VLDB 2026 Research / reviewers in the wild / expert
Vignesh Subbian
dblp:193/4470
· DBLP profile ↗
21ranked-venue papers
3as first author
15since 2021 · last 2026
0000-0001-9974-8382ORCID · corroborated
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 20 · 2 first-author · 15 since 2021Human-computer interaction and ubiquitous computing · 1 · 1 first-author
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2026 | Graph-spa: A Spatiotemporal Graph Neural Network based framework for ARDS prediction and interpretability
Shashank Yadav, Molly Douglas, Jarrod Mosier, Vignesh Subbian |
J. Biomed. Informatics | 4 |
| 2025 | Developing and sustaining inclusive language in biomedical informatics communications: an AMIA Board of Directors endorsed paper on the Inclusive Language and Context Style GuidelinesabstractOBJECTIVES: In 2023, AMIA's Inclusive Language and Context Style Guidelines (the "Guidelines") were approved by the Board of Directors and made a publicly available resource. This work began in 2021 through AMIA's DEI Task Force and subsequent DEI Committee; many members provided input, feedback, and time to create the Guidelines. In this paper, the authors provide a transparent account of the origin, development, contents, and dissemination of the Guidelines and share plans for their future development and use. MATERIALS AND METHODS: Our approach to drafting, refining, and distributing the Guidelines included consulting existing language guides, AMIA member reviews, external expert reviews, webinars, and workshops. Through an iterative approach to drafting and refining the Guidelines, the authors consulted relevant language guidelines and many experts throughout and beyond the AMIA community. RESULTS: The Inclusive Language Context Guidelines were formally approved by the AMIA Board of Directors on February 15, 2023. The Guidelines included four principles to be considered in scientific communications: Plurality, Precision, Transparency, and Destigmatization. DISCUSSION: A moment of vulnerability where an AMIA member raised concerns about the use of harmful language during a presentation resulted in the creation of a principled approach to support inclusive language within biomedical and health informatics communications. We envision that the Guidelines will support health equity by challenging dominant public narratives around health, fostering stronger interdisciplinary collaboration and critical thinking about the impact of language, and creating a more welcoming environment for the broader AMIA community. This work could not have been completed without the support of many AMIA members and other researchers in biomedical and health informatics. The Guidelines are a living document that will continue to be updated with input and feedback from the AMIA community into the future. Oliver J. Bear Don't Walk IV, Shefali Haldar, Duo Helen Wei, Hu Huang 0004, Rebecca L. Rivera, Jungwei Fan 0001, Vipina Kuttichi Keloth, Tiffany I. Leung, Pooja M. Desai, Diane M. Korngiebel, Lisa Grossman Liu, Adrienne Pichon, Vignesh Subbian, Tony Solomonides, Laura K. Wiley, Omolola Ogunyemi, Gretchen Purcell Jackson, Irene Dankwa-Mullan, Lisa Dirks, Avery Rose Everhart, Andrea G. Parker, Bradley E. Iott, Clair A. Kronk, Randi E. Foraker, Krista G. Martin, Tara Anand, Salvatore G. Volpe, Nathan Yung, Rubina F. Rizvi, Robert James Lucero, Tiffani J. Bright |
J. Am. Medical Informatics Assoc. | 13 |
| 2025 | National COVID Cohort Collaborative data enhancements: a path for expanding common data modelsabstractOBJECTIVE: To support long COVID research in National COVID Cohort Collaborative (N3C), the N3C Phenotype and Data Acquisition team created data designs to aid contributing sites in enhancing their data. Enhancements include long COVID specialty clinic indicator; Admission, Discharge, and Transfer transactions; patient-level social determinants of health; and in-hospital use of oxygen supplementation. MATERIALS AND METHODS: For each enhancement, we defined the scope and wrote guidance on how to prepare and populate the data in a standardized way. RESULTS: As of June 2024, 29 sites have added at least one data enhancement to their N3C pipeline. DISCUSSION: The use of common data models is critical to the success of N3C; however, these data models cannot account for all needs. Project-driven data enhancement is required. This should be done in a standardized way in alignment with common data model specifications. Our approach offers a useful pathway for enhancing data to improve fit for purpose. CONCLUSION: In this initiative, we rapidly produced project-specific data modeling guidance and documentation in support of long COVID research while maintaining a commitment to terminology standards and harmonized data. Kellie M. Walters, Marshall Clark, Sofia Dard, Stephanie S. Hong, Elizabeth Kelly, Kristin Kostka, Adam M. Lee, Robert T. Miller, Michele Morris, Matvey Palchuk, Emily R. Pfaff, Adam B. Wilcox, Alexis Graves, Alfred Anzalone, Amin Manna, Amit Saha, Amy Olex, Andrea Zhou, Andrew E. Williams, Andrew Southerland, Andrew T. Girvin, Anita Walden, Anjali A Sharathkumar, Benjamin R. C. Amor, Benjamin Bates, Brian Hendricks, Caleb Alexander, Carolyn T. Bramante, Cavin Ward-Caviness, Charisse R. Madlock-Brown, Christine Suver, Christopher G. Chute, Christopher Dillon, Chunlei Wu, Clare Schmitt, Cliff Takemoto, Dan Housman, Davera Gabriel, David Eichmann, Diego Mazzotti, Don Brown, Eilis A. Boudreau, Elaine L. Hill, Elizabeth Zampino, Emily Carlson Marti, Evan French, Farrukh M. Koraishy, Federico Mariona, Fred W. Prior, George Sokos, Greg Martin, Harold P. Lehmann, Heidi Spratt, Hemalkumar Mehta, Hythem Sidky, J. W. Awori Hayanga, Jami Pincavitch, Jaylyn Clark, Jeremy Richard Harper, Jessica Islam, Jin Ge, Joel Gagnier, Joel H. Saltz, Johanna Loomba, John Buse, Jomol P. Mathew, Joni L. Rutter, Julie A. McMurry, Justin Guinney, Justin Starren, Karen Crowley, Katie Rebecca Bradwell, Ken Wilkins, Kenneth R. Gersing, Kenrick Dwain Cato, Kimberly Murray, Lavance Northington, Lee Allan Pyles, Leonie Misquitta, Lesley Cottrell, Lili M. Portilla, Mariam Deacy, Mark M. Bissell, Mary Emmett, Mary Morrison Saltz, Melissa A. Haendel, Meredith C. B. Adams, Meredith Temple-O'Connor, Michael G. Kurilla, Nabeel Qureshi, Nasia Safdar, Nicole Garbarini, Noha Sharafeldin, Ofer Sadan, Patricia A. Francis, Penny Wung Burgoon, Peter N. Robinson, Philip R. O. Payne, Rafael Fuentes, Randeep Jawa, Rebecca Erwin-Cohen, Rena Patel, Richard A. Moffitt, Richard L. Zhu, Rishi Kamaleswaran, Robert Hurley, Saiju Pyarajan, Samuel G. Michael, Samuel Bozzette, Sandeep Mallipattu, Satyanarayana Vedula, Scott Chapman, Shawn T. O'Neil, Soko Setoguchi, Tellen D. Bennett, Tiffany Callahan, Umit Topaloglu, Usman Sheikh, Valery Gordon, Vignesh Subbian, Warren A. Kibbe, Wenndy Hernandez, Will Beasley, Will Cooper, William Hillegass, Xiaohan Tanner Zhang |
J. Am. Medical Informatics Assoc. | 123 |
| 2023 | A self-supervised learning-based approach to clustering multivariate time-series data with missing values (SLAC-Time): An application to TBI phenotyping
Hamid Ghaderi, Brandon Foreman, Amin Nayebi, Sindhu Tipirneni, Chandan K. Reddy, Vignesh Subbian |
