Thursday, April 8, 2021

Response to NIH RFI: Comments and Suggestions to Advance and Strengthen Racial Equity, Diversity, and Inclusion in the Biomedical Research Workforce and Advance Health Disparities and Health Equity Research

In addition to its public health problems, the COVID-19 pandemic has exposed other fault lines in society, not the least of which is systematic racism that still pervades American society. A more equitable society would ensure diversity and inclusion in all aspects of life, including in healthcare and in biomedical research. The National Institutes of Health (NIH), the premier US federal agency that funds biomedical research, has recognized the need for its activities to be more inclusive of all Americans from every background. Not only must biomedical research reflect the health issues for the entire US population, its workforce should ideally reflect the ethnic and racial makeup of our larger society. The NIH recently issued a request for information (RFI), asking for Comments and Suggestions to Advance and Strengthen Racial Equity, Diversity, and Inclusion in the Biomedical Research Workforce and Advance Health Disparities and Health Equity Research. This posting contains the comments I submitted in response to this RFI.

While others will likely comment on the need for biomedical research itself to address health disparities and move toward health equity, it is equally important to address the needs of the biomedical research workforce that will contribute solutions to these problems. The NIH has already made a tremendous commitment to diversity and inclusion, including in building career pathways the biomedical research workforce, but additional efforts must be made to facilitate access to these programs by extramural researchers and leaders.

One example is the Building Infrastructure Leading to Diversity (BUILD) Initiative, which has a prominent program in our region.

Nonetheless, there are still challenges for engaging the potential future biomedical research workforce. My particular concern is how to increase diversity and inclusion among faculty of academic health science centers.

One of the challenges is explaining to young minds the opportunity and the work of biomedical research. While most young people are familiar with healthcare professionals - i.e., physicians, nurses, and pharmacists - fewer are familiar with the work and importance of researchers. Schools and communities themselves may not be aware of career opportunities. There should be resources committed, and easy-to-use tools made available, so that academic health science centers and others can disseminate information about careers and the rewarding work of biomedical research.

A second challenge is for researchers themselves to have the time to engage in such mentoring and teaching. As demands for productivity by biomedical research faculty in academic health science centers increase - i.e., keep grants funded and students taught - there is less time in their busy schedules for this critical activity. Such activity is also unlikely to "count" toward promotion or lead to that next grant. There should be standards for promotion committees in academic health science centers to require diversity and inclusion outreach. Of course, this must not be an "unfunded mandate," and instead be an activity that has committed time from institutions.

A third challenge is that success in biomedical research typically requires a graduate degree. As such, the road to college and then graduate or professional school is long and can be expensive. There must be pathways for students, especially for those of limited resources with few parental or other role models, to be helped through that long path. There should be opportunities provided, along with appropriate mentoring, for students to enable them to stay engaged during the long journey. Students should not only be given sustained exposure, but also be taught knowledge and skills along the way.

My own work is as an academic faculty in biomedical and health informatics, where I daily experience the satisfaction of research and teaching. While my field has made some strides in diversity and inclusion, it still has a long way to go to reflect our the racial and ethnic distribution of our larger society. Many who want to spend time engaging with future diverse researchers and professionals in the field need help in overcoming the above barriers. This leads to questions that must be answered:

  1. How do we engage with schools, community organizations, and others to expose high school and perhaps even younger students to biomedical research?
  2. How do we provide academic faculty with the protected time and academic credit for this work of critical importance?
  3. How do we develop pathways to sustain the interest and achievement for students, especially those from backgrounds that include little exposure to higher education?

We can and should require our academic health science centers and their faculty and others to engage with historically underrepresented groups in biomedical research, but make sure that they have the time and the tools, with milestones and outcomes measured, to achieve these goals. This should consist of:

  1. The availability of resources and tools to engage young minds in the possibilities for careers in biomedical research
  2. Expectations and protected time for existing faculty to devote effort to engaging with young students, including requirements to achieve promotion
  3. Developing pathways to sustain interest and achievement toward careers in biomedical research

By making diversity and inclusion efforts an expected activity of all biomedical research faculty and providing such faculty the resources and opportunities, we can achieve the shared aim of the biomedical research workforce and its activities reflecting the larger population of our country.

Thursday, February 25, 2021

A New OHSU Course in Applied Clinical Data Science and Machine Learning for Health & Clinical Informatics (HCIN) Students

I have written over the years about the need for all who work in biomedical and health informatics to have appropriate knowledge and skills in data science, machine learning (ML), artificial intelligence (AI), and related topics. I am now excited to announce that our OHSU Biomedical Informatics Graduate Program is launching a new course in Applied Clinical Data Science and Machine Learning for Health & Clinical Informatics (HCIN) majors.

