An Automated System for Generating Situation-Specific Decision Support in Clinical Order Entry from Local Empirical Data

Indiana University-Purdue University Indianapolis (IUPUI)Clinical Decision Support is one of the only aspects of health information technology that has demonstrated decreased costs and increased quality in healthcare delivery, yet it is extremely expensive and time-consuming to create, maintain, and localize. Consequently, a majority of health care systems do not utilize it, and even when it is available it is frequently incorrect. Therefore it is important to look beyond traditional guideline-based decision support to more readily available resources in order to bring this technology into widespread use. This study proposes that the wisdom of physicians within a practice is a rich, untapped knowledge source that can be harnessed for this purpose. I hypothesize and demonstrate that this wisdom is reflected by order entry data well enough to partially reconstruct the knowledge behind treatment decisions. Automated reconstruction of such knowledge is used to produce dynamic, situation-specific treatment suggestions, in a similar vein to Amazon.com shopping recommendations. This approach is appealing because: it is local (so it reflects local standards); it fits into workflow more readily than the traditional local-wisdom approach (viz. the curbside consult); and, it is free (the data are already being captured). This work develops several new machine-learning algorithms and novel applications of existing algorithms, focusing on an approach called Bayesian network structure learning. I develop: an approach to produce dynamic, rank-ordered situation-specific treatment menus from treatment data; statistical machinery to evaluate their accuracy using retrospective simulation; a novel algorithm which is an order of magnitude faster than existing algorithms; a principled approach to choosing smaller, more optimal, domain-specific subsystems; and a new method to discover temporal relationships in the data. The result is a comprehensive approach for extracting knowledge from order-entry data to produce situation-specific treatment menus, which is applied to order-entry data at Wishard Hospital in Indianapolis. Retrospective simulations find that, in a large variety of clinical situations, a short menu will contain the clinicians' desired next actions. A prospective survey additionally finds that such menus aid physicians in writing order sets (in completeness and speed). This study demonstrates that clinical knowledge can be successfully extracted from treatment data for decision support

Patient-tailored prioritization for a pediatric care decision support system through machine learning

Objective Over 8 years, we have developed an innovative computer decision support system that improves appropriate delivery of pediatric screening and care. This system employs a guidelines evaluation engine using data from the electronic health record (EHR) and input from patients and caregivers. Because guideline recommendations typically exceed the scope of one visit, the engine uses a static prioritization scheme to select recommendations. Here we extend an earlier idea to create patient-tailored prioritization. Materials and methods We used Bayesian structure learning to build networks of association among previously collected data from our decision support system. Using area under the receiver-operating characteristic curve (AUC) as a measure of discriminability (a sine qua non for expected value calculations needed for prioritization), we performed a structural analysis of variables with high AUC on a test set. Our source data included 177 variables for 29 402 patients. Results The method produced a network model containing 78 screening questions and anticipatory guidance (107 variables total). Average AUC was 0.65, which is sufficient for prioritization depending on factors such as population prevalence. Structure analysis of seven highly predictive variables reveals both face-validity (related nodes are connected) and non-intuitive relationships. Discussion We demonstrate the ability of a Bayesian structure learning method to ‘phenotype the population’ seen in our primary care pediatric clinics. The resulting network can be used to produce patient-tailored posterior probabilities that can be used to prioritize content based on the patient's current circumstances. Conclusions This study demonstrates the feasibility of EHR-driven population phenotyping for patient-tailored prioritization of pediatric preventive care services

Query Health: standards-based, cross-platform population health surveillance

Objective: Understanding population-level health trends is essential to effectively monitor and improve public health. The Office of the National Coordinator for Health Information Technology (ONC) Query Health initiative is a collaboration to develop a national architecture for distributed, population-level health queries across diverse clinical systems with disparate data models. Here we review Query Health activities, including a standards-based methodology, an open-source reference implementation, and three pilot projects. Materials and methods Query Health defined a standards-based approach for distributed population health queries, using an ontology based on the Quality Data Model and Consolidated Clinical Document Architecture, Health Quality Measures Format (HQMF) as the query language, the Query Envelope as the secure transport layer, and the Quality Reporting Document Architecture as the result language. Results: We implemented this approach using Informatics for Integrating Biology and the Bedside (i2b2) and hQuery for data analytics and PopMedNet for access control, secure query distribution, and response. We deployed the reference implementation at three pilot sites: two public health departments (New York City and Massachusetts) and one pilot designed to support Food and Drug Administration post-market safety surveillance activities. The pilots were successful, although improved cross-platform data normalization is needed. Discussions This initiative resulted in a standards-based methodology for population health queries, a reference implementation, and revision of the HQMF standard. It also informed future directions regarding interoperability and data access for ONC's Data Access Framework initiative. Conclusions: Query Health was a test of the learning health system that supplied a functional methodology and reference implementation for distributed population health queries that has been validated at three sites

Feasibility of Homomorphic Encryption for Sharing I2B2 Aggregate-Level Data in the Cloud

The biomedical community is lagging in the adoption of cloud computing for the management of medical data. The primary obstacles are concerns about privacy and security. In this paper, we explore the feasibility of using advanced privacy-enhancing technologies in order to enable the sharing of sensitive clinical data in a public cloud. Our goal is to facilitate sharing of clinical data in the cloud by minimizing the risk of unintended leakage of sensitive clinical information. In particular, we focus on homomorphic encryption, a specific type of encryption that offers the ability to run computation on the data while the data remains encrypted. This paper demonstrates that homomorphic encryption can be used efficiently to compute aggregating queries on the ciphertexts, along with providing end-to-end confidentiality of aggregate-level data from the i2b2 data model

Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS): Architecture

We describe the architecture of the Patient Centered Outcomes Research Institute (PCORI) funded Scalable Collaborative Infrastructure for a Learning Healthcare System (SCILHS, http://www.SCILHS.org) clinical data research network, which leverages the $48 billion dollar federal investment in health information technology (IT) to enable a queryable semantic data model across 10 health systems covering more than 8 million patients, plugging universally into the point of care, generating evidence and discovery, and thereby enabling clinician and patient participation in research during the patient encounter. Central to the success of SCILHS is development of innovative ‘apps’ to improve PCOR research methods and capacitate point of care functions such as consent, enrollment, randomization, and outreach for patient-reported outcomes. SCILHS adapts and extends an existing national research network formed on an advanced IT infrastructure built with open source, free, modular components

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

OBJECTIVE: Coronavirus disease 2019 (COVID-19) poses societal challenges that require expeditious data and knowledge sharing. Though organizational clinical data are abundant, these are largely inaccessible to outside researchers. Statistical, machine learning, and causal analyses are most successful with large-scale data beyond what is available in any given organization. Here, we introduce the National COVID Cohort Collaborative (N3C), an open science community focused on analyzing patient-level data from many centers. MATERIALS AND METHODS: The Clinical and Translational Science Award Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level clinical data. We developed solutions to extract, aggregate, and harmonize data across organizations and data models, and created a secure data enclave to enable efficient, transparent, and reproducible collaborative analytics. RESULTS: Organized in inclusive workstreams, we created legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible COVID-19 cases; a data quality assurance and harmonization pipeline to create a single harmonized dataset; population of the secure data enclave with data, machine learning, and statistical analytics tools; dissemination mechanisms; and a synthetic data pilot to democratize data access. CONCLUSIONS: The N3C has demonstrated that a multisite collaborative learning health network can overcome barriers to rapidly build a scalable infrastructure incorporating multiorganizational clinical data for COVID-19 analytics. We expect this effort to save lives by enabling rapid collaboration among clinicians, researchers, and data scientists to identify treatments and specialized care and thereby reduce the immediate and long-term impacts of COVID-19

SCOR: A secure international informatics infrastructure to investigate COVID-19

Global pandemics call for large and diverse healthcare data to study various risk factors, treatment options, and disease progression patterns. Despite the enormous efforts of many large data consortium initiatives, scientific community still lacks a secure and privacy-preserving infrastructure to support auditable data sharing and facilitate automated and legally compliant federated analysis on an international scale. Existing health informatics systems do not incorporate the latest progress in modern security and federated machine learning algorithms, which are poised to offer solutions. An international group of passionate researchers came together with a joint mission to solve the problem with our finest models and tools. The SCOR Consortium has developed a ready-to-deploy secure infrastructure using world-class privacy and security technologies to reconcile the privacy/utility conflicts. We hope our effort will make a change and accelerate research in future pandemics with broad and diverse samples on an international scale

Computing Health Quality Measures Using Informatics for Integrating Biology and the Bedside

Abstract Background: The Health Quality Measures Format (HQMF) is a Health Level 7 (HL7) standard for expressing computable Clinical Quality Measures (CQMs). Creating tools to process HQMF queries in clinical databases will become increasingly important as the United States moves forward with its Health Information Technology Strategic Plan to Stages 2 and 3 of the Meaningful Use incentive program (MU2 and MU3). Informatics for Integrating Biology and the Bedside (i2b2) is one of the analytical databases used as part of the Office of the National Coordinator (ONC)'s Query Health platform to move toward this goal

Run manager module for Common Object Representation for Advanced Laboratories laboratory management

Thesis (M. Eng.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, June 2004.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.Includes bibliographical references (p. 101-102).This thesis describes a new module, the Run Manager (RM), for Stanford Nanofabrication Facility's Common Object Representation for Advanced Laboratories (CORAL). CORAL is the lab manager with which MIT's Microsystems Technology Laboratories hopes to replace its outmoded, fifteen-year-old lab manager. RM will be used to collect and store parameterized information about each step in the device fabrication process, which labs will use to automatically generate accounting, maintenance, and lot history reports. RM consists of an XML (Extensible Markup Language)- configurable Common Object Request Broker Architecture (CORBA) application server, database storage, and a Graphical User Interface (GUI) module which will be integrable with the existing CORAL Java client.by Jeffrey G. Klann.M.Eng

An intelligent listening framework for capturing encounter notes from a doctor-patient dialog

Background Capturing accurate and machine-interpretable primary data from clinical encounters is a challenging task, yet critical to the integrity of the practice of medicine. We explore the intriguing possibility that technology can help accurately capture structured data from the clinical encounter using a combination of automated speech recognition (ASR) systems and tools for extraction of clinical meaning from narrative medical text. Our goal is to produce a displayed evolving encounter note, visible and editable (using speech) during the encounter. Results This is very ambitious, and so far we have taken only the most preliminary steps. We report a simple proof-of-concept system and the design of the more comprehensive one we are building, discussing both the engineering design and challenges encountered. Without a formal evaluation, we were encouraged by our initial results. The proof-of-concept, despite a few false positives, correctly recognized the proper category of single-and multi-word phrases in uncorrected ASR output. The more comprehensive system captures and transcribes speech and stores alternative phrase interpretations in an XML-based format used by a text-engineering framework. It does not yet use the framework to perform the language processing present in the proof-of-concept. Conclusion The work here encouraged us that the goal is reachable, so we conclude with proposed next steps