 54 |
| B-Reptile | 1.000 | 1.000 | 1.000 | 18 |
| I-Reptile | 1.000 | 1.000 | 1.000 | 23 |
| B-Research Activity | 0.997 | 0.994 | 0.995 | 4768 |
| I-Research Activity | 0.999 | 0.999 | 0.999 | 3780 |
| B-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 4 |
| I-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 4 |
| B-Sign or Symptom | 0.996 | 0.999 | 0.998 | 1129 |
| I-Sign or Symptom | 0.999 | 0.998 | 0.998 | 807 |
| B-Spatial Concept | 0.997 | 0.997 | 0.997 | 4103 |
| I-Spatial Concept | 0.996 | 0.999 | 0.997 | 1473 |
| B-Therapeutic or Preventive Procedure | 0.998 | 0.998 | 0.998 | 6613 |
| I-Therapeutic or Preventive Procedure | 1.000 | 1.000 | 1.000 | 6523 |
| B-Tissue | 0.996 | 0.994 | 0.995 | 982 |
| I-Tissue | 0.995 | 0.998 | 0.997 | 597 |
| B-Vertebrate | 1.000 | 1.000 | 1.000 | 13 |
| I-Vertebrate | 0.000 | 0.000 | 0.000 | 3 |
| B-Virus | 0.999 | 1.000 | 0.999 | 696 |
| I-Virus | 1.000 | 1.000 | 1.000 | 1027 |
| B-Vitamin | 1.000 | 0.992 | 0.996 | 252 |
| I-Vitamin | 0.998 | 1.000 | 0.999 | 447 |
| macro avg | 0.959 | 0.959 | 0.959 | 805394 |
| weighted avg | 0.999 | 0.999 | 0.999 | 805394 |


# Performance on Validation Set

## Span Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| Acquired Abnormality | 0.109 | 0.182 | 0.136 | 33 |
| Amino Acid Sequence | 0.373 | 0.328 | 0.349 | 58 |
| Amino Acid, Peptide, or Protein | 0.310 | 0.278 | 0.293 | 187 |
| Amphibian | 1.000 | 0.143 | 0.250 | 7 |
| Anatomical Abnormality | 0.034 | 0.037 | 0.035 | 54 |
| Anatomical Structure | 0.625 | 0.263 | 0.370 | 38 |
| Animal | 0.615 | 0.747 | 0.675 | 75 |
| Antibiotic | 0.825 | 0.810 | 0.817 | 210 |
| Bacterium | 0.709 | 0.755 | 0.731 | 470 |
| Biologic Function | 0.389 | 0.479 | 0.429 | 142 |
| Biologically Active Substance | 0.583 | 0.641 | 0.611 | 1882 |
| Biomedical Occupation or Discipline | 0.584 | 0.475 | 0.524 | 198 |
| Biomedical or Dental Material | 0.395 | 0.428 | 0.411 | 304 |
| Bird | 0.846 | 0.759 | 0.800 | 116 |
| Body Location or Region | 0.288 | 0.393 | 0.332 | 163 |
| Body Part, Organ, or Organ Component | 0.639 | 0.665 | 0.652 | 1259 |
| Body Space or Junction | 0.442 | 0.476 | 0.458 | 145 |
| Body Substance | 0.641 | 0.725 | 0.681 | 269 |
| Body System | 0.611 | 0.629 | 0.620 | 105 |
| Cell | 0.713 | 0.733 | 0.723 | 1205 |
| Cell Component | 0.609 | 0.630 | 0.619 | 338 |
| Cell Function | 0.524 | 0.606 | 0.562 | 619 |
| Cell or Molecular Dysfunction | 0.635 | 0.595 | 0.614 | 111 |
| Chemical | 0.452 | 0.459 | 0.455 | 61 |
| Chemical Viewed Functionally | 0.362 | 0.382 | 0.372 | 55 |
| Chemical Viewed Structurally | 0.561 | 0.517 | 0.538 | 116 |
| Classification | 0.532 | 0.520 | 0.526 | 304 |
| Clinical Attribute | 0.545 | 0.522 | 0.534 | 404 |
| Congenital Abnormality | 0.481 | 0.694 | 0.568 | 36 |
| Diagnostic Procedure | 0.582 | 0.564 | 0.573 | 684 |
| Disease or Syndrome | 0.765 | 0.762 | 0.764 | 2365 |
| Drug Delivery Device | 0.000 | 0.000 | 0.000 | 6 |
| Element, Ion, or Isotope | 0.626 | 0.682 | 0.653 | 280 |
| Embryonic Structure | 0.698 | 0.769 | 0.732 | 39 |
| Enzyme | 0.647 | 0.728 | 0.685 | 569 |
| Eukaryote | 0.656 | 0.685 | 0.670 | 409 |
| Experimental Model of Disease | 0.377 | 0.547 | 0.446 | 53 |
| Finding | 0.355 | 0.348 | 0.351 | 2670 |
| Fish | 0.857 | 0.884 | 0.870 | 95 |
| Food | 0.585 | 0.641 | 0.611 | 259 |
| Fungus | 0.729 | 0.647 | 0.685 | 133 |
| Gene or Genome | 0.611 | 0.611 | 0.611 | 769 |
| Genetic Function | 0.644 | 0.680 | 0.662 | 519 |
| Geographic Area | 0.749 | 0.736 | 0.743 | 678 |
| Hazardous or Poisonous Substance | 0.598 | 0.620 | 0.609 | 221 |
| Health Care Activity | 0.450 | 0.446 | 0.448 | 981 |
| Health Care Related Organization | 0.532 | 0.559 | 0.545 | 367 |
| Hormone | 0.661 | 0.796 | 0.723 | 157 |
| Human | 0.766 | 0.883 | 0.820 | 137 |
| Immunologic Factor | 0.694 | 0.654 | 0.674 | 535 |
| Indicator, Reagent, or Diagnostic Aid | 0.342 | 0.385 | 0.363 | 231 |
