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Browse files- Dockerfile +13 -0
- app.py +292 -0
- requirements.txt +9 -0
Dockerfile
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FROM python:3.10-slim
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WORKDIR /app
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COPY requirements.txt .
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RUN pip install --no-cache-dir torch==2.2.2 --index-url https://download.pytorch.org/whl/cpu
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RUN pip install --no-cache-dir -r requirements.txt
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COPY app.py .
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EXPOSE 7860
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CMD ["uvicorn", "app:app", "--host", "0.0.0.0", "--port", "7860"]
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app.py
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from fastapi import FastAPI
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from fastapi.middleware.cors import CORSMiddleware
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from pydantic import BaseModel
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import torch
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from transformers import AutoTokenizer, AutoModelForSequenceClassification
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import time
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import json
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import numpy as np
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app = FastAPI(title="EdgeMed Clinical BERT API")
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app.add_middleware(
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CORSMiddleware,
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allow_origins=["*"],
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allow_methods=["*"],
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allow_headers=["*"],
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)
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# ββ Label maps (from your notebook) ββββββββββββββββββββββββββββββββββββββββββ
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id2label = {0: "ESI_1", 1: "ESI_2", 2: "ESI_3", 3: "ESI_4", 4: "ESI_5"}
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label2id = {v: k for k, v in id2label.items()}
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ESI_SLA = {"ESI_1": 2, "ESI_2": 10, "ESI_3": 30, "ESI_4": 60, "ESI_5": 120}
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ESI_LABEL = {"ESI_1": "Resuscitation", "ESI_2": "Emergent",
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"ESI_3": "Urgent", "ESI_4": "Less Urgent", "ESI_5": "Non-Urgent"}
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# ββ CAG keyword lookup (exact from your notebook) ββββββββββββββββββββββββββββ
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CAG_RULES = {
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"ESI_1": ["cardiac arrest","not breathing","no pulse","unresponsive",
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"unconscious","active seizure","anaphylaxis","major trauma",
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"respiratory arrest","hemorrhagic shock","arrest","cpr",
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"resus","apnea","shock","code"],
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"ESI_2": ["chest pain","acute stroke","stroke","altered mental status",
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"severe pain","overdose","sepsis","hypertensive emergency",
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"myocardial infarction","difficulty breathing",
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"shortness of breath","loss of consciousness","syncope",
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"fainting","high fever","sob","dyspnea","loc","seizure",
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"convulsion","palpitation","hypotension","ams","cp"],
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"ESI_3": ["moderate pain","fever","fracture","vomiting","dizziness",
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"weakness","wound","laceration","burn","abdominal pain",
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"back pain","headache","swelling","infection","urinary",
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"bleeding","trauma","injury","pain"],
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"ESI_4": ["mild pain","rash","sore throat","ear pain","eye pain",
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"minor","sprain","cough","cold","mild","ocular"],
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"ESI_5": ["prescription refill","routine","paperwork",
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"immunization","administrative","certificate"],
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}
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PRIORITY = ["ESI_1", "ESI_2", "ESI_3", "ESI_4", "ESI_5"]
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# Build flat lookup
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CAG_LOOKUP = {}
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for esi, keywords in CAG_RULES.items():
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for kw in keywords:
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CAG_LOOKUP[kw] = esi
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def cag_classify(text: str):
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t = text.lower()
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matched_esi, matched_kw = None, None
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for kw, esi in CAG_LOOKUP.items():
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if kw in t:
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if matched_esi is None or PRIORITY.index(esi) < PRIORITY.index(matched_esi):
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matched_esi = esi
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matched_kw = kw
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return matched_esi, matched_kw
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# ββ Keyword β specialty map (from your notebook) βββββββββββββββββββββββββββββ
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KEYWORD_SPECIALTY = {
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"cardiac": "Cardiology", "chest": "Cardiology",
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"heart": "Cardiology", "neuro": "Neurology",
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"stroke": "Neurology", "seizure": "Neurology",
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"head": "Neurology", "fracture": "Orthopedic",
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"bone": "Orthopedic", "joint": "Orthopedic",
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"abdom": "General Surgery","bowel": "Gastroenterology",
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"liver": "Gastroenterology","breath": "Pulmonology",
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"lung": "Pulmonology", "psych": "Psychiatry",
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"mental": "Psychiatry", "eye": "Ophthalmology",
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"ocular": "Ophthalmology", "ear": "ENT",
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"throat": "ENT", "urin": "Urology",
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"kidney": "Nephrology", "renal": "Nephrology",
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"burn": "General Surgery","wound": "General Surgery",
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}
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ESI_DEFAULT_SPECIALTY = {
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"ESI_1": "Emergency Medicine", "ESI_2": "Emergency Medicine",
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"ESI_3": "General Surgery", "ESI_4": "General Surgery",
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"ESI_5": "General Surgery",
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}
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def detect_specialty(symptom_text: str, esi_level: str) -> str:
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t = symptom_text.lower()
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for kw, spec in KEYWORD_SPECIALTY.items():
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if kw in t:
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return spec
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return ESI_DEFAULT_SPECIALTY.get(esi_level, "Emergency Medicine")
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# ββ Load BERT model βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
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print("Loading Mahdiya/edgemed-clinical-bert ...")