J. Biomed. Informatics | 6 |
| 2023 | WindowSHAP: An efficient framework for explaining time-series classifiers based on Shapley values
Amin Nayebi, Sindhu Tipirneni, Chandan K. Reddy, Brandon Foreman, Vignesh Subbian |
J. Biomed. Informatics | 5 |
| 2022 | Assessment of Real-World Health Applications on FHIR
Ashley C. Griffin, Anthony Sunjaya, Zubin Khan, Brian J. Douthit, Martin Nwadiugwu, Vignesh Subbian, Mark Braunstein, Viet Nguyen, Charles Jaffe, Titus Schleyer |
AMIA | 8 |
| 2022 | An Empirical Comparison of Explainable Artificial Intelligence Methods for Clinical Data: A Case Study on Traumatic Brain Injury
Amin Nayebi, Sindhu Tipirneni, Brandon Foreman, Chandan K. Reddy, Vignesh Subbian |
AMIA | 5 |
| 2022 | 25 Years of ELSI in Biomedical and Health Informatics
Vignesh Subbian, Melissa D. Clarkson, Carolyn Petersen, Tony Solomonides, Kenneth W. Goodman |
AMIA | 1 |
| 2022 | Selecting venues for AMIA events and conferences: guiding ethical principlesabstractA discussion and debate on the American Medical Informatics Association's (AMIA) Ethical, Legal, and Social Issues (ELSI) Working Group listserv in 2021 raised important issues related to a forthcoming conference in Texas. Texas had recently enacted a restrictive abortion law and restricted voting rights. Several AMIA members advocated for a boycott of the state and the scheduled conference. The discussion led the AMIA Board of Directors to request that the organization's Ethics Committee provide general guidance for principle-based venue selection. This document recommends overarching principles for the venue selection for future AMIA events and conferences. Discussions by the AMIA Board, the Ethics Committee, and the ELSI Working Group informed these recommendations, and this document on guiding principles was approved by the AMIA Board of Directors in April 2022. Christoph U. Lehmann, Kate Fultz Hollis, Carolyn Petersen, Paul DeMuro, Vignesh Subbian, Ross Koppel, Tony Solomonides, Eta S. Berner, Eric C. Pan, Julia Adler-Milstein, Kenneth W. Goodman |
J. Am. Medical Informatics Assoc. | 5 |
| 2022 | AMIA's code of professional and ethical conduct 2022abstractAMIA has a longstanding interest and a professional obligation to promote a strong ethical framework for its members and the field of biomedical and health informatics. This white paper presents the latest AMIA Code of Professional and Ethical Conduct. The original code was approved in 20071 by the AMIA Board of Directors and revised in 2013.2 Recognizing the need to regularly update the Code to ensure that it remains current and relevant, we present this document that constitutes a revision of and update to the third version, approved and published in the Journal of the American Medical Informatics Association in 2018.3 The code presented here remains an evolving document, with modifications expected as information technology, informatics, policy, and health care environments change over time. AMIA publishes on its web site the most recent version of the Code of Ethics as part of a process that seeks ongoing response from and involvement by AMIA members. Because the Code of Professional and Ethical Conduct (from now on “Code of Ethics”) is meant to be practical, applicable in real life, and easily understood, it is compact and uses general language. The AMIA Code of Ethics is not intended to be prescriptive or legislative; it is aspirational and extends beyond regulatory and legal obligations to provide the broad strokes of a set of important ethical principles pertinent to the field of biomedical and health informatics. The Code is organized around the common roles of AMIA members and the constituents they serve including patients, caregivers, colleagues and collaborators, clinicians, researchers, students, agencies, hospitals and practices, medical organizations, vendors, insurance companies, and others with whom they interact. The AMIA Board of Directors and the AMIA Ethics Committee encourage members to offer suggestions for improvements and changes. In this way, the Code will continue to evolve to best serve AMIA and the larger informatics community. AMIA members are professionally diverse,4,5 and include those who are, or are in training to be nurses, physicians, pharmacists, dentists, informaticians, computer scientists, analysts, implementation scientists, and other professionals. In many cases, these professions have their own codes of ethics.6–13 The International Medical Informatics Association, an international federation for which AMIA serves as the US membership organization, also has a revised “Code of Ethics for Health Information Professionals”.14 The AMIA Code of Ethics incorporates issues covered by other documents bearing on ethics and professional conduct: AMIA’s support for and efforts to incorporate and execute upon diversity, equity, inclusion, and accessibility goals and objectives throughout the organization.15 AMIA’s revised “Conflict of Interest Policy”, which governs the organization’s employees and leaders with regard to some of their financial and other interactions with outside entities.16 AMIA’s principles for selecting venues for conferences and other events, which affirm AMIA’s commitment to applying ethical principles and ensuring basic human rights when planning association events.17 AMIA’s “Meeting Anti-Harassment Policy”, which describes AMIA’s commitment to providing an atmosphere that is safe and welcoming to all members and supports learning and professional growth.18 AMIA’s principles for artificial intelligence (AI)19 and position on the appropriate development, use, and maintenance of adaptive clinical decision support.20 Members of the Ethics Committee are unanimous in their view that those who work in informatics, much as in other health professions, are duty-bound to embrace a patient-centered approach to their work, even if that work does not involve direct patient care or research involving human participants. As elsewhere in the health professions, vulnerable populations, historically and intentionally excluded/disinvested groups, and people with disabilities may reasonably expect additional considerations and support. The importance of professionalism and ethics has been recognized for millennia by health professionals and organizations,21 now including informaticians and information technology professionals. This code of ethics emphasizes AMIA’s commitment to adhere to and promote the highest standard of ethical and professional behavior. AMIA members acknowledge as their professional duty to uphold the following principles of and guidelines for ethical conduct. AMIA members are expected to know how to seek the advice of institutional ethics committees, AMIA’s Ethics Committee, or appropriate institutional review boards, as necessary. The following details address patient care, interactions with colleagues, responsibilities to employers, and roles regarding society and research. I. Key ethical guidelines regarding patients, guardians, and their authorized representatives (called here collectively “patients”) AMIA members involved in patient care should: Recognize that