Upload tokenizer

README.md

@@ -1,98 +1,86 @@
 ---
 language:
-  - en
+- en
 license: apache-2.0
 library_name: transformers
 tags:
-  - medical
-  - pharmacovigilance
-  - vaccines
+- medical
+- pharmacovigilance
+- vaccines
 datasets:
-  - chrisvoncsefalvay/vaers-outcomes
+- chrisvoncsefalvay/vaers-outcomes
 metrics:
-  - accuracy
-  - f1
-  - precision
-  - recall
+- accuracy
+- f1
+- precision
+- recall
 dataset: chrisvoncsefalvay/vaers-outcomes
 pipeline_tag: text-classification
 widget:
-  - text: >-
-      Patient is a 90 y.o. male with a PMH of IPF, HFpEF, AFib (Eliquis),
-      Metastatic Prostate Cancer who presented to Hospital 10/28/2023 following
-      an unwitnessed fall at his assisted living. He was found to have an AKI,
-      pericardial effusion, hypoxia, AMS, and COVID-19. His hospital course was
-      complicated by delirium and aspiration, leading to acute hypoxic
-      respiratory failure requiring BiPAP and transfer to the ICU. Palliative
-      Care had been following, and after goals of care conversations on
-      11/10/2023 the patient was transitioned to DNR-CC. Patient expired at 0107
-      11/12/23.
-    example_title: VAERS 2727645 (hospitalisation, death)
-  - text: >-
-      hospitalized for paralytic ileus a week after the vaccination; This
-      serious case was reported by a physician via call center representative
-      and described the occurrence of ileus paralytic in a patient who received
-      Rota (Rotarix liquid formulation) for prophylaxis. On an unknown date, the
-      patient received the 1st dose of Rotarix liquid formulation. On an unknown
-      date, less than 2 weeks after receiving Rotarix liquid formulation, the
-      patient experienced ileus paralytic (Verbatim: hospitalized for paralytic
-      ileus a week after the vaccination) (serious criteria hospitalization and
-      GSK medically significant). The outcome of the ileus paralytic was not
-      reported. It was unknown if the reporter considered the ileus paralytic to
-      be related to Rotarix liquid formulation. It was unknown if the company
-      considered the ileus paralytic to be related to Rotarix liquid
-      formulation. Additional Information: GSK Receipt Date: 27-DEC-2023 Age at
-      vaccination and lot number were not reported. The patient of unknown age
-      and gender was hospitalized for paralytic ileus a week after the
-      vaccination. The reporting physician was in charge of the patient.
-    example_title: VAERS 2728408 (hospitalisation)
-  - text: >-
-      Patient received Pfizer vaccine 7 days beyond BUD. According to Pfizer
-      manufacturer research data, vaccine is stable and effective up to 2 days
-      after BUD. Waiting for more stability data from PFIZER to determine if
-      revaccination is necessary.
-    example_title: VAERS 2728394 (no event)
-  - text: >-
-      Fever of 106F rectally beginning 1 hr after immunizations and lasting <24
-      hrs. Seen at ER treated w/tylenol & cool baths.
-    example_title: VAERS 25042 (ER attendance)
-  - text: >-
-      I had the MMR shot last week, and I felt a little dizzy afterwards, but it
-      passed after a few minutes and I'm doing fine now.
-    example_title: 'Non-sample example: simulated informal patient narrative (no event)'
-  - text: >-
-      My niece had the COVID vaccine. A few weeks later, she was T-boned by a
-      drunk driver. She called me from the ER. She's fully recovered now,
-      though.
-    example_title: >-
-      Non-sample example: simulated informal patient narrative (ER attendance,
-      albeit unconnected)
+- text: Patient is a 90 y.o. male with a PMH of IPF, HFpEF, AFib (Eliquis), Metastatic
+    Prostate Cancer who presented to Hospital 10/28/2023 following an unwitnessed
+    fall at his assisted living. He was found to have an AKI, pericardial effusion,
+    hypoxia, AMS, and COVID-19. His hospital course was complicated by delirium and
+    aspiration, leading to acute hypoxic respiratory failure requiring BiPAP and transfer
+    to the ICU. Palliative Care had been following, and after goals of care conversations
+    on 11/10/2023 the patient was transitioned to DNR-CC. Patient expired at 0107
+    11/12/23.
+  example_title: VAERS 2727645 (hospitalisation, death)
+- text: 'hospitalized for paralytic ileus a week after the vaccination; This serious
+    case was reported by a physician via call center representative and described
+    the occurrence of ileus paralytic in a patient who received Rota (Rotarix liquid
+    formulation) for prophylaxis. On an unknown date, the patient received the 1st
+    dose of Rotarix liquid formulation. On an unknown date, less than 2 weeks after
+    receiving Rotarix liquid formulation, the patient experienced ileus paralytic
+    (Verbatim: hospitalized for paralytic ileus a week after the vaccination) (serious
+    criteria hospitalization and GSK medically significant). The outcome of the ileus
+    paralytic was not reported. It was unknown if the reporter considered the ileus
+    paralytic to be related to Rotarix liquid formulation. It was unknown if the company
+    considered the ileus paralytic to be related to Rotarix liquid formulation. Additional
+    Information: GSK Receipt Date: 27-DEC-2023 Age at vaccination and lot number were
+    not reported. The patient of unknown age and gender was hospitalized for paralytic
+    ileus a week after the vaccination. The reporting physician was in charge of the
+    patient.'
+  example_title: VAERS 2728408 (hospitalisation)
+- text: Patient received Pfizer vaccine 7 days beyond BUD. According to Pfizer manufacturer
+    research data, vaccine is stable and effective up to 2 days after BUD. Waiting
+    for more stability data from PFIZER to determine if revaccination is necessary.
+  example_title: VAERS 2728394 (no event)
+- text: Fever of 106F rectally beginning 1 hr after immunizations and lasting <24
+    hrs. Seen at ER treated w/tylenol & cool baths.
+  example_title: VAERS 25042 (ER attendance)
+- text: I had the MMR shot last week, and I felt a little dizzy afterwards, but it
+    passed after a few minutes and I'm doing fine now.
+  example_title: 'Non-sample example: simulated informal patient narrative (no event)'
+- text: My niece had the COVID vaccine. A few weeks later, she was T-boned by a drunk
+    driver. She called me from the ER. She's fully recovered now, though.
+  example_title: 'Non-sample example: simulated informal patient narrative (ER attendance,
+    albeit unconnected)'
 model-index:
-  - name: daedra
-    results:
-      - task:
-          type: text-classification
-        dataset:
-          type: vaers-outcomes
-          name: vaers-outcomes
-        metrics:
-          - name: Accuracy, microaveraged
-            type: accuracy_microaverage
-            value: 0.885
-            verified: false
-          - name: F1 score, microaveraged
-            type: f1_microaverage
-            value: 0.885
-            verified: false
-          - name: Precision, macroaveraged
-            type: precision_macroaverage
-            value: 0.769
-            verified: false
-          - name: Recall, macroaveraged
-            type: recall_macroaverage
-            value: 0.688
-            verified: false
-
+- name: daedra
+  results:
+  - task:
+      type: text-classification
+    dataset:
+      name: vaers-outcomes
+      type: vaers-outcomes
+    metrics:
+    - type: accuracy_microaverage
+      value: 0.885
+      name: Accuracy, microaveraged
+      verified: false
+    - type: f1_microaverage
+      value: 0.885
+      name: F1 score, microaveraged
+      verified: false
+    - type: precision_macroaverage
+      value: 0.769
+      name: Precision, macroaveraged
+      verified: false
+    - type: recall_macroaverage
+      value: 0.688
+      name: Recall, macroaveraged
+      verified: false
 ---
 
