Update spaCy pipeline

.gitattributes

@@ -33,3 +33,5 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zst filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+es_breast_cancer_ehr_ner-any-py3-none-any.whl filter=lfs diff=lfs merge=lfs -text
+transformer/model filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,59 @@
+---
+tags:
+- spacy
+- token-classification
+language:
+- es
+license: mit
+model-index:
+- name: es_breast_cancer_ehr_ner
+  results:
+  - task:
+      name: NER
+      type: token-classification
+    metrics:
+    - name: NER Precision
+      type: precision
+      value: 0.9245630175
+    - name: NER Recall
+      type: recall
+      value: 0.9396914446
+    - name: NER F Score
+      type: f_score
+      value: 0.9320658474
+---
+Breast Cancer Diagnosis NER model
+
+| Feature | Description |
+| --- | --- |
+| **Name** | `es_breast_cancer_ehr_ner` |
+| **Version** | `0.0.0` |
+| **spaCy** | `>=3.5.0,<3.6.0` |
+| **Default Pipeline** | `transformer`, `ner` |
+| **Components** | `transformer`, `ner` |
+| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
+| **Sources** | n/a |
+| **License** | `mit` |
+| **Author** | [Álvaro García Barragán]() |
+
+### Label Scheme
+
+<details>
+
+<summary>View label scheme (21 labels for 1 components)</summary>
+
+| Component | Labels |
+| --- | --- |
+| **`ner`** | `CANCER_CONCEPT`, `CANCER_EXP`, `CANCER_GRADE`, `CANCER_INTRTYPE`, `CANCER_LOC`, `CANCER_MET`, `CANCER_REC`, `CANCER_STAGE`, `CANCER_SUBTYPE`, `CANCER_TYPE`, `DATE`, `IMPLICIT_DATE`, `MOLEC_MARKER`, `SURGERY`, `TNM`, `TRAT`, `TRAT_DRUG`, `TRAT_FREQ`, `TRAT_INTERVAL`, `TRAT_QUANTITY`, `TRAT_SHEMA` |
+
+</details>
+
+### Accuracy
+
+| Type | Score |
+| --- | --- |
+| `ENTS_F` | 93.21 |
+| `ENTS_P` | 92.46 |
+| `ENTS_R` | 93.97 |
+| `TRANSFORMER_LOSS` | 45014.63 |
+| `NER_LOSS` | 1216054.67 |

