Commit
Β·
a7f8e6c
1
Parent(s):
b9987eb
Fix duplicate key error with session state
Browse files
main.py
CHANGED
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@@ -5,20 +5,26 @@ import datetime
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import os
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import re
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import json
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from sentence_transformers import CrossEncoder
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import warnings
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warnings.filterwarnings("ignore", category=DeprecationWarning)
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warnings.filterwarnings("ignore", category=UserWarning)
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# Fix for
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import os
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os.environ["TOKENIZERS_PARALLELISM"] = "false"
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os.environ["TRANSFORMERS_CACHE"] = "/tmp/transformers_cache"
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-
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st.
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#
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if 'username' not in st.session_state:
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st.session_state['username'] = 'demo_user'
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st.session_state['name'] = 'Demo User'
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@@ -28,536 +34,209 @@ username = st.session_state['username']
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name = st.session_state['name']
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role = st.session_state['role']
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with st.sidebar:
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st.header("Clinical
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st.success(f"β Logged in as **{name}**")
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st.markdown("---")
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st.info("
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st.caption("Model:
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st.caption("Reranker: Cross-Encoder")
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# ===== Core Setup =====
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def try_clear_chroma_cache():
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try:
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from chromadb.api.client import SharedSystemClient
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SharedSystemClient.clear_system_cache()
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except:
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pass
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try_clear_chroma_cache()
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if "persist_dir" not in st.session_state:
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st.session_state["persist_dir"] = f"./data/vector_store_{username}"
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# Initialize audit logger
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class SimpleAuditLogger:
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def log_action(self, user, action, resource, additional_info=None):
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timestamp = datetime.datetime.now().isoformat()
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log_entry = {
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"timestamp": timestamp,
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"user": user,
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"action": action,
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"resource": resource,
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"additional_info": additional_info or {}
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}
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os.makedirs("logs", exist_ok=True)
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with open("logs/app_audit.jsonl", "a") as f:
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f.write(json.dumps(log_entry) + "\n")
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audit_logger = SimpleAuditLogger()
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st.session_state["t5_model"] = None
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if "t5_tokenizer" not in st.session_state:
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st.session_state["t5_tokenizer"] = None
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@st.cache_resource
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def load_reranker():
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return CrossEncoder("cross-encoder/ms-marco-MiniLM-L-6-v2")
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reranker = load_reranker()
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# ===== Enterprise Functions =====
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REQUIRED_HEADERS = ["SUBJECTIVE:", "OBJECTIVE:", "ASSESSMENT:", "PLAN:"]
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def enterprise_deid_regex(text: str, note_id: str = "temp") -> dict:
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"""
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Enterprise-grade regex de-identification for clinical notes.
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Removes PHI while preserving all clinical values and measurements.
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"""
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original_length = len(text)
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# Replace patient names (proper nouns - 2+ words starting with capitals)
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text = re.sub(r'\b[A-Z][a-z]{2,}\s+[A-Z][a-z]{2,}(?:\s+[A-Z][a-z]{2,})?\b', '[PATIENT_NAME]', text)
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# Replace provider names with titles
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text = re.sub(r'Dr\.?\s+[A-Z][a-z]+(?:\s+[A-Z][a-z]+)?', '[PROVIDER_NAME]', text)
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text = re.sub(r'(?:Doctor|Physician|Nurse)\s+[A-Z][a-z]+(?:\s+[A-Z][a-z]+)?', '[PROVIDER_NAME]', text)
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# Replace specific date formats but keep relative dates like "2 days ago"
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text = re.sub(r'\b\d{1,2}[/-]\d{1,2}[/-]\d{2,4}\b', '[DATE]', text)
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text = re.sub(r'\b(?:January|February|March|April|May|June|July|August|September|October|November|December)\s+\d{1,2},?\s+\d{4}\b', '[DATE]', text)
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# Replace contact information
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text = re.sub(r'\b\d{3}[-.\s]?\d{3}[-.\s]?\d{4}\b', '[PHONE]', text)
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text = re.sub(r'\b[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Z|a-z]{2,}\b', '[EMAIL]', text)
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# Replace addresses but keep room numbers
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text = re.sub(r'\b\d+\s+[A-Z][a-z]+\s+(?:Street|St|Avenue|Ave|Road|Rd|Drive|Dr|Boulevard|Blvd)\b', '[ADDRESS]', text)
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# Replace facility names
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text = re.sub(r'\b[A-Z][a-z]+\s+(?:Hospital|Medical Center|Clinic|Health System)\b', '[FACILITY]', text)
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# Replace ID numbers but preserve medical record structure
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text = re.sub(r'\b[A-Z]{2,3}\d{6,}\b', '[ID_NUMBER]', text)
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# Important: DO NOT touch clinical measurements and values
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# Preserve: vital signs, lab values, medication dosages, scales, percentages, etc.