| Injury or Poisoning | 0.621 | 0.625 | 0.623 | 435 |
| Inorganic Chemical | 0.688 | 0.688 | 0.688 | 285 |
| Intellectual Product | 0.480 | 0.465 | 0.472 | 1665 |
| Laboratory Procedure | 0.438 | 0.494 | 0.464 | 852 |
| Laboratory or Test Result | 0.144 | 0.189 | 0.163 | 132 |
| Mammal | 0.796 | 0.815 | 0.806 | 465 |
| Medical Device | 0.553 | 0.569 | 0.561 | 487 |
| Mental Process | 0.527 | 0.492 | 0.509 | 590 |
| Mental or Behavioral Dysfunction | 0.668 | 0.700 | 0.684 | 530 |
| Molecular Biology Research Technique | 0.510 | 0.667 | 0.578 | 195 |
| Molecular Function | 0.438 | 0.547 | 0.487 | 539 |
| Molecular Sequence | 0.071 | 0.125 | 0.091 | 8 |
| Neoplastic Process | 0.737 | 0.749 | 0.743 | 806 |
| Nucleic Acid, Nucleoside, or Nucleotide | 0.379 | 0.482 | 0.424 | 139 |
| Nucleotide Sequence | 0.404 | 0.423 | 0.414 | 130 |
| Organ or Tissue Function | 0.419 | 0.428 | 0.423 | 306 |
| Organic Chemical | 0.499 | 0.476 | 0.487 | 540 |
| Organism Function | 0.445 | 0.522 | 0.480 | 510 |
| Organization | 0.259 | 0.367 | 0.304 | 79 |
| Pathologic Function | 0.564 | 0.579 | 0.572 | 877 |
| Pharmacologic Substance | 0.634 | 0.682 | 0.657 | 1296 |
| Physiologic Function | 0.391 | 0.299 | 0.339 | 264 |
| Plant | 0.688 | 0.691 | 0.690 | 405 |
| Population Group | 0.661 | 0.620 | 0.640 | 1303 |
| Professional Society | 1.000 | 0.200 | 0.333 | 5 |
| Professional or Occupational Group | 0.643 | 0.734 | 0.685 | 365 |
| Receptor | 0.688 | 0.623 | 0.654 | 361 |
| Regulation or Law | 0.167 | 0.222 | 0.190 | 18 |
| Reptile | 1.000 | 0.222 | 0.364 | 18 |
| Research Activity | 0.590 | 0.525 | 0.556 | 1666 |
| Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 2 |
| Sign or Symptom | 0.581 | 0.634 | 0.607 | 350 |
| Spatial Concept | 0.431 | 0.439 | 0.435 | 1378 |
| Therapeutic or Preventive Procedure | 0.576 | 0.607 | 0.591 | 2131 |
| Tissue | 0.583 | 0.625 | 0.603 | 320 |
| Vertebrate | 1.000 | 0.500 | 0.667 | 6 |
| Virus | 0.690 | 0.777 | 0.731 | 224 |
| Vitamin | 0.860 | 0.607 | 0.712 | 61 |
| macro avg | 0.553 | 0.538 | 0.532 | 40864 |
| weighted avg | 0.575 | 0.588 | 0.580 | 40864 |

## Token Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| O | 0.938 | 0.939 | 0.939 | 187057 |
| B-Acquired Abnormality | 0.185 | 0.303 | 0.230 | 33 |
| I-Acquired Abnormality | 0.200 | 0.297 | 0.239 | 37 |
| B-Amino Acid Sequence | 0.522 | 0.414 | 0.462 | 58 |
| I-Amino Acid Sequence | 0.316 | 0.294 | 0.305 | 102 |
| B-Amino Acid, Peptide, or Protein | 0.346 | 0.292 | 0.317 | 185 |
| I-Amino Acid, Peptide, or Protein | 0.212 | 0.182 | 0.196 | 291 |
| B-Amphibian | 1.000 | 0.143 | 0.250 | 7 |
| I-Amphibian | 1.000 | 0.028 | 0.054 | 36 |
| B-Anatomical Abnormality | 0.041 | 0.038 | 0.039 | 53 |
| I-Anatomical Abnormality | 0.029 | 0.053 | 0.037 | 38 |
| B-Anatomical Structure | 0.625 | 0.263 | 0.370 | 38 |
| I-Anatomical Structure | 0.600 | 0.200 | 0.300 | 30 |
| B-Animal | 0.622 | 0.778 | 0.691 | 72 |
| I-Animal | 0.400 | 0.435 | 0.417 | 23 |
| B-Antibiotic | 0.856 | 0.832 | 0.844 | 208 |
| I-Antibiotic | 0.799 | 0.634 | 0.707 | 194 |
| B-Bacterium | 0.786 | 0.818 | 0.802 | 468 |
| I-Bacterium | 0.854 | 0.843 | 0.848 | 1112 |
| B-Biologic Function | 0.410 | 0.479 | 0.442 | 142 |
| I-Biologic Function | 0.328 | 0.367 | 0.346 | 60 |
| B-Biologically Active Substance | 0.633 | 0.674 | 0.653 | 1862 |
| I-Biologically Active Substance | 0.532 | 0.614 | 0.570 | 2209 |
| B-Biomedical Occupation or Discipline | 0.606 | 0.477 | 0.534 | 197 |
| I-Biomedical Occupation or Discipline | 0.615 | 0.370 | 0.462 | 173 |
| B-Biomedical or Dental Material | 0.438 | 0.486 | 0.461 | 292 |
| I-Biomedical or Dental Material | 0.427 | 0.262 | 0.325 | 447 |
| B-Bird | 0.875 | 0.798 | 0.835 | 114 |
| I-Bird | 0.938 | 0.822 | 0.876 | 219 |
| B-Body Location or Region | 0.323 | 0.429 | 0.368 | 163 |
| I-Body Location or Region | 0.333 | 0.417 | 0.370 | 144 |
| B-Body Part, Organ, or Organ Component | 0.690 | 0.712 | 0.701 | 1252 |