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tokenizer = AutoTokenizer.from_pretrained("Mahdiya/edgemed-clinical-bert")
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model = AutoModelForSequenceClassification.from_pretrained(
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"Mahdiya/edgemed-clinical-bert")
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model.eval()
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device = "cpu" # CPU Basic Space β no GPU available
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model.to(device)
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print(f"β
Model loaded on {device}")
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def bert_classify(text: str):
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enc = tokenizer(
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text[:400], return_tensors="pt",
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max_length=128, truncation=True, padding="max_length"
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).to(device)
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t0 = time.time()
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with torch.no_grad():
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logits = model(**enc).logits
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latency_ms = round((time.time() - t0) * 1000, 1)
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probs = torch.softmax(logits, dim=-1)[0].cpu().tolist()
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pred_id = int(torch.argmax(logits, dim=-1).item())
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pred_esi = id2label[pred_id]
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conf = round(probs[pred_id], 4)
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all_probs = {id2label[i]: round(p, 4) for i, p in enumerate(probs)}
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return pred_esi, conf, latency_ms, all_probs
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# ββ Hospital data (200 hospitals, 5 zones β from your notebook seed=42) βββββββ
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np.random.seed(42)
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SPECIALTIES_ALL = [
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"Cardiology","Neurology","Orthopedic","General Surgery",
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"Emergency Medicine","Gastroenterology","Pulmonology",
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"Nephrology","Psychiatry","Ophthalmology","ENT","Urology",
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"Oncology","Dermatology","Pediatrics","Gynecology",
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"Radiology","Anesthesiology","Hematology","Rheumatology"
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]
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ZONES = ["Zone-A","Zone-B","Zone-C","Zone-D","Zone-E"]
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HOSPITALS = []
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for i in range(200):
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zone = ZONES[i // 40]
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n_specs = int(np.random.randint(3, 7))
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specs = list(np.random.choice(SPECIALTIES_ALL, n_specs, replace=False))
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HOSPITALS.append({
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"hospital_id": f"H{str(i).zfill(3)}",
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"name": f"{zone.replace('Zone-','').strip()} Medical Center {i%40+1}",
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"zone": zone,
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"specialties": specs,
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"response_time": round(float(np.random.uniform(1, 30)), 1),
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"quality_score": round(float(np.random.uniform(0.5, 1.0)), 2),
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"current_load": round(float(np.random.uniform(0.1, 0.9)), 2),
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"availability": bool(np.random.random() > 0.2),
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})
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def routing_score(h: dict, alpha: float) -> float:
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"""Exact formula from your notebook."""
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speed = 1.0 - (h["response_time"] / 30.0)
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quality = h["quality_score"]
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load = h["current_load"] * 0.3
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return round((alpha * speed + (1 - alpha) * quality) * (1 - load), 4)
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def get_top_hospitals(specialty: str, zone: str, alpha: float,
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esi: str, top_n: int = 10) -> list:
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is_emergency = esi in ("ESI_1", "ESI_2")
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results = []
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for h in HOSPITALS:
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if not h["availability"]:
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continue
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if h["current_load"] > 0.85:
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continue
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spec_match = any(specialty.lower() in s.lower() for s in h["specialties"])
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zone_match = h["zone"] == zone
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if is_emergency:
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# Emergency β any available hospital with any specialty
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eff_alpha = 1.0 # pure speed
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score = routing_score(h, eff_alpha)
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results.append({**h, "score": score,
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"zone_match": zone_match,
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"spec_match": spec_match,
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"cross_zone": not zone_match})
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else:
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if spec_match:
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score = routing_score(h, alpha)
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results.append({**h, "score": score,
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"zone_match": zone_match,
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"spec_match": spec_match,
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"cross_zone": not zone_match})
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# Sort: zone-local first, then by score
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if is_emergency:
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results.sort(key=lambda x: x["response_time"])
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else:
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results.sort(key=lambda x: (-int(x["zone_match"]), -x["score"]))
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return results[:top_n]
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# ββ Request / Response models βββββββββββββββββββββββββββββββββββββββββββββββββ
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class TriageRequest(BaseModel):
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symptom_text: str
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zone: str
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alpha: float = 0.5
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class RouteRequest(BaseModel):
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symptom_text: str
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zone: str
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alpha: float
|
| 202 |
+
esi_level: str # already determined (from triage step)
|
| 203 |
+
specialty: str # already determined
|
| 204 |
+
|
| 205 |
+
# ββ Endpoints βββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββββ
|
| 206 |
+
@app.get("/")
|
| 207 |
+
def root():
|
| 208 |
+
return {"status": "EdgeMed API running",
|
| 209 |
+
"model": "Mahdiya/edgemed-clinical-bert",
|
| 210 |
+
"device": device}
|
| 211 |
+
|
| 212 |
+
@app.post("/triage")
|
| 213 |
+
def triage(req: TriageRequest):
|
| 214 |
+
"""
|
| 215 |
+
Full triage pipeline:
|
| 216 |
+
1. CAG keyword check
|
| 217 |
+
2. If no CAG hit β BERT inference (ESI 3-5)
|
| 218 |
+
Returns ESI level, confidence, method used, latency.
