Add two new covid_symptom GPT tasks

- covid_symptom__nlp_results_gpt35
- covid_symptom__nlp_results_gpt4

Both call out to Azure ChatGPT and detects COVID symptoms in clinical
notes, with the same cohort selection as the other covid_symptom
tasks (ED notes).

You will need to set the following two environment variables to use
them:
- AZURE_OPENAI_API_KEY
- AZURE_OPENAI_ENDPOINT

These tasks will also need to be added to your AWS config (see the new
template) and the Crawler run to detect their schemas.

The Library covid study has not yet been updated to consume the tables
yet, but will be.

compose.yaml

@@ -26,11 +26,15 @@ services:
       context: .
       target: cumulus-etl
     environment:
+      # Environment variobles to pull in from the host
       - AWS_ACCESS_KEY_ID
+      - AWS_DEFAULT_PROFILE
+      - AWS_PROFILE
       - AWS_SECRET_ACCESS_KEY
       - AWS_SESSION_TOKEN
-      - AWS_PROFILE
-      - AWS_DEFAULT_PROFILE
+      - AZURE_OPENAI_API_KEY
+      - AZURE_OPENAI_ENDPOINT
+      # Internal environment variobles
       - CUMULUS_HUGGING_FACE_URL=http://llama2:8086/
       - URL_CTAKES_REST=http://ctakes-covid:8080/ctakes-web-rest/service/analyze
       - URL_CNLP_NEGATION=http://cnlpt-negation:8000/negation/process

cumulus_etl/etl/studies/covid_symptom/__init__.py

@@ -1,3 +1,8 @@
 """The covid_symptom study"""
 
-from .covid_tasks import CovidSymptomNlpResultsTask, CovidSymptomNlpResultsTermExistsTask
+from .covid_tasks import (
+    CovidSymptomNlpResultsGpt35Task,
+    CovidSymptomNlpResultsGpt4Task,
+    CovidSymptomNlpResultsTask,
+    CovidSymptomNlpResultsTermExistsTask,
+)

cumulus_etl/etl/studies/covid_symptom/covid_ctakes.py

@@ -31,14 +31,11 @@ async def covid_symptoms_extract(
     :param cnlp_http_client: HTTPX client to use for the cNLP transformer server
     :return: list of NLP results encoded as FHIR observations
     """
-    docref_id = docref["id"]
-    _, subject_id = fhir.unref_resource(docref["subject"])
-
-    encounters = docref.get("context", {}).get("encounter", [])
-    if not encounters:
-        logging.warning("No encounters for docref %s", docref_id)
+    try:
+        docref_id, encounter_id, subject_id = nlp.get_docref_info(docref)
+    except KeyError as exc:
+        logging.warning(exc)
         return None
-    _, encounter_id = fhir.unref_resource(encounters[0])
 
     # cTAKES cache namespace history (and thus, cache invalidation history):
     #   v1: original cTAKES processing

cumulus_etl/etl/studies/covid_symptom/covid_tasks.py

@@ -1,14 +1,20 @@
 """Define tasks for the covid_symptom study"""
 
+import datetime
 import itertools
+import json
+import logging
+import os
 from typing import ClassVar
 
 import ctakesclient
+import openai
 import pyarrow
 import rich.progress
 from ctakesclient.transformer import TransformerModel
+from openai.types import chat
 
-from cumulus_etl import nlp, store
+from cumulus_etl import common, nlp, store
 from cumulus_etl.etl import tasks
 from cumulus_etl.etl.studies.covid_symptom import covid_ctakes
 
@@ -74,7 +80,7 @@ def is_ed_docref(docref):
     return any(is_ed_coding(x) for x in codings)
 
 
-class BaseCovidSymptomNlpResultsTask(tasks.BaseNlpTask):
+class BaseCovidCtakesTask(tasks.BaseNlpTask):
     """Covid Symptom study task, to generate symptom lists from ED notes using cTAKES + a polarity check"""
 
     # Subclasses: set name, tags, and polarity_model yourself
@@ -117,7 +123,7 @@ async def prepare_task(self) -> bool:
         bsv_path = ctakesclient.filesystem.covid_symptoms_path()
         success = nlp.restart_ctakes_with_bsv(self.task_config.ctakes_overrides, bsv_path)
         if not success:
-            print(f"Skipping {self.name}.")
+            print("  Skipping.")
             self.summaries[0].had_errors = True
         return success
 