| I-Body Part, Organ, or Organ Component | 0.644 | 0.677 | 0.660 | 969 |
| B-Body Space or Junction | 0.482 | 0.472 | 0.477 | 142 |
| I-Body Space or Junction | 0.508 | 0.682 | 0.583 | 176 |
| B-Body Substance | 0.647 | 0.710 | 0.677 | 269 |
| I-Body Substance | 0.464 | 0.593 | 0.520 | 118 |
| B-Body System | 0.642 | 0.648 | 0.645 | 105 |
| I-Body System | 0.711 | 0.667 | 0.688 | 81 |
| B-Cell | 0.758 | 0.761 | 0.760 | 1200 |
| I-Cell | 0.727 | 0.855 | 0.786 | 1263 |
| B-Cell Component | 0.687 | 0.663 | 0.675 | 338 |
| I-Cell Component | 0.544 | 0.511 | 0.527 | 266 |
| B-Cell Function | 0.590 | 0.663 | 0.624 | 614 |
| I-Cell Function | 0.510 | 0.518 | 0.514 | 533 |
| B-Cell or Molecular Dysfunction | 0.687 | 0.613 | 0.648 | 111 |
| I-Cell or Molecular Dysfunction | 0.524 | 0.581 | 0.551 | 93 |
| B-Chemical | 0.483 | 0.483 | 0.483 | 60 |
| I-Chemical | 0.500 | 0.083 | 0.143 | 24 |
| B-Chemical Viewed Functionally | 0.362 | 0.382 | 0.372 | 55 |
| I-Chemical Viewed Functionally | 0.476 | 0.400 | 0.435 | 50 |
| B-Chemical Viewed Structurally | 0.614 | 0.534 | 0.571 | 116 |
| I-Chemical Viewed Structurally | 0.171 | 0.128 | 0.146 | 47 |
| B-Classification | 0.577 | 0.560 | 0.569 | 300 |
| I-Classification | 0.460 | 0.388 | 0.421 | 147 |
| B-Clinical Attribute | 0.607 | 0.579 | 0.593 | 401 |
| I-Clinical Attribute | 0.470 | 0.345 | 0.398 | 275 |
| B-Congenital Abnormality | 0.481 | 0.694 | 0.568 | 36 |
| I-Congenital Abnormality | 0.562 | 0.581 | 0.571 | 62 |
| B-Diagnostic Procedure | 0.697 | 0.635 | 0.665 | 680 |
| I-Diagnostic Procedure | 0.638 | 0.648 | 0.643 | 1000 |
| B-Disease or Syndrome | 0.790 | 0.788 | 0.789 | 2335 |
| I-Disease or Syndrome | 0.754 | 0.779 | 0.766 | 2454 |
| B-Drug Delivery Device | 0.000 | 0.000 | 0.000 | 6 |
| I-Drug Delivery Device | 0.000 | 0.000 | 0.000 | 3 |
| B-Element, Ion, or Isotope | 0.691 | 0.716 | 0.703 | 278 |
| I-Element, Ion, or Isotope | 0.608 | 0.734 | 0.665 | 192 |
| B-Embryonic Structure | 0.698 | 0.833 | 0.759 | 36 |
| I-Embryonic Structure | 0.889 | 0.889 | 0.889 | 9 |
| B-Enzyme | 0.693 | 0.767 | 0.728 | 566 |
| I-Enzyme | 0.704 | 0.758 | 0.730 | 770 |
| B-Eukaryote | 0.782 | 0.830 | 0.805 | 406 |
| I-Eukaryote | 0.828 | 0.878 | 0.852 | 950 |
| B-Experimental Model of Disease | 0.431 | 0.596 | 0.500 | 52 |
| I-Experimental Model of Disease | 0.360 | 0.300 | 0.327 | 60 |
| B-Finding | 0.410 | 0.383 | 0.396 | 2640 |
| I-Finding | 0.343 | 0.278 | 0.307 | 2209 |
| B-Fish | 0.825 | 0.904 | 0.863 | 94 |
| I-Fish | 0.788 | 0.732 | 0.759 | 142 |
| B-Food | 0.663 | 0.715 | 0.688 | 256 |
| I-Food | 0.625 | 0.689 | 0.655 | 244 |
| B-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 0 |
| I-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 0 |
| B-Fungus | 0.842 | 0.722 | 0.777 | 133 |
| I-Fungus | 0.881 | 0.776 | 0.825 | 210 |
| B-Gene or Genome | 0.682 | 0.677 | 0.679 | 764 |
| I-Gene or Genome | 0.734 | 0.658 | 0.694 | 1317 |
| B-Genetic Function | 0.695 | 0.706 | 0.701 | 517 |
| I-Genetic Function | 0.585 | 0.478 | 0.526 | 316 |
| B-Geographic Area | 0.815 | 0.789 | 0.802 | 674 |
| I-Geographic Area | 0.703 | 0.790 | 0.744 | 542 |
| B-Hazardous or Poisonous Substance | 0.661 | 0.658 | 0.659 | 219 |
| I-Hazardous or Poisonous Substance | 0.590 | 0.630 | 0.610 | 311 |
| B-Health Care Activity | 0.506 | 0.496 | 0.501 | 970 |
| I-Health Care Activity | 0.523 | 0.451 | 0.484 | 730 |
| B-Health Care Related Organization | 0.589 | 0.610 | 0.599 | 359 |
| I-Health Care Related Organization | 0.649 | 0.647 | 0.648 | 519 |
| B-Hormone | 0.691 | 0.828 | 0.754 | 157 |
| I-Hormone | 0.474 | 0.688 | 0.561 | 80 |
| B-Human | 0.778 | 0.898 | 0.834 | 137 |
| I-Human | 0.419 | 0.464 | 0.441 | 28 |
| B-Idea or Concept | 0.000 | 0.000 | 0.000 | 0 |
| I-Idea or Concept | 0.000 | 0.000 | 0.000 | 0 |
| B-Immunologic Factor | 0.766 | 0.680 | 0.721 | 535 |
| I-Immunologic Factor | 0.688 | 0.680 | 0.684 | 753 |
