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# Complete Medical Literature Health Dataset Generator with Gradio Interface
#
# This creates a web-based interface for generating synthetic health optimization datasets
# =====================================================================
# STEP 1: INSTALLATIONS AND IMPORTS
# =====================================================================
# Install required packages
import subprocess
import sys
def install_packages():
"""Install required packages"""
packages = ['openai', 'gradio', 'python-dotenv', 'requests', 'pandas']
for package in packages:
try:
__import__(package)
except ImportError:
print(f"Installing {package}...")
subprocess.check_call([sys.executable, "-m", "pip", "install", package])
# Run installation
install_packages()
# Import libraries
import gradio as gr
import json
import random
import re
import time
import os
import io
import zipfile
from datetime import datetime
from typing import Dict, List, Any, Optional, Tuple
from openai import OpenAI
import pandas as pd
# =====================================================================
# STEP 2: CORE CLASSES (Same as before but with progress callbacks)
# =====================================================================
class MedicalLiteratureSimulator:
"""Simulates medical literature research for health dataset generation"""
def __init__(self):
self.research_domains = {
"longevity": {
"interventions": ["NAD+ supplementation", "resveratrol", "metformin", "caloric restriction"],
"biomarkers": ["telomere length", "cellular senescence", "inflammatory markers", "mitochondrial function"],
"outcomes": ["biological age reduction", "improved healthspan", "enhanced cellular repair"]
},
"metabolic_health": {
"interventions": ["berberine", "intermittent fasting", "alpha-lipoic acid", "chromium"],
"biomarkers": ["glucose levels", "insulin sensitivity", "HbA1c", "HOMA-IR"],
"outcomes": ["improved glucose control", "enhanced insulin sensitivity", "reduced inflammation"]
},
"cardiovascular": {
"interventions": ["omega-3 fatty acids", "coenzyme Q10", "magnesium", "nattokinase"],
"biomarkers": ["blood pressure", "cholesterol levels", "CRP", "endothelial function"],
"outcomes": ["reduced blood pressure", "improved lipid profile", "decreased inflammation"]
},
"cognitive": {
"interventions": ["lion's mane mushroom", "phosphatidylserine", "bacopa monnieri", "acetyl-L-carnitine"],
"biomarkers": ["cognitive performance", "BDNF levels", "neuroinflammation", "memory function"],
"outcomes": ["enhanced memory", "improved cognitive function", "neuroprotection"]
},
"hormonal": {
"interventions": ["ashwagandha", "vitamin D", "DHEA", "maca root"],
"biomarkers": ["cortisol levels", "thyroid hormones", "sex hormones", "stress markers"],
"outcomes": ["hormone balance", "improved energy", "better sleep quality"]
},
"inflammation": {
"interventions": ["curcumin", "omega-3", "quercetin", "boswellia"],
"biomarkers": ["CRP", "IL-6", "TNF-alpha", "oxidative stress"],
"outcomes": ["reduced inflammation", "improved immune function", "enhanced recovery"]
}
}
def generate_study_data(self, domain: str) -> Dict[str, Any]:
"""Generate realistic medical study data"""
if domain not in self.research_domains:
domain = "longevity"
domain_data = self.research_domains[domain]
study = {
"pmid": f"PMID{random.randint(35000000, 40000000)}",
"title": self._generate_study_title(domain, domain_data),
"abstract": self._generate_study_abstract(domain, domain_data),
"journal": random.choice([
"Nature Medicine", "Cell Metabolism", "Journal of Clinical Medicine",
"Circulation", "Aging Cell", "Nutrients", "Clinical Nutrition"
]),
"year": random.choice([2023, 2024]),
"domain": domain,
"interventions": random.sample(domain_data["interventions"], min(2, len(domain_data["interventions"]))),
"biomarkers": random.sample(domain_data["biomarkers"], min(3, len(domain_data["biomarkers"]))),
"outcomes": random.sample(domain_data["outcomes"], min(2, len(domain_data["outcomes"]))),
"participant_count": random.randint(50, 300),
"duration_weeks": random.choice([8, 12, 16, 24]),
"dosages": self._generate_dosages(domain_data["interventions"][0])
}
return study
def _generate_study_title(self, domain: str, domain_data: Dict) -> str:
intervention = random.choice(domain_data["interventions"])
outcome = random.choice(domain_data["outcomes"])
titles = [
f"Effects of {intervention} on {outcome}: A randomized controlled trial",
f"{intervention} supplementation improves {outcome} in healthy adults",
f"Clinical evaluation of {intervention} for {outcome} optimization",
f"Randomized trial of {intervention} in {outcome} enhancement"
]
return random.choice(titles)
def _generate_study_abstract(self, domain: str, domain_data: Dict) -> str:
intervention = domain_data["interventions"][0]
biomarker = random.choice(domain_data["biomarkers"])
outcome = random.choice(domain_data["outcomes"])
abstract = f"""
Background: {intervention} has shown promise in preliminary studies for health optimization.
