News and Events

Chair’s Message

pth-use-this-oneWe 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

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.

https://urldefense.com/v3/__https://www.press.jhu.edu/journals/journal-health-care-poor-and-underserved/author-guidelines__;!!BZ50a36bapWJ!8OgCX71HpHYjqg9H5GDRb8if6jIDucvrVwZl_dadwWeQ8ErjiU1SkojADpIrog$

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:

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.

March 16-20, 2020

NEWS

Congratulations to YiFan Wu, Yue Guo, Regina Casanova Perez and Hannah Burkhardt who have been chosen to represent UW at the 2020 IPHIE Master Class hosted by BIME in June.

UPCOMING GENERAL EXAM

Chethan Jujjavarapu

Friday, March 20, 2020; 3:00 pm; Zoom: https://washington.zoom.us/j/471915232

Title:  Moving the Learning Healthcare System Forward using Data Science and Application Development in the Fields of Lower Back Pain and Genetic Medicine

Abstract: Precision Medicine (PM) is one of the most important goals in recent years in the healthcare field. The approach is to guide healthcare providers to administer treatments specific to patients based on their demographics and health characteristics so as to avoid unnecessary testing and therapies. To achieve this goal, a culture of sharing clinical data is needed in the healthcare system. Electronic health record (EHR) research needs to inform clinical practice and both need to engage patient participation. The learning healthcare system (LHS) is a framework that addresses this symbiotic relationship among clinical researchers, healthcare providers, and patients. The LHS framework is a cycle that can harness the power of the electronic health record (EHR), engage patients and clinicians to ask meaningful questions, and ensure that the knowledge that is produced is quickly integrated into care to improve health. However, there is an underrepresentation of research that links EHR research to patient engagement. Therefore, we propose to build a framework that can link EHR research with patient engagement. Our strategy is to achieve this link by addressing specific challenges in two independent clinical problem spaces: lower back pain (LBP) and genetic medicine (GM). For LBP, patients routinely start with conservative treatments and if these fail then are given surgery, such as decompression surgery, however literature indicates the timing of surgery can greatly affect patients’ short-term health outcomes, specifically for disc herniation and stenosis patients (subgroups of LBP). To address this concern, we propose to predict decompression surgery for patients by applying deep learning to patients’ structured and unstructured EHR data (free-text image reports) (Aim 2). To build our two patient subgroups, we will need to rely on both patients’ diagnosis codes and free-text imaging reports. To utilize free-text imaging reports, we propose to compare different natural language processing-based feature extraction methods coupled with logistic regression to classify imaging reports for these subgroups (Aim 1). For GM, there is interest in motivating patients to share their genetic test results with their biological relatives, so that their results may inform and motivate their relatives to also get tested for possible Mendelian diseases. To address this, we will build a smartphone application, ShareDNA, to securely share genetic test results and educational material with patients and their family members to help engage and educate them on importance of genetic testing (Aim 3). While Aim 3 is specific for genetic testing, our application can be easily tailored to any clinical information, such as the results from Aim 2, to disseminate information to patients and their family members.

March 9-13, 2020

NEWS

AMIA 2020 Clinical Informatics Conference Student Volunteer Program, May 19-21, 2020; Seattle, WA

AMIA CIC Student Volunteer opportunities:

https://www.amia.org/cic2020/student-volunteer-program

UPCOMING GENERAL EXAMS

Andrew Teng

Wednesday, March 18, 2020; 11:00 am; Zoom: https://bit.ly/AdamZoom

Title: Acute care sepsis prediction: Analyzing the predictive influence of social determinants