patients and their loved ones and caregivers have the right to know about the existence and use of electronic records containing their personal health and healthcare information, to access these records as written, and have the right to create and maintain their own personal health records and manage personal health information using a variety of platforms including mobile devices. In this context AMIA members should: Not mislead patients about the collection, use, or communication of their health information. Educate—when requested and within reason and the scope of their position—patients on the type, amount, and use of health information collected. Enable and—as appropriate, within reason and the scope of their position and in accord with independent ethical and legal standards—facilitate patients’ rights and ability to access, review, and correct their electronic health information, including clinicians’ notes. Recognize that patient-provided/generated health data, such as those collected on mobile devices and wearable devices, deserve the same diligence and protection as biomedical and health data gathered in the process of providing health care. Ensure that patients and their care team members are made aware of the role and use of AI and other complex automated tools that are not clearly apparent when such systems are involved in medical decision-making or care planning.19,20 Advocate and work as appropriate to ensure that protected health information (PHI),22 personally identifiable information (PII), and other biomedical data are acquired, recorded, stored, maintained, analyzed, transmitted, and communicated in an appropriately safe, reliable, secure, and confidential manner, and that such data management is consistent with applicable laws, local privacy and security policies, and accepted informatics standards. Never knowingly disclose PHI, PII, or biomedical or health data in violation of legal requirements or accepted local confidentiality practices, or in ways that are inconsistent with the explanation of data disclosure and use to the patient.23 AMIA members should understand that inappropriate disclosure of biomedical information can cause harm, and so should work to prevent such disclosures. AMIA members should avoid acquiring data through means that run the risk of, or fail to prevent, inappropriate disclosure. AMIA members should not accept, use, disseminate, or store data that they are aware were obtained in violation of applicable laws. Likewise, even if an action does not involve disclosure, one should not use or reuse—or through negligence permit the use of—patient information and data in ways inconsistent with the stated purposes, goals, or intentions of the patient or organization responsible for these data, except as appropriate for public health, previously approved and communicated research uses, quality improvement, or reporting as required under the law. Engage with patients, guardians, and their authorized representatives so as to support inclusion, promote equity, advance accessibility, and avoid bias and discrimination. II. Key ethical guidelines regarding colleagues AMIA members should: Endeavor, as appropriate, to support and foster colleagues’ and/or team members and their work, in a timely, respectful, and conscientious way to support their roles in healthcare and/or research and education. Support and foster the efforts of patients to be actively involved in the collection, management, and curation of their health data. Advise colleagues and others, as appropriate, about actual or potential information or systems issues (including system flaws, defects, usability or performance issues, etc.) that negatively affect patient safety, privacy, data security, or health outcomes or could hinder colleagues’ abilities to delegate responsibilities to patients, other colleagues, involved institutions, or other stakeholders. Actively support the inclusion of all professional colleagues and promote a diverse and inclusive environment in which all individuals have equitable access to resources, educational opportunities, and opportunities for professional advancement.15 An AMIA member in any leadership position should: Be familiar with these guidelines and their applicability to their practice, unit, or organization. Communicate as appropriate about these ethical guidelines to those they lead. Strive to promote familiarity with, and use of, these ethical guidelines. Use AMIA position statements to guide organizational decision-making with regard to diversity, equity, inclusion, and accessibility initiatives,15 including selection of event locations.17 Promote transparent and equitable decision-making among AMIA professional staff, volunteer member leaders, and others with whom they engage. Never allow personal political views or ideological stances to interfere with or impede their ability to represent AMIA and advocate for it. AMIA leaders who may pose a reputational liability to the organization due to criminal convictions should declare this information and be prepared to stand down from leadership positions. Members who may pose a reputational liability should recuse themselves from leadership positions. III. Key ethical guidelines regarding institutions, employers, business partners, and clients (called here collectively “employers”) AMIA members should: Understand their duties and obligations to current and former employers and fulfill them to the best of their abilities within the bounds of ethical and legal norms. Understand and appreciate that employers have legal and ethical rights and obligations, including those related to intellectual property. Understand and respect the obligations of their employers and comply with local policies and procedures to the extent that they do not violate ethical and legal norms. Consider the tradeoffs that occur with the configuration and use of technologies (eg, decision support systems) before implementation, and monitor, measure, and manage results when the optimal approach is unclear. Inform the employer and act in accordance with ethical-legal mandates and patient rights when employer actions, policies, or procedures would violate actual or understood ethical or legal obligations, contracts, or other agreements made with patients. Maintain a safe and high-quality environment even while implementing innovation, recognizing that all changes in a complex adaptive environment generate unanticipated consequences and potential harm. IV. Key ethical guidelines regarding society and regarding research AMIA members involved in research should: Be aware of the Declaration of Helsinki (Ethical Principles for Medical Research Involving Human Subjects), the Nuremberg Report, and the Belmont Report, which should guide all human subjects research, including research that involves users of informatics tools and interventions as participants (eg, workflow analysis studies, evaluation of clinical decision support systems, patient care innovations, analysis, etc.).24–27 Recognize that duty and care to individuals such as patients and colleagues exist regardless of whether such responsibilities are acknowledged by