Objective: To evaluate the effects of {intervention} supplementation on {biomarker} and related health outcomes.
Methods: Randomized, double-blind, placebo-controlled trial with {random.randint(120, 250)} participants aged 40-65 years.
Subjects received {intervention} or placebo for {random.randint(12, 24)} weeks.
Results: {intervention} supplementation significantly improved {outcome} compared to placebo (p<0.05).
{biomarker.capitalize()} showed {random.randint(15, 35)}% improvement from baseline.
Secondary outcomes included improved quality of life and no serious adverse events.
Conclusions: {intervention} supplementation provides significant benefits for {outcome} with excellent safety profile.
""".strip()
return abstract
def _generate_dosages(self, intervention: str) -> List[str]:
dosage_ranges = {
"NAD+": ["250mg", "500mg", "1000mg"],
"resveratrol": ["100mg", "250mg", "500mg"],
"berberine": ["500mg", "1000mg", "1500mg"],
"omega-3": ["1000mg", "2000mg", "3000mg"],
"magnesium": ["200mg", "400mg", "600mg"],
"curcumin": ["500mg", "1000mg", "1500mg"]
}
for key in dosage_ranges:
if key.lower() in intervention.lower():
return random.sample(dosage_ranges[key], min(2, len(dosage_ranges[key])))
return ["500mg", "1000mg"]
class HealthProfileGenerator:
"""Generates realistic health profiles based on medical studies"""
def __init__(self):
self.severity_levels = {
"optimal": {"multiplier": 1.0, "description": "excellent baseline health with optimization focus"},
"mild": {"multiplier": 1.2, "description": "minor health concerns with good overall function"},
"moderate": {"multiplier": 1.5, "description": "noticeable health issues requiring intervention"},
"severe": {"multiplier": 2.0, "description": "significant health challenges needing intensive protocols"}
}
def generate_profile_from_study(self, study: Dict[str, Any], severity: str = "moderate") -> Dict[str, Any]:
"""Generate complete health profile based on study data and severity level"""
domain = study.get("domain", "longevity")
severity_data = self.severity_levels.get(severity, self.severity_levels["moderate"])
multiplier = severity_data["multiplier"]
age = random.randint(35, 65)
gender = random.choice(["male", "female"])
labs = self._generate_lab_values(domain, multiplier)
health_profile = {
"user_tests_result_data": {
"Labs": labs,
"gut_microbiome": self._generate_gut_microbiome(severity),
"epigenetics": self._generate_epigenetics(severity),
"wearables": self._generate_wearables(severity),
"cgm": self._generate_cgm(severity)
},
"user_query": self._generate_user_query(study, age, gender, severity),
"source_study": {
"pmid": study.get("pmid"),
"domain": domain,
"severity": severity,
"title": study.get("title")
}
}
return health_profile
def _generate_lab_values(self, domain: str, multiplier: float) -> Dict[str, Any]:
"""Generate realistic lab values based on domain and severity"""
base_labs = {
"blood_tests": {
"systolic_bp": int(random.randint(120, 140) * multiplier),
"diastolic_bp": int(random.randint(70, 90) * multiplier),
"total_cholesterol": int(random.randint(180, 220) * multiplier),
"ldl": int(random.randint(100, 140) * multiplier),
"hdl": int(random.randint(40, 60) / multiplier),
"triglycerides": int(random.randint(80, 150) * multiplier),
"apoB": int(random.randint(70, 110) * multiplier),
"lp_a": random.randint(10, 50)
},
"inflammatory": {
"hscrp": round(random.uniform(1.0, 4.0) * multiplier, 1),
"esr": int(random.randint(5, 25) * multiplier),
"il6": round(random.uniform(1.0, 5.0) * multiplier, 1),
"tnf_alpha": round(random.uniform(1.0, 3.0) * multiplier, 1),
"oxidative_stress_markers": "elevated" if multiplier > 1.3 else "normal",
"homocysteine": round(random.uniform(8, 15) * multiplier, 1)
},
"nutritional": {
"vitamin_d": int(random.randint(25, 50) / multiplier),
"b12": random.randint(250, 400),
"folate": round(random.uniform(6, 14), 1),
"iron": random.randint(60, 120),
"ferritin": random.randint(30, 100),
"selenium": random.randint(80, 120),
"zinc": random.randint(70, 110),
"magnesium": round(random.uniform(1.5, 2.2), 1),