Abstract: The Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 established guidelines to help improve patient safety and efficacy by laying the framework for electronic healthcare record (EHR) adoption in the United States through financial incentives. Through the HITECH Act, basic EHR adoption skyrocketed domestically and large databases of clinical information were created. Currently, many institutions have large quantities of data,that have been under-analyzed, ripe for biomedical exploration and discovery. Within the hospital setting, sepsis is a leading cause of mortality. Annually, sepsis affects more than 1.7 million adults and is present in about 30 to 50 percent of hospitalizations that end with death. Despite the high occurrence and prevalence, detection and diagnosis of sepsis remain a challenge due to its non-specific early-onset symptoms. However, as it can quickly progress to a life-threatening stage, it is important to detect sepsis patients earlier to increase outcomes. With the recently increased adoption of EHRs, many institutions now have large amounts of patient data being collected and have created their own customized sepsis detection and mortality tools using various machine learning (ML) techniques. Additionally, those who experience more socioeconomic challenges are more susceptible to chronic illnesses, including sepsis. However, structured coding of social features is often underutilized and unreliable. First, in order to understand the current environment of predictive analytics solutions for sepsis, we will systematically identify various studies that utilize different models or ML techniques and analyze their approach and results. Second, we will propose a framework that utilizes natural language processing text classification from clinical text notes to extract social determinants of health and other social features. Third, we will develop and assess classification methods that utilize currently established sepsis definitions to establish a baseline and integrate the results from Aim Two to determine if social determinants of health features can help enhance predictive performance for sepsis detection and post-acute care readmission.

March 2-6, 2020

NEWS

AMIA 2020 Clinical Informatics Conference Student Volunteer Program, May 19-21, 2020; Seattle, WA

AMIA CIC Student Volunteer opportunities:

https://www.amia.org/cic2020/student-volunteer-program

UPCOMING LECTURES AND SEMINARS

BIME 590A – Biomedical & Health Informatics Lecture Series

Thursday, 11:00am-11:50am, UW Medicine South Lake Union, Building C, Orin Smith Auditorium

March 12, 2020: No Seminar

BIME 591A-Information Visualization in Health Care

Tuesdays, 12:30 pm-1:20 pm; Will be held remotely, see class page for more information

Facilitator: Ari Pollack

BIME 591B-Exploring Epidemic Modelling

Wednesdays, 12:30 pm-1:20 pm; Will be held remotely, see class page for more information

Facilitators: Juandalyn Burke

UPCOMING GENERAL EXAM

Jason Thomas

Thursday, March 12, 2020; South Lake Union, Building E, Room E130B (could change to remote)

Title: Assessing the fitness for use of real-world electronic health records and log data: Utility and privacy tradeoffs of privacy preserving technologies

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, richness) 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 methodological transparency(9). Thus, users of electronic health record and log data remain uninformed as to the FFU of their data at baseline and are unable to effectively assess subsequent tradeoffs between utility and privacy when applying preserving technologies.

Our long-term goal is to enable the Data Utility Assessment (DUA) of EHR data – both records and logs – before and after the application of privacy preserving technologies (PPT). The overall objective of this proposal is two-fold: 1) build a novel fitness for use framework and paired interoperable, open-source DUA tool that can be used across organizations, data networks, and among synthetic datasets created with PPT for health records and 2) Assess utility and privacy tradeoffs within methodologically transparent private and non-private analyses of log data that adheres to emerging log data standards. To do so, I will propose creation of (Aim 1) a repository of clinical ‘facts’ to be (Aim 2) mined from the EHR by our DUA tool and (Aim 3) conducting a retrospective, observational analysis of clinical workstation authentication behaviors to inform customized solutions that balance usability and security. PPT in the form of synthetic data generation and ε-differentially private queries will be applied to Aims 2 & 3 to allow for the evaluation of tradeoffs between privacy and utility.

OTHER

On Thursday, February 27, 2020, University of Washington eScience Institute held the inaugural Non-Ableist Data Science workshop. Community participants used AI Blindspots Cards as a framework address potential oversights in planning, building, and deployment phases of data science tools. 17 facilitators and over 90 attendees joined in on nine small groups co-designing solutions to counter AI biases that may disadvantage people with disabilities. BIME alumni and students Jimmy Phuong, Lauren Snyder, Nick Reid, and Chethan Jejjavarapu facilitated small groups on Privacy, Explainability, and Abusibility issues in AI. BIME alumni Mandi (Amanda) Hall and CIPCT student Megan Laine participated as attendees in small group discussions on Purpose and Explainability issues in AI. This event was supported by eScience institute Non-Ableist Data Science Special Interest Group and the Taskar Center for Accessible Technologies.

February 24-February 28, 2020

NEWS

AMIA 2020 Clinical Informatics Conference Student Volunteer Program, May 19-21, 2020; Seattle, WA

AMIA CIC Student Volunteer opportunities will be available sometime next week. An announcement will be sent out as soon as the information becomes available.