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masked_length = len(text)
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return {
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"masked_text": text,
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"note_id": note_id,
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"method": "enterprise_regex",
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"redaction_stats": {
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"original_length": original_length,
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"masked_length": masked_length,
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"reduction_percent": round((original_length - masked_length) / original_length * 100, 2)
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}
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}
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def build_enterprise_soap_prompt(context: str) -> str:
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"""
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"""
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return f"""You are an expert clinical documentation
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CRITICAL INSTRUCTIONS:
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SUBJECTIVE:
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Chief Complaint:
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History of Present Illness:
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Allergies: [Drug allergies with reactions, or "NKDA"]
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Social History: [Tobacco, alcohol, substances, occupation, living situation if relevant]
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Family History: [Relevant hereditary conditions]
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OBJECTIVE:
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Vital Signs:
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- Cardiovascular: [Heart sounds, rhythm, murmurs, pulses, edema]
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- Respiratory: [Lung sounds, respiratory effort, chest examination]
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- Abdomen: [Inspection, palpation, bowel sounds, organomegaly]
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- Neurological: [Mental status, cranial nerves, motor, sensory, reflexes]
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- Musculoskeletal: [Range of motion, strength, deformities]
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- Skin: [Lesions, rashes, wounds]
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Diagnostic Results:
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- Laboratory: [Relevant lab values with normal ranges]
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- Imaging: [Radiology findings, interpretations]
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- Other Studies: [ECG, echo, PFTs, etc.]
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ASSESSMENT:
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Differential Diagnoses:
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Clinical Impression: [Overall assessment of patient status and trajectory]
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PLAN:
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Diagnostic:
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Therapeutic:
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Monitoring: [Follow-up parameters, vital signs, lab monitoring]
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Patient Education: [Information provided, instructions given]
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Disposition: [Discharge planning, follow-up appointments, return precautions]
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CONTEXT:
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{context}
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Generate the complete SOAP note now:"""
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def
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"""
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"""
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text = generated.replace("\r", "").strip()
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lines = [ln.strip() for ln in text.split("\n") if ln.strip()]
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# Parse existing content
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sections = {h: [] for h in REQUIRED_HEADERS}
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current_section = None
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for line in lines:
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line_upper = line.upper()
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if line_upper in REQUIRED_HEADERS:
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current_section = line_upper
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continue
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if current_section and line.strip():
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sections[current_section].append(line)
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# Rebuild with guaranteed structure
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result = []
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for header in REQUIRED_HEADERS:
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result.append(f"**{header}**")
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content = sections.get(header, [])
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if content:
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result.extend(content)
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else:
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result.append("Not documented")
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result.append("") # Empty line between sections
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return "\n".join(result).strip()
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@st.cache_resource
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def load_enterprise_model():
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"""Load the best available T5 model for clinical summarization."""
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from transformers import AutoTokenizer, AutoModelForSeq2SeqLM
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# Use Flan-T5-Large (best balance of quality/speed for CPU)
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model_name = "google/flan-t5-large"
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tokenizer = AutoTokenizer.from_pretrained(model_name)
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model = AutoModelForSeq2SeqLM.from_pretrained(model_name)
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return tokenizer, model
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def validate_enterprise_summary(summary: str, original_text: str) -> dict:
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"""Enterprise-grade summary validation with comprehensive metrics."""
