Training in progress epoch 0

README.md

@@ -15,9 +15,9 @@ probably proofread and complete it, then remove this comment. -->
 
 This model is a fine-tuned version of [bert-base-cased](https://huggingface.co/bert-base-cased) on an unknown dataset.
 It achieves the following results on the evaluation set:
-- Train Loss: 0.0097
-- Validation Loss: 0.0036
-- Epoch: 2
+- Train Loss: 0.3570
+- Validation Loss: 0.0236
+- Epoch: 0
 
 ## Model description
 
@@ -43,9 +43,7 @@ The following hyperparameters were used during training:
 
 | Train Loss | Validation Loss | Epoch |
 |:----------:|:---------------:|:-----:|
-| 0.3378     | 0.0268          | 0     |
-| 0.0222     | 0.0048          | 1     |
-| 0.0097     | 0.0036          | 2     |
+| 0.3570     | 0.0236          | 0     |
 
 
 ### Framework versions

config.json

@@ -11,118 +11,138 @@
   "hidden_size": 768,
   "id2label": {
     "0": "O",
-    "1": "B-ACCESSION_NUM",
-    "2": "I-ACCESSION_NUM",
-    "3": "B-ALLELE_FREQ",
-    "4": "I-ALLELE_FREQ",
-    "5": "B-AMINO_ACID_CHANGE",
-    "6": "I-AMINO_ACID_CHANGE",
-    "7": "B-ASSAY",
-    "8": "I-ASSAY",
-    "9": "B-BIOMARKER",
-    "10": "I-BIOMARKER",
-    "11": "B-CDNA_CHANGE",
-    "12": "I-CDNA_CHANGE",
-    "13": "B-CF_DNA_OR_AMP",
-    "14": "I-CF_DNA_OR_AMP",
-    "15": "B-CHROM",
-    "16": "I-CHROM",
-    "17": "B-COPY_NUM",
-    "18": "I-COPY_NUM",
-    "19": "B-COSMIC_ID",
-    "20": "I-COSMIC_ID",
-    "21": "B-COVERAGE",
-    "22": "I-COVERAGE",
-    "23": "B-DATE",
-    "24": "I-DATE",
-    "25": "B-EFFECT",
-    "26": "I-EFFECT",
-    "27": "B-EXON",
-    "28": "I-EXON",
-    "29": "B-GENE",
-    "30": "I-GENE",
-    "31": "B-NEG_BIOMARKER",
-    "32": "I-NEG_BIOMARKER",
-    "33": "B-OTHER_SENSITIVE_DRUGS",
-    "34": "I-OTHER_SENSITIVE_DRUGS",
-    "35": "B-PATIENT_ID",
-    "36": "I-PATIENT_ID",
-    "37": "B-PATIENT_NAME",
-    "38": "I-PATIENT_NAME",
-    "39": "B-POS_BIOMARKER",
-    "40": "I-POS_BIOMARKER",
-    "41": "B-REPORT_NO",
-    "42": "I-REPORT_NO",
-    "43": "B-RESISTANT_DRUGS",
-    "44": "I-RESISTANT_DRUGS",
-    "45": "B-RESULTS",
-    "46": "I-RESULTS",
-    "47": "B-SENSITIVE_DRUGS",
-    "48": "I-SENSITIVE_DRUGS",
-    "49": "B-THERAPIES",
-    "50": "I-THERAPIES",
-    "51": "B-TUMOR_TYPE",
-    "52": "I-TUMOR_TYPE",
-    "53": "B-VARIATION",
-    "54": "I-VARIATION"
+    "1": "B-BIOMARKER_ACTIONABLE_DRUG",
+    "2": "I-BIOMARKER_ACTIONABLE_DRUG",
+    "3": "B-BIOMARKER_CANDIDATE_DRUG",
+    "4": "I-BIOMARKER_CANDIDATE_DRUG",
+    "5": "B-BIOMARKER_EFFECT",
+    "6": "I-BIOMARKER_EFFECT",
+    "7": "B-BIOMARKER_MUTATION",
+    "8": "I-BIOMARKER_MUTATION",
+    "9": "B-CHROMOSOME",
+    "10": "I-CHROMOSOME",