@@ -197,7 +203,7 @@ def get_schema(cls, resource_type: str | None, rows: list[dict]) -> pyarrow.Sche
         )
 
 
-class CovidSymptomNlpResultsTask(BaseCovidSymptomNlpResultsTask):
+class CovidSymptomNlpResultsTask(BaseCovidCtakesTask):
     """Covid Symptom study task, to generate symptom lists from ED notes using cTAKES and cnlpt negation"""
 
     name: ClassVar = "covid_symptom__nlp_results"
@@ -210,7 +216,7 @@ async def init_check(cls) -> None:
         nlp.check_negation_cnlpt()
 
 
-class CovidSymptomNlpResultsTermExistsTask(BaseCovidSymptomNlpResultsTask):
+class CovidSymptomNlpResultsTermExistsTask(BaseCovidCtakesTask):
     """Covid Symptom study task, to generate symptom lists from ED notes using cTAKES and cnlpt termexists"""
 
     name: ClassVar = "covid_symptom__nlp_results_term_exists"
@@ -224,3 +230,206 @@ class CovidSymptomNlpResultsTermExistsTask(BaseCovidSymptomNlpResultsTask):
     async def init_check(cls) -> None:
         nlp.check_ctakes()
         nlp.check_term_exists_cnlpt()
+
+
+class BaseCovidGptTask(tasks.BaseNlpTask):
+    """Covid Symptom study task, using GPT"""
+
+    tags: ClassVar = {"covid_symptom", "cpu"}
+    outputs: ClassVar = [tasks.OutputTable(resource_type=None)]
+
+    # Overridden by child classes
+    model_id: ClassVar = None
+
+    async def prepare_task(self) -> bool:
+        api_key = os.environ.get("AZURE_OPENAI_API_KEY")
+        endpoint = os.environ.get("AZURE_OPENAI_ENDPOINT")
+        if not api_key or not endpoint:
+            if not api_key:
+                print("  The AZURE_OPENAI_API_KEY environment variable is not set.")
+            if not endpoint:
+                print("  The AZURE_OPENAI_ENDPOINT environment variable is not set.")
+            print("  Skipping.")
+            self.summaries[0].had_errors = True
+            return False
+        return True
+
+    async def read_entries(self, *, progress: rich.progress.Progress = None) -> tasks.EntryIterator:
+        """Passes clinical notes through NLP and returns any symptoms found"""
+        async for orig_docref, docref, clinical_note in self.read_notes(
+            progress=progress, doc_check=is_ed_docref
+        ):
+            try:
+                docref_id, encounter_id, subject_id = nlp.get_docref_info(docref)
+            except KeyError as exc:
+                logging.warning(exc)
+                self.add_error(orig_docref)
+                continue
+
+            client = openai.AsyncAzureOpenAI(api_version="2024-06-01")
+            try:
+                response = await nlp.cache_wrapper(
+                    self.task_config.dir_phi,
+                    f"{self.name}_v{self.task_version}",
+                    clinical_note,
+                    lambda x: chat.ChatCompletion.model_validate_json(x),
+                    lambda x: x.model_dump_json(
+                        indent=None, round_trip=True, exclude_unset=True, by_alias=True
+                    ),
+                    client.chat.completions.create,
+                    messages=[
+                        {"role": "system", "content": "You are a helpful assistant."},
+                        {"role": "user", "content": self.get_prompt(clinical_note)},
+                    ],
+                    model=self.model_id,
+                    seed=12345,  # arbitrary, only specified to improve reproducibility
+                    response_format={"type": "json_object"},
+                )
+            except openai.APIError as exc:
+                logging.warning(f"Could not connect to GPT for DocRef {docref['id']}: {exc}")
+                self.add_error(orig_docref)
+                continue
+
+            if response.choices[0].finish_reason != "stop":
+                logging.warning(
+                    f"GPT response didn't complete for DocRef {docref['id']}: "
+                    f"{response.choices[0].finish_reason}"
+                )
+                self.add_error(orig_docref)
+                continue
+
+            try:
+                symptoms = json.loads(response.choices[0].message.content)
+            except json.JSONDecodeError as exc:
+                logging.warning(f"Could not parse GPT results for DocRef {docref['id']}: {exc}")
+                self.add_error(orig_docref)
+                continue
+
+            yield {
+                "id": docref_id,  # keep one results entry per docref
+                "docref_id": docref_id,
+                "encounter_id": encounter_id,
+                "subject_id": subject_id,
+                "generated_on": common.datetime_now().isoformat(),
+                "task_version": self.task_version,
+                "system_fingerprint": response.system_fingerprint,
+                "symptoms": {
+                    "congestion_or_runny_nose": bool(symptoms.get("Congestion or runny nose")),
+                    "cough": bool(symptoms.get("Cough")),
+                    "diarrhea": bool(symptoms.get("Diarrhea")),
+                    "dyspnea": bool(symptoms.get("Dyspnea")),
+                    "fatigue": bool(symptoms.get("Fatigue")),
+                    "fever_or_chills": bool(symptoms.get("Fever or chills")),
+                    "headache": bool(symptoms.get("Headache")),
+                    "loss_of_taste_or_smell": bool(symptoms.get("Loss of taste or smell")),
+                    "muscle_or_body_aches": bool(symptoms.get("Muscle or body aches")),
+                    "nausea_or_vomiting": bool(symptoms.get("Nausea or vomiting")),
+                    "sore_throat": bool(symptoms.get("Sore throat")),
+                },
+            }
+
+    @staticmethod
+    def get_prompt(clinical_note: str) -> str:
+        instructions = (
+            "You are a helpful assistant identifying symptoms from emergency "