"omega3_index": round(random.uniform(4, 8) / multiplier, 1)
}
}
if domain == "metabolic_health":
base_labs["metabolic"] = {
"fasting_glucose": int(random.randint(85, 110) * multiplier),
"hba1c": round(random.uniform(5.2, 6.0) * min(multiplier, 1.4), 1),
"insulin_fasting": round(random.uniform(5, 15) * multiplier, 1),
"homa_ir": round(random.uniform(1.5, 4.0) * multiplier, 1)
}
return base_labs
def _generate_gut_microbiome(self, severity: str) -> str:
scores = {
"optimal": random.uniform(8.5, 9.5),
"mild": random.uniform(7.0, 8.5),
"moderate": random.uniform(5.5, 7.0),
"severe": random.uniform(3.5, 5.5)
}
score = scores.get(severity, 6.5)
descriptions = {
"optimal": "excellent diversity with optimal bacterial balance",
"mild": "good diversity with minor imbalances",
"moderate": "moderate dysbiosis with reduced beneficial bacteria",
"severe": "significant dysbiosis with pathogenic overgrowth"
}
desc = descriptions.get(severity, "moderate dysbiosis")
return f"Diversity score {score:.1f}/10, {desc}, beneficial bacteria {random.randint(60, 90)}%"
def _generate_epigenetics(self, severity: str) -> str:
age_acceleration = {
"optimal": random.randint(-2, 1),
"mild": random.randint(1, 3),
"moderate": random.randint(3, 6),
"severe": random.randint(6, 12)
}
acceleration = age_acceleration.get(severity, 4)
telomere_percentile = max(10, random.randint(30, 80) - acceleration * 5)
return f"Biological age acceleration: {acceleration} years, telomere length: {telomere_percentile}th percentile, DunedinPACE: {round(random.uniform(0.9, 1.4), 2)}"
def _generate_wearables(self, severity: str) -> Dict[str, int]:
base_ranges = {
"optimal": {"hrv": (55, 75), "rhr": (45, 60), "sleep": (85, 95)},
"mild": {"hrv": (45, 65), "rhr": (55, 70), "sleep": (75, 85)},
"moderate": {"hrv": (30, 50), "rhr": (65, 80), "sleep": (60, 75)},
"severe": {"hrv": (20, 35), "rhr": (75, 95), "sleep": (45, 65)}
}
ranges = base_ranges.get(severity, base_ranges["moderate"])
return {
"hrv_avg": random.randint(*ranges["hrv"]),
"rhr": random.randint(*ranges["rhr"]),
"sleep_score": random.randint(*ranges["sleep"]),
"recovery_score": random.randint(ranges["sleep"][0]-10, ranges["sleep"][1]-5),
"stress_score": random.randint(100-ranges["sleep"][1], 100-ranges["sleep"][0]+20),
"vo2_max": random.randint(25, 50),
"fitness_age": random.randint(30, 65)
}
def _generate_cgm(self, severity: str) -> str:
glucose_ranges = {
"optimal": (80, 95, 92, 98),
"mild": (85, 105, 85, 95),
"moderate": (95, 120, 70, 85),
"severe": (110, 140, 55, 75)
}
avg_min, avg_max, tir_min, tir_max = glucose_ranges.get(severity, glucose_ranges["moderate"])
return f"Average glucose {random.randint(avg_min, avg_max)} mg/dL, time in range {random.randint(tir_min, tir_max)}%"
def _generate_user_query(self, study: Dict[str, Any], age: int, gender: str, severity: str) -> str:
domain = study.get("domain", "longevity")
base_queries = {
"longevity": f"I'm a {age}-year-old {gender} interested in longevity optimization and anti-aging protocols",
"metabolic_health": f"I'm a {age}-year-old {gender} with metabolic dysfunction seeking evidence-based glucose control",
"cardiovascular": f"I'm a {age}-year-old {gender} with cardiovascular risk factors wanting heart health optimization",
"cognitive": f"I'm a {age}-year-old {gender} seeking cognitive enhancement and brain health optimization",
"hormonal": f"I'm a {age}-year-old {gender} with hormonal imbalances needing optimization protocols",
"inflammation": f"I'm a {age}-year-old {gender} with chronic inflammation seeking anti-inflammatory interventions"
}
base_query = base_queries.get(domain, base_queries["longevity"])
severity_context = {
"optimal": "I have excellent baseline health but want to push the boundaries of optimization",
"mild": "I have minor health concerns and want targeted interventions",
"moderate": "I have noticeable health issues and need comprehensive protocols",
"severe": "I have significant health challenges and require intensive interventions"
}
context = severity_context.get(severity, "")
return f"{base_query}. {context}."
