My research interest lies in applying data science for actionable transformation of human health from the bench to bedside. Current research focus areas include cutting edge single-cell sequencing informatics and genomics; precision medicine through integration of multi-omics data types; novel modeling and computational methods for biomarker research; public health genomics. I apply my biomedical informatics and analytical expertise to study diseases such as cancers, as well the impact of pregnancy/early life complications on later life diseases.
Biodiversity in nature can be puzzlingly high in the light of competition between species, which arguably should eventually result in a single winner. The coexistence mechanisms that allow for this biodiversity shape the dynamics of communities and ecosystems. My research focuses on understanding the mechanisms of competitive coexistence, how competition influences community structure and diversity, and what insights observed patterns of community structure might provide about competitive coexistence.
I am interested in the use and development of data science approaches to draw insights regarding coexistence mechanisms from the structural patterns of ecological communities with respect to species’ functional traits, relative abundance, spatial distribution, and phylogenetic relatedness, through as community dynamics proceed. I am also interested in the use of Maximum Likelihood and Bayesian approaches for fitting demographic models to forest census data sets, demographic models that can then be used to quantitatively assess the role of different competitive coexistence mechanisms.
The current goal of our research is to learn enough about the physiology and ecology of microbes and microbial communities in the gut that we are able to engineer the gut microbiome to improve human health. The first target of our engineering is the production of butyrate – a common fermentation product of some gut microbes that is essential for human health. Butyrate is the preferred energy source for mitochondria in the epithelial cells lining the gut and it also regulates their gene expression.
One of the most effective ways to influence the composition and metabolism of the gut microbiota is through diet. In an interventional study, we have tracked responses in the composition and fermentative metabolism of the gut microtiota in >800 healthy individuals. Emerging patterns suggest several configurations of the microbiome that can result in increased production of butyrate acid. We have isolated the microbes that form an anaerobic food web to convert dietary fiber to butyrate and continue to make discoveries about their physiology and interactions. Based on these results, we have initiated a clinical trial in which we are hoping to prevent the development of Graft versus Host Disease following bone marrow transplants by managing butyrate production by the gut microbiota.
We are also beginning to track hundreds of other metabolites from the gut microbiome that may influence human health. We use metagenomes and metabolomes to identify patterns that link the microbiota with their metabolites and then test those models in human organoids and gnotobiotic mice colonized with synthetic communities of microbes. This blend of wet-lab research in basic microbiology, data science and in ecology is moving us closer to engineering the gut microbiome to improve human health.
My research is at the intersection of neuroscience and artificial intelligence. My group uses neuroscience or brain-inspired principles to design models and algorithms for computer vision and language processing. In turn, we uses neural network models to test hypotheses in neuroscience and explain or predict human perception and behaviors. My group also develops and uses machine learning algorithms to improve the acquisition and analysis of medical images, including functional magnetic resonance imaging of the brain and magnetic resonance imaging of the gut.
We use brain-inspired neural networks models to predict and decode brain activity in humans processing information from naturalistic audiovisual stimuli.
My research focuses on the application of data science in educational research, so called learning analytics. I have experience analyzing educational data on a large-scale to understand a) how course design influence students’ learning behavior and b) how students form peer networks. My work involves using multiple educational data sources such as log-data in online learning environment, course information, students’ academic records, and location data gathered from campus WiFi networks. I am interested in network analysis, time-series analysis, and machine learning.
My research focuses on the causes, dynamics and outcomes of conflict, at the international and local levels. My methodological areas of interest include spatial statistics, mathematical/computational modeling and text analysis.
Map/time-series/network plot, showing the flow of information across battles in World War II. Z axis is time, X and Y axes are longitude and latitude, polygons are locations of battles, red lines are network edges linking battles involving the same combatants. Source: https://doi.org/10.1017/S0020818318000358
I use machine-learning techniques to implement decision support systems and tools that facilitate more personalized care for disease management and healthcare utilization to ultimately deliver efficient, effective, and equitable therapy for chronic diseases. To test and advance these general principles, I have built operational programs that are guiding—and improving—patient care in costly in low resource settings, including emerging countries.
Dr. Dempsey’s research focuses on statistical methods for digital and mobile health. My current work involves three complementary research themes: (1) experimental design and data analytic methods to inform multi-stage decision making in health; (2) statistical modeling of complex longitudinal and survival data; and (3) statistical modeling of complex relational structures such as interaction networks. Current directions include (1) integration of sequential multiple assignment randomized trials (SMARTs) and micro-randomized trials (MRTs) and associated causal inference methods; (2) recurrent event analysis in the presence of high-frequency sensor data; and (3) temporal models for, community detection of, and link prediction using complex interaction data.
My research is focused on a wide range of topics from computational social sciences to bioinformatics where I do pattern recognition, perform data analysis, and build prediction models. At the core of my effort, there lie machine learning methods by which I have been trying to address problems related to social networks, opinion mining, biomarker discovery, pharmacovigilance, drug repositioning, security analytics, genomics, food contamination, and concussion recovery. I’m particularly interested in and eager to collaborate on cyber security aspect of social media analytics that includes but not limited to misinformation, bots, and fake news. In addition, I’m still pursuing opportunities in bioinformatics, especially about next generation sequencing analysis that can be also leveraged for phenotype predictions by using machine learning methods.
A typical pipeline for developing and evaluating a prediction models to identify malicious Android mobile apps in the market
My research focuses on issues in data collection with hard-to-reach populations. In particular, she examines 1) nontraditional sampling approaches for minority or stigmatized populations and their statistical properties and 2) measurement error and comparability issues for racial, ethnic and linguistic minorities, which also have implications for cross-cultural research/survey methodology. Most recently, my research has been dedicated to respondent driven sampling that uses existing social networks to recruit participants in both face-to-face and Web data collection settings. I plan to expand my research scope in examining representation issues focusing on the racial/ethnic minority groups in the U.S. in the era of big data.