BIME will be hosting 22 Prospective PhD students March 5-6, 2020 for Visit Days. They will meet with various faculty, current students, attend the BIME 590 seminar, attend a Poster Session, and tour the UW main campus.

UPCOMING LECTURES AND SEMINARS

BIME 590A – Biomedical & Health Informatics Lecture Series

Thursday, 11:00am-11:50am, UW Medicine South Lake Union, Building C, Orin Smith Auditorium

March 5, 2020: Ari Robicsek, MD, Chief Medical Analytics Officer, Providence St. Joseph Health

Title: Endless Forms Most Beautiful: notes from the wild world of clinical practice variation

BIME 591A-Information Visualization in Health Care

Tuesdays, 12:30 pm-1:20 pm; Heath Sciences Building, Room RR134

Facilitator: Ari Pollack

 BIME 591B-Exploring Epidemic Modelling

Wednesdays, 12:30 pm-1:20 pm; Health Sciences Building, Room T 360+A

Facilitators: Juandalyn Burke

February 17-February 21, 2020

PUBLICATIONS

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. Poster to be presented at 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. Poster to be presented at 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. Poster to be presented at AMIA Clinical Informatics Conference 2020.

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. Poster to be presented at AMIA Clinical Informatics Conference 2020.

Kim, S, Appelbaum, NP, Baker, N, Bajwa, NM, Chu, F, Pal, JD, Cochran, N, Bochatay, N. Patient Safety over Power Hierarchy: A Scoping Review of Healthcare Professionals’ Speaking-Up Skills Training. Accepted to Journal of Healthcare Quality.

February 10-February 14, 2020

PUBLICATIONS

William R. Kearns, Nai-Ching Chi, Yong K. Choi, Shih-Yin Lin, Hilaire Thompson, George Demiris. A Systematic Review of Health Dialog Systems. Methods of Information in Medicine. 2020.

William R. Kearns, Neha Kaura, Myra Divina, Cuong Vo, Dong Si, Teresa, M Ward, Weichao Yuwen. A Wizard-of-Oz Interface and Persona-based Methodology for Collecting Health Counseling Dialog. In: Proceedings of the 2020 CHI Conference on Human Factors.

February 3-February 7, 2020

PUBLICATIONS

LeRouge, C.,  Sangameswaran, S., Frogner, B., Snyder, C., Rubenstein V. L., Kirsh, S., Sayre, G., The Group Practice Manager in the VHA: A View From the Field, Federal Practitioner 37(2).

UPCOMING GENERAL EXAM

Will Kearns

Friday, February 14 at 9:30 am; South Lake Union, Orin Smith Auditorium

Title: Enhancing Empathy: Toward Emotionally Aware Conversational Agents for Caregivers

Abstract: Chronic health conditions affect one in four children in the United States. Their family caregivers are more likely to experience mental health symptoms related to anxiety and depression. These symptoms can reduce the ability of caregivers to provide treatment according to clinical recommendations which leads to poorer health outcomes and increased risk of hospitalization for the child. Yet, these conditions often go undiagnosed and untreated since caregiver mental health status is not part of standard practice. This contributes to health disparity between families with regular access to care and those without. While telemedicine solutions have the potential to increase access to mental health therapy, the cost of these services may be prohibitive for many patients.

Health dialog systems (HDS) can help to scale mental health therapy to more patients at reduced cost. Already, HDS have seen increased adoption by patients, hospital systems, and researchers due to a confluence of advancements in machine learning and the ubiquity of high-performance hardware that supports real-time speech recognition, high-fidelity text-to-speech, and semantic understanding of natural language. Commercial digital assistant platforms have made HIPAA-compliant HDS accessible to patients that allow them to update their care team on their recovery progress, track their blood sugar, and receive educational health information. HDS have no practical scale limitations and can be delivered as a mobile application to increase global access to on-demand mental health support. However, maintaining patient engagement with these systems will require addressing the current inability for HDS to achieve theory of mind and to respond empathetically based on this understanding.

The central hypothesis of this work is that recent advances in knowledge-based language models can be leveraged to achieve clinical empathy in HDS by inferring and verifying the mental states of a patient in health counseling dialog and generating responses conditioned on these states to improve rapport and provide relevant therapeutic content. Further, this work develops and evaluates a tool and framework to support health practitioners in training statistical HDS that support this capability, thus relieving the burden of maintaining rule-based systems that have been superseded by data-driven approaches in the general domain.

