We are moving toward our vision with a number of activities across our various programs. We have updated our strategic plan in response to the 10-year academic program review that we recently completed. For our research-oriented MS and PhD programs, we have recently added a specialization in Data Science. We are completing a curriculum revision for our on line applied clinical informatics MS which will be effective Fall 2020. The work of our fellows in the clinical informatics fellowship program has received plaudits from clinical administrators and faculty, and we are currently recruiting a new faculty member in our department to assist with this program (view position description). We are also recruiting a faculty member in medical education to start Summer 2020 (view position description). This is the beginning of a new cycle of admissions to our graduate programs, and we look forward to another productive year, and new growth in our department.
Peter Tarczy-Hornoch, MD
Chair and Professor, Department of Biomedical Informatics and Medical Education
Biomedical Informatics and Medical Education Newsletter
July 26-30, 2021
It is with regret that we announce that Adam Wilcox will be leaving the University of Washington to take on the role of Director of the Applied Clincal Informatics Institute at Washington University St. Louis starting August 27th. During his time at UW as a core BIME faculty member and as UW Medicine Chief Analytics Officer Adam has made many important contributions to UW in all aspects of the BIME mission (research, education, praxis and fiscal/other). Please congratulate Adam on this new opportunity. He wanted us to convey that while he is excited for this upcoming opportunity he will miss the members of the Department
Mike Leu was selected to participate in the development of the American Academy of Pediatrics’ (AAP) next clinical practice guideline, on “Failure to Thrive (Faltering Growth)”.
PUBLICATIONS AND PRESENTATIONS
Mark Phillips is presenting work on a national effort to establish an ontology for the domain of radiation oncology at the annual meeting of the American Association of Physicists in Medicine:
“Radiation Therapy Ontology: A report of the AAPM Working Group”, Mark Phillips, J Bona, A Dekker, P Gabriel, C Mayo.
Weinberg ST, Monsen C, Lehmann CU, Leu MG, Council on Clinical Information Technology. Policy Statement. Integrating Web Services / Applications to Improve Pediatric Functionalities in Electronic Health Records. Pediatrics. 2021 June 28; e2021052047. doi: 10.1542/peds.2021-052047. PMID: 34183360.
Leu MG, Weinberg ST, Monsen C, Lehmann CU. Technical Report: Web Services and Cloud Computing in Pediatric Care. Pediatrics. 2021 June 28; e2021052048. doi: 10.1542/peds.2021-052048. PMID: 34183361.
UPCOMING FINAL EXAMS
Thursday, August 12, 2021; 3:00 PM
Title: Improving Design and Usability of Interactive Vulnerability Mapping for Global Health Preparedness
Abstract: Global health preparedness –the ability of organizations and governments to anticipate risks and respond to disease outbreaks– presents both an imperative and a challenging opportunity for public health informatics interventions. Addressing risks of vector-borne and zoonotic disease (VBZD) outbreaks is especially complex as it involves the careful integration of human, animal, entomological, environmental, and infrastructure data. Presentation and understanding of those risks require usable tools and technology. Spatial Systems for Decision Support (SSDS) are a type of visualization tool that enable public health practitioners to make critical decisions informed by timely access to pertinent, analyzed data. In my dissertation research, I introduce a new type of SSDS, interactive vulnerability mapping tools, which can help decision makers in global health preparedness identify spatial areas that are at risk for VBZD outbreaks and have a lower capacity to contain spread. Decision makers include epidemiologists, public health planners, vector control specialists, and directors, who might use this information to allocate vaccine resources or plan intervention activities to high risk regions. Unfortunately, SDSS tools are not routinely developed using a human centered design (HCD) approach, and there is a lack of deliberate consideration of sociotechnical factors. In my doctoral research, I have applied principles of HCD and information visualization to design and evaluate the usability of interactive mapping tools for dengue vulnerability in Peru (Aim 1) and Rift Valley fever vulnerability in Kenya (Aim 2). To situate my Aim 1-2 findings in the literature, I conducted a scoping review of SDSS for VBZD preparedness (Aim 3) that describes data, users, technology, and use cases in published SDSS studies as well as gaps in the existing literature. This work contributes: 1) usable SDSS tools designed for public health decision makers in Peru and Kenya, 2) empirical data on the design, data visualization preferences, usability, and acceptance of SSDS for disease vulnerability in global health settings, and 3) a reproducible search of the literature on SDSS for VBZD that maps the current state of the literature, characterizes health informatics factors, and identifies opportunities for future research.