class AIProtocolGenerator:
"""Uses OpenAI to generate health optimization protocols"""
def __init__(self, api_key: str, model: str = "gpt-4"):
self.client = OpenAI(api_key=api_key)
self.model = model
self.total_cost = 0.0
def generate_protocol(self, health_profile: Dict[str, Any], study_context: Dict[str, Any], progress_callback=None) -> Optional[str]:
"""Generate comprehensive health optimization protocol"""
system_prompt = self._create_system_prompt(study_context)
user_prompt = self._create_user_prompt(health_profile, study_context)
try:
if progress_callback:
progress_callback(f"π Generating protocol using {self.model}...")
response = self.client.chat.completions.create(
model=self.model,
messages=[
{"role": "system", "content": system_prompt},
{"role": "user", "content": user_prompt}
],
max_tokens=4000,
temperature=0.7,
top_p=0.9
)
self._update_cost(response.usage)
if progress_callback:
progress_callback(f"β
Protocol generated ({response.usage.total_tokens} tokens)")
return response.choices[0].message.content
except Exception as e:
if progress_callback:
progress_callback(f"β Error generating protocol: {e}")
return None
def _create_system_prompt(self, study_context: Dict[str, Any]) -> str:
domain = study_context.get("domain", "health")
interventions = ", ".join(study_context.get("interventions", []))
return f"""You are an advanced AI health optimization system specializing in evidence-based medicine and personalized protocols.
RESEARCH CONTEXT:
- Domain: {domain} optimization
- Key Interventions: {interventions}
- Evidence Level: Peer-reviewed clinical research
PROTOCOL REQUIREMENTS:
1. Executive Summary with current health assessment
2. Multi-Phase Protocol:
- Phase 1: Foundation (0-3 months)
- Phase 2: Optimization (3-6 months)
- Phase 3: Advanced Enhancement (6-12 months)
3. Specific supplement protocols with dosages and timing
4. Lifestyle interventions (exercise, nutrition, sleep)
5. Monitoring and assessment plans
6. Expected outcomes with realistic timelines
STYLE: Professional, authoritative, using Medicine 3.0 terminology. Reference biological age, biomarkers, and cellular health.
SAFETY: Keep dosages within evidence-based safe ranges. Include monitoring recommendations.
Generate comprehensive protocols (3000+ words) with actionable precision medicine recommendations."""
def _create_user_prompt(self, health_profile: Dict[str, Any], study_context: Dict[str, Any]) -> str:
return f"""
COMPREHENSIVE HEALTH OPTIMIZATION REQUEST:
Health Profile Analysis:
{json.dumps(health_profile, indent=2)}
Research Context:
- Study: {study_context.get('title', 'Health Optimization Study')}
- Domain: {study_context.get('domain', 'general health')}
- Key Findings: Based on clinical research showing significant improvements in health biomarkers
Please analyze this health profile and generate a detailed, personalized optimization protocol. Address the specific biomarker patterns, deficiencies, and health challenges identified in the data. Provide targeted interventions with precise dosing, timing, and monitoring protocols.