OTHER

The New York Times Data Editor, Amanda Cox, will be speaking at UW May 7th. Topic will be on communicating data and models to mass audiences.

Registration opens March 4th. These talks tend to book quickly (like a few days after tickets are offered) so it is worth announcing now so people can mark their calendars for March 4th.

https://grad.uw.edu/public-lecture-series/amanda-cox/

January 22-January 31, 2020

NEWS

In early 2019, the Clinical Sequencing Evidence-Generating Research (CSER) consortium’s U01 projects and the coordinating center (CC; P.I.s: Jarvik, Veenstra, Nickerson, Fullerton, Tarczy-Hornoch) signed a data use agreement (DUA) outlining processes and procedures for the sharing of data within CSER for scientific projects. Building on this effort, and to further support the sharing of data within, the CSER CC requested and received a multi-year supplemental award in late 2019 to manage the harmonized outcomes and measures, and sequence data, and to have the CC serve as a data coordinating center (DCC).  The proposed ecosystem is one of the first National Human Genome Research Institute (NHGRI) programs to leverage the Genomic Analysis, Visualization, and Informatics Lab-space (AnVIL) resource for data deposition, storage, and retrieval. University of Washington investigators Kathleen Muenzen and David Crosslin are leading these efforts at the CSER CC.

PUBLICATIONS

MONROE-WISE, Aliza et al. Improving Information and Communications Technology (ICT) Knowledge and Skills to Develop Health Research Capacity in Kenya. Online Journal of Public Health Informatics, [S.l.], v. 11, n. 3, dec. 2019. ISSN 1947-2579. Aliza Monroe-Wise, John Kinuthia, Sherrilynne Fuller, Matthew Dunbar, David Masuda, Elisha Opiyo, Betty Muchai, Christopher Chepken, Elijah Omwenga, Robert Oboko, Alfred Osoti, Daniel Masys, Michael H Chung

Available at: <https://journals.uic.edu/ojs/index.php/ojphi/article/view/10323>. Date accessed: 30 Jan. 2020. doi:https://doi.org/10.5210/ojphi.v11i3.10323.

Shefali Haldar, Sonali R. Mishra, Yoojung Kim, Andrea Hartzler, Ari H Pollack, Wanda Pratt. Use and Impact of an Online Community for Hospital Patients. Journal of the American Medical Informatics Association (JAMIA). https://doi.org/10.1093/jamia/ocz212

OTHER

Population Health Initiative: Feature Wall Content for the Hans Rosling Center for Population Health

A key component of the new Hans Rosling Center for Population Health – opening this summer – is telling the story of the major advances, achievements, and contributors to improvements in population health (i.e., human health, environmental resilience, social and economic equity) that have occurred both domestically and internationally.

We’re hoping to secure broad input to help show how each of the university’s disciplines have contributed to improvements in health and well-being. This input will be converted to short passages of text that are laser engraved on wooden blocks that make up the feature walls next to main building entrances.

Feedback is welcome from all faculty, students, and staff of the UW. The survey will close at 5 p.m. (Pacific) on Tuesday, February 18, 2020. More information can be found by visiting our website (link) or the survey itself (https://is.gd/rosling_center).

January 20-January 24, 2020

NEWS

Please join the University of Washington School of Medicine at the Western Group on Educational Affairs (WGEA) annual meeting, March 28-31, 2020, at the beautiful Asilomar Conference Center in Pacific Grove, CA.

WGEA Conference Co-Chairs: Lynne Robins, Ph.D., Joshua Jauregui, M.D.

This conference will celebrate the many ways WGEA members are working toward “Finding Common Ground” within and across communities. Our theme borrows principles from improvisational theater to provide a language for discussing the attitudes and skills that allow collaborative exchange and advancement within medical education.

https://www.wgea2020.com/

January 13-January 17, 2020

NEWS

UWFM Research Section Head Matthew Thompson and colleagues awarded funding by Gordon & Betty Moore Foundation. Kari Stephens, PhD, Meliha Yetisgen, PhD

https://depts.washington.edu/fammed/blog/uwfm-research-section-head-matthew-thompson-and-colleagues-awarded-funding-by-gordon-betty-moore-foundation/

PUBLICATIONS AND PRESENTATIONS

Mittler, John E., James T. Murphy, Sarah E. Stansfield, Kathryn Peebles, Geoffrey S. Gottlieb, Neil F. Abernethy, Molly C. Reid, Steven M. Goodreau, and Joshua T. Herbeck. “Large benefits to youth-focused HIV treatment-as-prevention efforts in generalized heterosexual populations: An agent-based simulation model.” PLoS Computational Biology 15, no. 12 (2019).

