Initial state perturbations as a validation method for data-driven fuzzy models of cellular networks

BMC Bioinformatics
Lidija MagdevskaMiha Moskon

Abstract

Data-driven methods that automatically learn relations between attributes from given data are a popular tool for building mathematical models in computational biology. Since measurements are prone to errors, approaches dealing with uncertain data are especially suitable for this task. Fuzzy models are one such approach, but they contain a large amount of parameters and are thus susceptible to over-fitting. Validation methods that help detect over-fitting are therefore needed to eliminate inaccurate models. We propose a method to enlarge the validation datasets on which a fuzzy dynamic model of a cellular network can be tested. We apply our method to two data-driven dynamic models of the MAPK signalling pathway and two models of the mammalian circadian clock. We show that random initial state perturbations can drastically increase the mean error of predictions of an inaccurate computational model, while keeping errors of predictions of accurate models small. With the improvement of validation methods, fuzzy models are becoming more accurate and are thus likely to gain new applications. This field of research is promising not only because fuzzy models can cope with uncertainty, but also because their run time is short compared to...Continue Reading

References

May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·A LevchenkoP W Sternberg
Oct 4, 2000·Physiological Genomics·P J Woolf, Y Wang
Feb 22, 2001·Annual Review of Physiology·S M Reppert, D R Weaver
May 31, 2003·Proceedings of the National Academy of Sciences of the United States of America·Jean-Christophe Leloup, Albert Goldbeter
Dec 6, 2003·Proceedings of the National Academy of Sciences of the United States of America·Daniel B Forger, Charles S Peskin
Jan 31, 2004·Biochemical and Biophysical Research Communications·Satoshi YamadaAkihiko Yoshimura
Jun 10, 2004·Microbiology and Molecular Biology Reviews : MMBR·Philippe P Roux, John Blenis
Jan 13, 2006·Current Opinion in Chemical Biology·Kevin A Janes, Douglas A Lauffenburger
Nov 24, 2006·Nature·Alex SigalUri Alon
Feb 20, 2008·PLoS Computational Biology·Joshua F ApgarBruce Tidor
Jan 20, 2009·Bio Systems·Michael HeckerReinhard Guthke
Apr 4, 2009·PLoS Computational Biology·Bree B AldridgeDouglas A Lauffenburger
Jun 25, 2009·Proceedings of the National Academy of Sciences of the United States of America·Henry P MirskyFrancis J Doyle
Sep 16, 2009·Cancer Research·Qi CaoH Phillip Koeffler
Jan 19, 2010·Biochimica Et Biophysica Acta·Eun Kyung Kim, Eui-Ju Choi
Aug 21, 2010·The Journal of Biological Chemistry·Yuji KamiokaMichiyuki Matsuda
Sep 27, 2012·Journal of Biological Rhythms·Michael J McCarthy, David K Welsh
Jul 23, 2014·Scientific Reports·Anja KorenčičHanspeter Herzel
Apr 23, 2015·Journal of Biological Rhythms·Nathalie Labrecque, Nicolas Cermakian
Oct 10, 2015·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Jure BordonMiha Mraz
Oct 6, 2016·Progress in Biophysics and Molecular Biology·Eann A Patterson, Maurice P Whelan
Jan 4, 2017·Scientific Reports·Marek KochańczykTomasz Lipniacki
Nov 4, 2017·Journal of Biological Rhythms·Michael E HughesJohn B Hogenesch

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

MAFTS
MATLAB

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.