Now showing items 1-20 of 28

    • A Mathematics Pipeline to Student Success in Data Analytics through Course-Based Undergraduate Research 

      Bennett, Kristin P.; Erickson, John S.; Svirsky, Amy; Seddon, Josephine (The Mathematics Enthusiast, 2021-12-16)
      This paper reports on Data Analytics Research (DAR), a course-based undergraduate research experience (CURE) in which undergraduate students conduct data analysis research on open real- world problems for industry, university, ...
    • Addressing Scientific Rigor in Data Analytics Using Semantic Workflows 

      Erickson, John S.; Sheehan, John; Bennett, Kristin P.; McGuinness, Deborah L. (Springer, Cham, 2016-06-16)
      New NIH grants require establishing scientific rigor, i.e. applicants must provide evidence of strict application of the scientific method to ensure robust and unbiased experimental design, methodology, analysis, interpretation ...
    • Augmenting Functional Microbiome Research using a Semantically-Enabled Analytical Infrastructure 

      Patton, Evan; Ravichandar, Divya; Urschel, Matthew; Bennett, Kristin P.; Dyson, Anna; Rogers, Karyn; Collins, Cynthia; McGuinness, Deborah L. (BMC, 2016)
    • Automating Population Health Studies through Semantics and Statistics Semantic Statistics (SemStats) 

      New, Alexander; Qi, Miao; Chari, Shruthi; Rashid, Sabbir; Seneviratne, Oshani; McCusker, Jamie; Erickson, John S.; McGuinness, Deborah L.; Bennett, Kristin P. (Springer, 2019-10)
      With the rapid development of the Semantic Web, machines are able to understand the contextual meaning of data, including in the field of automated semantics-driven statistical reasoning. This paper introduces a ...
    • Characterizing Common Quarterly Behaviors In DeFi Lending Protocols 

      Green, Aaron; Giannattasio, Michael; Wang, Keran; Erickson, John S.; Seneviratne, Oshani; Bennett, Kristin P. (Springer, Cham., 2023-07)
      The emerging decentralized financial ecosystem (DeFi) is comprised of numerous protocols, one type being lending protocols. People make transactions in lending protocols, each of which is attributed to a specific blockchain ...
    • DeFi Survival Analysis: Insights into Risks and User Behavior 

      Green, Aaron; Cammilleri, Christopher; Erickson, John S.; Seneviratne, Oshani; Bennett, Kristin P. (Springer, 2022-06)
      We propose a decentralized finance (DeFi) survival analysis approach for discovering and characterizing user behavior and risks in lending protocols. We demonstrate how to gather and prepare DeFi transaction data for ...
    • Developing Scientific Knowledge Graphs Using Whyis 

      McCusker, Jamie; Rashid, Sabbir; Agu, Nkechinyere; Bennett, Kristin P.; McGuinness, Deborah L. (SemSci, 2018)
      We present Whyis, the first framework for creating custom provenance-driven knowledge graphs. Whyis knowledge graphs are based on nanopublications, which simplifies and standardizes the production of structured, ...
    • Eat4Genes: A Bioinformatic Rational Gene Targeting App and Prototype Model for Improving Human Health 

      Ford, M.L.; Cooley, J.M.; Sripada, V.; Erickson, John S.; Bennett, Kristin P.; Crawford, Dana R. (Frontiers in Nutrition, 2023-05-04)
      Eat4Genes is a prototype diet recommendation web app for patients, healthcare providers, and researchers that aids in the selection of a healthy diet to help treat and prevent numerous health conditions. Our approach is ...
    • Identifying Windows of susceptibility by temporal Gene Analysis 

      Bennett, Kristin P.; Brown, Elisabeth; De Los Santos, Hannah; Poegel, Matt; Kiehl, Thomas; Patton, Evan; Norris, Spencer; Temple, Sally; Erickson, John S.; McGuinness, Deborah L.; Boles, Nathan (Scientific Reports, 2019-02-01)
      Increased understanding of developmental disorders of the brain has shown that genetic mutations, environmental toxins and biological insults typically act during developmental windows of susceptibility. Identifying these ...
    • Integrating Semantics and Numerics: Case Study on Enhancing Genomic and Disease Data Using Linked Data Technologies 

      McGuinness, Deborah L.; Bennett, Kristin P. (2015-08-18)
      Bioinformatics was an early adopter of semantic technologies and provided many ontologies and datasets in semantic formats to aid integration of biological and biochemical data. There is a lack of tooling support however ...
    • Knowledge Integration for Disease Characterization: A Breast Cancer Example 