config.cfg

@@ -0,0 +1,148 @@
+[paths]
+train = "/home/alvaro/Desktop/NLP/Spacy-NLP/dataset/mama_JD_JC_550_V2/train.spacy"
+dev = "/home/alvaro/Desktop/NLP/Spacy-NLP/dataset/mama_JD_JC_550_V2/test.spacy"
+vectors = null
+init_tok2vec = null
+
+[system]
+gpu_allocator = "pytorch"
+seed = 0
+
+[nlp]
+lang = "es"
+pipeline = ["transformer","ner"]
+batch_size = 128
+disabled = []
+before_creation = null
+after_creation = null
+after_pipeline_creation = null
+tokenizer = {"@tokenizers":"spacy.Tokenizer.v1"}
+
+[components]
+
+[components.ner]
+factory = "ner"
+incorrect_spans_key = null
+moves = null
+scorer = {"@scorers":"spacy.ner_scorer.v1"}
+update_with_oracle_cut_size = 100
+
+[components.ner.model]
+@architectures = "spacy.TransitionBasedParser.v2"
+state_type = "ner"
+extra_state_tokens = false
+hidden_width = 64
+maxout_pieces = 2
+use_upper = false
+nO = null
+
+[components.ner.model.tok2vec]
+@architectures = "spacy-transformers.TransformerListener.v1"
+grad_factor = 1.0
+pooling = {"@layers":"reduce_mean.v1"}
+upstream = "*"
+
+[components.transformer]
+factory = "transformer"
+max_batch_items = 4096
+set_extra_annotations = {"@annotation_setters":"spacy-transformers.null_annotation_setter.v1"}
+
+[components.transformer.model]
+@architectures = "spacy-transformers.TransformerModel.v3"
+name = "bert-base-multilingual-uncased"
+mixed_precision = false
+
+[components.transformer.model.get_spans]
+@span_getters = "spacy-transformers.strided_spans.v1"
+window = 128
+stride = 96
+
+[components.transformer.model.grad_scaler_config]
+
+[components.transformer.model.tokenizer_config]
+use_fast = true
+
+[components.transformer.model.transformer_config]
+
+[corpora]
+
+[corpora.dev]
+@readers = "spacy.Corpus.v1"
+path = ${paths.dev}
+max_length = 0
+gold_preproc = false
+limit = 0
+augmenter = null
+
+[corpora.train]
+@readers = "spacy.Corpus.v1"
+path = ${paths.train}
+max_length = 0
+gold_preproc = false
+limit = 0
+augmenter = null
+
+[training]
+accumulate_gradient = 3
+dev_corpus = "corpora.dev"
+train_corpus = "corpora.train"
+seed = ${system.seed}
+gpu_allocator = ${system.gpu_allocator}
+dropout = 0.1
+patience = 1600
+max_epochs = 0
+max_steps = 20000
+eval_frequency = 200
+frozen_components = []
+annotating_components = []
+before_to_disk = null
+before_update = null
+
+[training.batcher]
+@batchers = "spacy.batch_by_padded.v1"
+discard_oversize = true
+size = 2000
+buffer = 256
+get_length = null
+
+[training.logger]
+@loggers = "spacy.ConsoleLogger.v1"
+progress_bar = false
+
+[training.optimizer]
+@optimizers = "Adam.v1"
+beta1 = 0.9
+beta2 = 0.999
+L2_is_weight_decay = true
+L2 = 0.01
+grad_clip = 1.0
+use_averages = false
+eps = 0.00000001
+
+[training.optimizer.learn_rate]
+@schedules = "warmup_linear.v1"
+warmup_steps = 250
+total_steps = 20000
+initial_rate = 0.00005
+
+[training.score_weights]
+ents_f = 1.0
+ents_p = 0.0
+ents_r = 0.0
+ents_per_type = null
+
+[pretraining]
+
+[initialize]
+vectors = ${paths.vectors}
+init_tok2vec = ${paths.init_tok2vec}
+vocab_data = null
+lookups = null
+before_init = null
+after_init = null
+
+[initialize.components]
+
+[initialize.components.ner]
+
+[initialize.tokenizer]

es_breast_cancer_ehr_ner-any-py3-none-any.whl

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:11e3c88b1225b51735788869c55327da9c888fd50430a89840ccb8bf778d69fb
+size 622795991