|
| 219 |
+
"""
|
| 220 |
+
t_total = time.time()
|
| 221 |
+
|
| 222 |
+
# Step 1: CAG
|
| 223 |
+
cag_esi, cag_kw = cag_classify(req.symptom_text)
|
| 224 |
+
|
| 225 |
+
if cag_esi in ("ESI_1", "ESI_2"):
|
| 226 |
+
# Bypass BERT β critical keyword found
|
| 227 |
+
specialty = detect_specialty(req.symptom_text, cag_esi)
|
| 228 |
+
return {
|
| 229 |
+
"esi_level": cag_esi,
|
| 230 |
+
"esi_label": ESI_LABEL[cag_esi],
|
| 231 |
+
"sla_minutes": ESI_SLA[cag_esi],
|
| 232 |
+
"confidence": 1.0,
|
| 233 |
+
"method": "CAG_BYPASS",
|
| 234 |
+
"cag_keyword": cag_kw,
|
| 235 |
+
"specialty": specialty,
|
| 236 |
+
"bert_probs": None,
|
| 237 |
+
"latency_ms": round((time.time() - t_total) * 1000, 1),
|
| 238 |
+
}
|
| 239 |
+
|
| 240 |
+
# Step 2: BERT inference
|
| 241 |
+
bert_esi, conf, bert_latency, all_probs = bert_classify(req.symptom_text)
|
| 242 |
+
|
| 243 |
+
# CAG may have a lower-priority hint (ESI 3-5) β use whichever is more urgent
|
| 244 |
+
final_esi = bert_esi
|
| 245 |
+
method = "BERT"
|
| 246 |
+
if cag_esi and PRIORITY.index(cag_esi) < PRIORITY.index(bert_esi):
|
| 247 |
+
final_esi = cag_esi
|
| 248 |
+
method = "CAG+BERT"
|
| 249 |
+
|
| 250 |
+
specialty = detect_specialty(req.symptom_text, final_esi)
|
| 251 |
+
|
| 252 |
+
return {
|
| 253 |
+
"esi_level": final_esi,
|
| 254 |
+
"esi_label": ESI_LABEL[final_esi],
|
| 255 |
+
"sla_minutes": ESI_SLA[final_esi],
|
| 256 |
+
"confidence": conf,
|
| 257 |
+
"method": method,
|
| 258 |
+
"cag_keyword": cag_kw,
|
| 259 |
+
"specialty": specialty,
|
| 260 |
+
"bert_probs": all_probs,
|
| 261 |
+
"latency_ms": round((time.time() - t_total) * 1000, 1),
|
| 262 |
+
}
|
| 263 |
+
|
| 264 |
+
@app.post("/route")
|
| 265 |
+
def route(req: RouteRequest):
|
| 266 |
+
"""
|
| 267 |
+
KAG routing: given ESI + specialty + zone + alpha,
|
| 268 |
+
returns top 10 hospitals ranked by routing score.
|
| 269 |
+
"""
|
| 270 |
+
hospitals = get_top_hospitals(
|
| 271 |
+
specialty=req.specialty,
|
| 272 |
+
zone=req.zone,
|
| 273 |
+
alpha=req.alpha,
|
| 274 |
+
esi=req.esi_level,
|
| 275 |
+
top_n=10,
|
| 276 |
+
)
|
| 277 |
+
return {
|
| 278 |
+
"zone": req.zone,
|
| 279 |
+
"specialty": req.specialty,
|
| 280 |
+
"esi_level": req.esi_level,
|
| 281 |
+
"alpha": req.alpha,
|
| 282 |
+
"hospitals": hospitals,
|
| 283 |
+
"total": len(hospitals),
|
| 284 |
+
}
|
| 285 |
+
|
| 286 |
+
@app.get("/zones")
|
| 287 |
+
def zones():
|
| 288 |
+
counts = {}
|
| 289 |
+
for z in ZONES:
|
| 290 |
+
avail = sum(1 for h in HOSPITALS if h["zone"] == z and h["availability"])
|
| 291 |
+
counts[z] = {"total": 40, "available": avail}
|
| 292 |
+
return {"zones": ZONES, "counts": counts}
|
requirements.txt
ADDED
|
@@ -0,0 +1,9 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
fastapi
|
| 2 |
+
uvicorn
|
| 3 |
+
transformers==4.40.0
|
| 4 |
+
torch==2.2.2
|
| 5 |
+
numpy
|
| 6 |
+
pydantic
|
| 7 |
+
huggingface-hub
|
| 8 |
+
safetensors
|
| 9 |
+
tokenizers
|