      Seneviratne, Oshani; Rashid, Sabbir; Chari, Shruthi; Bennett, Kristin P.; Hendler, James A.; McGuinness, Deborah L. (2018-07-20)
      With the rapid advancements in cancer research, the information that is useful for characterizing disease, staging tumors, and creating treatment and survivorship plans has been changing at a pace that creates challenges ...
    • Making Study Populations Visible through Knowledge Graphs 

      Chari, Shruthi; Qim, Miao; Agu, Nkechinyere; Seneviratne, Oshani; McCusker, Jamie; Bennett, Kristin P.; Das, Amar; McGuinness, Deborah L. (2019-10-12)
    • An Ontology for Fairness Metrics 

      Franklin, Jade S; Bhanot, Karan; Ghalwash, Mohamed; Bennett, Kristin P.; McCusker, Jamie; McGuinness, Deborah L. (ACM, 2022-07)
      Recent research has revealed that many machine-learning models and the datasets they are trained on suffer from various forms of bias, and a large number of different fairness metrics have been created to measure this bias. ...
    • Ontology-enabled Analysis of Study Populations 

      Chari, Shruthi; Qim, Miao; Agu, Nkechinyere; Seneviratne, Oshani; McCusker, Jamie; Bennett, Kristin P.; Das, Amar; McGuinness, Deborah L. (2019-10-01)
      We address the problem of modeling study populations in research studies in a declarative manner. Research studies often have a great degree of variability in the reporting of population descriptions. To make study populations ...
    • Ontology-enabled Breast Cancer Characterization 

      Seneviratne, Oshani; Rashid, Sabbir; Chari, Shruthi; McCusker, Jamie; Bennett, Kristin P.; Hendler, James A.; McGuinness, Deborah L. (2018-10-01)
      We address the problem of characterizing breast cancer, which today is done using staging guidelines. Our demo will show different breast cancer staging results that leverage the Whyis semantic nanopublication knowledge ...
    • The Problem of Fairness in Synthetic Healthcare Data 

      Bhanot, Karan; Qi, Miao; Erickson, John S.; Guyon, Isabelle; Bennett, Kristin P. (Entropy (Basel, Switzerland), 2021-09)
      Access to healthcare data such as electronic health records (EHR) is often restricted by laws established to protect patient privacy. These restrictions hinder the reproducibility of existing results based on private ...
    • Semantalytics: Multi-modal Experimental Data Integration and Analysis through Semantic Alignment 

      Erickson, John S.; Shang, Yao; Jackson, Meredith; Fede, Halley; Shahir, Munira; McCrae, Sarah; New, Alexander; Draper, Josh; Walf, Alicia A.; Arpels-Josiah, Ranjit; Rosner, Andrew; Pinheiro, Paulo; Dyson, Anna; McGuinness, Deborah L.; Bennett, Kristin P. (DSpace at RPI, 2017-12)
      We describe an event-based semantics-driven framework for heterogeneous dataset integration, alignment and data analysis. The testbed for this semantalytics prototype was the pilot study of a multi-step experiment examining ...
    • Semantically enabling clinical decision support recommendations 

      Seneviratne, Oshani; Das, Amar K.; Chari, Shruthi; Agu, Nkechinyere N.; Rashid, Sabbir M.; McCusker, Jamie P.; Franklin, Jade S.; Qi, Miao; Bennett, Kristin P.; Chen, Ching-Hua; Hendler, James A.; McGuinness, Deborah L. (BMC/Springer Nature, 2023-07-18)
      Background Clinical decision support systems have been widely deployed to guide healthcare decisions on patient diagnosis, treatment choices, and patient management through evidence-based recommendations. These recommendations ...
    • Semantically-aware population health risk analyses 

      New, Alexander; Rashid, Sabbir; Erickson, John S.; McGuinness, Deborah L.; Bennett, Kristin P. (arXiv, 2018-11-27)
      One primary task of population health analysis is the identification of risk factors that, for some subpopulation, have a significant association with some health condition. Examples include finding lifestyle factors ...
    • Semantically-targeted analytics for reproducible scientific discovery 

      New, Alexander; Chari, Shruthi; Qim, Miao; Rashid, Sabbir; Erickson, John S.; McGuinness, Deborah L.; Bennett, Kristin P. (2019-05-13)
      We develop a semantics-driven, automated approach for dynamically performing rigorous scientific studies. This framework may be applied to a wide variety of data and study types; here, we demonstrate its suitability for ...