Chair’s Message
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.
Cordially,
Peter Tarczy-Hornoch, MD
Chair and Professor, Department of Biomedical Informatics and Medical Education
Biomedical Informatics and Medical Education Newsletter
October 26-October 30, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursday, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/92138508055
November 5, 2020:
Speaker: Brian Piening, PhD
Title: Molecular Tracking of SARS-CoV-2 in Oregon and Beyond
Abstract: Until the availability of a vaccine against SARS-CoV-2, molecular diagnostics represent some of our most effective tools in the COVID-19 pandemic. Here I will discuss work from our group in launching rapid diagnostics, SARS-CoV-2 genome sequencing and large-scale COVID-19 serological testing in the Providence Health System. These efforts have revealed a wealth of data regarding the molecular trajectories of SARS-CoV-2 in Oregon and I will discuss ongoing efforts linking SARS-CoV-2 molecular information with electronic health record data to better predict outcomes.
Speaker Bio: : Brian Piening, PhD is technical director for clinical genomics in the Providence Molecular Genomics Laboratory, which provides clinical genomics testing across the multi-state nonprofit Providence/Swedish Health Network. Dr. Piening is also research faculty at the Providence Cancer Institute in Portland, OR and his research laboratory utilizes multi-omic and computational methods to develop predictive and prognostic biomarkers associated with cancer immunotherapeutics. Dr. Piening performed his PhD training in Molecular and Cellular Biology at UW and Fred Hutch and his postdoctoral training in the department of genetics at Stanford University. He has recently contributed to several large multi-omic studies including the NIH Human Microbiome Project and the NASA Twins Study.
BIME 591B – Reproducibility in Research
Tuesdays, 11:30-12:20
Facilitators: Hannah Burkhardt, Jake Portanova (BHI PhD Students) with Trevor Cohen (faculty sponsor)
October 19-October 23, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursday, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/92138508055
October 29: Speaker: Jason Moore, PhD, University of Pennsylvania
Title: Accessible Artificial Intelligence for Data Science
Abstract: Artificial intelligence (AI) has finally emerged as a useful tool for big data analytics. This is due to decades of research that have provided powerful algorithms and the availability of plentiful computing resources. Despite these advances, AI is not widely accessible due to a steep learning curve and the expense and black box nature of software provided by commercial vendors. In response to this need, we have developed an accessible, open-source, and user-friendly AI system at the University of Pennsylvania (PennAI) to bring AI and automated machine learning technology to everyone who wants to incorporate this technology into their big data analytics agenda.
Speaker Bio: Jason Moore is the Edward Rose Professor of Informatics and Director of the Penn Institute for Biomedical Informatics. He also serves as Senior Associate Dean for Informatics and Chief of the Division of Informatics in the Department of Biostatistics, Epidemiology, and Informatics. He came to Penn in 2015 from Dartmouth where he was Director of the Institute for Quantitative Biomedical Sciences. Prior to Dartmouth he served as Director of the Advanced Computing Center for Research and Education at Vanderbilt University where he launched their first high-performance computer. He has a Ph.D. in Human Genetics and an M.S. in Applied Statistics from the University of Michigan. He leads an active NIH-funded research program focused on the development of artificial intelligence and machine learning algorithms for the analysis of complex biomedical data. He is an elected fellow of the American Association for the Advancement of Science (AAAS), an elected fellow of the American College of Medical Informatics (ACMI), and an elected fellow of the American Statistical Association (ASA). He serves as Editor-in-Chief of the journal BioData Mining.
BIME 591B – Reproducibility in Research
Tuesdays, 11:30-12:20
Facilitators: Hannah Burkhardt, Jake Portanova (BHI PhD Students) with Trevor Cohen (faculty sponsor)
PUBLICATIONS
Shefali Haldar, Yoojung Kim, Sonali R. Mishra, Andrea L. Hartzler, Ari H Pollack, and Wanda Pratt. 2020. The Patient Advice System: A Technology Probe Study to Enable Peer Support in the Hospital. Proc. ACM Hum.-Comput. Interact. 4, CSCW2, Article 112 (October 2020). https://doi.org/10.1145/3415183
Lauren Snyder, Ayan Anandkumar Saraf, Regina Casanova-Perez, Sarah E. Connor, Sheba George, Amelia Wang, Darwin Jones, Georgina Mendoza, John Gore, Mark S. Litwin and Andrea Hartzler. Visualization Co-Design with Prostate Cancer Survivors who have Limited Graph Literacy. Accepted for VAHC 2020.
Regina Casanova-Perez, Calvin Apodaca, Cezanne Lane, Drishti Vidyarthi, Erin Beneteau, Steven R. Rick, Colleen Emmenegger, Cindy Schairer, Janice Sabin, Wanda Pratt, Nadir Weibel, Andrea L Hartzler. Patients’ perspectives on implicit bias in clinical interactions with healthcare providers. Poster presentation at Workshop on Interactive Systems in Healthcare (WISH) 2020.
Steven R. Rick, Colleen Emmenegger, Cynthia E. Schairer, Alex Andreiu, Sam Fleet, Kimberly Sladek, James Ricketts, Calvin Apodaca, Regina Casanova-Perez, Cezanne Lane, Erin Beneteau, Drishti Vidyarthi, Janice Sabin, Wanda Pratt, Andrea Hartzler, Nadir Weibel. Seeing Beyond Patient-Centeredness: Searching for a Signal of Bias and Empathy in Patient-Provider Interaction. Poster presentation at Workshop on Interactive Systems in Healthcare (WISH) 2020.
Luo, C.L. Nau, W.W. Crawford, M. Schatz, R.S. Zeiger, E. Rozema, and C. Koebnick. Developing a Predictive Model for Asthma-Related Hospital Encounters in Patients with Asthma in a Large Integrated Healthcare System: Secondary Analysis. JMIR Medical Informatics, 2020
Tong, A.I. Messinger, and G. Luo. Testing the Generalizability of an Automated Method for Explaining Machine Learning Predictions on Asthma Patients’ Asthma Hospital Visits to an Academic Healthcare System. IEEE Access, 2020.
Adam Wilcox: article that came out of an interview with The Verge:
NEWS
UW jumps two spots to No. 8 in US News Best Global Universities ranking
The University of Washington moved up two spots to No. 8 on the U.S. News & World Report’s Best Global Universities rankings, released Tuesday. The UW maintained its No. 2 ranking among U.S. public institutions. In addition, 10 subjects at the UW are ranked in the top 10 in the world, including infectious diseases (No. 6), immunology (No. 6) and social sciences and public health (No. 7) — all fields that are playing critical roles in the COVID-19 pandemic response.
https://www.washington.edu/news/
October 12-October 16, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursday, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/92138508055
October 22: Speaker: TBD
BIME 591B – Reproducibility in Research
Tuesdays, 11:30-12:20
Facilitators: Hannah Burkhardt, Jake Portanova (BHI PhD Students) with Trevor Cohen (faculty sponsor)
OTHER
The UW School of Medicine AI Seminars
We are excited to announce the first AI in Medicine Seminar featuring Prof. Sean Mooney with an introduction by School of Medicine Dean and UW Medicine CEO Dr. Paul Ramsey and Biomedical Informatics and Medical Education Chair, Peter Tarczy-Hornoch. Please register at this link.
The meeting will be held on Zoom: October 19th, Monday at 1:00-2:30pm; https://uw-phi.zoom.us/j/91367210948
October 5-October 9, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursday, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/92138508055
October 15: Speaker: TBD
BIME 591B – Reproducibility in Research
Tuesdays, 11:30-12:20: Zoom: https://washington.zoom.us/j/98333515649
Facilitators: Hannah Burkhardt, Jake Portanova (BHI PhD Students) with Trevor Cohen (faculty sponsor)
Guest Speaker 10/13/2020: Dr. Ariel Rokem from the eScience reproducibility in science group
OTHER
The UW School of Medicine AI Seminars
We are excited to announce the first AI in Medicine Seminar featuring Prof. Sean Mooney with an introduction by School of Medicine Dean and UW Medicine CEO Dr. Paul Ramsey and Biomedical Informatics and Medical Education Chair, Peter Tarczy-Hornoch. Please register at this link.
The meeting will be held on Zoom: October 19th, Monday at 1:00-2:30pm; https://uw-phi.zoom.us/j/91367210948
September 28-October 2, 2020
PUBLICATIONS
Choi, Y.K., Demiris, G., & Thompson, H.J. (in press). Use of an Internet-of-Things smart home system for healthy aging of older adults in their residential setting: A feasibility study. JMIR Aging.