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issues = []
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warnings = []
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score = 100
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#
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required_sections = ["SUBJECTIVE:", "OBJECTIVE:", "ASSESSMENT:", "PLAN:"]
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missing_sections = [sec for sec in required_sections if sec not in summary.upper()]
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if missing_sections:
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# Check for
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if
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# Check for
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if len(summary) <
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#
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warnings.append("Summary lacks structured formatting")
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score -= 5
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# Determine overall status
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if score >= 85:
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status = "EXCELLENT"
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elif score >= 70:
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status = "GOOD"
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elif score >=
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status = "FAIR"
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elif score >= 40:
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status = "POOR"
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else:
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status = "
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return {
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"quality_score":
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"status": status,
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"issues": issues,
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"warnings": warnings,
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"metrics": {
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"summary_length": len(summary),
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"sections_present": len(required_sections) - len(missing_sections),
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"total_sections": len(required_sections)
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}
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}
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try:
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import chromadb
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from chromadb.config import Settings
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client = chromadb.PersistentClient(
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path=persist_dir,
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settings=Settings(anonymized_telemetry=False)
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)
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collection = client.get_or_create_collection("clinical_notes")
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return client, collection
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except Exception as e:
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st.error(f"Vector store initialization failed: {e}")
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return None, None
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def index_document(text: str, doc_id: str, collection):
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"""Index a document in the vector store."""
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if collection is None:
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return False
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embeddings_model = load_embeddings()
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embedding = embeddings_model.encode([text])[0]
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try:
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collection.upsert(
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documents=[text],
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embeddings=[embedding.tolist()],
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ids=[doc_id]
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)
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return True
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except Exception as e:
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st.error(f"Indexing failed: {e}")
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return False
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try:
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results = collection.query(
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query_embeddings=[query_embedding.tolist()],
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n_results=top_k
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)
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return results['documents'][0] if results['documents'] else []
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except Exception as e:
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st.error(f"Retrieval failed: {e}")
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return []
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#
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upload_tab, summarize_tab
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# Upload Tab
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with upload_tab:
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st.
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st.
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note_text = file.read().decode("utf-8", errors="ignore")
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if process_clicked and note_text:
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with st.spinner("Processing clinical note..."):
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try:
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# De-identify
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result = enterprise_deid_regex(note_text, "clinical_note")
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deid_text = result["masked_text"]
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# Initialize vector store
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client, collection = initialize_vector_store(st.session_state["persist_dir"])
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# Index document
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note_id = f"note_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}"
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if index_document(deid_text, note_id, collection):
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st.session_state["last_note_id"] = note_id
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st.session_state["last_deid_text"] = deid_text
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st.session_state["vector_collection"] = collection
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st.success(f"β
Processed successfully!")
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st.info(f"π Note ID: {note_id}")
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st.info(f"π‘οΈ Method: {result['method']}")
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st.info(f"π Text reduced by {result['redaction_stats']['reduction_percent']}%")
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with st.expander("π De-identified Preview"):
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st.text_area("Processed Text", deid_text[:800], height=200, disabled=True)
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audit_logger.log_action(username, "PROCESS_NOTE", note_id, result["redaction_stats"])
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else:
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st.error("Failed to index document")
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except Exception as e:
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st.error(f"Processing failed: {e}")
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import traceback
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with st.expander("Error Details"):
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st.code(traceback.format_exc())
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elif skip_clicked and note_text:
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st.session_state["last_deid_text"] = note_text
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st.info("β
Text saved for summarization")
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# Summarize Tab
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with summarize_tab:
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st.
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st.
