Explainable artificial intelligence for omics data: a systematic mapping study.

Researchers increasingly turn to explainable artificial intelligence (XAI) to analyze omics data and gain insights into the underlying biological processes. Yet, given the interdisciplinary nature of the field, many findings have only been shared in their respective research community. An overview of XAI for omics data is needed to highlight promising approaches and help detect common issues. Toward this end, we conducted a systematic mapping study. To identify relevant literature, we queried Scopus, PubMed, Web of Science, BioRxiv, MedRxiv and arXiv. Based on keywording, we developed a coding scheme with 10 facets regarding the studies' AI methods, explainability methods and omics data. Our mapping study resulted in 405 included papers published between 2010 and 2023. The inspected papers analyze DNA-based (mostly genomic), transcriptomic, proteomic or metabolomic data by means of neural networks, tree-based methods, statistical methods and further AI methods. The preferred post-hoc explainability methods are feature relevance (n = 166) and visual explanation (n = 52), while papers using interpretable approaches often resort to the use of transparent models (n = 83) or architecture modifications (n = 72). With many research gaps still apparent for XAI for omics data, we deduced eight research directions and discuss their potential for the field. We also provide exemplary research questions for each direction. Many problems with the adoption of XAI for omics data in clinical practice are yet to be resolved. This systematic mapping study outlines extant research on the topic and provides research directions for researchers and practitioners.

Perceived fairness of direct-to-consumer genetic testing business models.

Although consumers and experts often express concerns regarding the questionable business practices of direct-to-consumer (DTC) genetic testing services (e.g., reselling of consumers' genetic data), the DTC genetic testing market keeps expanding rapidly. We employ retail fairness as our theoretical lens to address this seeming paradox and conduct a discrete choice experiment with 16 attributes to better understand consumers' fairness perceptions of DTC genetic testing business models. Our results suggest that, while consumers perceive privacy-preserving DTC genetic testing services fairer, price is the main driver for fairness perception. We contribute to research on consumer perceptions of DTC genetic testing by investigating consumer preferences of DTC genetic testing business models and respective attributes. Further, this research contributes to knowledge about disruptive business models in healthcare and retail fairness by contextualizing the concept of retail fairness in the DTC genetic testing market. We also demonstrate how to utilize discrete choice experiments to elicit perceived fairness. Supplementary Information: The online version contains supplementary material available at 10.1007/s12525-022-00571-x.

A scoping review of distributed ledger technology in genomics: thematic analysis and directions for future research.

OBJECTIVE: Rising interests in distributed ledger technology (DLT) and genomics have sparked various interdisciplinary research streams with a proliferating number of scattered publications investigating the application of DLT in genomics. This review aims to uncover the current state of research on DLT in genomics, in terms of focal research themes and directions for future research. MATERIALS AND METHODS: We conducted a scoping review and thematic analysis. To identify the 60 relevant papers, we queried Scopus, Web of Science, PubMed, ACM Digital Library, IEEE Xplore, arXiv, and BiorXiv. RESULTS: Our analysis resulted in 7 focal themes on DLT in genomics discussed in literature, namely: (1) Data economy and sharing; (2) Data management; (3) Data protection; (4) Data storage; (5) Decentralized data analysis; (6) Proof of useful work; and (7) Ethical, legal, and social implications. DISCUSSION: Based on the identified themes, we present 7 future research directions: (1) Investigate opportunities for the application of DLT concepts other than Blockchain; (2) Explore people's attitudes and behaviors regarding the commodification of genetic data through DLT-based genetic data markets; (3) Examine opportunities for joint consent management via DLT; (4) Investigate and evaluate data storage models appropriate for DLT; (5) Research the regulation-compliant use of DLT in healthcare information systems; (6) Investigate alternative consensus mechanisms based on Proof of Useful Work; and (7) Explore DLT-enabled approaches for the protection of genetic data ensuring user privacy. CONCLUSION: While research on DLT in genomics is currently growing, there are many unresolved problems. This literature review outlines extant research and provides future directions for researchers and practitioners.

Direct-to-Consumer Genetic Testing on Social Media: Topic Modeling and Sentiment Analysis of YouTube Users' Comments.

Background: With direct-to-consumer (DTC) genetic testing enabling self-responsible access to novel information on ancestry, traits, or health, consumers often turn to social media for assistance and discussion. YouTube, the largest social media platform for videos, offers an abundance of DTC genetic testing-related videos. Nevertheless, user discourse in the comments sections of these videos is largely unexplored. Objective: This study aims to address the lack of knowledge concerning user discourse in the comments sections of DTC genetic testing-related videos on YouTube by exploring topics discussed and users' attitudes toward these videos. Methods: We employed a 3-step research approach. First, we collected metadata and comments of the 248 most viewed DTC genetic testing-related videos on YouTube. Second, we conducted topic modeling using word frequency analysis, bigram analysis, and structural topic modeling to identify topics discussed in the comments sections of those videos. Finally, we employed Bing (binary), National Research Council Canada (NRC) emotion, and 9-level sentiment analysis to identify users' attitudes toward these DTC genetic testing-related videos, as expressed in their comments. Results: We collected 84,082 comments from the 248 most viewed DTC genetic testing-related YouTube videos. With topic modeling, we identified 6 prevailing topics on (1) general genetic testing, (2) ancestry testing, (3) relationship testing, (4) health and trait testing, (5) ethical concerns, and (6) YouTube video reaction. Further, our sentiment analysis indicates strong positive emotions (anticipation, joy, surprise, and trust) and a neutral-to-positive attitude toward DTC genetic testing-related videos. Conclusions: With this study, we demonstrate how to identify users' attitudes on DTC genetic testing by examining topics and opinions based on YouTube video comments. Shedding light on user discourse on social media, our findings suggest that users are highly interested in DTC genetic testing and related social media content. Nonetheless, with this novel market constantly evolving, service providers, content providers, or regulatory authorities may still need to adapt their services to users' interests and desires.

