Catalina M. Medina | Searcharxiv

arXiv2025

A Systematic Literature Review of Undergraduate Data Science Education Research

The presence of data science has been profound in the scientific community in almost every discipline. An important part of the data science education expansion has been at the undergraduate level. We conducted a systematic literature review to (1) portray current evidence and knowledge gaps in self-proclaimed undergraduate data science education research and (2) inform policymakers and the data science education community about what educators may encounter when searching for literature using the general keyword 'data science education.' While open-access publications that target a broader audience of data science educators and include multiple examples of data science programs and courses are a strength, significant knowledge gaps remain. The undergraduate data science literature that we identified often lacks empirical data, research questions and reproducibility. Certain disciplines are less visible. We recommend that we should (1) cherish data science as an interdisciplinary field; (2) adopt a consistent set of keywords/terminology to ensure data science education literature is easily identifiable; (3) prioritize investments in empirical studies.

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arXiv2024

Accounting for reporting delays in real-time phylodynamic analyses with preferential sampling

The COVID-19 pandemic demonstrated that fast and accurate analysis of continually collected infectious disease surveillance data is crucial for situational awareness and policy making. Coalescent-based phylodynamic analysis can use genetic sequences of a pathogen to estimate changes in its effective population size, a measure of genetic diversity. These changes in effective population size can be connected to the changes in the number of infections in the population of interest under certain conditions. Phylodynamics is an important set of tools because its methods are often resilient to the ascertainment biases present in traditional surveillance data (e.g., preferentially testing symptomatic individuals). Unfortunately, it takes weeks or months to sequence and deposit the sampled pathogen genetic sequences into a database, making them available for such analyses. These reporting delays severely decrease precision of phylodynamic methods closer to present time, and for some models can lead to extreme biases. Here we present a method that affords reliable estimation of the effective population size trajectory closer to the time of data collection, allowing for policy decisions to be based on more recent data. Our work uses readily available historic times between sampling and sequencing for a population of interest, and incorporates this information into the sampling model to mitigate the effects of reporting delay in real-time analyses. We illustrate our methodology on simulated data and on SARS-CoV-2 sequences collected in the state of Washington in 2021.

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