| B-Indicator, Reagent, or Diagnostic Aid | 0.450 | 0.476 | 0.463 | 227 |
| I-Indicator, Reagent, or Diagnostic Aid | 0.512 | 0.533 | 0.522 | 450 |
| B-Injury or Poisoning | 0.654 | 0.614 | 0.633 | 433 |
| I-Injury or Poisoning | 0.543 | 0.698 | 0.611 | 315 |
| B-Inorganic Chemical | 0.704 | 0.711 | 0.708 | 284 |
| I-Inorganic Chemical | 0.718 | 0.685 | 0.701 | 257 |
| B-Intellectual Product | 0.539 | 0.506 | 0.522 | 1653 |
| I-Intellectual Product | 0.557 | 0.486 | 0.519 | 2089 |
| B-Laboratory Procedure | 0.516 | 0.544 | 0.530 | 847 |
| I-Laboratory Procedure | 0.574 | 0.600 | 0.587 | 1237 |
| B-Laboratory or Test Result | 0.217 | 0.250 | 0.232 | 132 |
| I-Laboratory or Test Result | 0.199 | 0.224 | 0.211 | 152 |
| B-Mammal | 0.831 | 0.838 | 0.834 | 457 |
| I-Mammal | 0.840 | 0.849 | 0.844 | 345 |
| B-Medical Device | 0.604 | 0.603 | 0.604 | 486 |
| I-Medical Device | 0.605 | 0.604 | 0.605 | 685 |
| B-Mental Process | 0.567 | 0.523 | 0.544 | 583 |
| I-Mental Process | 0.609 | 0.533 | 0.568 | 304 |
| B-Mental or Behavioral Dysfunction | 0.711 | 0.735 | 0.723 | 529 |
| I-Mental or Behavioral Dysfunction | 0.700 | 0.670 | 0.685 | 397 |
| B-Molecular Biology Research Technique | 0.576 | 0.718 | 0.639 | 195 |
| I-Molecular Biology Research Technique | 0.712 | 0.724 | 0.718 | 409 |
| B-Molecular Function | 0.501 | 0.596 | 0.544 | 539 |
| I-Molecular Function | 0.449 | 0.483 | 0.466 | 532 |
| B-Molecular Sequence | 0.143 | 0.250 | 0.182 | 8 |
| I-Molecular Sequence | 0.222 | 0.286 | 0.250 | 7 |
| B-Neoplastic Process | 0.778 | 0.793 | 0.786 | 794 |
| I-Neoplastic Process | 0.774 | 0.788 | 0.781 | 905 |
| B-Nucleic Acid, Nucleoside, or Nucleotide | 0.453 | 0.600 | 0.517 | 130 |
| I-Nucleic Acid, Nucleoside, or Nucleotide | 0.392 | 0.396 | 0.394 | 197 |
| B-Nucleotide Sequence | 0.446 | 0.425 | 0.435 | 127 |
| I-Nucleotide Sequence | 0.316 | 0.524 | 0.394 | 103 |
| B-Organ or Tissue Function | 0.459 | 0.447 | 0.453 | 304 |
| I-Organ or Tissue Function | 0.478 | 0.481 | 0.480 | 270 |
| B-Organic Chemical | 0.537 | 0.484 | 0.509 | 539 |
| I-Organic Chemical | 0.450 | 0.363 | 0.402 | 1105 |
| B-Organism Function | 0.466 | 0.540 | 0.500 | 506 |
| I-Organism Function | 0.389 | 0.379 | 0.384 | 272 |
| B-Organization | 0.287 | 0.403 | 0.335 | 77 |
| I-Organization | 0.250 | 0.330 | 0.284 | 91 |
| B-Pathologic Function | 0.598 | 0.595 | 0.597 | 872 |
| I-Pathologic Function | 0.467 | 0.487 | 0.477 | 532 |
| B-Pharmacologic Substance | 0.670 | 0.718 | 0.693 | 1274 |
| I-Pharmacologic Substance | 0.602 | 0.666 | 0.633 | 1991 |
| B-Physiologic Function | 0.437 | 0.317 | 0.367 | 262 |
| I-Physiologic Function | 0.271 | 0.172 | 0.211 | 186 |
| B-Plant | 0.781 | 0.779 | 0.780 | 403 |
| I-Plant | 0.824 | 0.845 | 0.834 | 676 |
| B-Population Group | 0.712 | 0.659 | 0.684 | 1289 |
| I-Population Group | 0.489 | 0.467 | 0.478 | 486 |
| B-Professional Society | 0.500 | 0.200 | 0.286 | 5 |
| I-Professional Society | 1.000 | 0.250 | 0.400 | 8 |
| B-Professional or Occupational Group | 0.683 | 0.786 | 0.731 | 359 |
| I-Professional or Occupational Group | 0.631 | 0.613 | 0.622 | 302 |
| B-Receptor | 0.755 | 0.657 | 0.702 | 361 |
| I-Receptor | 0.686 | 0.647 | 0.666 | 541 |
| B-Regulation or Law | 0.286 | 0.333 | 0.308 | 18 |
| I-Regulation or Law | 0.640 | 0.627 | 0.634 | 51 |
| B-Reptile | 1.000 | 0.222 | 0.364 | 18 |
| I-Reptile | 1.000 | 0.115 | 0.207 | 52 |
| B-Research Activity | 0.639 | 0.559 | 0.597 | 1650 |
| I-Research Activity | 0.605 | 0.542 | 0.572 | 1274 |
| B-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 2 |
| I-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 4 |
| B-Sign or Symptom | 0.616 | 0.646 | 0.630 | 350 |
| I-Sign or Symptom | 0.504 | 0.513 | 0.509 | 232 |
| B-Spatial Concept | 0.485 | 0.481 | 0.483 | 1371 |
| I-Spatial Concept | 0.434 | 0.389 | 0.410 | 570 |
| B-Therapeutic or Preventive Procedure | 0.618 | 0.637 | 0.628 | 2112 |