"""
def _update_cost(self, usage):
pricing = {
"gpt-3.5-turbo": {"input": 0.0015, "output": 0.002},
"gpt-4": {"input": 0.03, "output": 0.06},
"gpt-4-turbo": {"input": 0.01, "output": 0.03}
}
model_pricing = pricing.get(self.model, pricing["gpt-4"])
input_cost = usage.prompt_tokens * model_pricing["input"] / 1000
output_cost = usage.completion_tokens * model_pricing["output"] / 1000
self.total_cost += input_cost + output_cost
class HealthDatasetGenerator:
"""Complete system that orchestrates the entire dataset generation process"""
def __init__(self, api_key: str, model: str = "gpt-4"):
self.literature_sim = MedicalLiteratureSimulator()
self.profile_gen = HealthProfileGenerator()
self.protocol_gen = AIProtocolGenerator(api_key, model)
self.generated_examples = []
def generate_dataset(self,
domains: List[str] = None,
examples_per_domain: int = 2,
rate_limit_delay: float = 2.0,
progress_callback=None) -> Tuple[List[Dict[str, Any]], str]:
"""Generate complete health optimization dataset with progress updates"""
if domains is None:
domains = ["longevity", "metabolic_health", "cardiovascular", "cognitive"]
if progress_callback:
progress_callback(f"π Starting Health Dataset Generation")
progress_callback(f"Domains: {domains}")
progress_callback(f"Examples per domain: {examples_per_domain}")
progress_callback(f"Total examples to generate: {len(domains) * examples_per_domain}")
examples = []
total_examples = len(domains) * examples_per_domain
current_example = 0
for domain in domains:
if progress_callback:
progress_callback(f"\nπ Processing domain: {domain}")
for i in range(examples_per_domain):
current_example += 1
try:
if progress_callback:
progress_callback(f" Creating example {i+1}/{examples_per_domain} (Overall: {current_example}/{total_examples})")
# Generate study data
study = self.literature_sim.generate_study_data(domain)
if progress_callback:
progress_callback(f" π Generated study: {study['title'][:50]}...")
# Create health profile
severity = random.choice(["mild", "moderate", "severe"])
health_profile = self.profile_gen.generate_profile_from_study(study, severity)
if progress_callback:
progress_callback(f" π€ Created {severity} health profile")
# Generate protocol
protocol = self.protocol_gen.generate_protocol(health_profile, study, progress_callback)
if protocol:
training_example = {
"user_context": health_profile,
"response": protocol,
"citations": self._generate_citations(study),
"metadata": {
"domain": domain,
"severity": severity,
"study_pmid": study["pmid"],
"generated_at": datetime.now().isoformat()
}
}
examples.append(training_example)
if progress_callback:
progress_callback(f" β
Complete example generated")
# Rate limiting
if i < examples_per_domain - 1:
if progress_callback:
progress_callback(f" β³ Rate limit delay: {rate_limit_delay}s")
time.sleep(rate_limit_delay)
except Exception as e:
if progress_callback:
progress_callback(f" β Error generating example: {e}")
continue
if progress_callback:
progress_callback(f"\nπ Dataset generation complete!")
progress_callback(f"Generated: {len(examples)} examples")
progress_callback(f"Total cost: ${self.protocol_gen.total_cost:.4f}")
self.generated_examples = examples
return examples, f"Generated {len(examples)} examples. Total cost: ${self.protocol_gen.total_cost:.4f}"
def _generate_citations(self, study: Dict[str, Any]) -> Dict[str, List[str]]:
return {
"tier_1_peer_reviewed": [study["pmid"], f"PMC{random.randint(1000000, 9999999)}"],
"tier_2_rct": [f"{study['domain'].upper()}.2024.{random.randint(100000, 999999)}"],
"tier_3_cohort": [f"HEALTH.2023.{random.randint(100000, 999999)}"],
"real_world_cases": ["Evidence-based health optimization protocols"]
}
def export_dataset(self, filename: str = None) -> Tuple[str, List[str]]:
"""Export dataset and return zip file path and file list"""
if not filename:
timestamp = datetime.now().strftime("%Y%m%d_%H%M%S")
filename = f"health_dataset_{timestamp}"
# Create all files in memory
files_created = []
# Raw dataset
raw_data = json.dumps(self.generated_examples, indent=2, ensure_ascii=False)
files_created.append((f"{filename}.json", raw_data))
# Fine-tuning format
fine_tune_lines = []
for example in self.generated_examples:
fine_tune_example = {
"messages": [
{
"role": "system",
"content": "You are an advanced AI health optimization system that creates evidence-based protocols."