 # DAEDRA: Determining Adverse Event Disposition for Regulatory Affairs

special_tokens_map.json

@@ -1,7 +1,37 @@
 {
-  "cls_token": "[CLS]",
-  "mask_token": "[MASK]",
-  "pad_token": "[PAD]",
-  "sep_token": "[SEP]",
-  "unk_token": "[UNK]"
+  "cls_token": {
+    "content": "[CLS]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "mask_token": {
+    "content": "[MASK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "pad_token": {
+    "content": "[PAD]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "sep_token": {
+    "content": "[SEP]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  },
+  "unk_token": {
+    "content": "[UNK]",
+    "lstrip": false,
+    "normalized": false,
+    "rstrip": false,
+    "single_word": false
+  }
 }

tokenizer_config.json

@@ -8,7 +8,7 @@
       "single_word": false,
       "special": true
     },
-    "100": {
+    "1": {
       "content": "[UNK]",
       "lstrip": false,
       "normalized": false,
@@ -16,7 +16,7 @@
       "single_word": false,
       "special": true
     },
-    "101": {
+    "2": {
       "content": "[CLS]",
       "lstrip": false,
       "normalized": false,
@@ -24,7 +24,7 @@
       "single_word": false,
       "special": true
     },
-    "102": {
+    "3": {
       "content": "[SEP]",
       "lstrip": false,
       "normalized": false,
@@ -32,7 +32,7 @@
       "single_word": false,
       "special": true
     },
-    "103": {
+    "4": {
       "content": "[MASK]",
       "lstrip": false,
       "normalized": false,