| I-Therapeutic or Preventive Procedure | 0.611 | 0.623 | 0.617 | 1917 |
| B-Tissue | 0.620 | 0.649 | 0.634 | 319 |
| I-Tissue | 0.571 | 0.563 | 0.567 | 215 |
| B-Vertebrate | 1.000 | 0.500 | 0.667 | 6 |
| I-Vertebrate | 0.000 | 0.000 | 0.000 | 2 |
| B-Virus | 0.760 | 0.856 | 0.805 | 222 |
| I-Virus | 0.699 | 0.843 | 0.764 | 267 |
| B-Vitamin | 0.886 | 0.639 | 0.743 | 61 |
| I-Vitamin | 0.889 | 0.681 | 0.771 | 94 |
| macro avg | 0.560 | 0.533 | 0.533 | 269146 |
| weighted avg | 0.839 | 0.840 | 0.839 | 269146 |


# Performance on Testing Set

## Span Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| Acquired Abnormality | 0.273 | 0.240 | 0.255 | 50 |
| Amino Acid Sequence | 0.303 | 0.357 | 0.328 | 84 |
| Amino Acid, Peptide, or Protein | 0.258 | 0.277 | 0.267 | 166 |
| Anatomical Abnormality | 0.190 | 0.145 | 0.164 | 76 |
| Anatomical Structure | 0.160 | 0.308 | 0.211 | 13 |
| Animal | 0.605 | 0.742 | 0.667 | 93 |
| Antibiotic | 0.835 | 0.784 | 0.808 | 148 |
| Bacterium | 0.752 | 0.732 | 0.742 | 448 |
| Biologic Function | 0.341 | 0.369 | 0.355 | 157 |
| Biologically Active Substance | 0.586 | 0.640 | 0.612 | 2080 |
| Biomedical Occupation or Discipline | 0.437 | 0.444 | 0.441 | 196 |
| Biomedical or Dental Material | 0.369 | 0.452 | 0.406 | 197 |
| Bird | 0.810 | 0.819 | 0.814 | 83 |
| Body Location or Region | 0.386 | 0.461 | 0.420 | 232 |
| Body Part, Organ, or Organ Component | 0.565 | 0.604 | 0.584 | 1092 |
| Body Space or Junction | 0.272 | 0.311 | 0.290 | 90 |
| Body Substance | 0.542 | 0.731 | 0.622 | 212 |
| Body System | 0.554 | 0.511 | 0.532 | 90 |
| Cell | 0.680 | 0.737 | 0.708 | 924 |
| Cell Component | 0.589 | 0.637 | 0.612 | 311 |
| Cell Function | 0.484 | 0.599 | 0.535 | 499 |
| Cell or Molecular Dysfunction | 0.607 | 0.657 | 0.631 | 99 |
| Chemical | 0.348 | 0.333 | 0.340 | 72 |
| Chemical Viewed Functionally | 0.286 | 0.432 | 0.344 | 37 |
| Chemical Viewed Structurally | 0.443 | 0.427 | 0.435 | 82 |
| Classification | 0.520 | 0.544 | 0.532 | 309 |
| Clinical Attribute | 0.596 | 0.625 | 0.610 | 323 |
| Congenital Abnormality | 0.438 | 0.443 | 0.440 | 79 |
| Diagnostic Procedure | 0.672 | 0.648 | 0.660 | 735 |
| Disease or Syndrome | 0.757 | 0.774 | 0.766 | 2199 |
| Element, Ion, or Isotope | 0.713 | 0.657 | 0.684 | 385 |
| Embryonic Structure | 0.587 | 0.509 | 0.545 | 53 |
| Enzyme | 0.766 | 0.761 | 0.763 | 681 |
| Eukaryote | 0.745 | 0.793 | 0.768 | 397 |
| Experimental Model of Disease | 0.286 | 0.356 | 0.317 | 45 |
| Finding | 0.391 | 0.388 | 0.389 | 2759 |
| Fish | 1.000 | 0.947 | 0.973 | 19 |
| Food | 0.556 | 0.455 | 0.501 | 336 |
| Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 1 |
| Fungus | 0.819 | 0.798 | 0.809 | 119 |
| Gene or Genome | 0.551 | 0.539 | 0.545 | 912 |
| Genetic Function | 0.598 | 0.646 | 0.621 | 652 |
| Geographic Area | 0.673 | 0.712 | 0.692 | 598 |
| Hazardous or Poisonous Substance | 0.513 | 0.522 | 0.518 | 293 |
| Health Care Activity | 0.487 | 0.458 | 0.472 | 1061 |
| Health Care Related Organization | 0.531 | 0.642 | 0.581 | 296 |
| Hormone | 0.806 | 0.746 | 0.775 | 189 |
| Human | 0.799 | 0.880 | 0.837 | 158 |
| Idea or Concept | 0.000 | 0.000 | 0.000 | 1 |
| Immunologic Factor | 0.674 | 0.606 | 0.638 | 434 |
| Indicator, Reagent, or Diagnostic Aid | 0.427 | 0.451 | 0.439 | 182 |
| Injury or Poisoning | 0.617 | 0.703 | 0.657 | 357 |
| Inorganic Chemical | 0.611 | 0.680 | 0.643 | 256 |
| Intellectual Product | 0.495 | 0.485 | 0.490 | 2075 |
| Laboratory Procedure | 0.445 | 0.452 | 0.448 | 908 |
| Laboratory or Test Result | 0.183 | 0.196 | 0.190 | 112 |
| Mammal | 0.778 | 0.838 | 0.807 | 456 |
| Medical Device | 0.434 | 0.437 | 0.435 | 355 |
| Mental Process | 0.546 | 0.546 | 0.546 | 740 |
| Mental or Behavioral Dysfunction | 0.710 | 0.774 | 0.741 | 518 |
| Molecular Biology Research Technique | 0.500 | 0.539 | 0.519 | 206 |
| Molecular Function | 0.504 | 0.555 | 0.528 | 719 |
