We fine-tuned and deployed specialised LLMs for the organisation's surveillance workflows over 14 weeks. Training dataset preparation (weeks 1-4). Epidemiological corpus: training dataset assembled from — 48,000 surveillance reports (5 years of archived reports across all programmes), 8,600 outbreak investigation reports, 2,200 published research papers from the organisation's researchers, CDC MMWR reports and surveillance summaries (10 years), and expert-annotated examples of information extraction, report classification, and narrative generation. The corpus: representing the specific epidemiological language, report formats, and analytical patterns used in public health surveillance. Expert annotation: 3 senior epidemiologists providing annotation and quality review — marking key findings in surveillance reports, coding outbreak parameters, and rating narrative output quality. The annotation: ensuring the model learned the expert-level judgement that distinguished important findings from routine data.
Domain vocabulary integration: specialised vocabulary — ICD-10 codes, pathogen nomenclature, epidemiological methodology terms, geographic health jurisdictions, and surveillance programme-specific terminology — incorporated into the model's understanding. The integration: enabling the model to correctly interpret and generate the technical language of epidemiological surveillance. Surveillance report processing model (weeks 3-8). Report intake automation: fine-tuned model processing incoming surveillance reports — extracting disease counts, trend indicators (increasing, decreasing, stable), notable events (outbreaks, unusual clusters, novel findings), and geographic patterns. The extraction: structured data pulled from narrative reports in under 30 seconds (vs. 15-25 minutes of analyst reading). Priority flagging: model identifying reports requiring urgent analyst attention — significant trend changes, novel pathogen detections, unusual cluster patterns, and findings that crossed surveillance programme boundaries. The flagging: ensuring that high-priority findings received immediate expert attention while routine reports were processed automatically.
Cross-report synthesis: model comparing current reports against historical baselines — identifying when current disease activity deviated from expected seasonal patterns and flagging jurisdictions with unusual trends. The synthesis: automated pattern detection across the 2,400 weekly reports that no analyst team could manually monitor. Outbreak analysis model (weeks 5-10). Outbreak parameter extraction: fine-tuned model extracting standardised parameters from outbreak investigation reports — pathogen identification, exposure source, setting type, attack rate, hospitalisation rate, control measures implemented, and investigation outcome. The extraction: structured data from narrative text enabling database entry and cross-outbreak analysis. Pattern identification: model comparing current outbreak parameters against the historical database — identifying recurring outbreak patterns (same pathogen-source combinations, repeated venue types, seasonal clustering). The identification: detecting outbreak patterns that manual review missed because no analyst could hold 340+ annual investigations in memory.
Outbreak narrative generation: model generating standardised outbreak summary narratives from structured investigation data — producing the formatted reports that communicated findings to health departments and partner agencies. The generation: consistent, thorough outbreak summaries produced in minutes rather than the 45-60 minutes of analyst writing time. Literature monitoring model (weeks 7-12). Automated literature screening: fine-tuned model monitoring published literature — screening abstracts against each programme's surveillance priorities, relevance-scoring publications, and generating weekly literature digests for each research team. The screening: systematic coverage of 14,000 annual publications rather than the 15-20% that manual monitoring achieved. Relevance extraction: for high-relevance publications, the model extracting key findings, methodology, and implications for the organisation's surveillance programmes — enabling researchers to quickly assess relevance without reading full papers. The extraction: 2-minute relevance assessment replacing 15-30 minutes of paper reading for initial screening.
Cross-domain identification: model identifying publications relevant to multiple surveillance programmes — an environmental study with infectious disease implications, or an injury research paper with chronic disease correlations. The identification: systematic cross-programme literature connection that informal communication could not achieve. Report generation assistance (weeks 9-14). Draft narrative generation: model generating first drafts of surveillance summaries, programme reports, and policy briefs from structured data and analyst notes — producing narrative text that analysts reviewed and refined rather than wrote from scratch. The generation: reducing report writing time by an estimated 60% while maintaining the analytical voice and accuracy that these documents required. Cross-programme synthesis: model generating cross-programme synthesis reports — identifying and narrating connections between findings across surveillance programmes that would otherwise require manual meetings and discussion to discover.