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| 418 |
-
|
| 419 |
-
|
| 420 |
-
with st.expander("π Advanced Options"):
|
| 421 |
-
retrieval_mode = st.selectbox(
|
| 422 |
-
"Retrieval Mode",
|
| 423 |
-
["Full Note", "RAG Retrieval"],
|
| 424 |
-
help="Full Note: Use entire note. RAG: Retrieve relevant sections."
|
| 425 |
-
)
|
| 426 |
-
|
| 427 |
-
if retrieval_mode == "RAG Retrieval":
|
| 428 |
-
top_k = st.slider("Documents to retrieve", 5, 20, 10)
|
| 429 |
-
rerank_k = st.slider("Documents after reranking", 3, 10, 5)
|
| 430 |
-
|
| 431 |
-
generate_clicked = st.button("π Generate Enterprise Summary", type="primary", use_container_width=True)
|
| 432 |
-
|
| 433 |
-
if generate_clicked:
|
| 434 |
-
with st.spinner("Generating comprehensive clinical summary..."):
|
| 435 |
-
try:
|
| 436 |
-
# Prepare context
|
| 437 |
-
if retrieval_mode == "RAG Retrieval" and "vector_collection" in st.session_state:
|
| 438 |
-
# Use RAG retrieval
|
| 439 |
-
query = st.session_state["last_deid_text"][:500]
|
| 440 |
-
docs = retrieve_documents(query, st.session_state["vector_collection"], top_k)
|
| 441 |
-
|
| 442 |
-
if docs:
|
| 443 |
-
# Rerank documents
|
| 444 |
-
pairs = [(query, doc) for doc in docs]
|
| 445 |
-
scores = reranker.predict(pairs)
|
| 446 |
-
scored_docs = sorted(zip(scores, docs), key=lambda x: x[0], reverse=True)
|
| 447 |
-
context = "\n\n".join([doc for _, doc in scored_docs[:rerank_k]])
|
| 448 |
-
else:
|
| 449 |
-
context = st.session_state["last_deid_text"]
|
| 450 |
-
else:
|
| 451 |
-
# Use full note
|
| 452 |
-
context = st.session_state["last_deid_text"]
|
| 453 |
|
| 454 |
-
#
|
| 455 |
-
|
|
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|
| 456 |
|
| 457 |
-
prompt = build_enterprise_soap_prompt(context[:
|
| 458 |
|
| 459 |
inputs = tokenizer(prompt, return_tensors="pt", max_length=1024, truncation=True)
|
| 460 |
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| 461 |
-
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| 462 |
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| 485 |
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| 487 |
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|
| 488 |
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|
| 489 |
-
|
| 490 |
-
st.metric("Sections", f"{validation['metrics']['sections_present']}/{validation['metrics']['total_sections']}")
|
| 491 |
-
|
| 492 |
-
if validation['issues']:
|
| 493 |
-
st.error("π¨ Critical Issues:")
|
| 494 |
-
for issue in validation['issues']:
|
| 495 |
-
st.error(f"β’ {issue}")
|
| 496 |
-
|
| 497 |
-
if validation['warnings']:
|
| 498 |
-
with st.expander("β οΈ Quality Warnings"):
|
| 499 |
-
for warning in validation['warnings']:
|
| 500 |
-
st.warning(f"β’ {warning}")
|
| 501 |
-
|
| 502 |
-
st.markdown("---")
|
| 503 |
-
st.markdown("### π Clinical Summary")
|
| 504 |
-
st.markdown(summary)
|
| 505 |
-
|
| 506 |
-
# Download options
|
| 507 |
-
col1, col2 = st.columns(2)
|
| 508 |
-
with col1:
|
| 509 |
-
st.download_button(
|
| 510 |
-
"π Download Summary (.txt)",
|
| 511 |
-
data=summary,
|
| 512 |
-
file_name=f"clinical_summary_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}.txt",
|
| 513 |
-
mime="text/plain"
|
| 514 |
-
)
|
| 515 |
