- NER using vector knowledge graph search
- Semantic similarity to find a consistent set of related conditions, diseases, etc
- Graph-based measures to find a consistent set of related conditions, diseases, etc
- Various combinations of the above
HF_HOME=/workspace genius InPatientAPI rise\
batch \
--input_s3_bucket geniusrise-test-healthcare \
--input_s3_folder model \
batch \
--output_s3_bucket geniusrise-test-healthcare \
--output_s3_folder model \
none \
listen \
--args \
endpoint="*" \
port=2180 \
llm_model="/workspace/Llama-2-70B-chat-GPTQ" \
ner_model="emilyalsentzer/Bio_ClinicalBERT" \
networkx_graph="./saved/snomed.graph" \
faiss_index="./saved/faiss.index.Bio_ClinicalBERT" \
concept_id_to_concept="./saved/concept_id_to_concept.pickle" \
description_id_to_concept="./saved/description_id_to_concept.pickle" \
cors_domain="*"curl -s -X POST \
-H "Content-Type: application/json" \
-d '{"user_input": "i feel a bit light headed and have some difficulty breathing and some pain in chest"}' \
https://yauiuxmk8rlxkj-2180.proxy.runpod.net/api/v1/ner | jq{
"query": "i feel a bit light headed and have some difficulty breathing and some pain in chest",
"symptoms_diseases": ["light headed", "difficulty breathing", "pain in chest"]
}curl -s -X POST \
-H "Content-Type: application/json" \
-d '{
"user_input": "i feel a bit light headed and have some difficulty breathing and some pain in chest",
"symptoms_diseases": [
"shortness_of_breath",
"chest_pain",
"lightheadedness"
],
"semantic_similarity_cutoff": 0.9
}' \
https://yauiuxmk8rlxkj-2180.proxy.runpod.net/api/v1/semantic_search | jq{
"query": "i feel a bit light headed and have some difficulty breathing and some pain in chest",
"symptoms_diseases": [
"light headed",
"difficulty breathing",
"pain in chest"
],
"snomed_concept_ids": [
[371268001, 22601002, 56242006],
[230145002, 161945003],
[29857009, 139228007]
],
"snomed_concepts": [
["light", "light (weight)", "light, electromagnetic radiation"],
["difficulty breathing", "difficulty breathing"],
["chest pain", "chest pain"]
]
}curl -s -X POST \
-H "Content-Type: application/json" \
-d '{
"symptoms_diseases": [
"light headed",
"difficulty breathing",
"pain in chest"
],
"snomed_concept_ids": [
[
371268001,
22601002,
56242006
],
[
230145002,
161945003
],
[
29857009,
139228007
]
]
}' \
https://yauiuxmk8rlxkj-2180.proxy.runpod.net/api/v1/follow_up | jq[
{
"snomed_concept_ids": [
371268001,
22601002,
56242006
],
"snomed_concepts": [
"light",
"light (weight)",
"light, electromagnetic radiation"
],
"questions": [
"Do you feel lightheaded?",
"Do you feel dizzy?",
"Do you feel nauseous?"
]
},
{
"snomed_concept_ids": [
230145002,
161945003
],
"snomed_concepts": [
"difficulty breathing",
"difficulty breathing"
],
"questions": [
"How long have you had difficulty breathing?",
"Is the pain in your chest constant, or does it come and go?"
]
},
{
"snomed_concept_ids": [
29857009,
139228007
],
"snomed_concepts": [
"chest pain",
"chest pain"
],
"questions": [
"When did you first notice the symptoms?",
"Are you allergic to any medication?"
]
}
]curl -s -X POST \
-H "Content-Type: application/json" \
-d '{
"snomed_concept_ids": [
[
139200001,
161945003,
230145002
],
[
139228007,
29857009
]
],
"symptoms_diseases": [
"light headed",
"difficulty breathing",
"chest pain"
],
"qa": {
"Do you feel lightheaded?": "yes",
"Do you feel dizzy?": "a little bit",
"Do you feel nauseous?": "no",
"How long have you had difficulty breathing?": "for the past 2 days",
"Is the pain in your chest constant, or does it come and go?": "it comes and goes",
"When did you first notice the symptoms?": "yesterday",
"Are you allergic to any medication?": "not that i know of"
}
}' \
https://yauiuxmk8rlxkj-2180.proxy.runpod.net/api/v1/summary | jq{
"conditions": [
"difficulty breathing",
"difficulty breathing",
"difficulty breathing",
"chest pain",
"chest pain"
],
"qa": {
"Do you feel lightheaded?": "yes",
"Do you feel dizzy?": "a little bit",
"Do you feel nauseous?": "no",
"How long have you had difficulty breathing?": "for the past 2 days",
"Is the pain in your chest constant, or does it come and go?": "it comes and goes",
"When did you first notice the symptoms?": "yesterday",
"Are you allergic to any medication?": "not that i know of"
},
"summary": "# In-Patient Report
## Summary
### Patient's Observations
The patient presented with the following complaints:
['light headed', 'difficulty breathing', 'chest pain']
of which these are the conditions identified from SNOMED:
- difficulty breathing
- difficulty breathing
- difficulty breathing
- chest pain
- chest pain
### Questions and Answers
Subsequently, on further questioning, the patient had these to add on:
- **Question**: Do you feel lightheaded?