+    "11": "B-COPY_NUMBER",
+    "12": "I-COPY_NUMBER",
+    "13": "B-FUSION_GENE",
+    "14": "I-FUSION_GENE",
+    "15": "B-FUSION_BREAKPOINT",
+    "16": "I-FUSION_BREAKPOINT",
+    "17": "B-FUSION_TRANSCRIPT",
+    "18": "I-FUSION_TRANSCRIPT",
+    "19": "B-FUSION_VARIANT",
+    "20": "I-FUSION_VARIANT",
+    "21": "B-GENE",
+    "22": "I-GENE",
+    "23": "B-MSI_RESULT",
+    "24": "I-MSI_RESULT",
+    "25": "B-NEG_BIOMARKER",
+    "26": "I-NEG_BIOMARKER",
+    "27": "B-POS_BIOMARKER",
+    "28": "I-POS_BIOMARKER",
+    "29": "B-REPORT_DATE",
+    "30": "I-REPORT_DATE",
+    "31": "B-REPORT_DIAGNOSIS",
+    "32": "I-REPORT_DIAGNOSIS",
+    "33": "B-REPORT_ID",
+    "34": "I-REPORT_ID",
+    "35": "B-REPORT_PATIENT_ID",
+    "36": "I-REPORT_PATIENT_ID",
+    "37": "B-REPORT_PATIENT_NAME",
+    "38": "I-REPORT_PATIENT_NAME",
+    "39": "B-REPORT_PHYSICIAN",
+    "40": "I-REPORT_PHYSICIAN",
+    "41": "B-REPORT_TEST_ASSAY",
+    "42": "I-REPORT_TEST_ASSAY",
+    "43": "B-TMB_RESULT",
+    "44": "I-TMB_RESULT",
+    "45": "B-VARIANT_ACCESSION",
+    "46": "I-VARIANT_ACCESSION",
+    "47": "B-VARIANT_ALLELE_AMPLIFICATION",
+    "48": "I-VARIANT_ALLELE_AMPLIFICATION",
+    "49": "B-VARIANT_ALLELE_FRACTION",
+    "50": "I-VARIANT_ALLELE_FRACTION",
+    "51": "B-VARIANT_ALLELE_FREQUENCY",
+    "52": "I-VARIANT_ALLELE_FREQUENCY",
+    "53": "B-VARIANT_AMINO_ACID_CHANGE",
+    "54": "I-VARIANT_AMINO_ACID_CHANGE",
+    "55": "B-VARIANT_COSMIC",
+    "56": "I-VARIANT_COSMIC",
+    "57": "B-VARIANT_COVERAGE",
+    "58": "I-VARIANT_COVERAGE",
+    "59": "B-VARIANT_EXON",
+    "60": "I-VARIANT_EXON",
+    "61": "B-VARIANT_FORM",
+    "62": "I-VARIANT_FORM",
+    "63": "B-VARIANT_HGVS",
+    "64": "I-VARIANT_HGVS"
   },
   "initializer_range": 0.02,
   "intermediate_size": 3072,
   "label2id": {
-    "B-ACCESSION_NUM": 1,
-    "B-ALLELE_FREQ": 3,
-    "B-AMINO_ACID_CHANGE": 5,
-    "B-ASSAY": 7,
-    "B-BIOMARKER": 9,
-    "B-CDNA_CHANGE": 11,
-    "B-CF_DNA_OR_AMP": 13,
-    "B-CHROM": 15,
-    "B-COPY_NUM": 17,
-    "B-COSMIC_ID": 19,
-    "B-COVERAGE": 21,
-    "B-DATE": 23,
-    "B-EFFECT": 25,
-    "B-EXON": 27,
-    "B-GENE": 29,
-    "B-NEG_BIOMARKER": 31,
-    "B-OTHER_SENSITIVE_DRUGS": 33,
-    "B-PATIENT_ID": 35,
-    "B-PATIENT_NAME": 37,
-    "B-POS_BIOMARKER": 39,
-    "B-REPORT_NO": 41,
-    "B-RESISTANT_DRUGS": 43,
-    "B-RESULTS": 45,
-    "B-SENSITIVE_DRUGS": 47,
-    "B-THERAPIES": 49,
-    "B-TUMOR_TYPE": 51,
-    "B-VARIATION": 53,
-    "I-ACCESSION_NUM": 2,
-    "I-ALLELE_FREQ": 4,
-    "I-AMINO_ACID_CHANGE": 6,
-    "I-ASSAY": 8,
-    "I-BIOMARKER": 10,
-    "I-CDNA_CHANGE": 12,
-    "I-CF_DNA_OR_AMP": 14,
-    "I-CHROM": 16,