meta.json

@@ -0,0 +1,174 @@
+{
+  "lang":"es",
+  "name":"breast_cancer_ehr_ner",
+  "version":"0.0.0",
+  "description":"Breast Cancer Diagnosis NER model",
+  "author":"\u00c1lvaro Garc\u00eda Barrag\u00e1n",
+  "email":"[email protected]",
+  "url":"",
+  "license":"mit",
+  "spacy_version":">=3.5.0,<3.6.0",
+  "spacy_git_version":"Unknown",
+  "vectors":{
+    "width":0,
+    "vectors":0,
+    "keys":0,
+    "name":null
+  },
+  "labels":{
+    "transformer":[
+
+    ],
+    "ner":[
+      "CANCER_CONCEPT",
+      "CANCER_EXP",
+      "CANCER_GRADE",
+      "CANCER_INTRTYPE",
+      "CANCER_LOC",
+      "CANCER_MET",
+      "CANCER_REC",
+      "CANCER_STAGE",
+      "CANCER_SUBTYPE",
+      "CANCER_TYPE",
+      "DATE",
+      "IMPLICIT_DATE",
+      "MOLEC_MARKER",
+      "SURGERY",
+      "TNM",
+      "TRAT",
+      "TRAT_DRUG",
+      "TRAT_FREQ",
+      "TRAT_INTERVAL",
+      "TRAT_QUANTITY",
+      "TRAT_SHEMA"
+    ]
+  },
+  "pipeline":[
+    "transformer",
+    "ner"
+  ],
+  "components":[
+    "transformer",
+    "ner"
+  ],
+  "disabled":[
+
+  ],
+  "performance":{
+    "ents_f":0.9320658474,
+    "ents_p":0.9245630175,
+    "ents_r":0.9396914446,
+    "ents_per_type":{
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+        "r":0.9627329193,
+        "f":0.9779179811
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+        "r":0.9901960784,
+        "f":0.9901960784
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+      "CANCER_EXP":{
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+        "r":1.0,
+        "f":0.9779411765
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+      "CANCER_GRADE":{
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+      "MOLEC_MARKER":{
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+        "r":0.9375,
+        "f":0.9333333333
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+      "TNM":{
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+        "r":0.8951612903,
+        "f":0.8671875
+      },
+      "CANCER_STAGE":{
+        "p":0.9545454545,
+        "r":0.9130434783,
+        "f":0.9333333333
+      },
+      "CANCER_LOC":{
+        "p":0.9247910864,
+        "r":0.9299719888,
+        "f":0.9273743017
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+      "DATE":{
+        "p":0.9378881988,
+        "r":0.9741935484,
+        "f":0.9556962025
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+      "SURGERY":{
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+        "f":0.9205479452
+      },
+      "TRAT_DRUG":{
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+        "r":0.9775280899,
+        "f":0.9304812834
+      },
+      "TRAT_INTERVAL":{
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+        "f":0.9189189189
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+      "IMPLICIT_DATE":{
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+        "f":0.9079754601
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+      "CANCER_REC":{
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+        "r":1.0,
+        "f":1.0
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+      "CANCER_INTRTYPE":{
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+        "f":0.9411764706
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+      "CANCER_MET":{
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+        "f":0.9277108434
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+      "TRAT_SHEMA":{
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+      "CANCER_SUBTYPE":{
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+        "r":0.75,
+        "f":0.75
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+      "TRAT_QUANTITY":{
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+        "f":0.8333333333
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+      "TRAT_FREQ":{
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+        "r":1.0,
+        "f":0.9411764706
+      }
+    },
+    "transformer_loss":450.1462650569,
+    "ner_loss":12160.5466765245
+  },
+  "requirements":[
+    "spacy-transformers>=1.3.5,<1.4.0"
+  ]
+}

ner/cfg

@@ -0,0 +1,13 @@
+{
+  "moves":null,
+  "update_with_oracle_cut_size":100,
+  "multitasks":[
+
+  ],
+  "min_action_freq":1,
+  "learn_tokens":false,
+  "beam_width":1,
+  "beam_density":0.0,
+  "beam_update_prob":0.0,
+  "incorrect_spans_key":null
+}