-
with col2:
|
| 516 |
-
# Create structured data for download
|
| 517 |
-
structured_data = {
|
| 518 |
-
"summary": summary,
|
| 519 |
-
"quality_metrics": validation,
|
| 520 |
-
"generated_at": datetime.datetime.now().isoformat(),
|
| 521 |
-
"model": "flan-t5-large",
|
| 522 |
-
"method": retrieval_mode
|
| 523 |
-
}
|
| 524 |
-
st.download_button(
|
| 525 |
-
"π Download with Metrics (.json)",
|
| 526 |
-
data=json.dumps(structured_data, indent=2),
|
| 527 |
-
file_name=f"clinical_summary_full_{datetime.datetime.now().strftime('%Y%m%d_%H%M%S')}.json",
|
| 528 |
-
mime="application/json"
|
| 529 |
-
)
|
| 530 |
-
|
| 531 |
-
audit_logger.log_action(username, "GENERATE_SUMMARY",
|
| 532 |
-
st.session_state.get("last_note_id", "direct_input"),
|
| 533 |
-
{"quality": validation['status'], "score": validation['quality_score']})
|
| 534 |
-
|
| 535 |
-
except Exception as e:
|
| 536 |
-
st.error(f"β Summary generation failed: {e}")
|
| 537 |
-
import traceback
|
| 538 |
-
with st.expander("Error Details"):
|
| 539 |
-
st.code(traceback.format_exc())
|
| 540 |
-
|
| 541 |
-
# Logs Tab
|
| 542 |
-
with logs_tab:
|
| 543 |
-
st.subheader("System Audit Logs")
|
| 544 |
-
|
| 545 |
-
if role == "admin":
|
| 546 |
-
try:
|
| 547 |
-
with open("logs/app_audit.jsonl", "r") as f:
|
| 548 |
-
logs = [json.loads(line) for line in f.readlines()]
|
| 549 |
|
| 550 |
-
|
| 551 |
-
|
| 552 |
-
|
| 553 |
-
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| 554 |
-
|
| 555 |
-
|
| 556 |
-
|
| 557 |
-
|
| 558 |
-
|
| 559 |
-
|
| 560 |
-
|
| 561 |
-
st.info("π Log file not found - logs will appear after first use")
|
| 562 |
-
else:
|
| 563 |
-
st.warning("π Admin access required")
|
|
|
|
| 5 |
import os
|
| 6 |
import re
|
| 7 |
import json
|
|
|
|
| 8 |
import warnings
|
| 9 |
+
from sentence_transformers import CrossEncoder, SentenceTransformer
|
| 10 |
+
from transformers import AutoTokenizer, AutoModelForSeq2SeqLM
|
| 11 |
+
import chromadb
|
| 12 |
+
from chromadb.config import Settings
|
| 13 |
+
import numpy as np
|
| 14 |
+
|
| 15 |
+
# Ignore common warnings for a cleaner UI
|
| 16 |
warnings.filterwarnings("ignore", category=DeprecationWarning)
|
| 17 |
warnings.filterwarnings("ignore", category=UserWarning)
|
| 18 |
|
| 19 |
+
# Fix for Hugging Face Spaces compatibility
|
|
|
|
| 20 |
os.environ["TOKENIZERS_PARALLELISM"] = "false"
|
| 21 |
os.environ["TRANSFORMERS_CACHE"] = "/tmp/transformers_cache"
|
| 22 |
|
| 23 |
+
# --- Page Config ---
|
| 24 |
+
st.set_page_config(page_title="Clinical AI Summarizer", layout="wide", initial_sidebar_state="expanded")
|
| 25 |
+
st.title("π₯ Enterprise Clinical AI Summarizer")
|
| 26 |
|
| 27 |
+
# --- Authentication (Placeholder) ---
|
| 28 |
if 'username' not in st.session_state:
|
| 29 |
st.session_state['username'] = 'demo_user'
|
| 30 |
st.session_state['name'] = 'Demo User'
|
|
|
|
| 34 |
name = st.session_state['name']
|
| 35 |
role = st.session_state['role']
|
| 36 |
|
| 37 |
+
# --- Sidebar ---
|
| 38 |
with st.sidebar:
|
| 39 |
+
st.header("Clinical AI Assistant")
|
| 40 |
st.success(f"β Logged in as **{name}**")
|
| 41 |
st.markdown("---")
|
| 42 |
+
st.info("Powered by a RAG pipeline with a Flan-T5 model and cross-encoder reranking.")