Choi, Y.K., Thompson, H.J. & Demiris, G. (in press). Internet-of-Things (IoT) smart home technology to support aging-in-place: older adults’ perceptions and attitudes. Journal of Gerontological Nursing.
OTHER
Microsoft is hiring interns for next summer. The job description is posted here:
It is a rather generic job posting for all of Microsoft, but the Healtcare NeXT team, has internship openings. We work on building an open source FHIR server, DICOM server and related tools. We are part of Microsoft Research which allows for some fun activities during the summer and exposure to other research teams.
If anyone is interested, they can reach out to Jared Erwin, erwinj@uw.edu, but will also need to apply online using the link above. You can mention the Healthcare NeXT team, and the hiring manager is Joyce Cunningham.
September 21-September 25, 2020
NEWS
A message from Paul Ramsey, MD: After 10 years of serving as Associate Dean for Curriculum Dr. Michael Ryan is stepping down from his role effective 9/16/20. He recently moved from Seattle to Spokane where he has continued his outstanding work. I am pleased to report that Dr. Ryan will continue working with the curriculum team making additional improvements and changes to the curriculum starting with the 2022-23 academic year. Dr. Mark Whipple, assistant to the dean for clinical education, has agreed to serve as the acting associate dean for curriculum. In the near future, I will announce the search process for a permanent associate dean for curriculum. Please join me in thanking Dr. Ryan for his superb contributions and remarkable vision.
Trevor Cohen MBChB, PhD, received a Notification of Award for from the National Institute on Aging indicating the award of a $442 K grant to develop novel approaches to quantify the coherence of language produced by patients with Dementia of the Alzheimer’s Type, in order to facilitate the study of fluctuations in lucidity over time that have been observed in this condition. The award is for is a multi-PI grant with Serguei Pakhomov, PhD at the University of Minnesota and Trevor as the two PIs.
Project Description: The focus of the proposed project is to enable automated detection and analysis of episodes of unexpected lucidity in individuals with late-stage dementia in which the individual long thought to have succumbed to dementia and lost most of his or her cognitive abilities temporarily regains the ability to communicate in a clear and coherent fashion. The very low frequency and unexpected nature of these episodes make it challenging to capture objective evidence in the form of audio or video recordings of these events needed to enable systematic and comprehensive investigations. Thus, it is necessary to develop technological solutions for automated linguistic analysis that can be used for long-term continuous monitoring of individuals in late stages of dementia. In this feasibility project, we will develop technology to address two challenging issues: a) accurate conversion of continuous speech to text, and b) automated analysis of the text to measure the degree of coherence.
Dr. Anne Turner, Dr. Uba Backonja, and fellow investigators were awarded supplemental funding by the Health and Human Services Office of Minority Health to integrate data and training on COVID-19 and related social determinants of health into their project, SHARE-NW: Solutions in Health Analytics for Rural Equity across the Northwest.
Casey Overby Taylor, PhD, received one of the NIH/NHGRI-funded Genomic Innovator Awards this year.
It will provide some funding for Casey and team members over the next 5 years to study genomic clinical decision support.
The story from Hopkins BME is here: https://www.bme.jhu.edu/news-events/news/casey-overby-taylor-earns-genomic-innovator-award/
OTHER
Houda Benlhabib, PhD, announced the birth of her baby girl “Noor” born on 09/20/2020: 8 pounds and 1.7 oz, mom and baby are healthy.
September 14-September 18, 2020
PUBLICATIONS AND PRESENTATIONS
Thomas H Payne, Lue Ping Zhao, Calvin Le, Peter Wilcox, Troy Yi, Jesse Hinshaw, Duncan Hussey, Alex Kostrinsky-Thomas, Malika Hale, John Brimm, Fuki M Hisama. Electronic health records contain dispersed risk factor information that could be used to prevent breast and ovarian cancer. Journal of the American Medical Informatics Association, ocaa152, https://doi.org/10.1093/jamia/ocaa152
Fox S, Menking A, Eschler J, Backonja U. Modules Over Models: Participatory Explorations of the Menstrual Tracking Application. ToCHI special issue on Special Issue on HCI and the Body: Reimagining Women’s Health). 2020; 27(4): article 22. https://doi.org/10.1145/3397178
OTHER
We are growing the Informatics team at DOH (Shoreline) Please consider joining us and helping in the COVID response.
Bryant Thomas Karras M.D.
Chief Informatics Officer
Office of the State Health Officer/Chief Science Officer
Washington State Department of Health
bryant.karras@doh.wa.gov
Here are the direct links and blurbs:
Informatics Specialist (all levels)
Public Health Informatics Specialist (Epidemiologist) positions will support development, maintenance, operation, enhancement, and configuration of data systems and informatics capabilities to address the needs of the Department of Health and in service to the 35 Local Health Jurisdictions, 29 federally-recognized Tribes, and other public health and healthcare sector partners across Washington State. These include laboratory and case reporting, systems which support case management and case and contact investigation, and other critical informatics and data science capabilities that support all aspects of the COVID-19 response in Washington State.
https://www.governmentjobs.com/careers/washington/doh/jobs/2855022
Informatics System Support Supervisor WMS1:
COVID-19 Informatics Systems Support Unit Lead will support priority capacity in COVID-19 response by serving as the Systems Support Unit Supervisor. The Systems Support Unit supports the ongoing surveillance system design, development, and integration tasks. This position leads teams charged with maintaining and operating key data systems and capabilities, and leading process improvements and system enhancements for state-led surveillance applications. They are responsible for a staff of eleven (11) professionals and will coordinate with private and public sector partners to expand surveillance capacity within the state.
https://www.governmentjobs.com/careers/washington/doh/jobs/2861017
RHINO Program Manager WMS1:
Rapid Health Information NetwOrk (RHINO) Program Manager is the program manager for the Rapid Health Information NetwOrk (RHINO) program, Washington state’s syndromic surveillance program. This position has the authority to act on behalf of the agency to public and elected officials, media, and others, regarding issues of high visibility or sensitivity. The RHINO Program Manager will conduct supervisory activities, and coordinate public health surveillance activities for syndromic surveillance, for communicable diseases and non-communicable conditions. This position is directly responsible for supervising professional-level staff responsible for meeting federal grant deliverables around developing, sustaining, and enhancing Washington’s syndromic surveillance capacity. The RHINO Program Manager will coordinate efforts with cross-agency workgroups and other key stakeholders to ensure robust data systems are in place to address syndromic surveillance needs throughout the Department of Health and in service to Local Health Jurisdictions and Tribal health authorities.
https://www.governmentjobs.com/careers/washington/doh/jobs/2860963
August 31-September 4, 2020
NEWS
2020 UW FHIR® Conference
Data > Information > Evidence > Knowledge through FHIR
September 11 – 12, 2020 (Friday & Saturday)
The current times have brought unexpected shifts in what we do, where and how we work, and how health systems and public health operate and interact. This complex time offers a unique opportunity to explore how FHIR can support the changes all around us. The 2020 UW FHIR Conference builds on innovations and collaborations that are working to expand public health, health systems, and research use of FHIR, and will address topics including:
- Rapid interoperability during the COVID-19 pandemic
- Public health disease surveillance and reporting
- Implementing Clinical Decision Support
- Access to care and health equity
During a half day of tutorials, and a day of talks, we will bring together a broad audience of faculty, staff, students, administrators, and software developers from clinical, research, and public health disciplines. Participants will learn about the healthcare standard FHIR (Fast Health Interoperability Resources), the related technologies of SMART and CDS Hooks, and their use in health informatics applications supporting clinical care, research, and public health practice.
The 2020 conference will be innovative and dynamic, with all sessions carried out virtually. Friday, September 11 will feature a half day of hands-on learning opportunities through workshops and tutorials. Saturday, September 12 will feature keynotes, panels, and opportunities for direct participation and discussion. Registration is free and open to all.
https://uwfhir.org/workshops/2020/
The conference is organized and sponsored by the University of Washington Clinical Health Informatics Group (CIRG) and Institute for Translational Health Science (ITHS), in collaboration with the Washington State Department of Health.
