Translational utility of a hierarchical classification strategy in biomolecular data analytics

Scientific Reports
Dieter GaleaKirill A Veselkov

Abstract

Hierarchical classification (HC) stratifies and classifies data from broad classes into more specific classes. Unlike commonly used data classification strategies, this enables the probabilistic prediction of unknown classes at different levels, minimizing the burden of incomplete databases. Despite these advantages, its translational application in biomedical sciences has been limited. We describe and demonstrate the implementation of a HC approach for "omics-driven" classification of 15 bacterial species at various taxonomic levels achieving 90-100% accuracy, and 9 cancer types into morphological types and 35 subtypes with 99% and 76% accuracy, respectively. Unknown bacterial species were probabilistically assigned with 100% accuracy to their respective genus or family using mass spectra (n = 284). Cancer types were predicted by mRNA data (n = 1960) for most subtypes with 95-100% accuracy. This has high relevance in clinical practice where complete datasets are difficult to compile with the continuous evolution of diseases and emergence of new strains, yet prediction of unknown classes, such as bacterial species, at upper hierarchy levels may be sufficient to initiate antimicrobial therapy. The algorithms presented here can b...Continue Reading

References

Jan 18, 2006·Bioinformatics·Zafer BarutcuogluOlga G Troyanskaya
Mar 11, 2006·IEEE Transactions on Neural Networks·Haifeng LiKeshu Zhang
Mar 28, 2006·Systematic and Applied Microbiology·Didier HutsebautPaul de Vos
Jul 28, 2006·BMC Bioinformatics·Tadayoshi FushikiShinto Eguchi
Dec 17, 2009·Nature Reviews. Microbiology·Sascha Sauer, Magdalena Kliem
Jul 20, 2010·Clinical Microbiology and Infection : the Official Publication of the European Society of Clinical Microbiology and Infectious Diseases·A Bizzini, G Greub
Jan 20, 2012·The New England Journal of Medicine·Reza MirnezamiAra Darzi
May 3, 2013·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkGreg Eley
Jun 25, 2013·Nature·UNKNOWN Cancer Genome Atlas Research Network
Jul 3, 2013·European Journal of Clinical Microbiology & Infectious Diseases : Official Publication of the European Society of Clinical Microbiology·S S RichterG W Procop
Oct 15, 2013·Cell·Cameron W BrennanUNKNOWN TCGA Research Network
Jan 9, 2014·Proceedings of the National Academy of Sciences of the United States of America·Kirill A VeselkovZoltan Takats
Jan 31, 2014·Nature·UNKNOWN Cancer Genome Atlas Research Network
Aug 1, 2014·Nature·UNKNOWN Cancer Genome Atlas Research Network
May 21, 2015·BMC Genomics·Ankit Gupta, Vineet K Sharma
Jun 11, 2015·The New England Journal of Medicine·UNKNOWN Cancer Genome Atlas Research NetworkJianan Zhang
Nov 5, 2015·The New England Journal of Medicine·W Marston LinehanUNKNOWN Cancer Genome Atlas Research Network
Nov 7, 2015·Cell·UNKNOWN Cancer Genome Atlas Research Network

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Methods Mentioned

BETA
PCA

Software Mentioned

LIBSVM
MATLAB

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