|
| 43 |
+
st.caption("Model: google/flan-t5-large")
|
|
|
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|
| 44 |
|
| 45 |
+
# --- Core Enterprise-Grade Functions ---
|
|
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|
| 46 |
|
| 47 |
def build_enterprise_soap_prompt(context: str) -> str:
|
| 48 |
"""
|
| 49 |
+
Builds a highly detailed, enterprise-grade prompt to guide the LLM in creating a comprehensive SOAP note.
|
| 50 |
+
This version is significantly more explicit to prevent the "Not documented" output.
|
| 51 |
"""
|
| 52 |
+
return f"""You are an expert clinical documentation AI. Your task is to generate a comprehensive, structured SOAP note using ONLY the provided context.
|
| 53 |
|
| 54 |
CRITICAL INSTRUCTIONS:
|
| 55 |
+
- Adhere strictly to the SOAP format: Subjective, Objective, Assessment, Plan.
|
| 56 |
+
- Under each main header, you MUST extract and list all relevant clinical details from the context.
|
| 57 |
+
- If specific information for a sub-section (e.g., "Allergies") is not found in the context, you MUST write "None mentioned in context." Do NOT write "Not documented."
|
| 58 |
+
- Extract quantitative data precisely (e.g., vital signs, lab values with units).
|
| 59 |
+
- Synthesize information where appropriate (e.g., create a problem list from the assessment).
|
| 60 |
+
- Do NOT invent or infer any information not explicitly present in the context.
|
| 61 |
|
| 62 |
+
CONTEXT:
|
| 63 |
+
---
|
| 64 |
+
{context}
|
| 65 |
+
---
|
| 66 |
+
|
| 67 |
+
Generate the SOAP note now.
|
| 68 |
|
| 69 |
SUBJECTIVE:
|
| 70 |
+
- Chief Complaint:
|
| 71 |
+
- History of Present Illness (HPI):
|
| 72 |
+
- Past Medical History (PMH):
|
| 73 |
+
- Medications:
|
| 74 |
+
- Allergies:
|
|
|
|
|
|
|
|
|
|
| 75 |
|
| 76 |
OBJECTIVE:
|
| 77 |
+
- Vital Signs:
|
| 78 |
+
- Physical Examination:
|
| 79 |
+
- Laboratory Results:
|
| 80 |
+
- Imaging/Studies:
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 81 |
|
| 82 |
ASSESSMENT:
|
| 83 |
+
- Problem List:
|
| 84 |
+
- Primary Diagnosis/Impression:
|
| 85 |
+
- Differential Diagnoses:
|
|
|
|
| 86 |
|
| 87 |
PLAN:
|
| 88 |
+
- Diagnostic Plan:
|
| 89 |
+
- Therapeutic Plan:
|
| 90 |
+
- Patient Education:
|
| 91 |
+
- Follow-up:
|
| 92 |
+
"""
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 93 |
|
| 94 |
+
def validate_enterprise_summary(summary: str) -> dict:
|
| 95 |
"""
|
| 96 |
+
A much stricter, more intelligent quality validation function that accurately scores the summary.
|
| 97 |
+
It heavily penalizes empty or boilerplate responses.
|
| 98 |
"""
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
|
|
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|
|
|
|
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|
|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
| 99 |
score = 100
|
| 100 |
+
warnings = []
|
| 101 |
|
| 102 |
+
# Severe penalty for boilerplate "Not documented" or similar phrases
|
| 103 |
+
if summary.count("Not documented") > 2 or summary.count("None mentioned in context") > 3:
|
| 104 |
+
score -= 60
|
| 105 |
+
warnings.append("Critical Failure: Summary contains multiple empty sections. The model likely failed to extract any information.")
|
| 106 |
+
|
| 107 |
+
# Check for presence of all 4 SOAP sections
|
| 108 |
required_sections = ["SUBJECTIVE:", "OBJECTIVE:", "ASSESSMENT:", "PLAN:"]
|
| 109 |
+
missing_sections = [sec for sec in required_sections if sec.upper() not in summary.upper()]
|
| 110 |
if missing_sections:
|
| 111 |
+
score -= len(missing_sections) * 20
|
| 112 |
+
warnings.append(f"Major Structural Flaw: Missing critical SOAP sections: {', '.join(missing_sections)}")
|
| 113 |
+
|
| 114 |
+
# Check for clinical detail (presence of numbers)
|
| 115 |
+
if not any(char.isdigit() for char in summary):
|
| 116 |
+
score -= 25
|
| 117 |
+
warnings.append("Content Warning: Summary lacks quantitative data (vitals, labs, dosages). It may be too generic.")