| Molecular Sequence | 0.417 | 0.556 | 0.476 | 9 |
| Neoplastic Process | 0.761 | 0.745 | 0.753 | 918 |
| Nucleic Acid, Nucleoside, or Nucleotide | 0.331 | 0.450 | 0.381 | 109 |
| Nucleotide Sequence | 0.320 | 0.491 | 0.387 | 110 |
| Organ or Tissue Function | 0.482 | 0.425 | 0.452 | 247 |
| Organic Chemical | 0.396 | 0.464 | 0.427 | 511 |
| Organism Function | 0.462 | 0.518 | 0.488 | 471 |
| Organization | 0.270 | 0.442 | 0.335 | 77 |
| Pathologic Function | 0.541 | 0.541 | 0.541 | 669 |
| Pharmacologic Substance | 0.577 | 0.623 | 0.599 | 1258 |
| Physiologic Function | 0.283 | 0.286 | 0.284 | 182 |
| Plant | 0.603 | 0.618 | 0.610 | 403 |
| Population Group | 0.710 | 0.711 | 0.711 | 1263 |
| Professional Society | 0.000 | 0.000 | 0.000 | 7 |
| Professional or Occupational Group | 0.599 | 0.725 | 0.656 | 360 |
| Receptor | 0.614 | 0.686 | 0.648 | 271 |
| Regulation or Law | 0.182 | 0.125 | 0.148 | 16 |
| Reptile | 1.000 | 0.318 | 0.483 | 22 |
| Research Activity | 0.559 | 0.540 | 0.549 | 1653 |
| Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 2 |
| Sign or Symptom | 0.629 | 0.647 | 0.638 | 340 |
| Spatial Concept | 0.474 | 0.483 | 0.479 | 1282 |
| Therapeutic or Preventive Procedure | 0.609 | 0.617 | 0.613 | 2036 |
| Tissue | 0.562 | 0.525 | 0.543 | 259 |
| Vertebrate | 0.000 | 0.000 | 0.000 | 1 |
| Virus | 0.678 | 0.831 | 0.747 | 172 |
| Vitamin | 0.706 | 0.511 | 0.593 | 47 |
| macro avg | 0.507 | 0.525 | 0.512 | 40144 |
| weighted avg | 0.571 | 0.589 | 0.578 | 40144 |

## Token Level

| Label | Precision | Recall | F1-score | Support |
| --- | --- | --- | --- | --- |
| O | 0.940 | 0.938 | 0.939 | 188640 |
| B-Acquired Abnormality | 0.279 | 0.240 | 0.258 | 50 |
| I-Acquired Abnormality | 0.371 | 0.283 | 0.321 | 46 |
| B-Amino Acid Sequence | 0.368 | 0.390 | 0.379 | 82 |
| I-Amino Acid Sequence | 0.525 | 0.503 | 0.514 | 189 |
| B-Amino Acid, Peptide, or Protein | 0.321 | 0.325 | 0.323 | 166 |
| I-Amino Acid, Peptide, or Protein | 0.173 | 0.211 | 0.190 | 161 |
| B-Amphibian | 0.000 | 0.000 | 0.000 | 0 |
| I-Amphibian | 0.000 | 0.000 | 0.000 | 0 |
| B-Anatomical Abnormality | 0.231 | 0.158 | 0.188 | 76 |
| I-Anatomical Abnormality | 0.296 | 0.154 | 0.203 | 104 |
| B-Anatomical Structure | 0.154 | 0.333 | 0.211 | 12 |
| I-Anatomical Structure | 0.000 | 0.000 | 0.000 | 11 |
| B-Animal | 0.646 | 0.793 | 0.712 | 92 |
| I-Animal | 0.500 | 0.512 | 0.506 | 41 |
| B-Antibiotic | 0.846 | 0.782 | 0.813 | 147 |
| I-Antibiotic | 0.727 | 0.566 | 0.636 | 99 |
| B-Bacterium | 0.836 | 0.791 | 0.813 | 446 |
| I-Bacterium | 0.904 | 0.822 | 0.861 | 1311 |
| B-Biologic Function | 0.381 | 0.394 | 0.387 | 155 |
| I-Biologic Function | 0.165 | 0.195 | 0.179 | 77 |
| B-Biologically Active Substance | 0.632 | 0.675 | 0.652 | 2070 |
| I-Biologically Active Substance | 0.581 | 0.633 | 0.606 | 2623 |
| B-Biomedical Occupation or Discipline | 0.532 | 0.508 | 0.520 | 195 |
| I-Biomedical Occupation or Discipline | 0.509 | 0.446 | 0.475 | 130 |
| B-Biomedical or Dental Material | 0.431 | 0.513 | 0.468 | 195 |
| I-Biomedical or Dental Material | 0.416 | 0.537 | 0.469 | 203 |
| B-Bird | 0.902 | 0.892 | 0.897 | 83 |
| I-Bird | 0.886 | 0.951 | 0.917 | 163 |
| B-Body Location or Region | 0.455 | 0.504 | 0.479 | 232 |
| I-Body Location or Region | 0.255 | 0.351 | 0.295 | 174 |
| B-Body Part, Organ, or Organ Component | 0.610 | 0.643 | 0.626 | 1086 |
| I-Body Part, Organ, or Organ Component | 0.579 | 0.630 | 0.604 | 865 |
| B-Body Space or Junction | 0.271 | 0.299 | 0.284 | 87 |
| I-Body Space or Junction | 0.383 | 0.500 | 0.434 | 108 |
| B-Body Substance | 0.546 | 0.722 | 0.622 | 212 |
| I-Body Substance | 0.529 | 0.618 | 0.570 | 102 |
| B-Body System | 0.605 | 0.557 | 0.580 | 88 |
| I-Body System | 0.629 | 0.619 | 0.624 | 63 |
| B-Cell | 0.721 | 0.765 | 0.743 | 920 |
| I-Cell | 0.747 | 0.750 | 0.748 | 1142 |
| B-Cell Component | 0.658 | 0.688 | 0.673 | 311 |