Committee: Drs. Andrea Hartzler (Chair), Uba Backonja, Nancy Puttkammer, Peter Rabinowitz, Christopher Adolph
Friday, August 20, 2021; 10:00 AM
Title: Assessing the fitness for use of real and synthetic electronic health record data for observational research
Abstract: Over the past decade, electronic health record (EHR) adoption has led to an explosion in the volume of Electronic health record and log data, then efforts to effectively harness the potential of these data for knowledge discovery (KD) and quality improvement (QI). In parallel, recent gains in artificial intelligence have produced powerful methods to analyze, use, and even create synthetic data. However, limitations in data utility (e.g. bias, data quality, comprehensiveness) and accessibility (e.g. privacy, interoperability, availability), as well as limited means to measure and manage tradeoffs between the two are significant barriers to using these data effectively. Determining whether data are suitable to be used in a specific analysis or context, known as “fitness for use” is not included in current frameworks for general health record data quality characterization nor evaluated by data quality assessment (DQA) tools. EHR log data use is particularly unrefined for QI and KD due to an absence of validated standards and methods. Thus, users of electronic health record and log data remain uninformed as to the fitness for use of their data at baseline and are unable to effectively assess subsequent tradeoffs between utility and privacy when applying preserving technologies.
First, we 1) developed a framework for data utility assessment of electronic health records, then 2) adapted open-source tools to make use of this framework which we then applied to assess the utility of real and synthetic EHR data for observational research related to COVID-19 and/or future influenza pandemics. Second, we evaluated whether synthetic data derived from a national COVID-19 data set could be used for geospatial and temporal epidemic analyses. To do so we conducted replication of studies and computed general summary statistics on original and synthetic data, then compared the similarity of results between the two datasets. Third, we conducted a retrospective, observational analysis – with and without privacy preserving technology – of clinical workstation authentication behaviors from the UW Medicine health system to inform customized solutions that balance usability and security.
Committee: Drs. Adam Wilcox (Chair), Gang Luo, Matthew Thomas Trunnell, Larry Kessler
July 12-16, 2021
Dr. Janice Sabin has been asked by Dean Ramsey to serve on a new task force to review existing practices for faculty search processes in the School of Medicine (SoM) that support equity, diversity, and inclusion in recruitment and to propose modifications and improvements to establish best practices in this area.
Dr. Janice Sabin has joined the guest editorial team for a special issue of Frontiers in Psychology, Title: “Implicit Social Cognition: malleability and change.” The team of guest editors also includes: Maddalena Marini, (Italian Institute of Technology, Italy), Brian O’Shea (University of Amsterdam, Netherlands), Michelangelo Vianello (Padua University, Italy), and Sarah Redfield (University of New Hampshire School of Law, USA). The special issue will give a multidisciplinary view of the topic, not only research but also ethical, legal, medical, and practical aspects.
Dr. Anne M. Turner has been asked to serve as a member of the NLM Extramural Program Biomedical Informatics, Library and Data Sciences Review Committee (BILDS) Committee. She will start this June as an ad hoc member and as a standing member (4-year term) starting in November 2021. This is a big honor recognizing Dr. Turner’s sustained research and leadership contributions over the years.
As Associate Direction of the CDC funded UW Health Promotion Research Center (UW HPRC), Dr. Turner will be participating in a CDC funded project focusing on COVID-19 access and hesitance in King County. The UW HPRC has received $500K in supplemental grant funding to support three projects funded under the award which focus on improved communication with limited English proficiency groups, fostering vaccine access to communities of color, and strengthening community partnerships. Additional information about the projects and the award can be found at Collaborating to Increase King County Vaccination Rates | Health Promotion Research Center (washington.edu).