institutional review boards, vendors, and others involved in informatics activities. Be mindful and respectful of the social or public health implications of their work, ensuring that the greatest good for society is balanced by ethical obligations to individual patients. Uphold standards for publication and authorship, including the International Committee of Medical Journal Editors’ “Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals.”28 These recommendations are paralleled by the editorial policies for the past29 and current30 publishers of the Journal of the American Medical Informatics Association, as well as the publisher of Applied Clinical Informatics31 and their open access companion journals. Such efforts include, but are not limited to, avoiding any plagiarism or self-plagiarism or other misrepresentations of the truth in the publication of research and other work. Disseminate new knowledge—both positive and negative findings—expeditiously, to allow the field to advance and to permit others to take advantage of novel discoveries and understanding to improve patient care. Strive, as appropriate, in the context of one’s position to foster the generation of knowledge and biomedical advances through appropriate support for ethical and institutionally approved research efforts facilitated through informed consent and robust data governance, including disclosure processes and procedures, particularly when third-party entities not meeting the definition of business associates are involved. Know and abide by the applicable governmental regulations and institutional policies that define ethical research in their professional environment. V. General professional and ethical guidelines AMIA members should: Maintain competence as informatics professionals: Obtain applicable continuing education and be dedicated to a culture of lifelong learning and self-improvement. Recognize technical and ethical limitations and seek consultation when needed, particularly in ethically conflicting situations. Contribute to the education and mentoring of students, early-career members, and others, as appropriate. Promote a culture of diversity, equity, inclusion, and accessibility in their work and professional conduct. Strive to encourage the adoption of informatics approaches supported by adequate evidence to improve health and healthcare; and to encourage and support efforts to improve the amount and quality of such evidence. Treat all individuals with respect and not discriminate against anyone based on age, race, ethnicity, gender identity, disability (visible or invisible), national origin, sexual orientation, religion, or residency status. Be mindful that their work and actions reflect on the profession and on AMIA. The Code’s authors are aware that all professionals will, from time to time, find themselves in situations shaped by what has been called “dual agency” or “multiple agency”. In these circumstances, a professional encounters conflicting commitments, duties, or loyalties. An informatics professional may have conflicting duties to patients, to colleagues, to society, and to an employer. No code of ethics can resolve contradictions, but a well-crafted code may enable priorities to be set down explicitly and so provide a guide to action. In addition to this Code of Ethics, the AMIA’s Ethics Committee and its Conflict of Interest Panel are primary resources for members who find themselves in ethically unclear or challenging situations. For scholarship and education related to ethical issues in the broader field of medical information, the AMIA Ethical, Legal, and Social Issues (ELSI) Working Group serves as a community forum for members. As a matter of personal and professional integrity, adherence to the principles laid out here is expected of all who have the privilege of serving in the field of biomedical and health informatics. Those whose skills allow them to contribute in one way or another to the health of individuals and populations carry important responsibilities. This code of ethics provides guidance about how informaticians may best do so. All authors participated in the revision, review, and approval of this manuscript. Because this work is a revision of AMIA’s Code of Professional and Ethical Conduct 2018, no author can be considered to be responsible for the conception or design of the work. The authors and the AMIA Ethics Committee would like to thank the AMIA Board of Directors for its continuing interest in refining and publishing these guidelines. Phyllis Burchman, AMIA’s former Director of Office Operations and Human Resources, long provided invaluable support to the Ethics Committee in its work. Members of the AMIA Ethics Committee who contributed to the third version of the code in 2018 and are not otherwise listed here include Peter Embi, Harold Lehmann, Sarah A. Maulden, Kyle A. McGregor, and Enrique Terrazas. This version of the code also owes much to the members of AMIA’s Ethical, Legal, and Social Issues (ELSI) Working Group. None declared. Carolyn Petersen, Eta S. Berner, Anthony Cardillo, Kate Fultz Hollis, Kenneth W. Goodman, Ross Koppel, Diane M. Korngiebel, Christoph U. Lehmann, Tony Solomonides, Vignesh Subbian |
J. Am. Medical Informatics Assoc. | 10 |
| 2021 | Fighting COVID-19 with FHIR: Latest Developments from the COVID-19 Knowledge Accelerator (COKA)
Brian S. Alper, Harold P. Lehmann, Joanne Dehnbostel, Andrey Soares, Vignesh Subbian |
AMIA | 5 |
| 2021 | Impact of COVID-19 Pandemic on Emergency Department Visits: A Regional Case Study of Informatics Challenges and Opportunities
Hamid Ghaderi, Jeffrey Stowell, Murtaza Akhter, Craig Norquist, Paul E. Pugsley, Vignesh Subbian |
AMIA | 6 |
| 2021 | Recurrent Neural Network based Time-Series Modeling for Long-term Prognosis Following Acute Traumatic Brain Injury
Amin Nayebi, Sindhu Tipirneni, Brandon Foreman, Jonathan J. Ratcliff, Chandan K. Reddy, Vignesh Subbian |
AMIA | 6 |
| 2021 | Ethics and informatics in the age of COVID-19: challenges and recommendations for public health organization and public policyabstractThe COVID-19 pandemic response in the United States has exposed significant gaps in information systems and processes that prevent timely clinical and public health decision-making. Specifically, the use of informatics to mitigate the spread of SARS-CoV-2, support COVID-19 care delivery, and accelerate knowledge discovery bring to the forefront issues of privacy, surveillance, limits of state powers, and interoperability between public health and clinical information systems. Using a consensus-building process, we critically analyze informatics-related ethical issues in light of the pandemic across 3 themes: (1) public health reporting and data sharing, (2) contact tracing and tracking, and (3) clinical scoring tools for critical care. We provide context and rationale for ethical considerations and recommendations that are actionable during the pandemic and conclude with recommendations calling for longer-term, broader change (beyond the pandemic) for public health organization and policy reform. Vignesh Subbian, Tony Solomonides, Melissa D. Clarkson, Vasiliki Nataly Rahimzadeh, Carolyn Petersen, Richard Schreiber, Paul DeMuro, Prerna Dua, Kenneth W. Goodman, Bonnie Kaplan, Ross Koppel, Christoph U. Lehmann, Eric C. Pan, Yalini Senathirajah |