| I-Cell Component | 0.637 | 0.594 | 0.615 | 293 |
| B-Cell Function | 0.545 | 0.643 | 0.590 | 498 |
| I-Cell Function | 0.549 | 0.491 | 0.518 | 483 |
| B-Cell or Molecular Dysfunction | 0.684 | 0.677 | 0.680 | 99 |
| I-Cell or Molecular Dysfunction | 0.656 | 0.468 | 0.546 | 126 |
| B-Chemical | 0.371 | 0.361 | 0.366 | 72 |
| I-Chemical | 0.000 | 0.000 | 0.000 | 24 |
| B-Chemical Viewed Functionally | 0.340 | 0.459 | 0.391 | 37 |
| I-Chemical Viewed Functionally | 0.149 | 0.412 | 0.219 | 17 |
| B-Chemical Viewed Structurally | 0.545 | 0.512 | 0.528 | 82 |
| I-Chemical Viewed Structurally | 0.162 | 0.107 | 0.129 | 56 |
| B-Classification | 0.556 | 0.582 | 0.569 | 306 |
| I-Classification | 0.292 | 0.226 | 0.255 | 177 |
| B-Clinical Attribute | 0.612 | 0.637 | 0.624 | 322 |
| I-Clinical Attribute | 0.558 | 0.502 | 0.529 | 219 |
| B-Congenital Abnormality | 0.500 | 0.481 | 0.490 | 79 |
| I-Congenital Abnormality | 0.463 | 0.479 | 0.471 | 169 |
| B-Diagnostic Procedure | 0.731 | 0.686 | 0.708 | 732 |
| I-Diagnostic Procedure | 0.775 | 0.692 | 0.732 | 1102 |
| B-Disease or Syndrome | 0.788 | 0.803 | 0.795 | 2185 |
| I-Disease or Syndrome | 0.742 | 0.755 | 0.749 | 2326 |
| B-Drug Delivery Device | 0.000 | 0.000 | 0.000 | 0 |
| I-Drug Delivery Device | 0.000 | 0.000 | 0.000 | 0 |
| B-Element, Ion, or Isotope | 0.737 | 0.669 | 0.702 | 381 |
| I-Element, Ion, or Isotope | 0.714 | 0.622 | 0.665 | 225 |
| B-Embryonic Structure | 0.595 | 0.472 | 0.526 | 53 |
| I-Embryonic Structure | 0.545 | 0.486 | 0.514 | 37 |
| B-Enzyme | 0.791 | 0.781 | 0.786 | 680 |
| I-Enzyme | 0.823 | 0.779 | 0.801 | 1051 |
| B-Eukaryote | 0.820 | 0.899 | 0.858 | 396 |
| I-Eukaryote | 0.894 | 0.938 | 0.916 | 892 |
| B-Experimental Model of Disease | 0.353 | 0.400 | 0.375 | 45 |
| I-Experimental Model of Disease | 0.392 | 0.328 | 0.357 | 61 |
| B-Finding | 0.449 | 0.424 | 0.436 | 2741 |
| I-Finding | 0.353 | 0.323 | 0.337 | 2236 |
| B-Fish | 0.857 | 0.947 | 0.900 | 19 |
| I-Fish | 0.944 | 1.000 | 0.971 | 17 |
| B-Food | 0.650 | 0.499 | 0.564 | 335 |
| I-Food | 0.580 | 0.375 | 0.455 | 299 |
| B-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 1 |
| I-Fully Formed Anatomical Structure | 0.000 | 0.000 | 0.000 | 1 |
| B-Fungus | 0.913 | 0.890 | 0.901 | 118 |
| I-Fungus | 0.917 | 0.948 | 0.933 | 328 |
| B-Gene or Genome | 0.653 | 0.629 | 0.641 | 911 |
| I-Gene or Genome | 0.558 | 0.577 | 0.567 | 1329 |
| B-Genetic Function | 0.659 | 0.683 | 0.671 | 652 |
| I-Genetic Function | 0.523 | 0.372 | 0.435 | 489 |
| B-Geographic Area | 0.727 | 0.763 | 0.744 | 594 |
| I-Geographic Area | 0.672 | 0.698 | 0.685 | 557 |
| B-Hazardous or Poisonous Substance | 0.589 | 0.570 | 0.579 | 291 |
| I-Hazardous or Poisonous Substance | 0.427 | 0.527 | 0.472 | 300 |
| B-Health Care Activity | 0.548 | 0.498 | 0.522 | 1055 |
| I-Health Care Activity | 0.576 | 0.462 | 0.513 | 795 |
| B-Health Care Related Organization | 0.582 | 0.682 | 0.628 | 296 |
| I-Health Care Related Organization | 0.633 | 0.754 | 0.688 | 411 |
| B-Hormone | 0.831 | 0.757 | 0.792 | 189 |
| I-Hormone | 0.744 | 0.782 | 0.762 | 119 |
| B-Human | 0.824 | 0.892 | 0.856 | 157 |
| I-Human | 0.535 | 0.719 | 0.613 | 32 |
| B-Idea or Concept | 0.000 | 0.000 | 0.000 | 1 |
| I-Idea or Concept | 0.000 | 0.000 | 0.000 | 2 |
| B-Immunologic Factor | 0.738 | 0.653 | 0.693 | 432 |
| I-Immunologic Factor | 0.741 | 0.690 | 0.715 | 720 |
| B-Indicator, Reagent, or Diagnostic Aid | 0.469 | 0.462 | 0.465 | 182 |
| I-Indicator, Reagent, or Diagnostic Aid | 0.598 | 0.699 | 0.645 | 196 |
| B-Injury or Poisoning | 0.672 | 0.749 | 0.708 | 347 |
| I-Injury or Poisoning | 0.683 | 0.709 | 0.695 | 398 |
| B-Inorganic Chemical | 0.656 | 0.707 | 0.680 | 256 |
| I-Inorganic Chemical | 0.599 | 0.809 | 0.689 | 220 |
| B-Intellectual Product | 0.547 | 0.517 | 0.532 | 2065 |
| I-Intellectual Product | 0.552 | 0.541 | 0.547 | 2378 |
| B-Laboratory Procedure | 0.538 | 0.513 | 0.525 | 907 |