PUBLICATIONS AND PRESENTATIONS
W. Zhou, G. Luo. Parameter Sensitivity Analysis for the Progressive Sampling-Based Bayesian Optimization Method for Automated Machine Learning Model Selection. Proc. 2020 International Workshop on Data Management and Analytics for Medicine and Healthcare, 15 pages
OTHER
Study Participation Opportunity
The Disruptions to Laboratory Life (DLL) study at UCSF is investigating the ways in which laboratory life has shifted in the wake of COVID-19. We would like to interview you to learn more about your experiences since the outbreak of the COVID-19 pandemic, particularly those related to your laboratory-based research and responsibilities. We want to understand how COVID-19 has impacted your work and laboratory dynamics, and to get your reflections on these changes. This study is being conducted by researchers at UCSF in the Department of Social and Behavioral Sciences.
Participation in this study is voluntary. Participation in the study entails two (2) interviews and the completion of a brief questionnaire (during the first interview). Each interview will last about 45-60 minutes. If you choose to participate in this study, you will be provided with a $25 gift card for your participation, following the completion of your follow-up interview.
Read More: https://www.meljeske.com/dll-study/
August 24-28, 2020
PUBLICATIONS AND PRESENTATIONS
Lin, S-Y., Thompson, H.J., Hart, L., Fu, M., & Demiris, G. (in press). Evaluation of pharmaceutical pictograms by older “Turkers”: A cross-sectional crowdsourced study. Research in Social and Administrative Pharmacy.
Epub ahead of print: https://doi.org/10.1016/j.sapharm.2020.08.006
Phuong J, Bandaragoda CJ, Haldar S, Stephens KA, Ordonez P, Mooney SD, Hartzler AL. Information needs and priority use-cases of population health researchers to improve preparedness for future hurricanes and floods. Accepted: Journal of the American Medical Informatics Association.
August 17-21, 2020
NEWS
Mike Leu was invited to serve on the UW Graduate Medical Education Committee for the 2020-2021 academic year, which is responsible for overseeing the ACGME-accreditation of UW and its accredited training programs.
Janice Sabin received funding for two research projects: Center for Health Workforce Studies. HRSA 2020-2022, U81 HP32114: Cooperative Agreement for a Regional Center for Health Workforce Studies: Health Equity, Frogner, B. PI
Lasting Effects of Continuing Education on the Topic of Implicit Bias in the Clinical and Learning Environment
Lead: Janice Sabin, PhD, MSW
Exploring Health Workforce Influence on Equitable Care Delivery and Stigmatization toward COVID-19 Positive People of Color and People with Disabilities
Co-leads: Danbi Lee, PhD, OTD, OTR/L, Janice Sabin, PhD, MSW
August 10-14, 2020
NEWS
Andrea Hartzler, and co-Investigators Abhi Pratap (Sage Bionetworks), Sean Mooney, and Cynthia Chen (Engineering) received an NSF grant from the Smart and Connected Communities program: ”Building capacity for data-driven physical activity interventions in communities with depression and obesity hotspots”. This project combines EHR data analytics with community engagement to co-design tailored lifestyle interventions with communities in need.
NBC Today Show: Janice Sabin, July 27, 2020
https://www.today.com/health/implicit-bias-medicine-how-it-hurts-black-women-t187866
Janice Sabin: UW Radiology Grand Rounds, August 10, 2020, Title: Radiology Virtual Grand Rounds Lecture: “Implicit Bias in the Clinical and Learning Environment: The Implicit Revolution”
The BHI first year Clinical Informatics Fellows, Jeehoon Jang, Zach Liao, and Sarah Stewart all took the accelerated physician builder class and all of them are now certified physician builders!
PUBLICATIONS AND PRESENTATIONS
Benson, R., Hu, M., Chen, A. T., Nag, S., Zhu, S.-H., Conway, M. (accepted). Investigating the attitudes of adolescents and young adults towards JUUL: A computational study using Twitter data. JMIR Public Health and Surveillance.
August 3-7, 2020
NEWS
Reza Sadeghian MD, MBA, MSc, FAAP, Attending Physician- Department of Pediatrics, Arrowhead Regional Medical Center has been named Chief Medical Information Officer.
https://en.calameo.com/read/0061675719ee3ddf6d7ef
PUBLICATIONS AND PRESENTATIONS
Chen, A. T., Ge, S., Cho, S., Teng, A. K., Chu, F., Demiris, G., Zaslavsky, O. (accepted). Reactions to COVID-19, information and technology use, and social connectedness among older adults with pre-frailty and frailty. Geriatric Nursing.
Bowen, J., Klaich, A., Chen, A. T., Rockhill, C. (accepted). The PEACE Project: Emotional dysregulation, depression, and functional impairment at baseline and 6 month follow-up in youth admitted to an inpatient psychiatric unit for aggression or depression. Poster to be presented at American Academy of Child & Adolescent Psychiatry 67th Annual Meeting (virtual due to COVID-19).
UPCOMING GENERAL EXAM
Wilson Lau
Monday, August 17; 1:00 PM; Zoom: https://washington.zoom.us/j/99052030074
Title: Clinical Finding Extraction from Radiology Reports
Abstract: Radiology reports in electronic health record systems provide valuable opportunities for biomedical research on both individual level and population level. They are the principal means of communication and documentation for diagnostic imaging results. Because they exist as free-text narratives, important clinical information described in the reports, such as findings, are not readily retrievable for secondary use applications. Information Extraction (IE) methods provide opportunities to automatically extract structured information from natural human languages and potentially generate insights to biomedical research questions. The goal of this dissertation is to develop deep learning based IE approaches to extract findings reported by radiologists in radiology reports. To ensure the generalizability of the proposed approaches, radiology reports from four hospitals within University of Washington medical system (University of Washington Medical Center (UWMC), Harborview Medical Center (HMC), Seattle Cancer Care Alliance (SCCA), and Northwest Hospital and Medical Center (NWMC)) and from Beth Israel Deaconess Medical Center (MIMIC-III dataset) will be included in the research dataset. Aim 1. Creating a gold standard dataset annotated with findings: In this aim, I will focus on creating the gold standard corpus for training and testing the machine learning models to extract findings in radiology reports. First, I will create a detailed representation of findings with frame semantics. Based on this representation, I will create a detailed annotation guideline that describes the extraction task. To ensure maximum gain by the models and minimum annotation effort by annotators, active learning will be used during the annotation process. Aim 2. Developing deep-learning based IE approaches to extract findings from radiology reports: In this aim, I will implement deep-learning based IE approaches to extract findings from radiology reports. Each finding frame will be defined with a trigger and multiple attributes. Each attribute is linked to the frame trigger with a specific relation. I will first train state-of-the-art named-entity recognition (attribute and trigger extraction) and relation extraction models as baselines. To improve the baselines, I will then experiment with various deep learning approaches, including character / word / deep contextualized embeddings and pre-trained language models to identify the best architecture for each frame and relation extraction task. Frames that describe the same findings will be merged using co-reference resolution approaches.
Expected outcomes: At the conclusion of this dissertation, we will have (1) a detailed frame representation of imaging test findings with rich semantics; (2) a gold standard corpus annotated with an active learning approach which will facilitate the creation of quality frame representation; (3) high performance open-source NLP methods for automatically identifying information from radiology reports.
July 27-July 31, 2020
NEWS
Professor Wanda Pratt has been appointed Acting Associate Dean for Diversity, Equity, and Inclusion for the Information School.
New Electronic Patient-Reported Outcomes Toolkit Available:
Danielle Lavallee, PharmD, PhD, Cynthia LeRouge, MS, PhD, Elizabeth Austin, MPH, Andrea Hartzler, PhD, Joseph Heim, PhD, William Lober, MD, Jenney Lee, MA, Savitha Sangameswaran, MS, Courtney Segal, PhD(c)
A new toolkit funded by AHRQ’s Digital Healthcare Research Program is available to help healthcare systems integrate electronic patient-reported outcomes (ePROs) into care delivery.
http://epros.becertain.org/introduction/project-background/about-the-team
PUBLICATIONS AND PRESENTATIONS
Erin Beneteau, Shefali Haldar, Sonali Mishra, Wanda Pratt. “Eavesdropping: An Information Source for Inpatients.” Computers, Informatics, Nursing (CIN) 2020 Jun 18. doi:
10.1097/CIN.0000000000000640. Online ahead of print.