PUBLICATIONS AND PRESENTATIONS
AMIA Paper presentation:
Older adults’ personal health information management: The role and perspective of various healthcare providers Alyssa L. Bosold, MPH, Shih-Yin Lin, PhD, Jean O. Taylor, PhD George Demiris, PhD, Anne M. Turner, MD, MLIS, MPH
SHARE-NW: An Innovative Public Health Informatics Tool. Uba Backonja, PhD, RN , Anne M. Turner, MD, MLIS, MPH , Betty Bekemeier, PhD, MPH, RN Northwest Center for Public Health Practice, University of Washington, Seattle, WA
Burkhardt H, Alexopoulos G, Pullmann M, Hull T, Areán P, Cohen T. Behavioral Activation and Depression Symptomatology: Longitudinal Assessment of Linguistic Indicators in Text-Based Therapy Sessions. J Med Internet Res 2021;23(7):e28244. http://dx.doi.org/10.2196/28244
Burkhardt HA, Alexopoulos GS, Pullmann MD, Hull TD, Areán PA, Cohen T. Linguistic indicators of Behavioral Activation in text-based therapy sessions anticipate changes in depression symptomatology. Podium abstract accepted for AMIA 2021.
June 21-June 25, 2021
PUBLICATIONS AND PRESENTATIONS
Sangameswaran S, Segal C, Rosenberg D, Casanova-Perez R, Cronkite D, Gore J, Hartzler AL. Design of digital walking programs that engage prostate cancer survivors: Needs and preferences from focus groups. Paper accepted for AMIA 2021.
Casanova-Perez R, Apodaca C, Bascom E, Mohanraj D, Lane C, Vidyarthi D, Beneteau E, Sabin J, Pratt W, Weibel N, Hartzler AL. Broken down by bias: Healthcare biases experienced by BIPOC and LGBTQ+ patients. Paper accepted for AMIA 2021.
Patel H. Henrikson NB, Ralston JD, Leppig K, Scrol A, Jarvik GP, DeVange S, Larson EB, Hartzler AL. Implementation matters: How patient experiences differ when genetic counseling accompanies the return of genetic variants of uncertain significance. Paper accepted for AMIA 2021.
Snyder L, Phan D, Connor SE, George S, Williams KC, Villatoro J, Saraf A, Kwan L, Reid N, Gore GL, Litwin MS, Hartzler AL. User Evaluation of Interactive Longitudinal PRO Visualizations Designed by Prostate Cancer Survivors with Limited Graph Literacy. Podium abstract accepted for AMIA 2021.
Reed N, Ramos KJ, Hobler MR, Bartlett LE, Kpanadak SG, Hartzler AL. Usability Study of a Decision Support Website to Support People Living with Cystic Fibrosis in Shared Decision Making about Lung Transplant. Poster accepted for AMIA 2021.
Rahmatullah I, Stephens KA, Cole AM, Hartzler AL. Primary Care Providers’ Needs for Usable Clinical Prediction Rule Presentations. Poster accepted for AMIA 2021.
UPCOMING FINAL EXAM
Wednesday, June 30, 2021; 3:00 PM
Title: Genetic Association to Adverse Drug Events in the eMERGE Pharmacogenomics Cohort
Abstract: Adverse drug events (ADEs) are a serious problem causing over 100,000 hospitalizations in the U.S. annually. One key component in the response to a drug is our genetic variation. Identifying and using genetic information to avoid ADEs is an already proven method that needs further expansion. The eMERGE PGx project collected electronic medical records (EMR) along with targeted DNA variant data in order to create a useful dataset for pharmacogenetic studies. In this research, an automated approach to identify potential adverse drug events (ADE) in the eMERGE PGx cohort is presented. Data from the EMR is examined through the lens of a database of known adverse drug events: the Drug Evidence Base. Diagnosis codes that were known to be adverse events and appeared in a participant’s medical record following a medication order were labeled as a potential ADE. These potential ADEs were used as phenotypes for genetic associations tests at the single variant, gene, and gene-set level. The results were two findings of two single variants, 10 genes and one gene set having a significant association with one more adverse drug events. These results add to the body of knowledge that continues to grow around variation in drug response.