J. Am. Medical Informatics Assoc. | 1 |
| 2021 | Making science computable: Developing code systems for statistics, study design, and risk of biasabstractThe COVID-19 crisis led a group of scientific and informatics experts to accelerate development of an infrastructure for electronic data exchange for the identification, processing, and reporting of scientific findings. The Fast Healthcare Interoperability Resources (FHIR®) standard which is overcoming the interoperability problems in health information exchange was extended to evidence-based medicine (EBM) knowledge with the EBMonFHIR project. A 13-step Code System Development Protocol was created in September 2020 to support global development of terminologies for exchange of scientific evidence. For Step 1, we assembled expert working groups with 55 people from 26 countries by October 2020. For Step 2, we identified 23 commonly used tools and systems for which the first version of code systems will be developed. For Step 3, a total of 368 non-redundant concepts were drafted to become display terms for four code systems (Statistic Type, Statistic Model, Study Design, Risk of Bias). Steps 4 through 13 will guide ongoing development and maintenance of these terminologies for scientific exchange. When completed, the code systems will facilitate identifying, processing, and reporting research results and the reliability of those results. More efficient and detailed scientific communication will reduce cost and burden and improve health outcomes, quality of life, and patient, caregiver, and healthcare professional satisfaction. We hope the achievements reached thus far will outlive COVID-19 and provide an infrastructure to make science computable for future generations. Anyone may join the effort at https://www.gps.health/covid19_knowledge_accelerator.html. Brian S. Alper, Joanne Dehnbostel, Muhammad Afzal 0001, Vignesh Subbian, Andrey Soares, Ilkka Kunnamo, Khalid Shahin, Robert C. McClure |
J. Biomed. Informatics | 4 |
| 2020 | It is time for computable evidence synthesis: The COVID-19 Knowledge Accelerator initiativeabstractDear JAMIA Editors, A 2020 perspective article published in Journal of the American Medical Informatics Association (JAMIA) posed a timely question, “Is it time for computable evidence synthesis?”1 The shortest answer is, yes. The novel coronavirus disease 2019 (COVID-19) pandemic poses an immediate demand for evidence synthesis, given that nearly 30 000 articles have been published in fewer than 6 months since that first case in Wuhan, China.2 It provides the informatics community with a unique opportunity to accelerate development and interoperability of many systems to realize the aspirations of computable evidence synthesis. In this letter, we describe the origins and status of the COVID-19 Knowledge Accelerator (COKA). There are tremendous inefficiencies in our current scientific dissemination systems, in which many researchers compute the results then convert the data to various noncomputable forms for human-readable displays, and then many other knowledge processors work with the various human-readable displays to extract the data and enter it into computable form for evidence synthesis. This inefficient pattern is repeated incrementally across multiple steps in an extended series of processes while reports are re-evaluated and reused in subsequent reports. Thus, structured (computable) results directly from research and research publications would greatly accelerate evidence synthesis. Trial registries such as ClinicalTrials.gov are a good place for identifying early system developments for processing structured results data, but structured results data would be especially useful as a companion to scholarly publications, preprint publications, and derivative works in which systematic reviewers and other evidence processors are evaluating currently unstructured results data. For example, COVID-19 studies have already resulted in hundreds of systematic reviews. Achieving a state of structured results data as standard practice will not likely occur through a single universal repository, but we believe that it can be achieved with universal standards for data exchange, and multiple component standards that account for the many types of data that represent and support research results. Several groups—including the Guidelines International Network—seeking to accelerate evidence synthesis through collaborations set out to define standards for computable expressions of evidence, statistics, and evidence variables. In 2018, we started a project through Health Level Seven (HL7) International to extend the Fast Healthcare Interoperability Resources (FHIR) standard to achieve this. The group is called Evidence-Based Medicine on FHIR (EBMonFHIR).3 In less than 2 years, the EBMonFHIR project established draft standards for expression of evidence (http://build.fhir.org/evidence.html), evidence variables (http://build.fhir.org/evidencevariable.html), Statistics (http://build.fhir.org/statistic.html), and ordered distributions for statistical arrays (http://build.fhir.org/ordereddistribution.html). Recent developments to overcome the COVID-19 pandemic have stimulated many researchers, scholars, and information professionals to initiate large consortium-based efforts to share their work and advance our knowledge of the virus and the pandemic. Examples include the COVID-19 Open Research Dataset (CORD-19) (https://cset.georgetown.edu/research/covid-19-open-research-dataset-cord-19/), the COVID-19 Evidence Network to support Decision-making (COVID-END) (https://www.mcmasterforum.org/networks/covid-end), and the Australian National Clinical Evidence Taskforce (https://covid19evidence.net.au/). Several of these consortia asked to leverage EBMonFHIR efforts to provide standards for interoperable evidence syntheses. In response to these requests, our group initiated COKA (https://www.gps.health/covid19_knowledge_accelerator.html). The specific strategy of COKA is to establish universal standards for each component of knowledge exchanged and thus enable stakeholders to share and reuse their efforts by using the same format for electronic data exchange. As of May 11, 2020, COKA had 50 working meetings with more than 40 active participants from more than 25 organizations from academia, industry, government, and nonprofits in 7 countries. The group has created additional draft FHIR standards for expressions of citations (http://build.fhir.org/citation.html) and evidence reports (http://build.fhir.org/evidencereport.html) that provide compositions of all the preceding concepts. We strongly encourage developers of systems for evidence identification, evaluation, and dissemination to use these resources now as foundational elements to create a computational evidence ecosystem. This environment includes the building blocks for achieving computable evidence synthesis. Other resources not noted previously, such as resources for computational logic