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. 2020 Feb:117:103621.
doi: 10.1016/j.compbiomed.2020.103621. Epub 2020 Jan 20.

Extension of the Quantum Universal Exchange Language to precision medicine and drug lead discovery. Preliminary example studies using the mitochondrial genome

Barry Robson  1
Affiliations

Extension of the Quantum Universal Exchange Language to precision medicine and drug lead discovery. Preliminary example studies using the mitochondrial genome

Barry Robson. Comput Biol Med. 2020 Feb.

Abstract

The Quantum Universal Exchange Language (Q-UEL) based on Dirac notation and algebra from quantum mechanics, along with its associated data mining and Hyperbolic Dirac Net (HDN) for probabilistic inference, has proven to be a useful architectural principle for knowledge management, analysis and prediction systems in medicine. It has been described in several papers; here is described its extension to clinical genomics and precision medicine. Two use cases are studied: (a) bioinformatics in clinical decision support especially for risk for type 2 diabetes using mitochondrial patient DNA sequences, and (b) bioinformatics and computational biology (conformational) research examples related to drug discovery involving the recently discovered class of mitochondrial derived peptides (MDPs). MDPs were surprising when first discovered as coded in small open reading frames (sORFs), and are emerging as having a fundamental role in metabolic control, longevity and disease. This project originally represented a language specification study relating to what information related to genomics is essential or useful to carry, and what processing will be needed. However, novel aspects introduced or discovered include the HDN-like neural nets and their use, along with more established methods, for prediction of type 2 diabetes, and in particular for proposals for over 80 natural MDPs most of which that have not previously been described at the time of the study, as potential drug lead targets. Also, use of many medical records with simulated joining of mtDNA as performance tests led to some insightful observations regarding the behavior of HDN predictions where independent factors are involved.

Keywords: Bayes net; Bioinformatics; Clinical decision support; Data analytics; Data mining; Dirac notation; Genomics; Hyperbolic Dirac net; Inference net; Quantum mechanics; Universal exchange language.

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Conflict of interest statement

Declaration of competing interest This paper is provided to the community to promote the more general applications of the thinking of Professor Paul A. M. Dirac to human and animal medicine in accordance with the charter of The Dirac Foundation, to emphasize the advantages and simplicity of the basic form of the Hyperbolic Dirac Net, to encourage its use, and to propose at least some of the principles of the associated Q-UEL, a universal exchange language for medicine, as a basis for a standard for interoperability. These mathematical and engineering principles are used, amongst many others in an integrated way, in the algorithms and internal architectural features of the BioIngine.com, a distributed system developed by Ingine Inc. DE for the mining of, and inference from, Very Big Data for commercial purposes.

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