},
{
"role": "user",
"content": f"Create a health optimization protocol for this profile:\n\n{json.dumps(example['user_context'], indent=2)}"
},
{
"role": "assistant",
"content": example["response"]
}
]
}
fine_tune_lines.append(json.dumps(fine_tune_example, ensure_ascii=False))
fine_tune_data = '\n'.join(fine_tune_lines)
files_created.append((f"{filename}_fine_tuning.jsonl", fine_tune_data))
# Sample examples
sample_size = min(3, len(self.generated_examples))
sample_data = json.dumps(self.generated_examples[:sample_size], indent=2, ensure_ascii=False)
files_created.append((f"{filename}_samples.json", sample_data))
# Metadata
metadata = {
"generation_info": {
"generated_at": datetime.now().isoformat(),
"total_examples": len(self.generated_examples),
"total_cost": self.protocol_gen.total_cost,
"model_used": self.protocol_gen.model
},
"domains_covered": list(set(ex["metadata"]["domain"] for ex in self.generated_examples)),
"severity_distribution": {
severity: sum(1 for ex in self.generated_examples if ex["metadata"]["severity"] == severity)
for severity in ["mild", "moderate", "severe"]
}
}
metadata_data = json.dumps(metadata, indent=2, ensure_ascii=False)
files_created.append((f"{filename}_metadata.json", metadata_data))
# Create zip file
zip_buffer = io.BytesIO()
with zipfile.ZipFile(zip_buffer, 'w', zipfile.ZIP_DEFLATED) as zip_file:
for file_name, file_content in files_created:
zip_file.writestr(file_name, file_content)
# Save zip file
zip_filename = f"{filename}.zip"
with open(zip_filename, 'wb') as f:
f.write(zip_buffer.getvalue())
file_list = [f[0] for f in files_created]
return zip_filename, file_list
# =====================================================================
# STEP 3: GRADIO INTERFACE
# =====================================================================
class HealthDatasetGradioInterface:
"""Gradio web interface for the health dataset generator"""
def __init__(self):
self.generator = None
self.available_domains = list(MedicalLiteratureSimulator().research_domains.keys())
def estimate_cost(self, domains, examples_per_domain, model):
"""Estimate generation cost"""
if not domains:
return "Please select at least one domain"
total_examples = len(domains) * examples_per_domain
cost_per_example = {
"gpt-3.5-turbo": 0.05,
"gpt-4": 0.25,
"gpt-4-turbo": 0.15
}
estimated_cost = total_examples * cost_per_example.get(model, 0.25)
return f"π° Estimated cost: ${estimated_cost:.2f} for {total_examples} examples"
def validate_inputs(self, api_key, domains, examples_per_domain):
"""Validate user inputs"""
if not api_key or not api_key.strip():
return False, "β Please provide your OpenAI API key"
if not domains:
return False, "β Please select at least one domain"
if examples_per_domain < 1 or examples_per_domain > 10:
return False, "β Examples per domain must be between 1 and 10"
return True, "β
Inputs are valid"
def generate_dataset_interface(self, api_key, domains, examples_per_domain, model, rate_limit):
"""Main dataset generation function for Gradio interface"""
# Validate inputs
is_valid, message = self.validate_inputs(api_key, domains, examples_per_domain)
if not is_valid:
yield message, "", "", None, None
return
# Initialize generator
try:
self.generator = HealthDatasetGenerator(api_key.strip(), model)
except Exception as e:
yield f"β Error initializing generator: {e}", "", "", None, None
return
# Progress tracking
progress_messages = []
def progress_callback(message):
progress_messages.append(message)
progress_text = "\n".join(progress_messages[-20:]) # Keep last 20 messages
return progress_text
try:
# Generate dataset
yield "π Starting dataset generation...", "", "", None, None
dataset, summary = self.generator.generate_dataset(
domains=domains,
examples_per_domain=examples_per_domain,
rate_limit_delay=rate_limit,
progress_callback=progress_callback
)
if not dataset:
yield "β No examples generated", "", "", None, None
return
# Export dataset
progress_callback("πΎ Exporting dataset...")