Desai AD, Wang G, Wignall J, Kinard D, Singh V, Adams S, Pratt W. “User-Centered Design of a Longitudinal Care Plan for Children with Medical Complexity.” Journal of American Medical Informatics Association. (in press)
OTHER
Noah Benson, PhD, BHI Alumni, has rejoined the UW as a senior data scientist in the eScience department.
https://escience.washington.edu/people/noah-benson/
July 20-July 24, 2020
PUBLICATIONS AND PRESENTATIONS
Kneeman, S. Battalio, A. Korpak, D.C. Cherkin, G. Luo, S.D. Rundell, and P. Suri. Predicting Persistent Disabling Low Back Pain in Veterans Affairs Primary Care Using the STarT Back Tool. PM&R: The journal of injury, function and rehabilitation, 2020
Sean Mikles’ paper has been accepted for presentation at AMIA and publication in the 2020 AMIA Annual Proceedings:
Title: Why Should I Trust You? Supporting the Sharing of Health Data in the Interprofessional Space of Child Development. Authors: Mikles, SP, Snyder, LE, Kientz, JA, and Turner, AM
Recruiting older adult participants through crowdsourcing platforms: Mechanical Turk versus Prolific Academic has been accepted for presentation and publication for the 2020 AMIA Annual Proceeding. Authors: Turner, AM, Engelsma, T, Taylor, JO, Sharma, RK, Demiris, G.
OTHER
Research Assistantship opportunity:
The Clinical Sequencing Evidence-Generating Research Consortium (CSER) is seeking an RA to work with the CSER Coordinating Center. This position will offer a full year of funding starting in August 2020, with a high likelihood of a second year of funding through August 2022. If you are interested in this position, please contact Kathleen Muenzen (kmuenzen@uw.edu) for details.
Call for Abstracts
TechQuity Volume: Call for Abstracts
IBM, Brigham and Women’s Hospital (BWH), and Vanderbilt University Medical Center (VUMC) invite you to submit abstracts for papers to be included in a supplemental issue of the Journal of Health Care for the Poor and Underserved (JHCPU). This issue will focus on what has been termed “TechQuity”, or the consideration, design, development, and implementation of technology solutions that promote, assure and potentially enhance health equity.
The deadline for submission of abstracts is midnight Pacific time on August 20, 2020.
All abstracts should be submitted through REDCap using this link: https://urldefense.com/v3/__https://redcap.vanderbilt.edu/surveys/?s=ED79938LRH__;!!BZ50a36bapWJ!8OgCX71HpHYjqg9H5GDRb8if6jIDucvrVwZl_dadwWeQ8ErjiU1Skoh012lOVg$
The purpose of the supplemental issue is to describe how technology can transform health, public health, and healthcare to promote health equity (aka, “TechQuity”).
Process: Submitted abstracts will be scored by the sponsoring organizations. Of those received, no more than 50 will result in an invitation to submit completed papers to the Journal. Invited papers need to be submitted no later than October 15, 2020 for consideration. We anticipate accepting approximately 20 of the submitted papers to be published.
Criteria: Abstracts will be scored on the following criteria:
- Relevance for underserved populations
- Relevance to the topics suggested by the overview below
- Quality of research
- Implications for techquity research or its application
- New insights for techquity research or its application
- Clarity and completeness of abstract
- Evidence that the authors are knowledgeable about existing scholarship on the topic they address
Overview of Issue:
The topics we hope to see addressed in submitted abstracts include the following:
- The design and use of technology to promote and assure health equity (aka, “TechQuity”).
- People of technology, health, public health, and healthcare (e.g., Workforce Diversity)
- Data (e.g., data collection, data integration, data diversity)
- Design and/or usability considerations for non-majority populations
- Analytics (i.e., equity dashboards, racism/discrimination measures, etc.)
- Artificial intelligence (e.g., transparent, ethical, and equitable AI; reducing bias/racism through humans + AI solutions)
- System issues (e.g., structural racism, stress/psychosocial factors, and their impact on health, public health, and healthcare delivery and workforce)
- We invite authors with relevant work to submit abstracts. Achieving health equity through technology requires the use of interdisciplinary methods, stakeholders, data, and policies.
Editorial requirements:
Abstracts must be in English, no more than 250 words long, and sufficiently detailed for the scorers to evaluate the proposed paper in a fully informed way.
The authors should include, in addition to the abstract, a list of no fewer than five key words or phrases important for the proposed paper. For more information on the types of papers JHCPU accepts, please click the link below to view the author guidelines.
The authors must also include a cover letter, in which they supply the names, degrees, and affiliations of the authors, as well as any information they think it is important for the Guest Editors to know.
Population Parameters
To develop a topic, choosing among (or combining several of) the following population parameters may prove helpful. While the supplement will be organized in terms of race/ethnicity, we also welcome work that — while including information about race/ethnicity — also bear on other characteristics of underserved populations, including sexual orientation [LGBTQIA], mental health and cognitive development, disability, and others. Work framing identities in terms of intersectionality are welcome, but this approach is not required.
Race/ethnicity
African American (or Black)
Latino (or Hispanic) broken down by subgroups Non-Hispanic White (or White) American Indian/Alaska Native, broken down by subgroups Pacific Islander, broken down by subgroups Asian Americans, broken down by subgroups Multi-ethnic perspectives Age groups Children (pre-school, school age, or combined) Adolescents Adults Reproductive-aged women (including pregnancy, post-partum, gestational influences, and infancy) Elderly Other demographic characteristics Geographic regions Urban areas Rural areas Groups with low socioeconomic status
July 13-July 17, 2020
PUBLICATIONS AND PRESENTATIONS
Schubert, TM. Cohen, T. Fischer-Baum, S. Reading the written language environment: Learning orthographic structure from statistical regularities. To appear in: Journal of Memory and Language. Volume 114, October 2020. Currently available online at: https://authors.elsevier.com/c/1bPl2,H2pbYbzC
Bergquist, T., Yan, Y., Schaffter, T., Yu, T., Pejaver, V., Hammarlund, N., Prosser, J., Guinney, J., & Mooney, S. (2020). Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction. Journal of the American Medical Informatics Association: JAMIA. https://doi.org/10.1093/jamia/ocaa083
Qifei Dong had a paper accepted in VLDB DMAH 2020 Workshop: Enhancing Medical Word Sense Inventories Using Word Sense Induction: A Preliminary Study.
UPCOMING MASTER’S EXAM
Yiliang Ma
Thursday, July 23, 2020; 2:30 PM; Zoom: https://washington.zoom.us/j/9034274714
Title: Everyone’s Variant Annotation Tools: EVAT
Abstract: Currently, there is a lot of genetic variant information distributed in many different databases, and it will cost individuals plenty of time to retrieve data from those resources.
In this thesis, I develop EVAT(Everyone’s variant annotation tool), a tool aiming at helping individuals retrieve annotation information about their genetic variants. People with or without programming skills may choose different methods to get their genetic variant annotation information. For individuals who have program skills, EVAT offers Python APIs which connect to the backend directly to help them retrieve annotation information. The backend of the tool is built by four file interpreters that translate file format, a module that sends and receives information from MyVariant.info, a module that converts the JSON result from MyVariatn.info to Panda dataframe and three functions that support different queries. For individuals who don’t have program skills, EVAT offers a graphical user interface, which is the front end of the tool. This user interface allows users to upload files, read the annotation, and do the query by mouse so that they don’t need coding skills when doing genetic annotation.
EVAT can be used either as a backend only (for users with programming skills) or with a graphical user interface to easily query and retrieve annotation information. This annotation information could help people understand the effect of genetic variants or do further research about them.
Supervisory Committee:
Sean Mooney, Chair
John Gennari
July 6-July 10, 2020
NEWS
Peter Tarczy-Hornoch was appointed as a member of the National Library of Medicine Board of Scientific Counselors for a 4 year term starting July 1, 2020
Janice Sabin was interviewed by Vidya Rao, investigator with the NBC News/TODAY Show, about the history and impact of Black women’s pain being dismissed in healthcare settings. This is part of a larger series they are doing on systematic racism in healthcare to be aired in August.
Janice Sabin will be interviewed this week by reporter, Ajai Raj, with Pain Medicine News as part of a feature about racial disparities in pain treatment.
PUBLICATIONS AND PRESENTATIONS
Janice Sabin will present 3 posters July 28, 29, & 30, at the virtual Academy Health Annual Research Meeting.
Sabin, J.A., & Morales: Search Committee Education to Increase Faculty Diversity in Medicine Is Useful but Not Enough: Targeted, Long-Term, Systematic, Multifaceted Efforts Are Needed, poster presentation, Janice Sabin, PhD, MSW, Leo Morales, MD, PhD, MPH.
Sabin, J.A., Implicit Bias in the Clinical and Learning Environment: Evaluation of a Brief Course for Clinical Teaching Faculty, & Grace Geunther, Davis Patterson, India Ornelas, Bianca Frogner.