Committee: David Crosslin-Chair, John Gennari, Gail Jarvik, Ali Shojaie
Ronald W. Buie has completed his Master of Public Health, Health Systems and Policy . His thesis is titled, “Provider Perspectives on the Coordination of Care for Spinal Cord Injured Veterans”. This work is an analysis of a year of interviews with clinical and administrative leaders revealing gaps between policy, infrastructure, and collaborations with non VHA services within the VHA’s Spinal Cord Injured System of Care. Ron continues to pursue is PhD in Biomedical and Health Informatics under Annie Chen.
June 14-June 18, 2021
PUBLICATIONS AND PRESENTATIONS
UW-BioNLP group AMIA 2021 – Accepted papers and posters
Lybarger K, Mabrey L, Thau M, Bhatraju PK, Wurfel M, Yetisgen M. Identifying ARDS using the Hierarchical Attention Network with Sentence Objectives Framework.
Lau W, Altonen L, Gunn, M, Yetisgen M. Automatic Assignment of Radiology Examination Protocols Using Pre-trained Language Models with Knowledge Distillation.
Lau W, Wayne D, Lewis S, Uzuner O, Gunn M, Yetisgen M. A New Corpus for Clinical Findings in Radiology Reports.
Lybarger K, Qiao E, Yetisgen M. An exploration of information extraction models on transcribed patient visits.
Chakraborty A, Lybarger K, Long D, Shah VO, Yetisgen M. Automatic Detection of Surgical Site Infections Using EHR data.
Turner GK, Yetisgen M. Comparison of Different Phrase Chunking Approaches on Medical Concept Coverage in Clinical Text.
Welsh C, Nickerson DP, Rampadarath A, Neal ML, Sauro HM and Gennari JH (2021). LibOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics, in press.
Blinov ML, Gennari JH, Karr JR, Moraru II, Nickerson DP, and Sauro HM (2021). Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology. Current Opinion in Systems Biology, in press.
Dr. Uba Backonja and Dr. Anne Turner will present a system demonstration on November 2nd at 8:30 (S53) showing SHARE-NW: Solutions in Health Analytics for Rural Equity across the Northwest, a user-centered designed website with dashboard and trainings to support rural public health equity (launching August 2021; https://www.nwcphp.org/research/projects/share-nw).
Dr. Uba Backonja and Dr. Janice Sabin are part of a team running a preconference workshop on re: bias in informatics that will be held October 30, 2021 from 1:00 PM to 4:30 PM.
Technology to Support Collaborative Dissemination of Research with Alaska Native Communities by Lisa Dirks and Wanda Pratt
Broken down by bias: Healthcare biases experienced by BIPOC and LGBTQ+ patients by Reggie Casanova-Perez, Calvin Apodaca, Emily Bascom, Deepthi Mohanraj, Cezanne Lane, Drishti Vidyarthi, Erin Beneteau, Janice Sabin, Wanda Pratt, Nadir Weibel, and Andrea Hartzler
Children’s Designs for the Future of Telehealth by Erin Beneteau, Ann Paradiso, and Wanda Pratt
June 7-June 11, 2021
Sarah Stansfield, NLM Postdoctoral Fellow has accepted a new position as Postdoctoral Research Fellow in Mathematical Modeling at the Fred Hutch, in their Vaccine and Infectious Disease Division, working with Dr. Dobromir Dimitrov. She will begin her new position Monday, June 14, 2021.
Meliha Yetisgen & Martin Gunn’s NCI funded R01 on large scale clinical and economic impact analysis of incidental findings in radiology reports was on UW Medicine – Newsroom:
Meliha Yetisgen received funding for her new project titled “Extraction of Symptom Burden from Clinical Narratives of Cancer Patients using Natural Language Processing” from NCI.