zip_filename, file_list = self.generator.export_dataset()
# Create preview
preview = self.create_dataset_preview(dataset)
# Final progress
final_progress = progress_callback(f"π Generation complete! Files: {', '.join(file_list)}")
yield final_progress, summary, preview, zip_filename, file_list
except Exception as e:
yield f"β Error during generation: {e}", "", "", None, None
def create_dataset_preview(self, dataset):
"""Create a preview of the generated dataset"""
if not dataset:
return "No data to preview"
preview = "π **Dataset Preview**\n\n"
# Summary statistics
preview += f"**Total Examples:** {len(dataset)}\n"
# Domain distribution
domains = [ex['metadata']['domain'] for ex in dataset]
domain_counts = {d: domains.count(d) for d in set(domains)}
preview += f"**Domain Distribution:** {domain_counts}\n"
# Severity distribution
severities = [ex['metadata']['severity'] for ex in dataset]
severity_counts = {s: severities.count(s) for s in set(severities)}
preview += f"**Severity Distribution:** {severity_counts}\n\n"
# Sample example
if dataset:
example = dataset[0]
preview += "**Sample Example:**\n"
preview += f"- **Domain:** {example['metadata']['domain']}\n"
preview += f"- **Severity:** {example['metadata']['severity']}\n"
preview += f"- **User Query:** {example['user_context']['user_query'][:150]}...\n"
preview += f"- **Response Length:** {len(example['response'])} characters\n"
preview += f"- **PMID:** {example['metadata']['study_pmid']}\n"
return preview
def analyze_dataset_file(self, zip_file):
"""Analyze uploaded dataset file"""
if zip_file is None:
return "No file uploaded"
try:
# Read the zip file
with zipfile.ZipFile(zip_file.name, 'r') as zip_ref:
# Look for the main dataset file
json_files = [f for f in zip_ref.namelist() if f.endswith('.json') and not f.endswith('_samples.json') and not f.endswith('_metadata.json')]
if json_files:
dataset_file = json_files[0]
with zip_ref.open(dataset_file) as f:
dataset = json.load(f)
analysis = "π **Dataset Analysis**\n\n"
analysis += f"**Total Examples:** {len(dataset)}\n"
analysis += f"**Average Response Length:** {sum(len(ex['response']) for ex in dataset) / len(dataset):.0f} characters\n"
# Quality checks
long_responses = sum(1 for ex in dataset if len(ex['response']) > 2000)
has_phases = sum(1 for ex in dataset if "Phase" in ex['response'])
has_dosages = sum(1 for ex in dataset if re.search(r'\d+\s*mg', ex['response']))
analysis += f"**Quality Metrics:**\n"
analysis += f"- Responses >2000 chars: {long_responses}/{len(dataset)} ({long_responses/len(dataset)*100:.1f}%)\n"
analysis += f"- Responses with phases: {has_phases}/{len(dataset)} ({has_phases/len(dataset)*100:.1f}%)\n"
analysis += f"- Responses with dosages: {has_dosages}/{len(dataset)} ({has_dosages/len(dataset)*100:.1f}%)\n"
return analysis
else:
return "No dataset JSON file found in zip"
except Exception as e:
return f"Error analyzing file: {e}"
def create_interface(self):
"""Create the Gradio interface"""
with gr.Blocks(title="Medical Literature Health Dataset Generator", theme=gr.themes.Soft()) as interface:
gr.Markdown("""
# π₯ Medical Literature Health Dataset Generator
This tool generates synthetic health optimization datasets based on medical literature patterns.
Perfect for training AI models on evidence-based health protocols.
β οΈ **Important:** Generated content is for research/educational purposes only. Not medical advice.
""")
with gr.Tab("π Generate Dataset"):
with gr.Row():
with gr.Column(scale=1):
gr.Markdown("### βοΈ Configuration")
api_key = gr.Textbox(
label="OpenAI API Key",
placeholder="sk-...",
type="password",
info="Your OpenAI API key for generating protocols"
)
domains = gr.CheckboxGroup(
label="Research Domains",
choices=self.available_domains,
value=["longevity", "metabolic_health"],
info="Select medical research domains to include"
)
examples_per_domain = gr.Slider(
label="Examples per Domain",
minimum=1,
maximum=10,
value=2,
step=1,
info="Number of examples to generate for each domain"
)
model = gr.Dropdown(
label="OpenAI Model",
choices=["gpt-3.5-turbo", "gpt-4", "gpt-4-turbo"],
value="gpt-4",
info="Model for generating protocols (GPT-4 recommended for quality)"
)
rate_limit = gr.Slider(
label="Rate Limit Delay (seconds)",
minimum=0.5,
maximum=5.0,
value=2.0,
step=0.5,
info="Delay between API calls to avoid rate limits"
)
cost_estimate = gr.Textbox(
label="Cost Estimate",
value="Select domains and examples to see estimate",
interactive=False
)
generate_btn = gr.Button(
"π Generate Dataset",
variant="primary",
size="lg"
)
with gr.Column(scale=2):
gr.Markdown("### π Progress & Results")
progress_output = gr.Textbox(
label="Generation Progress",
lines=15,
max_lines=20,
value="Ready to generate dataset...",
interactive=False
)
summary_output = gr.Textbox(
label="Generation Summary",
lines=3,
interactive=False
)
preview_output = gr.Markdown(
label="Dataset Preview",
value="Dataset preview will appear here..."
