Update spaCy pipeline

.gitattributes

@@ -25,3 +25,10 @@ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
 *.zip filter=lfs diff=lfs merge=lfs -text
 *.zstandard filter=lfs diff=lfs merge=lfs -text
 *tfevents* filter=lfs diff=lfs merge=lfs -text
+*.whl filter=lfs diff=lfs merge=lfs -text
+*.npz filter=lfs diff=lfs merge=lfs -text
+*strings.json filter=lfs diff=lfs merge=lfs -text
+vectors filter=lfs diff=lfs merge=lfs -text
+model filter=lfs diff=lfs merge=lfs -text
+ner/moves filter=lfs diff=lfs merge=lfs -text
+tokenizer filter=lfs diff=lfs merge=lfs -text

README.md

@@ -0,0 +1,58 @@
+---
+tags:
+- spacy
+- token-classification
+language:
+- en
+model-index:
+- name: en_sdoh_roberta_cui
+  results:
+  - task:
+      name: NER
+      type: token-classification
+    metrics:
+    - name: NER Precision
+      type: precision
+      value: 0.8016997167
+    - name: NER Recall
+      type: recall
+      value: 0.7526595745
+    - name: NER F Score
+      type: f_score
+      value: 0.7764060357
+---
+CNN based Social determinants of health NER with a fine-grained window context bag-of-words classifier and a standard ontology extension interface (SNOMED_CT and CUI)
+
+| Feature | Description |
+| --- | --- |
+| **Name** | `en_sdoh_roberta_cui` |
+| **Version** | `0.0.0` |
+| **spaCy** | `>=3.2.1,<3.3.0` |
+| **Default Pipeline** | `transformer`, `ner`, `sdoh_cui` |
+| **Components** | `transformer`, `ner`, `sdoh_cui` |
+| **Vectors** | 0 keys, 0 unique vectors (0 dimensions) |
+| **Sources** | n/a |
+| **License** | n/a |
+| **Author** | [Dima Lituiev]() |
+
+### Label Scheme
+
+<details>
+
+<summary>View label scheme (52 labels for 1 components)</summary>
+
+| Component | Labels |
+| --- | --- |
+| **`ner`** | `Anxiety: GAD`, `Anxiety: Generalized Anxiety Disorder`, `Anxiety: Level of anxiety`, `Anxiety: NA`, `Anxiety: Signs and symptoms of anxiety`, `Anxiety: family hx: Anxiety state`, `Anxiety: hx of anxiety state`, `Depression: Family hx: Depression`, `Depression: Major depressive disorder`, `Depression: NA`, `Depression: PHQ`, `Depression: Symptoms of depression`, `Depression: hx of Depression`, `Financial_strain: Financial problem`, `Financial_strain: Financially secure`, `Financial_strain: NA`, `Financial_strain: Unable to afford medication`, `Food: Able to obtain food`, `Food: Fruit and vegetable intake`, `Food: NA`, `Housing: Homeless`, `Housing: Housing unsuited to needs`, `Housing: Marginally housed`, `Housing: NA`, `Housing: Stably housed`, `Housing: Subsidized housing`, `Housing: lives in facility`, `Insurance_status: Inadequate healthcare resources`, `Insurance_status: NA`, `Marital_or_partnership_status: Divorced`, `Marital_or_partnership_status: Engaged to be married`, `Marital_or_partnership_status: Married`, `Marital_or_partnership_status: NA`, `Marital_or_partnership_status: Partner`, `Marital_or_partnership_status: Partner relationship problem`, `Marital_or_partnership_status: Separated`, `Marital_or_partnership_status: Single person`, `Marital_or_partnership_status: Widowed`, `Social_isolation: At risk for loneliness`, `Social_isolation: Has social support`, `Social_isolation: Lives alone`, `Social_isolation: Lives with`, `Social_isolation: NA`, `Social_isolation: Personal relationship breakdown`, `Social_isolation: Social Isolation`, `Transportation: Has access to a car`, `Transportation: Has access to public transport vehicle`, `Transportation: NA`, `Transportation: Transportation problems`, `pain_and_disability: NA`, `pain_and_disability: Pain intensity rating scale, current`, `pain_and_disability: Pain intensity rating scale, worst` |
+
+</details>
+
+### Accuracy
+
+| Type | Score |
+| --- | --- |
+| `ENTS_F` | 77.64 |
+| `ENTS_P` | 80.17 |
+| `ENTS_R` | 75.27 |
+| `TRANSFORMER_LOSS` | 37708138.10 |
+| `NER_LOSS` | 1444086.80 |

config.cfg

@@ -0,0 +1,148 @@
+[paths]
+train = "./data/spacy-level-2/sdoh-cocoa-skippy-no-empty-2022-01-11-fold-2-train.spacy"
+dev = "./data/spacy-level-2/sdoh-cocoa-skippy-no-empty-2022-01-11-fold-2-val.spacy"
+vectors = null
+init_tok2vec = null
+
+[system]
+gpu_allocator = "pytorch"
+seed = 1
+
+[nlp]
+lang = "en"
+pipeline = ["transformer","ner","sdoh_cui"]
+batch_size = 16
+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.sdoh_cui]
+factory = "sdoh_cui"
+
+[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 = "roberta-base"
+mixed_precision = true
+
+[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]
+seed = ${system.seed}
+accumulate_gradient = 3
+dev_corpus = "corpora.dev"
+train_corpus = "corpora.train"
+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
+
+[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.tokenizer]

en_sdoh_roberta_cui-any-py3-none-any.whl

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+size 441082126

meta.json

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+{
+  "lang":"en",
+  "name":"sdoh_roberta_cui",
+  "version":"0.0.0",
+  "description":"CNN based Social determinants of health NER with a fine-grained window context bag-of-words classifier and a standard ontology extension interface (SNOMED_CT and CUI)",
+  "author":"Dima Lituiev",
+  "email":"d.lituiev@gmail.com",
+  "url":"",
+  "license":"",
+  "spacy_version":">=3.2.1,<3.3.0",
+  "spacy_git_version":"800737b41",
+  "vectors":{
+    "width":0,
+    "vectors":0,
+    "keys":0,
+    "name":null
+  },
+  "labels":{
+    "transformer":[
+
+    ],
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+      "Anxiety: GAD",
+      "Anxiety: Generalized Anxiety Disorder",
+      "Anxiety: Level of anxiety",
+      "Anxiety: NA",
+      "Anxiety: Signs and symptoms of anxiety",
+      "Anxiety: family hx: Anxiety state",
+      "Anxiety: hx of anxiety state",
+      "Depression: Family hx: Depression",
+      "Depression: Major depressive disorder",
+      "Depression: NA",
+      "Depression: PHQ",
+      "Depression: Symptoms of depression",
+      "Depression: hx of Depression",
+      "Financial_strain: Financial problem",
+      "Financial_strain: Financially secure",
+      "Financial_strain: NA",
+      "Financial_strain: Unable to afford medication",
+      "Food: Able to obtain food",
+      "Food: Fruit and vegetable intake",
+      "Food: NA",
+      "Housing: Homeless",
+      "Housing: Housing unsuited to needs",
+      "Housing: Marginally housed",
+      "Housing: NA",
+      "Housing: Stably housed",
+      "Housing: Subsidized housing",
+      "Housing: lives in facility",
+      "Insurance_status: Inadequate healthcare resources",
+      "Insurance_status: NA",
+      "Marital_or_partnership_status: Divorced",
+      "Marital_or_partnership_status: Engaged to be married",
+      "Marital_or_partnership_status: Married",
+      "Marital_or_partnership_status: NA",
+      "Marital_or_partnership_status: Partner",
+      "Marital_or_partnership_status: Partner relationship problem",
+      "Marital_or_partnership_status: Separated",
+      "Marital_or_partnership_status: Single person",
+      "Marital_or_partnership_status: Widowed",
+      "Social_isolation: At risk for loneliness",
+      "Social_isolation: Has social support",
+      "Social_isolation: Lives alone",
+      "Social_isolation: Lives with",
+      "Social_isolation: NA",
+      "Social_isolation: Personal relationship breakdown",
+      "Social_isolation: Social Isolation",
+      "Transportation: Has access to a car",
+      "Transportation: Has access to public transport vehicle",
+      "Transportation: NA",
+      "Transportation: Transportation problems",
+      "pain_and_disability: NA",
+      "pain_and_disability: Pain intensity rating scale, current",
+      "pain_and_disability: Pain intensity rating scale, worst"
+    ]
+  },
+  "pipeline":[
+    "transformer",
+    "ner",
+    "sdoh_cui"
+  ],
+  "components":[
+    "transformer",
+    "ner",
+    "sdoh_cui"
+  ],
+  "disabled":[
+
+  ],
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+  "requirements":[
+    "spacy-transformers>=1.1.4,<1.2.0"
+  ]
+}

ner/cfg

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+{
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+  "update_with_oracle_cut_size":100,
+  "multitasks":[
+
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+}

ner/model

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ner/moves

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sdoh_cui/mapping-ontology-to-umls.json

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+{"Anxiety: Level of anxiety": {"SNOMED_CT": 286644009, "CUI": "C0564474", "canonical_text": "Level of anxiety (finding)"}, "Anxiety: Signs and symptoms of anxiety": {"SNOMED_CT": 79823003, "CUI": "C0233481", "canonical_text": "Worry"}, "Anxiety: Anxiety": {"SNOMED_CT": 48694002, "CUI": "C0003467", "canonical_text": "Anxiety (finding)"}, "Anxiety: Generalized Anxiety Disorder": {"SNOMED_CT": 21897009, "CUI": "C0270549", "canonical_text": "Generalized Anxiety Disorder (disorder)"}, "Anxiety: family hx: Anxiety state": {"SNOMED_CT": 160332003, "CUI": "C0455385", "canonical_text": "Family history: Anxiety state (situation)"}, "Anxiety: hx of anxiety state": {"SNOMED_CT": 161470009, "CUI": "C0455504", "canonical_text": "History of anxiety state (situation)"}, "Anxiety: Assessment of anxiety": {"SNOMED_CT": 710841007, "CUI": "C4039089", "canonical_text": "Assessment of anxiety (procedure)"}, "Anxiety: GAD-7": {"SNOMED_CT": 445455005, "CUI": "C2919162", "canonical_text": "Generalized anxiety 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