- **Answer**: yes
- **Question**: Do you feel dizzy?
- **Answer**: a little bit
- **Question**: Do you feel nauseous?
- **Answer**: no
- **Question**: How long have you had difficulty breathing?
- **Answer**: for the past 2 days
- **Question**: Is the pain in your chest constant, or does it come and go?
- **Answer**: it comes and goes
- **Question**: When did you first notice the symptoms?
- **Answer**: yesterday
- **Question**: Are you allergic to any medication?
- **Answer**: not that i know of
## Recommended tests
### Tests for diagnosis
- blood test
- blood test
- blood test
- X-ray
- X-ray
- X-ray
### Tests for exclusion
- blood test
- blood test
- blood test
- X-ray
- X-ray
- X-ray
## Diseases to check for and narrow down the cause
- heart attack
- heart attack
- heart attack
- lung cancer
- lung cancer
- lung cancer",
"speciality": "### Department
The patient should visit the **Outpatient** department."
}http POST https://yauiuxmk8rlxkj-2180.proxy.runpod.net/api/v1/graph snomed_concepts:='
[
[
139200001,
161945003,
230145002
],
[
139228007,
29857009
]
]
' --downloadContent-Type: multipart/mixed; boundary="===============0359621490805120141=="
MIME-Version: 1.0
--===============0359621490805120141==
Content-Type: text/plain; charset="us-ascii"
MIME-Version: 1.0
Content-Transfer-Encoding: 7bit
Graph:
dyspnea --[is a]--> difficulty breathing
winded --[is a]--> difficulty breathing
labored breathing --[is a]--> difficulty breathing
respiratory distress --[is a]--> difficulty breathing
cannot blow --[is a]--> difficulty breathing
radiating chest pain --[is a]--> chest pain
microvascular angina --[is a]--> chest pain
pain of breast --[is a]--> chest pain
parasternal pain --[is a]--> chest pain
right sided chest pain --[is a]--> chest pain
assessment of chest pain --[has focus]--> chest pain
left sided chest pain --[is a]--> chest pain
thoracic back pain --[is a]--> chest pain
burning chest pain --[is a]--> chest pain
ischemic chest pain --[is a]--> chest pain
chest pain not present --[associated finding]--> chest pain
chest pain due to pericarditis --[is a]--> chest pain
crushing chest pain --[is a]--> chest pain
chest pain at rest --[is a]--> chest pain
localized chest pain --[is a]--> chest pain
retrosternal pain --[is a]--> chest pain
history of chest pain --[associated finding]--> chest pain
dull chest pain --[is a]--> chest pain
chest pain on breathing --[is a]--> chest pain
chronic chest pain --[is a]--> chest pain
pleuritic pain --[is a]--> chest pain
atypical chest pain --[is a]--> chest pain
musculoskeletal chest pain --[is a]--> chest pain
intercostal neuralgia --[is a]--> chest pain
upper chest pain --[is a]--> chest pain
angina --[is a]--> chest pain
noncardiac chest pain --[is a]--> chest pain
chest wall pain --[is a]--> chest pain
cardiac chest pain --[is a]--> chest pain
pleuropericardial chest pain --[is a]--> chest pain
precordial pain --[is a]--> chest pain
chest pain on exertion --[is a]--> chest pain
squeezing chest pain --[is a]--> chest pain
acute chest pain --[is a]--> chest pain
esophageal chest pain --[is a]--> chest pain
--===============0359621490805120141==
Content-Type: application/octet-stream; Name="image.png"
MIME-Version: 1.0
Content-Transfer-Encoding: base64
iVBORw0KGgoAAAANSUhEUgAAC/QAAAv0CAYAAACNCdhAAAAAOXRFWHRTb2Z0d2FyZQBNYXRwbG90
bGliIHZlcnNpb24zLjguMCwgaHR0cHM6Ly9tYXRwbG90bGliLm9yZy81sbWrAAAACXBIWXMAAC4j
--===============0359621490805120141==--