Somalee Datta

Jose D. Posada, David Love, Somalee Datta et al.

De-identification of clinical text remains essential for secondary use of electronic health records (EHRs), yet public benchmarks such as i2b2 2006/2014 are over a decade old and lack the semantic and demographic diversity of modern narratives. While Large Language Models (LLMs) achieve state-of-the-art zero-shot extraction, enterprise deployment is hindered by compute costs and governance restricting Protected Health Information (PHI) from cloud APIs. We introduce SHIELD (Synthetic Human-annotated Identifier-replaced Entries for Learning and De-identification), a diverse dataset of 1,394 notes with 10,505 gold-standard PHI spans across 9 categories, built via set-cover diversity sampling with human-in-the-loop adjudication. We evaluate four LLMs (two proprietary, two open-weight) to establish a performance ceiling, then distill these capabilities into locally deployable Small Language Models (SLMs). Distributional analysis using Frechet Text Distance and Jensen-Shannon Divergence confirms SHIELD occupies a distinct region of biomedical embedding and vocabulary space versus legacy benchmarks. Our best distilled model matches its teacher on structured PHI categories (DATE, DOCTOR, ID, PATIENT, PHONE) and achieves micro-averaged span-level precision of 0.88 and recall of 0.86 on standard workstation hardware. Cross-dataset evaluation shows diversity-trained models generalize well on universal structured PHI, while institution-specific entities remain hard to transfer, suggesting optimal deployment combines broad-coverage models with specialized models for high-volume notes. We publicly release the SHIELD dataset and the distilled DeBERTa v3 model.

Tina Seto, Lillian Sung, Jose Posada et al.

Flowsheet data presents unique challenges and opportunities for integration into standardized Common Data Models (CDMs) such as the Observational Medical Outcomes Partnership (OMOP) CDM from the Observational Health Data Sciences and Informatics (OHDSI) program. These data are a potentially rich source of detailed curated health outcomes data such as pain scores, vital signs, lines drains and airways (LDA) and other measurements that can be invaluable in building a robust model of patient health journey during an inpatient stay. We present two approaches to integration of flowsheet measures into the OMOP CDM. One approach was computationally straightforward but of potentially limited research utility. The second approach was far more computationally and labor intensive and involved mapping to standardized terms in controlled clinical vocabularies such as Logical Observation Identifiers Names and Codes (LOINC), resulting in a research data set of higher utility to population health studies.

Sanjay Malunjkar, Susan Weber, Somalee Datta

The advent of cost effective cloud computing over the past decade and ever-growing accumulation of high-fidelity clinical data in a modern hospital setting is leading to new opportunities for translational medicine. Machine learning is driving the appetite of the research community for various types of signal data such as patient vitals. Health care systems, however, are ill suited for massive processing of large volumes of data. In addition, due to the sheer magnitude of the data being collected, it is not feasible to retain all of the data in health care systems in perpetuity. This gold mine of information gets purged periodically thereby losing invaluable future research opportunities. We have developed a highly scalable solution that: a) siphons off patient vital data on a nightly basis from on-premises bio-medical systems to a cloud storage location as a permanent archive, b) reconstructs the database in the cloud, c) generates waveforms, alarms and numeric data in a research-ready format, and d) uploads the processed data to a storage location in the cloud ready for research. The data is de-identified and catalogued such that it can be joined with Electronic Medical Records (EMR) and other ancillary data types such as electroencephalogram (EEG), radiology, video monitoring etc. This technique eliminates the research burden from health care systems. This highly scalable solution is used to process high density patient monitoring data aggregated by the Philips Patient Information Center iX (PIC iX) hospital surveillance system for archival storage in the Philips Data Warehouse Connect enterprise-level database. The solution is part of a broader platform that supports a secure high performance clinical data science platform.

Somalee Datta, Jose Posada, Garrick Olson et al.

Stanford Medicine is building a new data platform for our academic research community to do better clinical data science. Hospitals have a large amount of patient data and researchers have demonstrated the ability to reuse that data and AI approaches to derive novel insights, support patient care, and improve care quality. However, the traditional data warehouse and Honest Broker approaches that are in current use, are not scalable. We are establishing a new secure Big Data platform that aims to reduce time to access and analyze data. In this platform, data is anonymized to preserve patient data privacy and made available preparatory to Institutional Review Board (IRB) submission. Furthermore, the data is standardized such that analysis done at Stanford can be replicated elsewhere using the same analytical code and clinical concepts. Finally, the analytics data warehouse integrates with a secure data science computational facility to support large scale data analytics. The ecosystem is designed to bring the modern data science community to highly sensitive clinical data in a secure and collaborative big data analytics environment with a goal to enable bigger, better and faster science.