expressions, may ultimately be needed for the complete ecosystem. If we can develop standards for each granular component, we can then weave together the many overlapping systems and consortia to accelerate realization of this complex evidence ecosystem. Computable evidence synthesis is not the endpoint, but rather is another step in a larger knowledge ecosystem. For instance, the EBMonFHIR project is closely related to a CPGonFHIR project (http://build.fhir.org/ig/HL7/cqf-recommendations/) extending FHIR to support clinical guidelines. Past and present consortia efforts that have or are considering advancements for this ecosystem include the Agency for Healthcare Research and Quality evidence-based Care Transformation Support (ACTS) initiative (https://digital.ahrq.gov/acts), the Centers for Disease Control and Prevention's Adapting Clinical Guidelines for the Digital Age (https://www.cdc.gov/ddphss/clinical-guidelines/), Logica (https://covid-19-ig.logicahealth.org/), Mobilizing Computable Biomedical Knowledge (MCBK) (http://mobilizecbk.org/), and the Patient-Centered Clinical Decision Support Learning Network (PCCDS LN) (https://pccds-ln.org/). Although creating a computational environment for evidence could be done for any domain or subject matter,4,5 COVID-19 currently presents a unique human interest with urgency and impact, thus providing a special openness to collaboration. We invite your participation at https://www.gps.health/covid19_knowledge_accelerator.html. VS is supported in part by the National Science Foundation under grant #1838745 and the Arizona Board of Regents’ Technology Research and Innovation Fund. All listed authors contributed to this correspondence. BSA was employed by EBSCO Information Services and owns Computable Publishing LLC but the COKA and EBMonFHIR efforts are open, noncommercial activities. The other authors have no competing interests to report. Brian S. Alper, Joshua E. Richardson, Harold P. Lehmann, Vignesh Subbian |
J. Am. Medical Informatics Assoc. | 4 |
| 2019 | DSL-TEACH: Data Science Literacy Training to Enhance Approaches for Clinical decision-making in Healthcare
Samir Rachid Zaim, Ahyoung Amy Kim, Colleen Kenost, Helen Zhang, Yves A. Lussier, Vignesh Subbian |
AMIA | 6 |
| 2019 | Translational bioinformatics in mental health: open access data sources and computational biomarker discoveryabstractMental illness is increasingly recognized as both a significant cost to society and a significant area of opportunity for biological breakthrough. As -omics and imaging technologies enable researchers to probe molecular and physiological underpinnings of multiple diseases, opportunities arise to explore the biological basis for behavioral health and disease. From individual investigators to large international consortia, researchers have generated rich data sets in the area of mental health, including genomic, transcriptomic, metabolomic, proteomic, clinical and imaging resources. General data repositories such as the Gene Expression Omnibus (GEO) and Database of Genotypes and Phenotypes (dbGaP) and mental health (MH)-specific initiatives, such as the Psychiatric Genomics Consortium, MH Research Network and PsychENCODE represent a wealth of information yet to be gleaned. At the same time, novel approaches to integrate and analyze data sets are enabling important discoveries in the area of mental and behavioral health. This review will discuss and catalog into an organizing framework the increasingly diverse set of MH data resources available, using schizophrenia as a focus area, and will describe novel and integrative approaches to molecular biomarker discovery that make use of mental health data. Jessica D. Tenenbaum, Krithika Bhuvaneshwar, Jane P. Gagliardi, Kate Fultz Hollis, Peilin Jia, Radhakrishnan Nagarajan, Gopalkumar Rakesh, Vignesh Subbian, Shyam Visweswaran, Zhongming Zhao, Leon Rozenblit |
Briefings Bioinform. | 9 |
| 2018 | AMIA's code of professional and ethical conduct 2018abstractAMIA has a longstanding interest in and a professional obligation to promote a strong ethical framework for the field of biomedical and health informatics. This white paper presents the latest AMIA Code of Professional and Ethical Conduct. The original Code was approved in 20071 by the AMIA Board of Directors. Recognizing the need to update the Code to ensure that it remains current and relevant, this document constitutes a revision of and update to the second code, approved in 2012 and published in the Journal of the American Medical Informatics Association in 2013.2 The code presented here remains an evolving document, with modifications expected as the information technology, informatics, and healthcare environments change over time. AMIA will publish on its web site the most recent version of the Code of Ethics as part of a process that seeks ongoing response from and involvement by AMIA members. Because the Code is meant to be practical, applicable in real life, and easily understood, it is compact and uses general language. The AMIA Code of Ethics is not intended to be prescriptive or legislative; it is aspirational and extends beyond regulatory and legal obligations to provide the broad strokes of a set of important ethical principles pertinent to the field of biomedical and health informatics. The Code is organized around the common roles of AMIA members and the constituents they serve, including patients, caregivers, clinicians, researchers, students, agencies, hospitals and practices, medical organizations, vendors, insurance companies, and others with whom they interact. The AMIA Board and the AMIA Ethics Committee encourage members to offer suggestions for improvements and changes. In this way, the Code will continue to evolve to best serve AMIA and the larger informatics community. The Code’s authors are aware that all professionals will, from time to time, find themselves in situations shaped by what has been called “dual agency” or “multiple agency.” In these circumstances, a professional encounters conflicting commitments, duties, or loyalties. An informatics professional may have conflicting duties to patients, to colleagues, to society, and to an employer. Few, if any, codes of ethics are nimble enough to provide guidance in such situations. Further, AMIA’s Ethics Committee is a resource to members who find themselves in ethically unclear or challenging situations. AMIA members may contact the AMIA Ethics Committee, which can provide guidance in some circumstances. AMIA members are professionally diverse,3,4 and include those who are, or are in training to be, nurses, physicians, pharmacists, dentists, informaticians, computer scientists, and others. In many cases, these professions have their own codes of ethics.5–12 The International Medical Informatics Association, an international federation for which AMIA serves as the U.S. membership organization, also has a revised “Code of Ethics for Health Information Professionals.”13 This document incorporates issues covered by other documents and laws bearing on ethics and professional conduct: AMIA’s “Conflict of Interest Policy,” which governs the organization’s employees and