Archetypes of Gamification: Analysis of mHealth Apps.

BACKGROUND: Nowadays, numerous health-related mobile apps implement gamification in an attempt to draw on the motivational potential of video games and thereby increase user engagement or foster certain health behaviors. However, research on effective gamification is still in its infancy and researchers increasingly recognize methodological shortcomings of existing studies. What we actually know about the phenomenon today stems from fragmented pieces of knowledge, and a variety of different perspectives. Existing research primarily draws on conceptual knowledge that is gained from research prototypes, and isolated from industry best practices. We still lack knowledge on how gamification has been successfully designed and implemented within the industry and whether certain gamification approaches have shown to be particularly suitable for certain health behaviors. OBJECTIVE: We address this lack of knowledge concerning best practices in the design and implementation of gamification for health-related mobile apps by identifying archetypes of gamification approaches that have emerged in pertinent health-related mobile apps and analyzing to what extent those gamification approaches are influenced by the underlying desired health-related outcomes. METHODS: A 3-step research approach is employed. As a first step, a database of 143 pertinent gamified health-related mobile apps from the Apple App Store and Google Play Store is set up. Second, the gamification approach of each app within the database is classified based on an established taxonomy for gamification in health-related apps. Finally, a 2-step cluster analysis is conducted in order to identify archetypes of the most dominant gamification approaches in pertinent gamified health-related mobile apps. RESULTS: Eight archetypes of gamification emerged from the analysis of health-related mobile apps: (1) competition and collaboration, (2) pursuing self-set goals without rewards, (3) episodical compliance tracking, (4) inherent gamification for external goals, (5) internal rewards for self-set goals, (6) continuous assistance through positive reinforcement, (7) positive and negative reinforcement without rewards, and (8) progressive gamification for health professionals. The results indicate a close relationship between the identified archetypes and the actual health behavior that is being targeted. CONCLUSIONS: By unveiling salient best practices and discussing their relationship to targeted health behaviors, this study contributes to a more profound understanding of gamification in mobile health. The results can serve as a foundation for future research that advances the knowledge on how gamification may positively influence health behavior change and guide practitioners in the design and development of highly motivating and effective health-related mobile health apps.

Valuable Genomes: Taxonomy and Archetypes of Business Models in Direct-to-Consumer Genetic Testing.

BACKGROUND: Recent progress in genome data collection and analysis technologies has led to a surge of direct-to-consumer (DTC) genetic testing services. Owing to the clinical value and sensitivity of genomic data, as well as uncertainty and hearsay surrounding business practices of DTC genetic testing service providers, DTC genetic testing has faced significant criticism by researchers and practitioners. Research in this area has centered on ethical and legal implications of providing genetic tests directly to consumers, but we still lack a more profound understanding of how businesses in the DTC genetic testing markets work and provide value to different stakeholders. OBJECTIVE: The aim of this study was to address the lack of knowledge concerning business models of DTC genetic testing services by systematically identifying the salient properties of various DTC genetic testing service business models as well as discerning dominant business models in the market. METHODS: We employed a 3-phased research approach. In phase 1, we set up a database of 277 DTC genetic testing services. In phase 2, we drew on these data as well as conceptual models of DTC genetic testing services and iteratively developed a taxonomy of DTC genetic testing service business models. In phase 3, we used a 2-stage clustering method to cluster the 277 services that we identified during phase 1 and derived 6 dominant archetypes of DTC genetic testing service business models. RESULTS: The contributions of this research are 2-fold. First, we provided a first of its kind, systematically developed taxonomy of DTC genetic testing service business models consisting of 15 dimensions in 4 categories. Each dimension comprises 2 to 5 characteristics and captures relevant aspects of DTC genetic testing service business models. Second, we derived 6 archetypes of DTC genetic testing service business models named as follows: (1) low-cost DTC genomics for enthusiasts, (2) high-privacy DTC genomics for enthusiasts, (3) specific information tests, (4) simple health tests, (5) basic low-value DTC genomics, and (6) comprehensive tests and low data processing. CONCLUSIONS: Our analysis paints a much more complex business landscape in the DTC genetic testing market than previously anticipated. This calls for further research on business models and their effects that underlie DTC genetic testing services and invites specific regulatory interventions to protect consumers and level the playing field.