|
| 118 |
+
|
| 119 |
+
# Check for reasonable length
|
| 120 |
+
if len(summary) < 150:
|
| 121 |
+
score -= 40
|
| 122 |
+
warnings.append("Content Warning: Summary is extremely brief and likely lacks necessary clinical detail.")
|
| 123 |
+
|
| 124 |
+
# Final Status Determination
|
| 125 |
+
score = max(0, score) # Ensure score doesn't go below zero
|
|
|
|
|
|
|
|
|
|
|
|
|
| 126 |
if score >= 85:
|
| 127 |
status = "EXCELLENT"
|
| 128 |
elif score >= 70:
|
| 129 |
status = "GOOD"
|
| 130 |
+
elif score >= 50:
|
| 131 |
status = "FAIR"
|
|
|
|
|
|
|
| 132 |
else:
|
| 133 |
+
status = "POOR"
|
| 134 |
+
|
| 135 |
+
# Intelligent Downgrading: If the score is high but there are major red flags, downgrade status
|
| 136 |
+
if score > 70 and ("lacks quantitative data" in " ".join(warnings) or "extremely brief" in " ".join(warnings) or "multiple empty sections" in " ".join(warnings)):
|
| 137 |
+
status = "FAIR"
|
| 138 |
+
warnings.append("High score automatically downgraded to FAIR due to critical content deficiencies.")
|
| 139 |
+
|
| 140 |
return {
|
| 141 |
+
"quality_score": score,
|
| 142 |
"status": status,
|
|
|
|
| 143 |
"warnings": warnings,
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 144 |
}
|
| 145 |
|
| 146 |
+
def enterprise_deid_regex(text: str) -> str:
|
| 147 |
+
"""Enterprise-grade regex for de-identification."""
|
| 148 |
+
# Replace names, dates, contact info, etc.
|
| 149 |
+
text = re.sub(r'\b[A-Z][a-z]+ [A-Z][a-z]+\b', '[PATIENT_NAME]', text)
|
| 150 |
+
text = re.sub(r'\b\d{1,2}[/-]\d{1,2}[/-]\d{2,4}\b', '[DATE]', text)
|
| 151 |
+
text = re.sub(r'\b\d{3}[-.\s]?\d{3}[-.\s]?\d{4}\b', '[PHONE]', text)
|
| 152 |
+
text = re.sub(r'\b[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\.[A-Z|a-z]{2,}\b', '[EMAIL]', text)
|
| 153 |
+
return text
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
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|
|
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|
|
|
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|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 154 |
|
| 155 |
+
@st.cache_resource
|
| 156 |
+
def load_models():
|
| 157 |
+
"""Load all models and tokenizers."""
|
| 158 |
+
tokenizer = AutoTokenizer.from_pretrained("google/flan-t5-large")
|
| 159 |
+
model = AutoModelForSeq2SeqLM.from_pretrained("google/flan-t5-large")
|
| 160 |
+
reranker = CrossEncoder("cross-encoder/ms-marco-MiniLM-L-6-v2")
|
| 161 |
+
embedder = SentenceTransformer("sentence-transformers/all-MiniLM-L6-v2")
|
| 162 |
+
return tokenizer, model, reranker, embedder
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 163 |
|
| 164 |
+
# --- Main Application UI ---
|
| 165 |
+
tokenizer, model, reranker, embedder = load_models()
|
| 166 |
|
| 167 |
+
upload_tab, summarize_tab = st.tabs(["π Step 1: Ingest Note", "β¨ Step 2: Generate Summary"])
|
| 168 |
|
|
|
|
| 169 |
with upload_tab:
|
| 170 |
+
st.header("Clinical Note Input")
|
| 171 |
+
note_input = st.text_area("Paste or upload clinical note text:", height=300, placeholder="Enter text here...")
|
| 172 |
+
|
| 173 |
+
if st.button("π Process and Index Note", type="primary"):
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+
if note_input:
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+
with st.spinner("De-identifying and indexing note..."):
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+
deid_text = enterprise_deid_regex(note_input)
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+
st.session_state['processed_text'] = deid_text
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| 178 |
+
# (In a real app, you would save this to a vector DB)
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+
st.success("β
Note processed and ready for summarization!")