The goal of this new course is not to provide students with the mastery of ML and AI tools and techniques; rather, it is to provide a conceptual understanding of their practical application in health and biomedicine. The course is not meant to be a substitute for the sequence of courses available in the other major in our program, Bioinformatics & Computational Biomedicine (BCB), whose offerings delve far more into the theory, mathematics, and programming of these topics and include:

  • BMI 551/651 - Statistical Methods
  • BMI 531/631 - Probability and Statistical Inference
  • BMI 543/643 - Machine Learning
  • BMI 525/625 - Principles and Practice of Data Visualization

The new HCIN course will be focused on applied data science and machine learning, with a focus on clinical data sets as well as clinical issues and challenges in their application. While the course will have some programming activity (requiring Python programming as a prerequisite), it will focus on a hands-on, high-level view of the different types of machine learning methods and their applications. It will also cover the topics of data management and selection, pitfalls in building and deploying models, and critical appraisal of clinical machine learning literature. The course will aim to provide an in-depth understanding for those who will work alongside experts who develop, build models, implement, and evaluate machine learning applications in health and clinical settings.

The textbook for the course will be: Hoyt, R. and Muenchen, R. (Eds.), 2019. Introduction to Biomedical Data Science, Lulu.com. The course syllabus provides further details on the topics to be covered.

The content of the course will be based on a combination of what faculty and students believe is most important for a course like this. Among the topics that be included are:

  • Data sources - electronic health records, registries (e.g., N3C, AllOfUs), patient-generated, social media, public health
  • Data preparation (wrangling) - cleaning, quality analysis, feature selection, de-biasing
  • Exploratory data analysis - summaries, correlations, visualizations
  • Machine learning approaches and models - supervised, unsupervised, reinforcement, deep learning
  • Software and tools available
  • Common pitfalls and misunderstandings of applying machine learning
  • Critical appraisal of clinical machine learning literature
  • Ethical issues and challenges

The 3-credit course will be taught in the OHSU spring academic quarter, which runs from late March to early June. The lead instructors will be Steven Chamberlin, ND and myself, with other department faculty contributing. As with all courses in the HCIN major, it will be mostly online and asynchronous, with some option synchronous activities (which will be recorded for those not able to attend). This course will be different from to complementary to other data science-related courses in the HCIN major, including:

  • BSTA 525 - Introduction to Biostatistics
  • BMI 540/640 - Computer Science and Programming for Clinical Informatics
  • BMI 544/644 - Databases
  • BMI 524/624 - Data Analytics for Healthcare
  • BMI 516/616 - Standards/Interoperability in Healthcare
  • BMI 537/637 - Healthcare Quality
  • BMI 525/625 - Principles and Practice of Data Visualization

I will be excited to see how this course is accepted and how it evolves based on feedback of students and others. I suspect there will be interest beyond our graduate program.

Monday, February 22, 2021

Vaccinated and Vaccinating: The End May Be Near?

I was delighted to learn in early January that my institution, Oregon Health & Science University (OHSU), made the decision like many medical centers to offer the SARS-CoV-2 vaccine to all employees, not just those at the front line of care delivery. I received my first and second doses of the Pfizer vaccine on January 2nd and 23rd. I had some minor malaise the day after the second dose, but was thrilled to have received the vaccine.

I also decided that since I received an early dose, I would do everything I could to support the national and global effort to disseminate the vaccine. To that end, I have volunteered to work shifts at the OHSU Portland International Airport Vaccine Clinic. While I thought I might put my medical training to use giving injections, it turns out that the greater need was for registration and check-in personnel. I suppose it is most appropriate for the Chair of the informatics department to be checking in and scheduling follow-up appointments in Epic for those coming for their shots. But I actually enjoy the job I am doing at the site, interacting with people driving through the site and expressing gratitude they are able to get vaccinated. It is also nice to put on a friendly face for our university.

Overall, I feel a sense that the end may be near for the worst of this pandemic that has upended our lives. While the complete end will not come any time soon, and we will likely need to be vigilant about SARS-CoV-2 for years to come, I am hopeful that the vaccine rollout will continue at a strong pace and allow us to gradually resume more normal living. I am also encouraged that the COVID-19 numbers of cases, hospitalizations, and deaths are trending downward, and that we have new science-driven leadership in our federal government.

Looking ahead, I yearn to be around people at work, in social settings, and, yes, traveling. Regarding the latter, it has been almost a year since I have been on an airplane, although I am planning to visit my elderly stepfather, my last living adult relative, next month in Florida. He will have received his second dose a couple weeks before I visit.

There are many unanswered questions about what life will be like in the long run. Will work move to a more virtual arrangement? What will come of city centers that have been hurt by the pandemic and resulting economic and social upheaval? What will come of academic meetings and conferences, many of which probably could be done more virtually? Even though I spend a great deal of work time in front of a computer, I am still a social being. Social media has taken the sting off of the interpersonal isolation, but there is nothing like being around other people, and I am hopeful that much of that will eventually return. We will see as 2021 unfolds.