Sabin, J.A., Minimizing Defensiveness in Clinician Education about Implicit Bias: Lessons Learned from a Community-Engaged Randomized Clinical Trial, & Joanne Calista, Elizabeth Dykhouse, Ethan Eisdorfer, Andrianna Foiles, Maria Garcia, Janet Hale, Geraldine Puerto, Lynley Rappaport, Jill Terrien, Olga Valdman, Majaid Yazdani and Jennifer Tjia
OTHER
From the Clinical Informatics Fellowship Program: We would like to celebrate our graduating fellows, and introduce our incoming fellows.
Arpit Patel MD, a General Surgeon, graduated from our program. During fellowship, Arpit practiced as a Fellow in Pediatric Surgery and supervised surgical residents at Seattle Children’s. He Arpit worked with IT Services on many projects, including: updating Depression note templates, working ITS leaders on determining order set content for the D:1 project, and determining how best to transition data from our Max transplant system and derivatives such as OHANA to Epic/Ellkay. As a physician builder, he took a leadership role in creating the decision support for opioid management of acute pain. He went to KenSci for additional training in machine learning, contributing to their thoughtful work on biases to which machine learning algorithms may be susceptible. His Master’s Project used machine learning to predict which patients with perforated appendicitis will develop post-operative complications. Arpit will be moving to Bakersfield, CA join his fiancée Laura; and where he is finalizing his negotiations with Dignity Health to be a General Surgeon and Regional CMIO.
Nikita Pozdeyev MD PhD, an Endocrinologist, graduated from our program. During fellowship, Nikita was very productive and worked on a plethora of projects in his service to the health system at UW. One project was implementing a regular expression generator to parse smoking history, to help determine patients in need of lung cancer screening. In this project, 5,500 of 24,000 patients had information that could only be parsed by Nikita’s logic – identifying 1,100 patients eligible for screening, where this work could potentially save 20 lives through detection of early stage lung cancer. As a physician builder, he improved the Diabetes and Hypertension Care Paths. In the latter project, an additional 5,000 UW Medicine patients transitioned to normal blood pressure with the implementation of the pathway. Nikita did his clinical work at Harborview, where he took care of patients with thyroid disease. His Master’s project, “Machine learning classifier of thyroid nodules based on the neural network analysis of thyroid ultrasound images”, relates closely to his clinical practice, determining whether thyroid nodules are likely to be cancerous or not from imaging. We will miss Nikita, Zhanna, and their children Maria and Daria they return to the University of Colorado, where Nikita will become the Head of Translational Informatics Services in the Colorado Center for Personalized Medicine/Division of Biomedical Informatics and Personalized Medicine, and practice clinically in their Division of Endocrinology.
Our new fellows:
Jeehoon Jang, MD finished his Internal Medicine residency in Englewood Hospital, NJ in 2020. He is interested in how mobile clinical decision support can improve healthcare providers’ efficiency and satisfaction at the point of care, in usability of clinical decision support, and in how machine learning algorithms transform healthcare. He likes to run, especially with his 10-month-old son’s jogging stroller, and sing Korean pop songs.
Zachary C. Liao, MD, MPH completed internal medicine residency at the University of Miami/Jackson Memorial Hospital. He is interested in machine learning, natural language processing, interoperability and public health informatics. He enjoys making music (piano, guitar and singing, in descending order of skill), and just bought a bicycle to explore Seattle on two wheels.
Sarah Stewart, MD grew up in Seattle and has spent the last 12 years in the Bay Area for college, medical school, and pediatric residency at Stanford University. In residency, she worked with patients and families to improve the safety of medication administration through EHR changes, and she is excited to continue learning how to use technology to improve pediatric care, empowering patients and their families to be involved in their child’s medical care. Dr. Stewart is our first fellow who is funded by Seattle Children’s Hospital.
June 29-July 3, 2020
NEWS
A team of UW investigators led by Dr. Gail Jarvik, and David Crosslin were just awarded a National Human Genome Research Institute (NHGRI) -funded grant to implement genomics into clinical practice. The local press release announcing the Electronic Medical Records and Genomics (eMERGE) Genomic Risk Assessment and Management Network is linked below. Drs. Meliha Yetisgen, Peter Tarczy-Hornoch, and Sean Mooney are a part of the UW team. https://bit.ly/2Bjzf6z
The BIME Diversity, Equity & Inclusion (DEI) Committee is pleased to welcome two new members: faculty: Andrea Hartzler and graduate student: Regina Casanova-Perez. Welcome! Janice Sabin, DEI Committee Chair
PUBLICATIONS AND PRESENTATIONS
Ding, X, Cohen, T. Retrofitting Vector Representations of Adverse Event Reporting Data to Structured Knowledge to Improve Pharmacovigilance Signal Detection. To appear in: Proceedings of the AMIA 2020 Virtual Annual Symposium
Xu, W. Portanova, J. Chander, A. Ben Ze-ev, D. Cohen, T. The Centroid Cannot Hold: Comparing Sequential and Global Estimates of Coherence as Indicators of Formal Thought Disorder. To appear in: Proceedings of the AMIA 2020 Virtual Annual Symposium
Usuyama, N., Larios Delgado, N., Hall, A. K., & Lundin, J. (2020). ePillID Dataset: A Low-Shot Fine-Grained Benchmark for Pill Identification. In Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition Workshops (pp. 910-911).
Washington KT, Demiris G, Parker Oliver D, Backonja U, Norfleet M, Han CJ, Popescu M. ENVISION: a tool for improving communication of interdisciplinary hospice teams. Journal of Gerontological Nursing. 2020;46(7):9-14. doi: 10.3928/00989134-20200605-03.
Brandt, PS, Kiefer, RC, Pacheco, JA, et al. Toward cross‐platform electronic health record‐driven phenotyping using Clinical Quality Language. Learn Health Sys. 2020;e10233. https://doi.org/10.1002/lrh2.10233
Mark Phillips will be presenting an invited paper “The Synergy of Ontologies and HL7-FHIR” at the annual meeting of the American Association of Physicists in Medicine.
June 22-26, 2020
PUBLICATIONS AND PRESENTATIONS
Kalet AM, Luk SM, Phillips MH. Radiation Therapy Quality Assurance Tasks and Tools: The Many Roles of Machine Learning. Medical Physics. 2020 Jun;47(5):e168-77.
Thomas, Jason | Burkhardt, Hannah | Chaudhry, Safina | Ngo, Anthony D.| Sharma, Saransh | Zhang, Larry | Au, Rhoda | Hosseini Ghomi, Reza. Assessing the Utility of Language and Voice Biomarkers to Predict Cognitive Impairment in the Framingham Heart Study Cognitive Aging Cohort Data. Journal of Alzheimer’s Disease, vol. Pre-press, no. Pre-press, pp. 1-17, 2020 https://content.iospress.com/articles/journal-of-alzheimers-disease/jad190783
June 15-19, 2020
NEWS
Neil Abernethy was quoted in a Seattle Times article about the challenges of contact tracing in Washington State https://www.seattletimes.com/seattle-news/times-watchdog/despite-army-of-newly-trained-workers-challenges-with-coronavirus-contact-tracing-in-washington-state-remain/
PUBLICATIONS AND PRESENTATIONS
White AA, Lee T, Garrison MM and Payne TH. A randomized trial of voice-generated inpatient progress notes: Effects on professional fee billing. Appl Clin Inform. 2020 May;11(3):427-432. doi: 10.1055/s-0040-1713134. Epub 2020 Jun 10. PMID: 32521556
Payne TH, Zhao LP, Le C, Wilcox P, Yi T, Hinshaw J, Hussey D, Kostrinsky-Thomas A, Hale M, Brimm J, Hisama FM. Electronic health records contain dispersed risk factor information that could be used to prevent breast and ovarian cancer. J Am Med Inform Assoc. 2020. Accepted for publication.
June 8-12, 2020
NEWS
Gang Luo is invited to attend the Microsoft Research Frontiers in Machine Learning event this July.
Anne Turner, MD, received the Notification of Award from the National Institute on Aging and was awarded a five year $3.3 M grant to develop novel strategies to involve older adults with Alzheimer’s Disease and Related Dementias (ADRD) in decisions about their care. Anne is the PI for the grant and Annie Chen, PhD is a co-investigator on the award. The grant is going through the Health Promotion Research Center in the Department of Health Services. The Project Summary is pasted below.