leaders in regard to some of their financial and other interactions with outside entities.14 AMIA’s “Meeting Anti-Harassment Policy,” which describes AMIA’s commitment to providing an atmosphere that is welcoming to all members and supports learning and professional growth.15 The International Committee of Medical Journal Editors’ “Recommendations for the Conduct, Reporting, Editing, and Publication of Scholarly Work in Medical Journals.”16 This document is widely accepted as identifying standards for publication and authorship, and is paralleled by the editorial policies for the past17 and current18 publishers of the Journal of the American Medical Informatics Association, as well as the publisher of Applied Clinical Informatics.19 Privacy laws. Several sections herein address patient privacy or the rights of patients to view and control access to their health information. These sections are intended to parallel and make explicit duties under the law. In the United States, for instance, the Privacy Rule under the Health Insurance Portability and Accountability Act20 lays out many duties for those who are entrusted with health information. Many other countries have similar laws to protect patient data. Informatics professionals are expected to be familiar with and follow the laws governing their practice. Members of the Ethics Committee are unanimous in their view that those who work in informatics, much as in other health professions, are duty-bound to embrace a patient-centered approach to their work, even if that work does not involve direct patient care or human subjects research. As elsewhere in the health professions, vulnerable populations or those with special needs may be entitled to additional considerations. The importance of professionalism and ethics has been recognized for millennia by health professionals and organizations,21 now including information technology professionals. This code of ethics emphasizes AMIA’s commitment to adhere to and promote the highest standard of ethical and professional behavior. AMIA members acknowledge as their professional duty to uphold the following principles of and guidelines for ethical conduct. AMIA members are expected to know to seek the advice of institutional ethics committees, AMIA’s Ethics Committee, or appropriate institutional review boards, as necessary. The following code details address patient care, interactions with colleagues, responsibilities to employers, and roles regarding society and research. I. Key ethical guidelines regarding patients, guardians, and their authorized representatives (called here collectively “patients”) AMIA members involved in patient care should: A. Recognize that patients and their loved ones and caregivers have the right to know about the existence and use of electronic records containing their personal healthcare information, and have the right to create and maintain their own personal health records and manage personal health information using a variety of platforms including mobile devices. In this context AMIA members should: Not mislead patients about the collection, use, or communication of their healthcare information. Enable and — as appropriate, within reason and the scope of their position and in accord with independent ethical and legal standards — facilitate patients’ rights and ability to access, review, and correct their electronic health information. Recognize that patient-provided/generated health data, such as those collected on mobile devices, deserve the same diligence and protection as biomedical and health data gathered in the process of providing health care. B. Advocate and work as appropriate to ensure that protected health information (PHI),20 personally identifiable information (PII), and other biomedical data are transmitted, acquired, recorded, stored, maintained, analyzed, and communicated in an appropriately safe, reliable, secure, and confidential manner, and that such data management is consistent with applicable laws, local privacy and security policies, and accepted informatics standards. C. Never knowingly disclose PHI, PII, or biomedical or health data in violation of legal requirements or accepted local confidentiality practices, or in ways that are inconsistent with the explanation of data disclosure and use to the patient. AMIA members should understand that inappropriate disclosure of biomedical information can cause harm, and so should work to prevent such disclosures. AMIA members should avoid acquiring data through means that run the risk of, or fail to prevent, inappropriate disclosure. Likewise, even if an action does not involve disclosure, one should not use — or through negligence permit the use of — patient information and data in ways inconsistent with the stated purposes, goals, or intentions of the patient or organization responsible for these data, except as appropriate for public health, previously approved and communicated research uses, or reporting as required under the law. II. Key ethical guidelines regarding colleagues AMIA members should: A. Endeavor, as appropriate, to support and foster colleagues’ and/or team members’ work, in a timely, respectful, and conscientious way to support their roles in healthcare and/or research and education. B. Support and foster the efforts of patients to be actively involved in the collection, management, and curation of their health data. C. Advise colleagues and others, as appropriate, about actual or potential information or systems issues (including system flaws, bugs, usability issues, etc.) that negatively affect patient safety, privacy, data security, or outcomes or could hinder colleagues’ ability to delegate responsibilities to patients, other colleagues, involved institutions, or other stakeholders. D. If a leader, an AMIA member should: Be familiar with these guidelines and their applicability to their practice, unit, or organization. Communicate as appropriate about these ethical guidelines to those they lead. Strive to promote familiarity with, and use of, these ethical guidelines. III. Key ethical guidelines regarding institutions, employers, business partners, and clients (called here collectively “employers”) AMIA members should: A. Understand their duties and obligations to current and former employers and fulfill them to the best of their abilities within the bounds of ethical and legal norms. B. Understand and appreciate that employers have legal and ethical rights and obligations, including those related to intellectual property. Understand and respect the obligations of their employers, and comply with local policies and procedures to the extent that they do not violate ethical and legal norms. Consider the tradeoffs that occur with the configuration and use of technologies (eg, decision support systems) before implementation, and monitor and manage results when the optimal approach is unclear. C. Inform the employer and act in accordance with ethico-legal mandates and patient rights when employer actions, policies, or procedures would violate ethical or legal obligations, contracts, or other agreements made with patients. Maintain a safe and high-quality