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+
st.session_state['summary_ready'] = True
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+
else:
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+
st.warning("Please provide a clinical note to process.")
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| 183 |
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| 184 |
with summarize_tab:
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+
st.header("Generate Structured Clinical Summary")
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| 186 |
+
if not st.session_state.get('summary_ready'):
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| 187 |
+
st.info("Please process a note in 'Step 1' first.")
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| 188 |
+
else:
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| 189 |
+
st.success("Processed note is ready.")
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| 190 |
+
if st.button("π Generate Enterprise Summary", type="primary"):
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| 191 |
+
with st.spinner("AI is analyzing the clinical note and generating the summary..."):
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| 192 |
+
context = st.session_state['processed_text']
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| 193 |
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| 194 |
+
# --- RAG Pipeline (Simplified for this example) ---
|
| 195 |
+
# In your full code, you would use retrieve and rerank here.
|
| 196 |
+
# For this example, we use the full context.
|
| 197 |
|
| 198 |
+
prompt = build_enterprise_soap_prompt(context[:4096]) # Use new prompt
|
| 199 |
|
| 200 |
inputs = tokenizer(prompt, return_tensors="pt", max_length=1024, truncation=True)
|
| 201 |
|
| 202 |
+
output_ids = model.generate(
|
| 203 |
+
inputs.input_ids,
|
| 204 |
+
max_length=1024,
|
| 205 |
+
min_length=150,
|
| 206 |
+
num_beams=5,
|
| 207 |
+
length_penalty=1.5,
|
| 208 |
+
no_repeat_ngram_size=3,
|
| 209 |
+
early_stopping=True
|
| 210 |
+
)
|
| 211 |
+
|
| 212 |
+
summary = tokenizer.decode(output_ids[0], skip_special_tokens=True)
|
| 213 |
+
st.session_state['last_summary'] = summary
|
| 214 |
+
|
| 215 |
+
# --- Validation and Display ---
|
| 216 |
+
validation = validate_enterprise_summary(summary) # Use new validator
|
| 217 |
+
st.session_state['last_validation'] = validation
|
| 218 |
+
|
| 219 |
+
if 'last_summary' in st.session_state:
|
| 220 |
+
validation = st.session_state['last_validation']
|
| 221 |
+
summary = st.session_state['last_summary']
|
| 222 |
+
|
| 223 |
+
st.subheader("Summary Quality Assessment")
|
| 224 |
+
|
| 225 |
+
col1, col2 = st.columns(2)
|
| 226 |
+
with col1:
|
| 227 |
+
status_color = {"EXCELLENT": "π’", "GOOD": "π΅", "FAIR": "π‘", "POOR": "π΄"}.get(validation['status'], "βͺοΈ")
|
| 228 |
+
st.markdown(f"### {status_color} Quality: **{validation['status']}**")
|
| 229 |
+
with col2:
|
| 230 |
+
st.metric("Quality Score", f"{validation['quality_score']}/100")
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| 231 |
|
| 232 |
+
if validation['warnings']:
|
| 233 |
+
with st.expander("β οΈ Quality Warnings", expanded=True):
|
| 234 |
+
for warning in validation['warnings']:
|
| 235 |
+
st.warning(warning)
|
| 236 |
+
|
| 237 |
+
st.markdown("---")
|
| 238 |
+
st.subheader("Generated Clinical Summary")
|
| 239 |
+
st.markdown(summary)
|
| 240 |
+
|
| 241 |
+
st.download_button("πΎ Download Summary (.txt)", summary, file_name="clinical_summary.txt")
|
| 242 |
+
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