SIMON: Open-Source Knowledge Discovery Platform

Adriana Tomic; Ivan Tomic; Levi Waldron; Ludwig Geistlinger; Max Kuhn; Rachel L Spreng; Lindsay C Dahora; Kelly E Seaton; Georgia Tomaras; Jennifer Hill; Niharika A Duggal; Ross D Pollock; Norman R Lazarus; Stephen D R Harridge; Janet M Lord; Purvesh Khatri; Andrew J Pollard; Mark M Davis

doi:10.1016/j.patter.2020.100178

SIMON: Open-Source Knowledge Discovery Platform

Patterns (N Y). 2021 Jan 8;2(1):100178. doi: 10.1016/j.patter.2020.100178.

Authors

Adriana Tomic^{1

2}, Ivan Tomic³, Levi Waldron^{4

5}, Ludwig Geistlinger^{4

5}, Max Kuhn⁶, Rachel L Spreng⁷, Lindsay C Dahora⁷, Kelly E Seaton⁷, Georgia Tomaras⁷, Jennifer Hill¹, Niharika A Duggal⁸, Ross D Pollock⁹, Norman R Lazarus⁹, Stephen D R Harridge⁹, Janet M Lord^{8

10}, Purvesh Khatri^{2

11}, Andrew J Pollard¹, Mark M Davis^{2

12

13}

Affiliations

¹ Oxford Vaccine Group, Department of Paediatrics, University of Oxford, Oxford, UK.
² Institute of Immunity, Transplantation, and Infection, Stanford University School of Medicine, Stanford, CA, USA.
³ Deep Medicine, Nuffield Department of Women's and Reproductive Health, University of Oxford, Oxford, UK.
⁴ Graduate School of Public Health and Health Policy, City University of New York, New York, NY, USA.
⁵ Institute for Implementation Science and Population Health, City University of New York, New York, NY, USA.
⁶ RStudio, PBC, Boston, MA, USA.
⁷ Duke Human Vaccine Institute, Duke University, Durham, NC, USA.
⁸ MRC-Versus Arthritis Centre for Musculoskeletal Ageing Research, Institute of Inflammation and Ageing, University of Birmingham Research Labs, Birmingham, UK.
⁹ Centre for Human and Applied Physiological Sciences, King's College London, UK.
¹⁰ NIHR Birmingham Biomedical Research Centre, University Hospital Birmingham NHS Foundation Trust and University of Birmingham, Birmingham, UK.
¹¹ Center for Biomedical Informatics Research, Department of Medicine, Stanford University, Stanford, CA, USA.
¹² Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA.
¹³ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.

Abstract

Data analysis and knowledge discovery has become more and more important in biology and medicine with the increasing complexity of biological datasets, but the necessarily sophisticated programming skills and in-depth understanding of algorithms needed pose barriers to most biologists and clinicians to perform such research. We have developed a modular open-source software, SIMON, to facilitate the application of 180+ state-of-the-art machine-learning algorithms to high-dimensional biomedical data. With an easy-to-use graphical user interface, standardized pipelines, and automated approach for machine learning and other statistical analysis methods, SIMON helps to identify optimal algorithms and provides a resource that empowers non-technical and technical researchers to identify crucial patterns in biomedical data.

Keywords: artificial intelligence; autoML; bioinformatics; computational biology; data mining; data science; machine learning; software; systems biology.

Abstract

Grants and funding