+            "department notes that could relate to infectious respiratory diseases.\n"
+            "Output positively documented symptoms, looking out specifically for the "
+            "following: Congestion or runny nose, Cough, Diarrhea, Dyspnea, Fatigue, "
+            "Fever or chills, Headache, Loss of taste or smell, Muscle or body aches, "
+            "Nausea or vomiting, Sore throat.\nSymptoms only need to be positively "
+            "mentioned once to be included.\nDo not mention symptoms that are not "
+            "present in the note.\n\nFollow these rules:\nRule (1): Symptoms must be "
+            "positively documented and relevant to the presenting illness or reason "
+            "for visit.\nRule (2): Medical section headings must be specific to the "
+            "present emergency department encounter.\nInclude positive symptoms from "
+            'these medical section headings: "Chief Complaint", "History of '
+            'Present Illness", "HPI", "Review of Systems", "Physical Exam", '
+            '"Vital Signs", "Assessment and Plan", "Medical Decision Making".\n'
+            "Rule (3): Positive symptom mentions must be a definite medical synonym.\n"
+            'Include positive mentions of: "anosmia", "loss of taste", "loss of '
+            'smell", "rhinorrhea", "congestion", "discharge", "nose is '
+            'dripping", "runny nose", "stuffy nose", "cough", "tussive or '
+            'post-tussive", "cough is unproductive", "productive cough", "dry '
+            'cough", "wet cough", "producing sputum", "diarrhea", "watery '
+            'stool", "fatigue", "tired", "exhausted", "weary", "malaise", '
+            '"feeling generally unwell", "fever", "pyrexia", "chills", '
+            '"temperature greater than or equal 100.4 Fahrenheit or 38 celsius", '
+            '"Temperature >= 100.4F", "Temperature >= 38C", "headache", "HA", '
+            '"migraine", "cephalgia", "head pain", "muscle or body aches", '
+            '"muscle aches", "generalized aches and pains", "body aches", '
+            '"myalgias", "myoneuralgia", "soreness", "generalized aches and '
+            'pains", "nausea or vomiting", "Nausea", "vomiting", "emesis", '
+            '"throwing up", "queasy", "regurgitated", "shortness of breath", '
+            '"difficulty breathing", "SOB", "Dyspnea", "breathing is short", '
+            '"increased breathing", "labored breathing", "distressed '
+            'breathing", "sore throat", "throat pain", "pharyngeal pain", '
+            '"pharyngitis", "odynophagia".\nYour reply must be parsable as JSON.\n'
+            'Format your response using only the following JSON schema: {"Congestion '
+            'or runny nose": boolean, "Cough": boolean, "Diarrhea": boolean, '
+            '"Dyspnea": boolean, "Fatigue": boolean, "Fever or chills": '
+            'boolean, "Headache": boolean, "Loss of taste or smell": boolean, '
+            '"Muscle or body aches": boolean, "Nausea or vomiting": boolean, '
+            '"Sore throat": boolean}. Each JSON key should correspond to a symptom, '
+            "and each value should be true if that symptom is indicated in the "
+            "clinical note; false otherwise.\nNever explain yourself, and only reply "
+            "with JSON."
+        )
+        return f"### Instructions ###\n{instructions}\n### Text ###\n{clinical_note}"
+
+    @classmethod
+    def get_schema(cls, resource_type: str | None, rows: list[dict]) -> pyarrow.Schema:
+        return pyarrow.schema(
+            [
+                pyarrow.field("id", pyarrow.string()),
+                pyarrow.field("docref_id", pyarrow.string()),
+                pyarrow.field("encounter_id", pyarrow.string()),
+                pyarrow.field("subject_id", pyarrow.string()),
+                pyarrow.field("generated_on", pyarrow.string()),
+                pyarrow.field("task_version", pyarrow.int32()),
+                pyarrow.field("system_fingerprint", pyarrow.string()),
+                pyarrow.field(
+                    "symptoms",
+                    pyarrow.struct(
+                        [
+                            pyarrow.field("congestion_or_runny_nose", pyarrow.bool_()),
+                            pyarrow.field("cough", pyarrow.bool_()),
+                            pyarrow.field("diarrhea", pyarrow.bool_()),
+                            pyarrow.field("dyspnea", pyarrow.bool_()),
+                            pyarrow.field("fatigue", pyarrow.bool_()),
+                            pyarrow.field("fever_or_chills", pyarrow.bool_()),
+                            pyarrow.field("headache", pyarrow.bool_()),
+                            pyarrow.field("loss_of_taste_or_smell", pyarrow.bool_()),
+                            pyarrow.field("muscle_or_body_aches", pyarrow.bool_()),
+                            pyarrow.field("nausea_or_vomiting", pyarrow.bool_()),
+                            pyarrow.field("sore_throat", pyarrow.bool_()),
+                        ],
+                    ),
+                ),
+            ]
+        )
+
+
+class CovidSymptomNlpResultsGpt35Task(BaseCovidGptTask):
+    """Covid Symptom study task, using GPT3.5"""
+
+    name: ClassVar = "covid_symptom__nlp_results_gpt35"
+    model_id: ClassVar = "gpt-35-turbo-0125"
+
+    task_version: ClassVar = 1
+    # Task Version History:
+    # ** 1 (2024-08): Initial version **
+    #   model: gpt-35-turbo-0125
+    #   seed: 12345
+
+
+class CovidSymptomNlpResultsGpt4Task(BaseCovidGptTask):
+    """Covid Symptom study task, using GPT4"""
+
+    name: ClassVar = "covid_symptom__nlp_results_gpt4"
+    model_id: ClassVar = "gpt-4"
+
+    task_version: ClassVar = 1
+    # Task Version History:
+    # ** 1 (2024-08): Initial version **
+    #   model: gpt-4
+    #   seed: 12345