PUBLICATIONS AND PRESENTATIONS
X. Zhang, G. Luo. Ranking Rule-Based Automatic Explanations for Machine Learning Predictions on Asthma Hospital Encounters in Asthma Patients: Secondary Analysis. JMIR Medical Informatics, 2021.
Korngiebel DM, Mooney SD. Considering the possibilities and pitfalls of Generative Pre-trained Transformer 3 (GPT-3) in healthcare delivery. NPJ Digit Med. 2021 Jun 3;4(1):93. doi: 10.1038/s41746-021-00464-x. PMID: 34083689; PMCID: PMC8175735.
Dr. Thomas Payne, Professor, UW Department of Medicine; Adjunct Professor, Biomedical Informatics and Medical Education
“We have the means to prevent cancer and to detect it early. But we’re not fully using the resources we have.”
May 31-June 4, 2021
Andrea Hartzler was elected to serve a 3-year term on the Council of Academic Affairs for the UW School of Medicine.
The following faculty or staff (PI or collaborator) received a Garvey Institute for Brain Health Solutions Innovation Grant:
Biomedical Informatics and Medical Education
Trevor Cohen, MBChB, PhD, FACMI
Sean Mooney, PhD, FACMI
Andrea Hartzler, PhD
Bill Lober, MD, MS
The following BHI Students contributed to the publications:
List of projects and descriptions: https://gibhs.psychiatry.uw.edu/current-projects/
UW Medicine News Link: https://newsroom.uw.edu/news/garvey-institute-gives-13-million-advance-brain-health
PUBLICATIONS AND PRESENTATIONS
Augmenting aer2vec: Enriching Distributed Representations of Adverse Event Report Data with Orthographic and Lexical Information, Xiruo Ding, Justin Mower, Devika Subramanian, and Trevor Cohen. Accepted: JBI
Behavioral Activation and Depression Symptomatology: Longitudinal Assessment of Linguistic Indicators in Text-based Therapy Sessions, Hannah A Burkhardt, George S Alexopoulos, Michael D Pullmann; Thomas D Hull; Patricia A Areán, Trevor Cohen. Accepted: JMIR.
UW Undergraduate Research Symposium presentations (5/21/2021):
Fields, S., and Oei, C. Automatically identifying people and exploring social relations in the Svoboda Diaries. (Mentored by Dr. Annie Chen.)
Hallinan, S., Buie, R. W., Conway, M., Chen, A. T., Park, A. Understanding the public response to the coronavirus pandemic through topic modeling.
Chen, A. T. (accepted). Affect, cognition, and information behavior in the context of fibromyalgia. Journal of the Association for Information Science and Technology.
Du, J., Yuen, C., Slaughter, M., Chen, A. T. (accepted). The influence of familiarity with digital tools on user experience and perspective in the digital humanities. Annual meeting of the Association for Information Science and Technology (ASIS&T) 2021. October 30 – November 2, 2021.
Valdez, R., Chen, A. T., Hampton, A. J., Madathil, K. C., Papautsky, E. L., Rogers, C. C. (accepted). Leveraging Social Media for Human Factors Research in Health Care. Panel presentation at Human Factors and Ergonomics Society Annual Meeting (HFESAM) 2021. October 4-7, 2021. Baltimore, MD.
Chen, A. T., Cole, C., Fields, S., Perkins, A., Oei, C., Kuru, S. S. (2021). Introduction to network analysis for literary and historical research. Tutorial presented at Canadian Society for Digital Humanities/société canadienne des humanités numériques (CSDH/SCHN) 2021. May 30 – June 3, 2021.
language processing (NLP) methods to create novel measures of expressed emotional experience and mentalizing from transcribed speech responses of two streaming-based tasks. Furthermore, we propose to use these measures to evaluate the effectiveness of oxytocin for the abstraction of an overall pipeline for precision psychiatry. We believe the creation of this methodology will allow for a new approach to the diagnosis, monitoring, and treatment of people with schizophrenia that may be generalizable to other mental health issues.
to elucidate confounders for EHR-based pharmacovigilance, Journal of Biomedical Informatics, Volume 117, 2021