Ecole d'ingénieur et centre de recherche en Sciences du numérique

Parameter inference in differential equation models of biopathways using time warped gradient matching

Niu, Mu; Rogers, Simon; Filippone, Maurizio; Husmeier, Dirk

CIBB 2016, 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 1-3 September 2016, Stirling, UK / Also in LNCS, Vol.10477

Parameter inference in mechanistic models of biopathways based on systems of coupled differential equations is a topical yet computationally challenging problem due to the fact that each parameter adaptation involves a numerical integration of the differential equations. Techniques based on gradient matching, which aim to minimize the discrepancy between the slope of a data interpolant and the derivatives predicted from the differential equations, offer a computationally appealing shortcut to the inference problem. Gradient matching critically hinges on the smoothing scheme for function interpolation, with spurious oscillations in the interpolant having a dramatic effect on the subsequent inference. The present article demonstrates that a time warping approach that aims to homogenize intrinsic functional length scales can lead to a significant improvement in parameter estimation accuracy. We demonstrate the effectiveness of this scheme on noisy data from a dynamical system with periodic limit cycle, and a biopathway model.

Doi Bibtex

Titre:Parameter inference in differential equation models of biopathways using time warped gradient matching
Mots Clés:Biopathways; Differential equations; Gradient matching; Reproducing kernel hilbert space; Time warping; Optimisation
Type:Conférence
Langue:English
Ville:Stirling
Pays:ROYAUME-UNI
Date:
Département:Data Science
Eurecom ref:5355
Copyright: © Springer. Personal use of this material is permitted. The definitive version of this paper was published in CIBB 2016, 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, 1-3 September 2016, Stirling, UK / Also in LNCS, Vol.10477 and is available at : http://doi.org/10.1007/978-3-319-67834-4_12
Bibtex: @inproceedings{EURECOM+5355, doi = {http://doi.org/10.1007/978-3-319-67834-4_12}, year = {2016}, title = {{P}arameter inference in differential equation models of biopathways using time warped gradient matching}, author = {{N}iu, {M}u and {R}ogers, {S}imon and {F}ilippone, {M}aurizio and {H}usmeier, {D}irk}, booktitle = {{CIBB} 2016, 13th {I}nternational {M}eeting on {C}omputational {I}ntelligence {M}ethods for {B}ioinformatics and {B}iostatistics, 1-3 {S}eptember 2016, {S}tirling, {UK} / {A}lso in {LNCS}, {V}ol.10477}, address = {{S}tirling, {ROYAUME}-{UNI}}, month = {09}, url = {http://www.eurecom.fr/publication/5355} }
Voir aussi: