3.2.1
We are glad to announce that Spark NLP Healthcare 3.2.1 has been released!.
Highlights
- Deprecated ChunkEntityResolver.
- New BERT-Based NER Models
- HCC module added support for versions v22 and v23.
- Updated Notebooks for resolvers and graph builders.
- New TF Graph Builder.
New BERT-Based NER Models
We have two new BERT-based token classifier NER models. These models are the first clinical NER models that use the BertForTokenCLassification approach that was introduced in Spark NLP 3.2.0.
bert_token_classifier_ner_clinical: This model is BERT-based version ofner_clinicalmodel. This new model is 4% better than the legacy NER model (MedicalNerModel) that is based on BiLSTM-CNN-Char architecture.
Metrics:
precision recall f1-score support
PROBLEM 0.88 0.92 0.90 30276
TEST 0.91 0.86 0.88 17237
TREATMENT 0.87 0.88 0.88 17298
O 0.97 0.97 0.97 202438
accuracy 0.95 267249
macro avg 0.91 0.91 0.91 267249
weighted avg 0.95 0.95 0.95 267249
Example:
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols("sentence")\
.setOutputCol("token")
tokenClassifier = BertForTokenClassification.pretrained("bert_token_classifier_ner_clinical", "en", "clinical/models")\
.setInputCols("token", "sentence")\
.setOutputCol("ner")\
.setCaseSensitive(True)
ner_converter = NerConverter()\
.setInputCols(["sentence","token","ner"])\
.setOutputCol("ner_chunk")
pipeline = Pipeline(stages=[
documentAssembler,
sentenceDetector,
tokenizer,
tokenClassifier,
ner_converter
])
p_model = pipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
text = 'A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus ( T2DM ), one prior episode of HTG-induced pancreatitis three years prior to presentation , associated with an acute hepatitis , and obesity with a body mass index ( BMI ) of 33.5 kg/m2 , presented with a one-week history of polyuria , polydipsia , poor appetite , and vomiting . Two weeks prior to presentation , she was treated with a five-day course of amoxicillin for a respiratory tract infection . She was on metformin , glipizide , and dapagliflozin for T2DM and atorvastatin and gemfibrozil for HTG . She had been on dapagliflozin for six months at the time of presentation . Physical examination on presentation was significant for dry oral mucosa ; significantly , her abdominal examination was benign with no tenderness , guarding , or rigidity . Pertinent laboratory findings on admission were : serum glucose 111 mg/dl , bicarbonate 18 mmol/l , anion gap 20 , creatinine 0.4 mg/dL , triglycerides 508 mg/dL , total cholesterol 122 mg/dL , glycated hemoglobin ( HbA1c ) 10% , and venous pH 7.27 . Serum lipase was normal at 43 U/L . Serum acetone levels could not be assessed as blood samples kept hemolyzing due to significant lipemia . The patient was initially admitted for starvation ketosis , as she reported poor oral intake for three days prior to admission . However , serum chemistry obtained six hours after presentation revealed her glucose was 186 mg/dL , the anion gap was still elevated at 21 , serum bicarbonate was 16 mmol/L , triglyceride level peaked at 2050 mg/dL , and lipase was 52 U/L . The β-hydroxybutyrate level was obtained and found to be elevated at 5.29 mmol/L - the original sample was centrifuged and the chylomicron layer removed prior to analysis due to interference from turbidity caused by lipemia again . The patient was treated with an insulin drip for euDKA and HTG with a reduction in the anion gap to 13 and triglycerides to 1400 mg/dL , within 24 hours . Her euDKA was thought to be precipitated by her respiratory tract infection in the setting of SGLT2 inhibitor use . The patient was seen by the endocrinology service and she was discharged on 40 units of insulin glargine at night , 12 units of insulin lispro with meals , and metformin 1000 mg two times a day . It was determined that all SGLT2 inhibitors should be discontinued indefinitely . She had close follow-up with endocrinology post discharge .'
res = p_model.transform(spark.createDataFrame([[text]]).toDF("text")).collect()
res[0]['label']
bert_token_classifier_ner_jsl: This model is BERT-based version ofner_jslmodel. This new model is better than the legacy NER model (MedicalNerModel) that is based on BiLSTM-CNN-Char architecture.