)
with gr.Row():
download_file = gr.File(
label="π₯ Download Generated Dataset",
interactive=False
)
file_list = gr.Textbox(
label="Generated Files",
placeholder="Files included in download will be listed here",
interactive=False
)
with gr.Tab("π Analyze Dataset"):
gr.Markdown("### π Dataset Analysis")
gr.Markdown("Upload a generated dataset zip file to analyze its quality and structure.")
with gr.Row():
with gr.Column():
upload_file = gr.File(
label="Upload Dataset Zip File",
file_types=[".zip"]
)
analyze_btn = gr.Button(
"π Analyze Dataset",
variant="secondary"
)
with gr.Column():
analysis_output = gr.Markdown(
label="Analysis Results",
value="Upload a dataset file to see analysis..."
)
with gr.Tab("βΉοΈ Information"):
gr.Markdown("""
### π How It Works
1. **Literature Simulation**: Creates realistic medical studies with proper abstracts, interventions, and outcomes
2. **Health Profile Generation**: Generates comprehensive health profiles based on study domains and severity levels
3. **AI Protocol Generation**: Uses OpenAI to create detailed health optimization protocols
4. **Dataset Export**: Outputs data in multiple formats including OpenAI fine-tuning format
### π― Output Files
- **`dataset.json`**: Complete raw dataset
- **`dataset_fine_tuning.jsonl`**: OpenAI fine-tuning format
- **`dataset_samples.json`**: Sample examples for review
- **`dataset_metadata.json`**: Generation statistics and info
### π° Cost Information
- **GPT-3.5-turbo**: ~$0.05 per example
- **GPT-4**: ~$0.25 per example
- **GPT-4-turbo**: ~$0.15 per example
### β οΈ Important Notes
- Generated content is for **research/educational purposes only**
- **Not medical advice** - always consult healthcare professionals
- Include appropriate medical disclaimers when using generated content
- Review sample outputs before using in production
### π§ Recommended Settings
- **Start small**: Generate 2-4 examples first to test quality
- **Use GPT-4**: Better quality than GPT-3.5-turbo
- **Rate limiting**: Use 2+ second delays to avoid API limits
- **Multiple domains**: Include diverse domains for comprehensive dataset
""")
# Event handlers
# Update cost estimate when inputs change
def update_cost_estimate(domains, examples_per_domain, model):
return self.estimate_cost(domains, examples_per_domain, model)
for input_component in [domains, examples_per_domain, model]:
input_component.change(
fn=update_cost_estimate,
inputs=[domains, examples_per_domain, model],
outputs=[cost_estimate]
)
# Generate dataset
generate_btn.click(
fn=self.generate_dataset_interface,
inputs=[api_key, domains, examples_per_domain, model, rate_limit],
outputs=[progress_output, summary_output, preview_output, download_file, file_list]
)
# Analyze dataset
analyze_btn.click(
fn=self.analyze_dataset_file,
inputs=[upload_file],
outputs=[analysis_output]
)
return interface
# =====================================================================
# STEP 4: LAUNCH THE INTERFACE
# =====================================================================
def main():
"""Launch the Gradio interface"""
print("π Launching Medical Literature Health Dataset Generator")
print("This will start a web interface accessible through your browser")
# Create interface
interface_creator = HealthDatasetGradioInterface()
interface = interface_creator.create_interface()
# Launch with configuration
interface.launch(
share=True, # Creates public link for sharing
server_name="0.0.0.0", # Makes it accessible from other devices
server_port=7860, # Default Gradio port
show_error=True, # Show detailed errors
quiet=False # Show startup info
)
if __name__ == "__main__":
main()
# For Google Colab, uncomment the following:
# main() |