cumulus_etl/etl/studies/hftest/hf_tasks.py

@@ -63,7 +63,9 @@ async def read_entries(self, *, progress: rich.progress.Progress = None) -> task
             summary = await nlp.cache_wrapper(
                 self.task_config.dir_phi,
                 f"{self.name}_v{self.task_version}",
-                user_prompt,
+                clinical_note,
+                lambda x: x,  # from file: just store the string
+                lambda x: x,  # to file: just read it back
                 nlp.llama2_prompt,
                 system_prompt,
                 user_prompt,

cumulus_etl/etl/tasks/task_factory.py

@@ -22,6 +22,8 @@ def get_all_tasks() -> list[type[AnyTask]]:
     # Note: tasks will be run in the order listed here.
     return [
         *get_default_tasks(),
+        covid_symptom.CovidSymptomNlpResultsGpt35Task,
+        covid_symptom.CovidSymptomNlpResultsGpt4Task,
         covid_symptom.CovidSymptomNlpResultsTask,
         covid_symptom.CovidSymptomNlpResultsTermExistsTask,
         hftest.HuggingFaceTestTask,

cumulus_etl/nlp/__init__.py

@@ -2,7 +2,7 @@
 
 from .extract import TransformerModel, ctakes_extract, ctakes_httpx_client, list_polarity
 from .huggingface import hf_info, hf_prompt, llama2_prompt
-from .utils import cache_wrapper, is_docref_valid
+from .utils import cache_wrapper, get_docref_info, is_docref_valid
 from .watcher import (
     check_ctakes,
     check_negation_cnlpt,