Metrics:
precision recall f1-score support
Admission_Discharge 0.84 0.97 0.90 415
Age 0.96 0.96 0.96 2434
Alcohol 0.75 0.83 0.79 145
Allergen 0.33 0.16 0.22 25
BMI 1.00 0.77 0.87 26
Birth_Entity 1.00 0.17 0.29 12
Blood_Pressure 0.86 0.88 0.87 597
Cerebrovascular_Disease 0.74 0.77 0.75 266
Clinical_Dept 0.90 0.92 0.91 2385
Communicable_Disease 0.70 0.59 0.64 85
Date 0.95 0.98 0.96 1438
Death_Entity 0.83 0.83 0.83 59
Diabetes 0.95 0.95 0.95 350
Diet 0.60 0.49 0.54 229
Direction 0.88 0.90 0.89 6187
Disease_Syndrome_Disorder 0.90 0.89 0.89 13236
Dosage 0.57 0.49 0.53 263
Drug 0.91 0.93 0.92 15926
Duration 0.82 0.85 0.83 1218
EKG_Findings 0.64 0.70 0.67 325
Employment 0.79 0.85 0.82 539
External_body_part_or_region 0.84 0.84 0.84 4805
Family_History_Header 1.00 1.00 1.00 889
Fetus_NewBorn 0.57 0.56 0.56 341
Form 0.53 0.43 0.48 81
Frequency 0.87 0.90 0.88 1718
Gender 0.98 0.98 0.98 5666
HDL 0.60 1.00 0.75 6
Heart_Disease 0.88 0.88 0.88 2295
Height 0.89 0.96 0.92 134
Hyperlipidemia 1.00 0.95 0.97 194
Hypertension 0.95 0.98 0.97 566
ImagingFindings 0.66 0.64 0.65 601
Imaging_Technique 0.62 0.67 0.64 108
Injury_or_Poisoning 0.85 0.83 0.84 1680
Internal_organ_or_component 0.90 0.91 0.90 21318
Kidney_Disease 0.89 0.89 0.89 446
LDL 0.88 0.97 0.92 37
Labour_Delivery 0.82 0.71 0.76 306
Medical_Device 0.89 0.93 0.91 12852
Medical_History_Header 0.96 0.97 0.96 1013
Modifier 0.68 0.60 0.64 1398
O2_Saturation 0.84 0.82 0.83 199
Obesity 0.96 0.98 0.97 130
Oncological 0.88 0.96 0.92 1635
Overweight 0.80 0.80 0.80 10
Oxygen_Therapy 0.91 0.92 0.92 231
Pregnancy 0.81 0.83 0.82 439
Procedure 0.91 0.91 0.91 14410
Psychological_Condition 0.81 0.81 0.81 354
Pulse 0.85 0.95 0.89 389
Race_Ethnicity 1.00 1.00 1.00 163
Relationship_Status 0.93 0.91 0.92 57
RelativeDate 0.83 0.86 0.84 1562
RelativeTime 0.74 0.79 0.77 431
Respiration 0.99 0.95 0.97 221
Route 0.68 0.69 0.69 597
Section_Header 0.97 0.98 0.98 28580
Sexually_Active_or_Sexual_Orientation 1.00 0.64 0.78 14
Smoking 0.83 0.90 0.86 225
Social_History_Header 0.95 0.99 0.97 825
Strength 0.71 0.55 0.62 227
Substance 0.85 0.81 0.83 193
Substance_Quantity 0.00 0.00 0.00 28
Symptom 0.84 0.86 0.85 23092
Temperature 0.94 0.97 0.96 410
Test 0.84 0.88 0.86 9050
Test_Result 0.84 0.84 0.84 2766
Time 0.90 0.81 0.86 140
Total_Cholesterol 0.69 0.95 0.80 73
Treatment 0.73 0.72 0.73 506
Triglycerides 0.83 0.80 0.81 30
VS_Finding 0.76 0.77 0.76 588
Vaccine 0.70 0.84 0.76 92
Vital_Signs_Header 0.95 0.98 0.97 2223
Weight 0.88 0.89 0.88 306
O 0.97 0.96 0.97 253164
accuracy 0.94 445974
macro avg 0.82 0.82 0.81 445974
weighted avg 0.94 0.94 0.94 445974
Example:
documentAssembler = DocumentAssembler()\
.setInputCol("text")\
.setOutputCol("document")
sentenceDetector = SentenceDetectorDLModel.pretrained("sentence_detector_dl_healthcare","en","clinical/models")\
.setInputCols(["document"])\
.setOutputCol("sentence")
tokenizer = Tokenizer()\
.setInputCols("sentence")\
.setOutputCol("token")
tokenClassifier = BertForTokenClassification.pretrained("bert_token_classifier_ner_jsl", "en", "clinical/models")\
.setInputCols("token", "sentence")\
.setOutputCol("ner")\
.setCaseSensitive(True)
ner_converter = NerConverter()\
.setInputCols(["sentence","token","ner"])\
.setOutputCol("ner_chunk")
pipeline = Pipeline(stages=[
documentAssembler,
sentenceDetector,
tokenizer,
tokenClassifier,
ner_converter
])
p_model = pipeline.fit(spark.createDataFrame([[""]]).toDF("text"))