ner/moves

@@ -0,0 +1 @@
+��moves��{"0":{},"1":{"MOLEC_MARKER":3447,"CANCER_LOC":2210,"TNM":1722,"SURGERY":997,"DATE":888,"CANCER_CONCEPT":677,"CANCER_EXP":565,"CANCER_STAGE":559,"CANCER_GRADE":559,"CANCER_TYPE":470,"TRAT_DRUG":398,"TRAT_INTERVAL":370,"TRAT":342,"IMPLICIT_DATE":342,"CANCER_MET":303,"CANCER_SUBTYPE":86,"TRAT_QUANTITY":77,"TRAT_SHEMA":74,"TRAT_FREQ":46,"CANCER_INTRTYPE":44,"CANCER_REC":36},"2":{"MOLEC_MARKER":3447,"CANCER_LOC":2210,"TNM":1722,"SURGERY":997,"DATE":888,"CANCER_CONCEPT":677,"CANCER_EXP":565,"CANCER_STAGE":559,"CANCER_GRADE":559,"CANCER_TYPE":470,"TRAT_DRUG":398,"TRAT_INTERVAL":370,"TRAT":342,"IMPLICIT_DATE":342,"CANCER_MET":303,"CANCER_SUBTYPE":86,"TRAT_QUANTITY":77,"TRAT_SHEMA":74,"TRAT_FREQ":46,"CANCER_INTRTYPE":44,"CANCER_REC":36},"3":{"MOLEC_MARKER":3447,"CANCER_LOC":2210,"TNM":1722,"SURGERY":997,"DATE":888,"CANCER_CONCEPT":677,"CANCER_EXP":565,"CANCER_STAGE":559,"CANCER_GRADE":559,"CANCER_TYPE":470,"TRAT_DRUG":398,"TRAT_INTERVAL":370,"TRAT":342,"IMPLICIT_DATE":342,"CANCER_MET":303,"CANCER_SUBTYPE":86,"TRAT_QUANTITY":77,"TRAT_SHEMA":74,"TRAT_FREQ":46,"CANCER_INTRTYPE":44,"CANCER_REC":36},"4":{"MOLEC_MARKER":3447,"CANCER_LOC":2210,"TNM":1722,"SURGERY":997,"DATE":888,"CANCER_CONCEPT":677,"CANCER_EXP":565,"CANCER_STAGE":559,"CANCER_GRADE":559,"CANCER_TYPE":470,"TRAT_DRUG":398,"TRAT_INTERVAL":370,"TRAT":342,"IMPLICIT_DATE":342,"CANCER_MET":303,"CANCER_SUBTYPE":86,"TRAT_QUANTITY":77,"TRAT_SHEMA":74,"TRAT_FREQ":46,"CANCER_INTRTYPE":44,"CANCER_REC":36,"":1},"5":{"":1}}�cfg��neg_key�

tokenizer

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+  "10-12-2019",
+  "10-15%",
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+  "13/4/2018",
+  "13/9/19",
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+  "130",
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+  "14/05/18",
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+  "14/07/2020",
+  "14/08/2019",
+  "14/09/2016",
+  "14/10/2008",
+  "14/10/2016",
+  "14/11/2017",
+  "14/12/15",
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+  "15-04-2014",
+  "15-11-19",
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+  "15/04/2020",
+  "15/05/19",
+  "15/05/2019",
+  "15/05/2020",
+  "15/09/09",
+  "15/1/2015",
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+  "15/11/2019",
+  "15/2/2018",
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+  "16-04-2020",
+  "16/01/2014",
+  "16/01/2020",
+  "16/06/2017",
+  "16/09/2020",
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+  "16/12/2020",
+  "16/2/2021",
+  "160",
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+  "17/07/2017",
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+  "17/10/2017",
+  "17/11/",
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+  "18/05/16",
+  "18/05/2021",
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+  "18/08/2020",
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+  "18/12/2008",
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+  "250",
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+  "27/2/2019",
+  "27/3/2020",
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+  "30/04/2019",
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+  "zon",
+  "zona",
+  "zonas",
+  "zoster",
+  "zq+",
+  "zt",
+  "|",
+  "}",
+  "\u00a0",
+  "\u00ac",
+  "\u00ac_\u00ac",
+  "\u00af",
+  "\u00af\\(x)/\u00af",
+  "\u00af\\(\u30c4)/\u00af",
+  "\u00b0",
+  "\u00b0C",
+  "\u00b0C.",
+  "\u00b0F.",
+  "\u00b0K.",
+  "\u00b0X",
+  "\u00b0X.",
+  "\u00b0c",
+  "\u00b0c.",
+  "\u00b0f.",
+  "\u00b0k.",
+  "\u00b0x.",
+  "\u00e1g.",
+  "\u00e4",
+  "\u00e4.",
+  "\u00eda.",
+  "\u00f6",
+  "\u00f6.",
+  "\u00fam.",
+  "\u00fc",
+  "\u00fc.",
+  "\u0ca0",
+  "\u0ca0_\u0ca0",
+  "\u0ca0\ufe35\u0ca0",
+  "\u2014",
+  "\u2019",
+  "\u2019-(",
+  "\u2019-)",
+  "\u2019\u2019",
+  "\u2501",
+  "\u253b",
+  "\u253b\u2501\u253b",
+  "\u256f",
+  "\u25a1",
+  "\ufe35",
+  "\uff09"
+]

vocab/vectors.cfg

@@ -0,0 +1,3 @@
+{
+  "mode":"default"
+}