Byun J, Schliep KC, Peterson CM, Backonja U, Taylor RN, Stanford JB, Allen-Brady KL, Smith KR, Buck Louis GM. Adiposity and endometriosis severity and typology. The Journal of Minimally Invasive Gynecology (in press). 2020. doi: 10.1016/j.jmig.2020.01.002

Cheng SC, Backonja U, Buck B, Monroe-DeVita M, Walsh E. Facilitating pathways to care: A qualitative study of the self-reported needs and coping skills of caregivers of young adults diagnosed with early psychosis. Journal of Psychiatric and Mental Health Nursing (in press). 2020. doi: 10.1111/jpm.12591.

Ari H. Pollack, MD; Wanda Pratt, PhD. Association of Health Record Visualizations With Physicians’ Cognitive Load When Prioritizing Hospitalized Patients. https://jamanetwork.com/journals/jamanetworkopen/fullarticle/2758744

Timothy Bergquist, Vikas Pejaver, Noah Hammarlund, Sean D. Mooney & Stephen J. Mooney. Evaluation of the secondary use of electronic health records to detect seasonal, holiday-related, and rare events related to traumatic injury and poisoning. BMC Public Health volume 20, Article number: 46 (2020) https://bmcpublichealth.biomedcentral.com/articles/10.1186/s12889-020-8153-7

OTHER

BIME Happy Hour “Post-Holiday Blues” theme
Thursday, January 23, 5:00 p.m., South Lake Union, Reception Lounge

Please join us for our monthly departmental BYOB Happy Hour, held every third Thursday of the month. As always, please bring your own beverage; snacks will be provided. Games and Prizes!

January 6-January 10, 2020

NEWS

Bryant T. Karras, MD, Washington State Department of Health and Thomas H. Payne, MD, UW Medicine ITS/University of Washington are on the program committee … there may be student volunteer opportunity will let you know as soon as we hear.

Registration Open: AMIA 2020 Clinical Informatics Conference

The AMIA 2020 Clinical Informatics Conference (CIC) registration is now open! This is your chance to save with your members-only discount through March 26.

CIC, May 19-21 in Seattle, is where all members of the health care team come together. Our collective goal is to advance healthcare systems driven by data, evidence, and best practice with the explicit purpose of creating better health information technologies.

Last year’s conference was our largest to date, and this year we received nearly twice the number of submissions!

The program committee is working to create the best possible conference experience.

Register now to get your exclusive savings!

PUBLICATIONS AND PRESENTATIONS

J. Sabin. How we fail black patients in pain | AAMC. Half of white medical trainees believe such myths as black people have thicker skin or less sensitive nerve endings than white people. An expert looks at how false notions and hidden biases fuel inadequate treatment of minorities’ pain. www.aamc.org

Tsai, G., Chen, A. T., Garrett, L. T., Burke, W., Bowen, D. J., & Shirts, B. H. (in press). Exploring relatives’ perceptions of participation, ethics, and communication in a patient-driven familial genetics study. Journal of Genetic Counseling.DOI: 10.1002/jgc4.1215

Conway, M., Hu, M., Benson, R., Zhu, S.-H., Chen, A. T. (accepted). Tracking the evolving relationship between tobacco, marijuana, and e-cigarettes using Reddit. Poster to be presented at Society for Research on Nicotine and Tobacco (SRNT) 2020 Annual Meeting. New Orleans, Louisiana.

Lor M, Backonja U. Visualizations to Support Self-Management of Chronic Diseases in the Community: A Systematic Review. CIN: Computers, Informatics, Nursing. 2019 [Epub ahead of print]. doi: 10.1097/CIN.0000000000000583.

OTHER

BIME Happy Hour “Post-Holiday Blues” theme
Thursday, January 16, 5:00 p.m., South Lake Union, Reception Lounge

Please join us for our monthly departmental BYOB Happy Hour, held every third Thursday of the month. As always, please bring your own beverage; snacks will be provided. Games and Prizes!