The goal of this research is to advance our understanding of decision-making processes, and the preferences that influence decision-making, for older adults with ADRD and their caregivers. This goal will be met through the following aims: 1) Define decision-making processes and key factors influencing decision-making about transitions in care through qualitative interviews with older adults with mild to moderate ADRD, caregivers, and dementia care providers to gain a detailed understanding of the complexities of dementia care decision-making and related preferences. 2) Develop a dementia care preference elicitation tool for use in assessing the preferences of older adults with ADRD and their caregivers through novel application of discreet choice methodology in conjunction with visualization methods and human-centered design to ensure that the tool is responsive to the needs of older adults with ADRD. 3) Use developed and validated preference elicitation tool to ascertain preferences for dementia care-related decisions among older adults with ADRD and caregivers. Over a two year period, investigate the consistency of preferences regarding transitions in care among older adults with ADRD. The proposed research forms the basis for investigating novel strategies to keep older adults with ADRD meaningfully involved in decision-making, even as their dementia worsens.
PUBLICATIONS AND PRESENTATIONS
Bochatay, N, Kuna, A, Csupor, E, Pintér, JN, Muller-Juge, V, Hudelson, P, Nendaz, M, Csabai, M, Bajwa, NM, Kim, S. The role of power in healthcare conflict: recommendations for shifting towards constructive approaches. Accepted: Academic Medicine.
Daniel Y. Cho MD PhD , Cameron J. Kneib MD , Jonathan P. Massie MD. Danielle L. Sobol MD, Christopher S. Crowe MD ,Afaaf Shakir MD ,Jacob R. Burns MD ,Megan Lane MD , Shane D. Morrison MD MS. Janice Sabin PhD MSW , Janelle D. Sousa MD ,Visual Representation of Racial Diversity in Aesthetic Surgery Literature, Journal of Plastic, Recon-structive & Aesthetic Surgery(2020), doi: https://doi.org/10.1016/j.bjps.2020.05.04
Sawchuk, Russo, Ferguson, Williamson, Sabin, Goldberg, Lallemand, Hannon, Harris, Bogucki, & Buchwald (in press). A randomized controlled trial to address health outcomes in Alaska workplaces. Health Promotion and Practice, June 2020
Sabin, J.A., Minimizing Defensiveness in Clinician Education about Implicit Bias: Lessons Learned from a Community-Engaged Randomized Clinical Trial, oral presentation, Joanne Calista, Elizabeth Dykhouse, Ethan Eisdorfer, Andrianna Foiles, Maria Garcia, Janet Hale, Geraldine Puerto, Lynley Rappaport, Jill Terrien, Olga Valdman, Majaid Yazdani and Jennifer Tjia. Published online abstract; peer review Academy Health, July 2020 Health Services Research
Sawchuk CN, Russo J, Ferguson G, Williamson J, Sabin JA, Goldberg J, Lallemand O, Bogucki O, & Buchwald D (in press). Health promotion programs and policies in the workplace: an exploratory study with Alaska businesses. Preventing Chronic Disease
June 1-5, 2020
NEWS
Please welcome and congratulate the new chair of the Appointments & Promotions Council, Sean Mooney, PhD, Professor in Biomedical Informatics and Medical Education & Chief Research Information Officer (CRIO) at UW Medicine. Dr. Mooney begins his term as council chair on July 1, 2020.
PUBLICATIONS AND PRESENTATIONS
Heitkemper E, Bekemeier B, Schultz M, Backonja U, Whitman G. Development of a data visualization dashboard for public health using participatory design. Accepted for American Public Health Association Annual Conference. October 2020. San Francisco, CA.
May 25-May 29, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
June 4, 2020: Arpit Patel, MD
Title: Experiences of a Physician Informaticist with Predictive Machine Learning Models and Opioid Stewardship Efforts
Abstract: Physician informaticists straddle the boundary between clinicians and data scientists, providing valuable clinical insights to data analysts, as well as informatics insights to other clinicians. While attempting to create a machine learning model to predict post-operative outcomes in patients with perforated appendicitis, I take the role of a clinician to apply clinical knowledge to steps in the model development process. When supporting the Opioid Stewardship committee’s efforts to support the safe prescribing of opioid medications at UW Medicine, I provide technical knowledge of EHR architecture and tools. Each presents a set of challenges and need for deeper understanding in a different knowledge domain.
Speaker Bio: Arpit Patel is a board certified general surgeon, and a second-year fellow in the Clinical Informatics fellowship program at the University of Washington. Over the past two years, he has supported numerous projects at UW Medicine and ITS, including Opioid Stewardship efforts, expanding functionality of Epic tools, and supporting the Destination: One project. His clinical practice takes him to Seattle Children’s Hospital, where he works with the pediatric general surgery team to manage patients in the ED, OR, and ICU.
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
PUBLICATIONS AND PRESENTATIONS
Q. Dong, G. Luo, D. Haynor, M. O’Reilly, K. Linnau, Z. Yaniv, J.G. Jarvik, and N. Cross. DicomAnnotator: A Configurable Open-Source Software Program for Efficient DICOM Image Annotation. Journal of Digital Imaging (JDI), 2020
UPCOMING GENERAL EXAM
Savitha Sangameswaran
Date: Wednesday, June 3, 2020; 3:00pm; Zoom: https://washington.zoom.us/j/4028570225
Title: Design Recommendations for a Digital Mind-Body Based Tool to Mitigate Effects of Media Use on Sleep in Youth
Abstract: Sleep problems in youth due to pervasive media use presents an imperative public health problem with increasing prevalence. Current approaches to reducing media use have been met with many challenges. A “harm reduction model” based approach to reduce the adverse consequences of media use (i.e.., arousal from media use) without trying to eliminate media use is desirable. Such an approach might benefit youth with media use-induced sleep problems by mitigating the underlying mechanisms like increased arousal due to media use. Yet, very few studies have used the harm reduction model to target media use in youth. Mind-body interventions might be a potential harm reduction-based strategy to mitigate media-induced arousal. Mind-body approaches have shown to help youth in treatment or self-management of various conditions like chronic pain, eating disorders, insomnia and sleep disturbance. Existing mind-body approaches for youth have been delivered in person or at schools but are not readily accessible or scalable. There have been increasing calls to deliver mind-body approaches digitally to youth. Yet, research on utilizing mind-body approaches to regulate media use is scarce. With the growing prevalence and popularity of technology in youth, a digital mind-body approach is promising. Currently, there is very little guidance available on how to design mind-body based digital tools for youth. In my dissertation guided by Human-Centered Design (HCD), a methodological framework that emphasizes the participation of technology users in the design process, I will investigate the needs and design recommendations of a digital mind-body based tool for mitigating the effects of media use on sleep in youth (10 -14 years). I will describe and compare key stakeholder perspectives on media use, sleep and mind-body interventions (Aim 1) and Formulate design recommendations for a digital mind-body based tool through participatory design workshops with youth (Aim 2). Given the significant need to help youth with media-induced sleep problems and the scarcity in consumer health informatics research exploring harm reduction strategies for media use in youth, this project is a timely opportunity to advance research in consumer health informatics and sleep research.
Doctoral Supervisory Committee:
Andrea Hartzler, Chair (BIME)
Jason Yip (Information School)
Michelle Garrison (Health Services-Public Health)
Dori Rosenberg (Kaiser Permanente)
May 18-May 22, 2020
NEWS
BIME Associate Professor Neil Abernethy was quoted in the South Florida Sun-Sentinel about COVID-19 contact tracing: https://www.sun-sentinel.com/coronavirus/fl-ne-coronavirus-contract-tracing-consumer-guide-best-practices-20200506-53kpu4hrlrfozosofbyf6ivebe-story.html
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
May 28, 2020: Lydia Drumright, PhD, University Lecturer in Clinical informatics, Fellow of Hughes Hall,
Department of Medicine, University of Cambridge
Title: Harnessing Routine Health Data for Epidemiological Research in UK
Abstract: Routinely collected health data holds a wealth of opportunity to support better understanding of human health and the most effective delivery of interventions aimed at improving health. Yet, we are still in the nascent stages of harnessing the potential stored in these data. While the implementation of fully integrated, paperless electronic health records (EHRs) have provided an incredible opportunity for rapidly collating routinely collected healthcare data, we are still working on the challenge of making epidemiological sense of these data. Cambridge University NHS Foundation Trust (CUH) was the first hospital trust to go fully paperless, implementing Epic on October 26, 2014. With the aim of advancing both research and healthcare delivery, we developed an integrated research platform for harnessing clinical data, which has led to numerous translational studies for advancing clinical care, disease knowledge, and public health and altering practice and policy. In this talk, I will present two studies, one on hepatitis C virus (HCV) treatment outcomes in the era of directly acting antivirals (DAAs) and the other examining the molecular epidemiology of norovirus infection in healthcare settings, to highlight innovative use of routine data. Data processing techniques, including NLP, competing hazards models and molecular sequence analysis will be discussed, as well as how the complexities of working with clinical data were overcome.Speaker Bio: Dr Lydia Drumright, MPH PhD, is an infectious disease epidemiologist, the University Lecturer in Clinical Informatics at the University of Cambridge, and a Turing Fellow at The Alan Turing Institute, the UK’s national center for data science and artificial intelligence. Her work on transmission dynamics of infectious disease has spanned multiple disease systems, including HIV, viral hepatitis, influenza and healthcare-associated infections such as norovirus. She has employed multiple epidemiological strategies, including bio-behavioural surveys, geographic analyses, qualitative interviews, molecular epidemiology and analysis of routinely collected clinical data from new diagnostic platforms. More recently, she has combined many of these strategies to create a multidisciplinary epidemiological approach incorporating modern technologies to advance understanding of the natural history of infection and create clinical and public health interventions.
