Clinical Trial Document Search and Evidence Synthesis

import { Mixpeek } from 'mixpeek';

const client = new Mixpeek({ apiKey: process.env.MIXPEEK_API_KEY });

// Index clinical trial documents
await client.buckets.connect({
  collection_id: 'clinical-docs',
  bucket_uri: 's3://clinical/documents/',
  extractors: [
    'document-parser',     // PDFs, Word
    'table-extraction',    // Clinical data tables
    'figure-analysis',     // Efficacy/safety figures
    'medical-ner',         // Medical entity extraction
    'section-detection'    // Protocol/CSR sections
  ],
  settings: {
    medical_vocabularies: ['MedDRA', 'SNOMED', 'ICD-10'],
    document_types: ['protocol', 'csr', 'publication', 'sae_report', 'submission'],
    extract_references: true,
    hipaa_compliant: true
  }
});

// Search clinical documents semantically
async function searchClinicalDocs(query: string, filters?: {
  document_types?: string[];
  study_phases?: string[];
  date_range?: { start: string; end: string };
  indications?: string[];
}) {
  const results = await client.retrieve({
    collection_id: 'clinical-docs',
    query: {
      type: 'text',
      text: query,  // e.g., "hepatotoxicity signals in phase 3"
      expand_medical_terms: true  // Expand to synonyms
    },
    filters: filters,
    return_fields: [
      'content', 'document_type', 'study_id',
      'extracted_tables', 'extracted_figures',
      'medical_entities', 'section'
    ],
    limit: 100
  });

  return results;
}

// Monitor for safety signals across documents
async function findSafetySignals(drugProgram: string) {
  const signals = await client.retrieve({
    collection_id: 'clinical-docs',
    query: {
      type: 'safety_signal',  // Specialized safety query
      scope: drugProgram
    },
    filters: {
      document_type: { $in: ['sae_report', 'csr', 'dsmb_report'] }
    },
    return_fields: [
      'adverse_events', 'sae_details', 'causality_assessment',
      'frequency', 'severity', 'source_document'
    ],
    aggregate_by: 'adverse_event_term'
  });

  return {
    signals_by_term: signals.aggregations,
    new_signals: signals.results.filter(s => s.is_new),
    severity_distribution: calculateSeverityDistribution(signals.results)
  };
}

// Create evidence summary for regulatory submission
async function synthesizeEvidence(topic: string, drugProgram: string) {
  const evidence = await searchClinicalDocs(topic, {
    document_types: ['protocol', 'csr', 'publication']
  });

  // Group by study and extract key data
  const synthesis = {
    topic: topic,
    studies_included: [...new Set(evidence.map(e => e.study_id))],
    efficacy_data: evidence
      .filter(e => e.section === 'efficacy')
      .map(e => ({
        study: e.study_id,
        endpoint: e.extracted_tables[0]?.endpoint,
        result: e.extracted_tables[0]?.result
      })),
    safety_data: evidence
      .filter(e => e.section === 'safety')
      .map(e => ({
        study: e.study_id,
        aes: e.adverse_events
      })),
    references: evidence.map(e => ({
      document: e.document_type,
      location: e.page_number,
      citation: e.citation
    }))
  };

  return synthesis;
}