| I-Laboratory Procedure | 0.586 | 0.600 | 0.593 | 1390 |
| B-Laboratory or Test Result | 0.283 | 0.255 | 0.268 | 110 |
| I-Laboratory or Test Result | 0.189 | 0.174 | 0.181 | 132 |
| B-Mammal | 0.832 | 0.859 | 0.845 | 455 |
| I-Mammal | 0.649 | 0.633 | 0.641 | 278 |
| B-Medical Device | 0.508 | 0.460 | 0.483 | 354 |
| I-Medical Device | 0.451 | 0.470 | 0.460 | 566 |
| B-Mental Process | 0.582 | 0.585 | 0.583 | 727 |
| I-Mental Process | 0.419 | 0.545 | 0.474 | 299 |
| B-Mental or Behavioral Dysfunction | 0.741 | 0.798 | 0.768 | 515 |
| I-Mental or Behavioral Dysfunction | 0.670 | 0.670 | 0.670 | 412 |
| B-Molecular Biology Research Technique | 0.570 | 0.576 | 0.573 | 205 |
| I-Molecular Biology Research Technique | 0.621 | 0.598 | 0.609 | 353 |
| B-Molecular Function | 0.583 | 0.610 | 0.597 | 716 |
| I-Molecular Function | 0.526 | 0.526 | 0.526 | 741 |
| B-Molecular Sequence | 0.455 | 0.556 | 0.500 | 9 |
| I-Molecular Sequence | 0.600 | 0.833 | 0.698 | 18 |
| B-Neoplastic Process | 0.807 | 0.778 | 0.792 | 914 |
| I-Neoplastic Process | 0.792 | 0.772 | 0.782 | 1007 |
| B-Nucleic Acid, Nucleoside, or Nucleotide | 0.394 | 0.495 | 0.439 | 109 |
| I-Nucleic Acid, Nucleoside, or Nucleotide | 0.204 | 0.320 | 0.249 | 97 |
| B-Nucleotide Sequence | 0.365 | 0.532 | 0.433 | 109 |
| I-Nucleotide Sequence | 0.401 | 0.525 | 0.455 | 158 |
| B-Organ or Tissue Function | 0.551 | 0.457 | 0.500 | 247 |
| I-Organ or Tissue Function | 0.522 | 0.422 | 0.467 | 256 |
| B-Organic Chemical | 0.442 | 0.491 | 0.465 | 509 |
| I-Organic Chemical | 0.396 | 0.485 | 0.436 | 1003 |
| B-Organism Function | 0.495 | 0.537 | 0.515 | 471 |
| I-Organism Function | 0.314 | 0.338 | 0.326 | 207 |
| B-Organization | 0.293 | 0.442 | 0.352 | 77 |
| I-Organization | 0.327 | 0.467 | 0.385 | 75 |
| B-Pathologic Function | 0.569 | 0.558 | 0.564 | 661 |
| I-Pathologic Function | 0.517 | 0.469 | 0.492 | 512 |
| B-Pharmacologic Substance | 0.613 | 0.659 | 0.635 | 1248 |
| I-Pharmacologic Substance | 0.618 | 0.620 | 0.619 | 2121 |
| B-Physiologic Function | 0.288 | 0.282 | 0.285 | 181 |
| I-Physiologic Function | 0.393 | 0.315 | 0.350 | 111 |
| B-Plant | 0.702 | 0.712 | 0.707 | 403 |
| I-Plant | 0.650 | 0.763 | 0.702 | 528 |
| B-Population Group | 0.752 | 0.738 | 0.745 | 1261 |
| I-Population Group | 0.523 | 0.520 | 0.521 | 456 |
| B-Professional Society | 0.000 | 0.000 | 0.000 | 7 |
| I-Professional Society | 0.000 | 0.000 | 0.000 | 23 |
| B-Professional or Occupational Group | 0.639 | 0.760 | 0.695 | 359 |
| I-Professional or Occupational Group | 0.600 | 0.707 | 0.649 | 208 |
| B-Receptor | 0.648 | 0.730 | 0.686 | 270 |
| I-Receptor | 0.491 | 0.684 | 0.572 | 367 |
| B-Regulation or Law | 0.273 | 0.188 | 0.222 | 16 |
| I-Regulation or Law | 0.000 | 0.000 | 0.000 | 14 |
| B-Reptile | 1.000 | 0.136 | 0.240 | 22 |
| I-Reptile | 1.000 | 0.160 | 0.276 | 50 |
| B-Research Activity | 0.607 | 0.572 | 0.589 | 1642 |
| I-Research Activity | 0.658 | 0.619 | 0.638 | 1276 |
| B-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 2 |
| I-Self-help or Relief Organization | 0.000 | 0.000 | 0.000 | 2 |
| B-Sign or Symptom | 0.676 | 0.684 | 0.680 | 335 |
| I-Sign or Symptom | 0.457 | 0.500 | 0.478 | 204 |
| B-Spatial Concept | 0.504 | 0.503 | 0.503 | 1273 |
| I-Spatial Concept | 0.480 | 0.512 | 0.495 | 512 |
| B-Therapeutic or Preventive Procedure | 0.660 | 0.656 | 0.658 | 2017 |
| I-Therapeutic or Preventive Procedure | 0.687 | 0.660 | 0.673 | 2012 |
| B-Tissue | 0.633 | 0.559 | 0.593 | 256 |
| I-Tissue | 0.620 | 0.444 | 0.517 | 239 |
| B-Vertebrate | 1.000 | 1.000 | 1.000 | 1 |
| I-Vertebrate | 0.000 | 0.000 | 0.000 | 1 |
| B-Virus | 0.731 | 0.901 | 0.807 | 172 |
| I-Virus | 0.723 | 0.923 | 0.811 | 209 |
| B-Vitamin | 0.758 | 0.532 | 0.625 | 47 |
| I-Vitamin | 0.582 | 0.561 | 0.571 | 57 |
| macro avg | 0.525 | 0.527 | 0.519 | 270152 |
| weighted avg | 0.842 | 0.841 | 0.841 | 270152 |