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
May 21, 2020: TBA
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
PUBLICATIONS & PRESENTATIONS
AMIA CIC Posters
Ng, C., Shirts, B. H., Chen, A. T. (accepted). Facilitating family communication about genetic testing through ConnectMyVariant, an educational website: Development and preliminary usability assessment. AMIA Clinical Informatics Conference 2020.
Sharma, R. S., Tsui, S., Chen, A. T. (accepted). Involving stakeholders in the design of an interactive guide for patients with advanced cancer. AMIA Clinical Informatics Conference 2020.
Chen, A. T., Ornelas-Mendoza, M., Rockhill, C. (accepted). Examination of heart rate variability among psychiatric youth inpatients utilizing a technology-based Social Emotional Learning biofeedback intervention in an inpatient setting: data collection and analysis challenges, initial results and next steps. AMIA Clinical Informatics Conference 2020.
Bowen, J., Klaich, A., Chen, A. T., Rockhill, C. (accepted). Satisfaction of patients and implementers utilizing technology-based Social Emotional Learning interventions in a youth inpatient psychiatric setting. AMIA Clinical Informatics Conference 2020.
UW Undergraduate Research Symposium (May 15, 2020) Presentations and Posters mentored by Annie Chen:
Hallinan, S. Mapping User Trajectories to Examine Behavior and Outcomes in Digital Health Intervention Data
Tsui, S. Y. S. Use of User-Centered Design to Develop a Guide for Hospitalized Patients with Advanced Cancer
Lin, R.; Du, J.; Slaughter, M. M. Svoboda Diaries Project User Experience & Usability Rresearch.
Gazula, Y. Case Study of Social Networks in Ottoman Iraq
Bansal, S. Studying Information Behavior in Historical Corpus
NEWS
BIME Associate Professor Neil Abernethy was quoted in two news articles related to the COVID-19 pandemic:
- The coronavirus ‘infodemic’: How social media is shaping our perception of COVID-19 By Tania Bhatti The Daily
- Siphoning civil liberties in the name of COVID-19: A research roundup By Clark Merrefield
Eric Rose has joined the Department of Veterans Affairs Office of Health Informatics in the role of Chief Terminologist, where he will lead a team responsible for advancing clinical terminology knowledge and practice across the VA system and the larger healthcare community.
Sandra Johnston, PhD, RN (postdoc fellow 05-07) has joined the CLEAR center at the University of Washington, Department of Radiology as Research Scientist/Engineer-Senior in the role of Administrative Director. Clinical Learning, Evidence And Research (CLEAR) Center, is an NIH-funded P30 center, focusing on clinical trials in the musculoskeletal realm, especially spine disorders, with a strong emphasis on imaging. This is a multidisciplinary group with strong leadership in Biostats, Bioinformatics, PM&R as well as Radiology. The trials focus has been on large, pragmatic, effectiveness trials, as well as earlier stage translational trials as well. Here’s the link to the CLEAR center’s website: https://theclearcenter.org/about/
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
May 14, 2020: TBA
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
PUBLICATIONS
“Improving Biomedical Analogical Retrieval with Embedding of Structural Dependencies”, Amandalynne Paullada, Bethany Percha, and Trevor Cohen, to appear in the proceedings of the BioNLP 2020 Workshop on Biomedical Natural Language Processing. Virtual Conference.
April 27-May 1, 2020
NEWS
YiFan Wu, BHI PhD student, participated in the Dempsey startup competition, (The Dempsey Startup Competition, organized by the Buerk Center for Entrepreneurship, provides a real-world experience for student entrepreneurs, promoting student ideas and new venture creation to the entrepreneurial community) with other two students and ranked 31 out of 97 teams.
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
May 7, 2020: Ryan James
Title: Telerobotic Surgery, Mixed Reality and Artificial Intelligence
Abstract: According to the CDC, people who live in rural areas are more likely to die prematurely from all five leading causes of death when compared with urban residents. With over 46 million Americans living in rural areas—15% of the US population—the scope of the problem is considerable. The rural healthcare disparity is particularly acute for subspecialty surgical services. Telerobotic surgery involves a remote doctor performing surgery on a patient located in a distant location through a telerobotic interface. Recognizing that the widespread adoption of telerobotic surgery to perform subspecialty surgical procedures could have a profoundly positive impact on rural healthcare, I am doing research to shed light on what’s required to create this reality. During this talk, I plan to discuss my past and present research, then highlight plans for the future.
Speaker Bio:
Ryan James, PhD, is a healthcare researcher, engineer, and entrepreneur. He graduated in June, 2019 with a PhD in Biomedical and Health Informatics from the University of Washington. His dissertation explored the utility of a novel mixed reality user interface built to facilitate intra-procedural device navigation. He founded a company that is using telerobotics to improve access to care issues and he works at a startup, Pluto VR, that is helping humanity transcend physical location.
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
UPCOMING FINAL EXAM
Maher Khelifi
Monday, May 4, 2020; 2:00 PM, Zoom: https://washington.zoom.us/j/95355117450
Title: Supporting Hospitalized Patients through AI Technology
Abstract: Hospitalized patients of the 21st century are encouraged to actively engage in their care, manage their safety, make medical decisions, and monitor the quality of their treatments. However, engaged hospitalized patients face a dilemma. The complexity of their care makes their engagement more important yet harder to achieve. Patients with complex health problems are cognitively and physically impaired because of pain, stress, and medications. At the same time, the information related to their health situation is more abundant and more complex. Thus, hospitalized patients face an engagement gap that grows deeper with the complexity of their health problems. Artificial intelligence (AI) agents, technologies that automate information processing, could be a promising solution. Yet, we know little about how AI agents could support patients in hospital settings. In this thesis, first, I start by defining technological opportunities, especially AI applications, to support patient and information needs in hospital settings. I propose a new user-centered research method “Muse cards”. The method aims to inspire patients and their family caregiver to disrupt their hospital technologies with new designs that would accommodate their evolving roles in hospital settings. Second, I focus on the patient-clinician conversation, a core source of information in hospital settings. I report the factors that define the importance of verbally communicated information for patients, from the patients’ perspective and from the clinicians’ perspective. Third, I report the results of testing NURI, an AI agent to support hospitalized patients in understanding medical conversations with their clinicians. I report the perception of its usefulness and acceptance form the patients, caregivers, and clinician’s perspective. My work contributes to human computer interaction research a new toolkit to help users disrupt their attachment to existing technologies with new innovative ideas. Moreover, I provide design guidelines to implement AI agents in the hospital settings to support patients and their family caregivers. Furthermore, my work contributes to clinical speech processing research by providing an annotation framework to capture important information for patients’ use from the patient perspective and from the clinicians’ perspective.
Doctoral Supervisory Committee:
Wanda Pratt – Chair (iSchool Professor, adjunct BIME)
Andrea Hartzler (BIME)
Eric Horvitz (Microsoft Research)
James Fogarty – GSR (CSE)
April 20-24, 2020
NEWS
Hannah Burkhardt, BHI PhD student, has been accepted as a JAMIA student editorial board (SEB) member.