environment even while implementing innovation, recognizing that all changes in a complex adaptive environment generate unanticipated consequences and potential harm. IV. Key ethical guidelines regarding society and regarding research AMIA members involved in research should: A. Be aware of the Declaration of Helsinki (Ethical Principles for Medical Research Involving Human Subjects), which should guide all human subject research, including research that involves users of informatics tools and interventions as human subjects (eg, workflow analysis studies, clinical decision support systems analysis, patient care innovations, analysis, etc.).22,23 Recognize that duty and care to colleagues exist regardless of whether such responsibilities are acknowledged by institutional review boards, vendors, and others involved in informatics activities. B. Be mindful and respectful of the social or public health implications of their work, ensuring that the greatest good for society is balanced by ethical obligations to individual patients. C. Avoid any plagiarism or self-plagiarism or other misrepresentations of the truth in the publication of research and other work. D. Disseminate new knowledge — both positive and negative — expeditiously, to allow the field to advance and to permit others to take advantage of novel discoveries to improve patient care. E. Strive as appropriate in the context of one’s position to foster the generation of knowledge and biomedical advances through appropriate support for ethical and institutionally approved research efforts facilitated through informed consent and disclosure processes and procedures, particularly when third-party entities not meeting the definition of business associates are involved. F. Know and abide by the applicable governmental regulations and local policies that define ethical research in their professional environment. V. General professional and ethical guidelines AMIA members should: A. Maintain competence as informatics professionals: Obtain applicable continuing education and be dedicated to a culture of lifelong learning and improvement; Recognize technical and ethical limitations and seek consultation when needed, particularly in ethically conflicting situations; Contribute to the education and mentoring of students, junior members, and others, as appropriate; Promote a culture of inclusivity in their work and professional conduct. B. Strive to encourage the adoption of informatics approaches supported by adequate evidence to improve health and healthcare; and to encourage and support efforts to improve the amount and quality of such evidence. C. Be mindful that their work and actions reflect on the profession and on AMIA. As a matter of personal and professional integrity, adherence to the principles laid out here is expected of all who have the privilege of serving in the field of biomedical and health informatics. Those whose skills allow them to contribute in one way or another to the health of individuals and populations carry important responsibilities, and this Code of Ethics delineates how informaticians may best do so. None. Not commissioned; not peer reviewed. Conflict of interest statement. None. The authors and the AMIA Ethics Committee would like to thank the AMIA Board of Directors for its continuing interest in refining and publishing these guidelines. Phyllis Burchman, AMIA’s Director of Office Operations and Human Resources, provided invaluable support to the Ethics Committee in its work. Members of the AMIA Ethics Committee who contributed to the second version of the code in 2012 and are not otherwise listed here include Samantha Adams, Robert Hsiung, John Hurdle, and Dixie A. Jones. This version of the code also owes much to the members of AMIA’s Ethical, Legal, and Social Issues (ELSI) Working Group. Carolyn Petersen, Eta S. Berner, Peter J. Embí, Kate Fultz Hollis, Kenneth W. Goodman, Ross Koppel, Christoph U. Lehmann, Harold P. Lehmann, Sarah A. Maulden, Kyle A. McGregor, Tony Solomonides, Vignesh Subbian, Enrique Terrazas, Peter Winkelstein |
J. Am. Medical Informatics Assoc. | 12 |
| 2018 | Leveraging mobile health applications for biomedical research and citizen science: a scoping reviewabstractObjective: This systematic review aims to analyze current capabilities, challenges, and impact of self-directed mobile health (mHealth) research applications such as those based on the ResearchKit platform. Materials and Methods: A systematic review was conducted according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. English publications were included if: 1) mobile applications were used in the context of large-scale collection of data for biomedical research, and not as medical or behavioral intervention of any kind, and 2) all activities related to participating in research and data collection methods were executed remotely without any face-to-face interaction between researchers and study participants. Results: Thirty-six unique ResearchKit apps were identified. The majority of the apps were used to conduct observational studies on general citizens and generate large datasets for secondary research. Nearly half of the apps were focused on chronic conditions in adults. Discussion: The ability to generate large biomedical datasets on diverse populations that can be broadly shared and re-used was identified as a promising feature of mHealth research apps. Common challenges were low participation retention, uncertainty regarding how use patterns influence data quality, need for data validation, and privacy concerns. Conclusion: ResearchKit and other mHealth-based studies are well positioned to enhance development and validation of novel digital biomarkers as well as generate new biomedical knowledge through retrospective studies. However, in order to capitalize on these benefits, mHealth research studies must strive to improve retention rates, implement rigorous data validation strategies, and address emerging privacy and security challenges. Hannah Schmitz, Carol L. Howe, David G. Armstrong, Vignesh Subbian |
J. Am. Medical Informatics Assoc. | 4 |
| 2013 | Developing a new advanced microcontrollers course as a part of embedded systems curriculumabstractThis paper presents our experiences in developing a new advanced microcontrollers course within the Department of Electrical Engineering and Computing Systems at the University of Cincinnati (UC). This course was developed and offered for the first time in Spring 2013 to undergraduate seniors and first-year graduate students in electrical and computer engineering. It is also open to interested students in other relevant science and engineering programs. The course aims at providing advanced skills in designing and developing microcontroller-based embedded systems. It adopts an instruction model that integrates active learning techniques with in-class lectures and laboratory projects. The paper elaborates on the course structure and schedule, pedagogical techniques used in the course, and student feedback results. It also explains how this course fits in to the existing embedded systems curriculum at UC. Vignesh Subbian, Fred R. Beyette |
FIE | 1 |