City Research Online

Supporting shared hypothesis testing in the biomedical domain

Agibetov, A., Jimenez-Ruiz, E. ORCID: 0000-0002-9083-4599, Ondresik, M., Solimando, A., Banerjee, I., Guerrini, G., Catalano, C. E., Oliveira, J. M., Patane, G., Reis, R. L. and Spagnuolo, M. (2018). Supporting shared hypothesis testing in the biomedical domain. Journal of Biomedical Semantics, 9, 9.. doi: 10.1186/s13326-018-0177-x

Abstract

Background: Pathogenesis of inflammatory diseases can be tracked by studying the causality relationships among the factors contributing to its development. We could, for instance, hypothesize on the connections of the pathogenesis outcomes to the observed conditions. And to prove such causal hypotheses we would need to have the full understanding of the causal relationships, and we would have to provide all the necessary evidences to support our claims. In practice, however, we might not possess all the background knowledge on the causality relationships, and we might be unable to collect all the evidence to prove our hypotheses.

Results: In this work we propose a methodology for the translation of biological knowledge on causality relationships of biological processes and their effects on conditions to a computational framework for hypothesis testing. The methodology consists of two main points: hypothesis graph construction from the formalization of the background knowledge on causality relationships, and confidence measurement in a causality hypothesis as a normalized weighted path computation in the hypothesis graph. In this framework, we can simulate collection of evidences and assess confidence in a causality hypothesis by measuring it proportionally to the amount of available knowledge and collected evidences.

Conclusions: We evaluate our methodology on a hypothesis graph that represents both contributing factors which may cause cartilage degradation and the factors which might be caused by the cartilage degradation during osteoarthritis. Hypothesis graph construction has proven to be robust to the addition of potentially contradictory information on the simultaneously positive and negative effects. The obtained confidence measures for the specific causality hypotheses have been validated by our domain experts, and, correspond closely to their subjective assessments of confidences in investigated hypotheses. Overall, our methodology for a shared hypothesis testing framework exhibits important properties that researchers will find useful in literature review for their experimental studies, planning and prioritizing evidence collection acquisition procedures, and testing their hypotheses with different depths of knowledge on causal dependencies of biological processes and their effects on the observed conditions.

Publication Type: Article
Additional Information: © The Author(s). 2018Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, andreproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to theCreative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Publisher Keywords: Biomedical ontology; Ontology mapings; Network analysis; Hypothesis testing; Incomplete knowledge
Subjects: Q Science > QH Natural history > QH301 Biology
Departments: School of Mathematics, Computer Science & Engineering > Computer Science
URI: https://openaccess.city.ac.uk/id/eprint/22946
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