-    "I-COPY_NUM": 18,
-    "I-COSMIC_ID": 20,
-    "I-COVERAGE": 22,
-    "I-DATE": 24,
-    "I-EFFECT": 26,
-    "I-EXON": 28,
-    "I-GENE": 30,
-    "I-NEG_BIOMARKER": 32,
-    "I-OTHER_SENSITIVE_DRUGS": 34,
-    "I-PATIENT_ID": 36,
-    "I-PATIENT_NAME": 38,
-    "I-POS_BIOMARKER": 40,
-    "I-REPORT_NO": 42,
-    "I-RESISTANT_DRUGS": 44,
-    "I-RESULTS": 46,
-    "I-SENSITIVE_DRUGS": 48,
-    "I-THERAPIES": 50,
-    "I-TUMOR_TYPE": 52,
-    "I-VARIATION": 54,
+    "B-BIOMARKER_ACTIONABLE_DRUG": 1,
+    "B-BIOMARKER_CANDIDATE_DRUG": 3,
+    "B-BIOMARKER_EFFECT": 5,
+    "B-BIOMARKER_MUTATION": 7,
+    "B-CHROMOSOME": 9,
+    "B-COPY_NUMBER": 11,
+    "B-FUSION_BREAKPOINT": 15,
+    "B-FUSION_GENE": 13,
+    "B-FUSION_TRANSCRIPT": 17,
+    "B-FUSION_VARIANT": 19,
+    "B-GENE": 21,
+    "B-MSI_RESULT": 23,
+    "B-NEG_BIOMARKER": 25,
+    "B-POS_BIOMARKER": 27,
+    "B-REPORT_DATE": 29,
+    "B-REPORT_DIAGNOSIS": 31,
+    "B-REPORT_ID": 33,
+    "B-REPORT_PATIENT_ID": 35,
+    "B-REPORT_PATIENT_NAME": 37,
+    "B-REPORT_PHYSICIAN": 39,
+    "B-REPORT_TEST_ASSAY": 41,
+    "B-TMB_RESULT": 43,
+    "B-VARIANT_ACCESSION": 45,
+    "B-VARIANT_ALLELE_AMPLIFICATION": 47,
+    "B-VARIANT_ALLELE_FRACTION": 49,
+    "B-VARIANT_ALLELE_FREQUENCY": 51,
+    "B-VARIANT_AMINO_ACID_CHANGE": 53,
+    "B-VARIANT_COSMIC": 55,
+    "B-VARIANT_COVERAGE": 57,
+    "B-VARIANT_EXON": 59,
+    "B-VARIANT_FORM": 61,
+    "B-VARIANT_HGVS": 63,
+    "I-BIOMARKER_ACTIONABLE_DRUG": 2,
+    "I-BIOMARKER_CANDIDATE_DRUG": 4,
+    "I-BIOMARKER_EFFECT": 6,
+    "I-BIOMARKER_MUTATION": 8,
+    "I-CHROMOSOME": 10,
+    "I-COPY_NUMBER": 12,
+    "I-FUSION_BREAKPOINT": 16,
+    "I-FUSION_GENE": 14,
+    "I-FUSION_TRANSCRIPT": 18,
+    "I-FUSION_VARIANT": 20,
+    "I-GENE": 22,
+    "I-MSI_RESULT": 24,
+    "I-NEG_BIOMARKER": 26,
+    "I-POS_BIOMARKER": 28,
+    "I-REPORT_DATE": 30,
+    "I-REPORT_DIAGNOSIS": 32,
+    "I-REPORT_ID": 34,
+    "I-REPORT_PATIENT_ID": 36,
+    "I-REPORT_PATIENT_NAME": 38,
+    "I-REPORT_PHYSICIAN": 40,
+    "I-REPORT_TEST_ASSAY": 42,
+    "I-TMB_RESULT": 44,
+    "I-VARIANT_ACCESSION": 46,
+    "I-VARIANT_ALLELE_AMPLIFICATION": 48,
+    "I-VARIANT_ALLELE_FRACTION": 50,
+    "I-VARIANT_ALLELE_FREQUENCY": 52,
+    "I-VARIANT_AMINO_ACID_CHANGE": 54,
+    "I-VARIANT_COSMIC": 56,
+    "I-VARIANT_COVERAGE": 58,
+    "I-VARIANT_EXON": 60,
+    "I-VARIANT_FORM": 62,
+    "I-VARIANT_HGVS": 64,
     "O": 0
   },
   "layer_norm_eps": 1e-12,

tf_model.h5

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
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-size 431321252
+oid sha256:58f941172cb621d874def86a2ce824385c07262053e3ac593e18ef53202a2c0d
+size 431352012