text = 'A 28-year-old female with a history of gestational diabetes mellitus diagnosed eight years prior to presentation and subsequent type two diabetes mellitus ( T2DM ), one prior episode of HTG-induced pancreatitis three years prior to presentation , associated with an acute hepatitis , and obesity with a body mass index ( BMI ) of 33.5 kg/m2 , presented with a one-week history of polyuria , polydipsia , poor appetite , and vomiting . Two weeks prior to presentation , she was treated with a five-day course of amoxicillin for a respiratory tract infection . She was on metformin , glipizide , and dapagliflozin for T2DM and atorvastatin and gemfibrozil for HTG . She had been on dapagliflozin for six months at the time of presentation . Physical examination on presentation was significant for dry oral mucosa ; significantly , her abdominal examination was benign with no tenderness , guarding , or rigidity . Pertinent laboratory findings on admission were : serum glucose 111 mg/dl , bicarbonate 18 mmol/l , anion gap 20 , creatinine 0.4 mg/dL , triglycerides 508 mg/dL , total cholesterol 122 mg/dL , glycated hemoglobin ( HbA1c ) 10% , and venous pH 7.27 . Serum lipase was normal at 43 U/L . Serum acetone levels could not be assessed as blood samples kept hemolyzing due to significant lipemia . The patient was initially admitted for starvation ketosis , as she reported poor oral intake for three days prior to admission . However , serum chemistry obtained six hours after presentation revealed her glucose was 186 mg/dL , the anion gap was still elevated at 21 , serum bicarbonate was 16 mmol/L , triglyceride level peaked at 2050 mg/dL , and lipase was 52 U/L . The β-hydroxybutyrate level was obtained and found to be elevated at 5.29 mmol/L - the original sample was centrifuged and the chylomicron layer removed prior to analysis due to interference from turbidity caused by lipemia again . The patient was treated with an insulin drip for euDKA and HTG with a reduction in the anion gap to 13 and triglycerides to 1400 mg/dL , within 24 hours . Her euDKA was thought to be precipitated by her respiratory tract infection in the setting of SGLT2 inhibitor use . The patient was seen by the endocrinology service and she was discharged on 40 units of insulin glargine at night , 12 units of insulin lispro with meals , and metformin 1000 mg two times a day . It was determined that all SGLT2 inhibitors should be discontinued indefinitely . She had close follow-up with endocrinology post discharge .'
res = p_model.transform(spark.createDataFrame([[text]]).toDF("text")).collect()
res[0]['label']
HCC module added support for versions v22 and v23
Now we can use the version 22 and the version 23 for the new HCC module to calculate CMS-HCC Risk Adjustment score.
Added the following parameters elig, orec and medicaid on the profiles functions. These parameters may not be stored in clinical notes, and may require to be imported from other sources.
elig : The eligibility segment of the patient.
Allowed values are as follows:
- "CFA": Community Full Benefit Dual Aged
- "CFD": Community Full Benefit Dual Disabled
- "CNA": Community NonDual Aged
- "CND": Community NonDual Disabled
- "CPA": Community Partial Benefit Dual Aged
- "CPD": Community Partial Benefit Dual Disabled
- "INS": Long Term Institutional
- "NE": New Enrollee
- "SNPNE": SNP NE
orec: Original reason for entitlement code.
- "0": Old age and survivor's insurance
- "1": Disability insurance benefits
- "2": End-stage renal disease
- "3": Both DIB and ESRD
medicaid: If the patient is in Medicaid or not.