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
April 30, 2020: Jessica Ancker
Title: Making Numbers Meaningful: Improving the Way We Communicate About Numbers in Health
Abstract: People encounter numbers that are potentially important to their own health in personal devices and wearables data, lab results and medical record data, health risk information, genomic reports, environmental indicators, and nutrition and drug labels. Unfortunately, this flood of data primarily benefits well-educated individuals who have the numeracy skills to interpret it. A rich body of evidence is available about how to maximize comprehension of data, but most writers and developers know little about this evidence or about how to apply it to optimize documents and technologies. In this talk, Dr. Ancker will report on a set of interrelated projects to identify the multidisciplinary evidence on how data presentation formats affect comprehension, and to organize, synthesize, and disseminate it. Her long-term goal is to ensure that all people, including those with low numeracy, have the ability to benefit from the ever-increasing availability of health-related data.
Speaker Bio: Jessica S Ancker, MPH, PhD, is an associate professor of population health sciences (division of health informatics) at Weill Medical College of Cornell University. After a first career in journalism, she earned a master’s degree in biostatistics and a PhD in biomedical informatics from Columbia. Her research on health numeracy is supported by an R01 from the National Library of Medicine.
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
PUBLICATIONS
Chen, A. T., Slattery, K., Tomasino, K., Bardsley, L. R., Rubanovich, C., Mohr, D. (accepted). Challenges and benefits of an internet-based intervention with a peer support component for older adults with depression: Insights from a qualitative analysis of textual data. Journal of Medical Internet Research.
Chen, A. T., Flaherty, M. G., Threats, M. (accepted). Attitudes, provider and treatment selection of complementary and integrative health among individuals with pain-related conditions. Complementary Therapies in Medicine. DOI: 10.1016/j.ctim.2020.102410
Dong, G. Luo. Progress Indication for Deep Learning Model Training: A Feasibility Demonstration. IEEE Access, 2020, 33 pages.
April 13-17, 2020
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
April 23, 2020: Anne Turner
Title: Advancing Decision-Making in Dementia Care: Engaging Older Adults and Caregivers
Abstract: As older adults with Alzheimer’s disease and related dementias (ADRD) decline, they are often omitted from decisions regarding their care. The goal of this recently funded NIH R01 research is to apply novel methods developed for marketing, to elicit preferences from older adults with dementia regarding transitions in care. Our study will investigate factors that contribute to decision-making about transitions of care from older adults with mild to moderate dementia, their caregivers and staff. We will use this formative research to develop a DCE tool to elicit preferences and keep older adults with dementia involved in care decisions. For this presentation, I will discuss how our team seeks to understand decision-making among individuals with dementia, the role of informatics in creating preference tools, and ways we will be adapting our study to reach a high risk population in a COVID 19 environment.
Speaker Bio: Anne M. Turner, MD, MLIS, MPH, FACMI, is physician and professor at the University of Washington with a joint appointment in Health Services in the School of Public Health, and Biomedical Informatics and Medical Education in the School of Medicine. As a public health practice researcher, she has been involved in projects to improve public health practice for over 20 years. Her research has focused on applying information technology to improve the health of vulnerable populations, including older adults, individuals with limited English proficiency, and individuals with low health literacy. She was PI of the SOARing project investigating the personal health information management needs of older adults living in a variety of settings. The work described her is an offshoot of that five year project. Students that are interested in finding out more about this recently funded NIH project should contact Dr. Turner at amturner@uw.edu.
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
BIME Faculty Candidate – Lara Varpio, PhD
Monday, April 20, 11 a.m. via Zoom
Zoom: https://washington.zoom.us/j/292831010
Speaker: Lara Varpio, PhD
Professor, Department of Medicine
Associate Director of Research, Center for Health Professions Education
Uniformed Services University of the Health Sciences (USUHS), Bethesda, MD
Title: Achieving Growth By Being Nimble
Speaker Bio: Dr. Lara Varpio is Professor of Medicine, and Associate Director of Research for the Health Professions Education graduate degree program at the Uniformed Services University of the Health Sciences (USUHS). Dr. Varpio spent the first 6 years of her career at the University of Ottawa, Canada before moving to Washington DC, USA in 2013 to work at USUHS.
April 6-10, 2020
NEWS
University of Washington graduate and professional disciplines rank highly in US News’ Best Graduate School lists. https://www.washington.edu/news/2020/03/17/
The University of Washington’s graduate and professional degree programs were widely recognized as among the best in the nation, according to U.S. News & World Report’s 2021 Best Graduate School rankings released March 17.
Several schools and departments placed prominently in the 2021 rankings, including nursing, medicine, pharmacy and public affairs.
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/j/987140566
April 16, 2020: Christine Bandaragoda
Title: TBD
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
BIME Special Guest – Carol S. Hodgson, MS, PhD
Monday, April 13, 1 p.m. via Zoom
Zoom: https://washington.zoom.us/j/381584734
Speaker: Carol S. Hodgson, MS, PhD
Allan Gilbert Chair in Medical Education Research
Director, IDEAS Office
Associate Professor, Pediatrics
University of Alberta
Title: Professional Development in a Geographically Distributed & Multicultural World
Abstract: This talk will focus on ways to conceptualize various faculty development models to deliver educator development in a geographically distributed system. Almost all medical schools deliver content across multiple clinical sites, some a few miles away across town and others hundreds of miles away. How do you keep everyone on the same page in terms of what’s expected, learning objectives, what to teach and how to teach in a mutually safe and professional environment? This talk will offer a model to achieve these aims.
Speaker Bio: Carol Hodgson, Ph.D. is the J. Allan Gilbert Chair in Medical Education Research, Director of the IDEAS Office, directs the Teaching Scholars Program, and is an Associate Professor with tenure in Pediatrics at the University of Alberta Faculty of Medicine and Dentistry. She received a Master of Science degree in biochemistry from the University of California, Riverside and a doctorate in Education at UCLA. Before entering the field of medical education in 1992, she was a researcher in preventive medicine at the University of Southern California. Dr. Hodgson actively mentors numerous faculty members in the design and implementation of medical education research. Dr. Hodgson is an expert in curriculum design, program evaluation, educational research, and faculty development. Dr. Hodgson’s research focuses in the areas of professionalism, program evaluation, cancer education, and training for better care of people with disabilities.
PUBLICATIONS
Trevor Cohen* and Serguei Pakhomov*. A Tale of Two Perplexities: Sensitivity of Neural Language Models to Lexical Retrieval Deficits in Dementia of the Alzheimer’s Type (* denotes equal contribution). To appear in Proceedings of the Annual Meeting of the Association for Computational Linguistics (ACL 2020), virtual conference, July 2020.
Grange ES, Neil EJ, Stoffel M, Singh AP, Tseng E, Resco-Summers K, Fellner BJ, Lynch JB, Matthias PC, Mauritz-Miller K, Sutton PR, Leu MG. Responding to COVID-19: The UW Medicine IT Services Experience. Appl Clin Inform. Accepted. https://www.thiemeconnect.com/products/ejournals/abstract/10.1055/s-0040-1709715
March 30-April 3, 2020
NEWS
Neil Abernethy gave a live Youtube interview on contact tracing for Covid-19 to the local news outlet The Batavian: https://www.youtube.com/watch?v=YR5cKy3gFwk&feature=youtu.be&t=14
UPCOMING LECTURES AND SEMINARS
BIME 590A – Biomedical & Health Informatics Lecture Series
Thursdays, 11:00am-11:50am, Zoom: https://washington.zoom.us/s/756573880
April 9, 2020: David Heckerman Title: TBD
BIME 591A-Health Economics Theory and Applications in Informatics
Wednesdays, 12:30 pm-1:20 pm; Zoom
Facilitator: Noah Hammarlund
BIME 591C-Epigenetics and the Use of Omics Data in Clinical Care
Mondays, 12:30 pm-1:20 pm; Zoom
Facilitator: Houda Benlhabib
PUBLICATIONS
Dae Hyun Lee, Meliha Yetisgen, Lucy Vanderwende, Eric Horvitz. Predicting Severe Clinical Events by Learning about Life-Saving Actions and Outcomes using Distant Supervision. Accepted to Journal of Biomedical Informatics.
OTHER
Faculty looking for online Teaching resources can visit the CLIME website – clime.washington.edu
We have added a special section – COVID-19 Teaching Resource- https://clime.washington.edu/covid19-resources-1
Janice Sabin: With so many cancelled conferences, my UMass colleagues developed this language to place on CV. (with a tweak from Peter TH identifying why cancelled).
“Accepted, developed, scheduled to be delivered on <<date>>> yet not delivered due to conference cancellation due to COVID-19.”
Fred Carrle and Benedict Schilling, former Visiting Students of Gang Luo have successfully finished their time at the UW and would like to thank BIME for their support.