Required parameters should be stored in Spark dataframe.
df.show(truncate=False)
+---------------+------------------------------+---+------+-----------+----+--------+
|hcc_profileV24 |icd10_code |age|gender|eligibility|orec|medicaid|
+---------------+------------------------------+---+------+-----------+----+--------+
|{"hcc_lst":[...|[E1169, I5030, I509, E852] |64 |F |CFA |0 |true |
|{"hcc_lst":[...|[G629, D469, D6181] |77 |M |CND |1 |false |
|{"hcc_lst":[...|[D473, D473, D473, M069, C969]|16 |F |CPA |3 |true |
+---------------+------------------------------+---+------+-----------+----+--------+
The content of the hcc_profileV24 column is a JSON-parsable string, like in the following example,
{
"hcc_lst": [
"HCC18",
"HCC85_gDiabetesMellit",
"HCC85",
"HCC23",
"D3"
],
"details": {
"CNA_HCC18": 0.302,
"CNA_HCC85": 0.331,
"CNA_HCC23": 0.194,
"CNA_D3": 0.0,
"CNA_HCC85_gDiabetesMellit": 0.0
},
"hcc_map": {
"E1169": [
"HCC18"
],
"I5030": [
"HCC85"
],
"I509": [
"HCC85"
],
"E852": [
"HCC23"
]
},
"risk_score": 0.827,
"parameters": {
"elig": "CNA",
"age": 56,
"sex": "F",
"origds": false,
"disabled": false,
"medicaid": false
}
}
We can import different CMS-HCC model versions as seperate functions and use them in the same program.
from sparknlp_jsl.functions import profile,profileV22,profileV23
df = df.withColumn("hcc_profileV24", profile(df.icd10_code,
df.age,
df.gender,
df.eligibility,
df.orec,
df.medicaid
))
df.withColumn("hcc_profileV22", profileV22(df.codes, df.age, df.sex,df.elig,df.orec,df.medicaid))
df.withColumn("hcc_profileV23", profileV23(df.codes, df.age, df.sex,df.elig,df.orec,df.medicaid))
df.show(truncate=False)
+----------+------------------------------+---+------+-----------+----+--------+
|risk_score|icd10_code |age|gender|eligibility|orec|medicaid|
+----------+------------------------------+---+------+-----------+----+--------+
|0.922 |[E1169, I5030, I509, E852] |64 |F |CFA |0 |true |
|3.566 |[G629, D469, D6181] |77 |M |CND |1 |false |
|1.181 |[D473, D473, D473, M069, C969]|16 |F |CPA |3 |true |
+----------+------------------------------+---+------+-----------+----+--------+
Updated Notebooks for resolvers and graph builders
- We have updated the resolver notebooks on spark-nlp-workshop repo with new
BertSentenceChunkEmbeddingsannotator. This annotator lets users aggregate sentence embeddings and ner chunk embeddings to get more specific and accurate resolution codes. It works by averaging context and chunk embeddings to get contextual information. Input to this annotator is the context (sentence) and ner chunks, while the output is embedding for each chunk that can be fed to the resolver model. ThesetChunkWeightparameter can be used to control the influence of surrounding context. Example below shows the comparison of old vs new approach.
| text | ner_chunk | entity | icd10_code | all_codes | resolutions | icd10_code_SCE | all_codes_SCE | resolutions_SCE |
|---|---|---|---|---|---|---|---|---|
| Two weeks prior to presentation, she was treated with a five-day course of amoxicillin for a respiratory tract infection. | a respiratory tract infection | PROBLEM | J988 | [J988, J069, A499, J22, J209,…] | [respiratory tract infection, upper respiratory tract infection, bacterial respiratory infection, acute respiratory infection, bronchial infection,…] | Z870 | [Z870, Z8709, J470, J988, A499,… | [history of acute lower respiratory tract infection (situation), history of acute lower respiratory tract infection, bronchiectasis with acute lower respiratory infection, rti - respiratory tract infection, bacterial respiratory infection,… |
Here are the updated resolver notebooks:
You can also check for more examples of this annotator: 24.1.Improved_Entity_Resolution_with_SentenceChunkEmbeddings.ipynb
- We have updated TF Graph builder notebook to show how to create TF graphs with TF2.x.
Here is the updated notebook: 17.Graph_builder_for_DL_models.ipynb
To see more, please check: Spark NLP Healthcare Workshop Repo
New TF Graph Builder
TF graph builder to create graphs and train DL models for licensed annotators (MedicalNer, Relation Extraction, Assertion and Generic Classifier) is made compatible with TF2.x.
To see how to create TF Graphs, you can check here: 17.Graph_builder_for_DL_models.ipynb
Versions
- 5.5.1
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