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Systems Medicine Conference in Slovenia

Systems Medicine Conference in Slovenia: National Awareness Event,12th CFGBC Symposium and “Systems Medicine” Workshop took place from June 8th-9th 2017 at Hotel Slon, Ljubljana, Slovenia.

CASyM winter school of Systems Medicine

CASyM winter school of Systems Medicine took place between March 29th and April 1st 2017 in Ljubljana, Slovenia and is entitled »The 3rd SysBioMed hands-on tutorial: Systems Medicine Approaches in Personalized Medicine«

ELIXIR-SI launch & 11TH CFGBC Symposium

The event with motto “Data for Life” took place from September 20th - 21st 2016 at Cankarjev dom and the Faculty of Medicine, University of Ljubljana, Slovenia.

2017-06-07


Automatization of fuzzy inference system describing the dynamics of MAPK cascade

Lidija Magdevska1,Miha Mraz1,Nikolaj Zimic1,Miha Moškon1

1Faculty of Computer and Information Science, University of Ljubljana, Ljubljana, Slovenia

Introduction:
Fuzzy modelling is an approach to cope with uncertain data [1]. Models are built upon linguistic description, where for each linguistic variable its collection of fuzzy values and a membership functions are defined. A set of fuzzy rules has to be constructed to describe the relations between linguistic variables. Here we present an approach for automatic fuzzy model generation from known data.
 
Results:
The signaling pathway of the MAPK is a phosphorylation cascade [2]. The rules for a single phosphorylation cycle are automatically defined using a fuzzy c-means clustering algorithm. Here, data is firstly collected from a deterministic model. Experimental data could also be used. Data is generated by several runs of the deterministic model using different initial conditions. It needs to be resampled to be evenly distributed. The resampled data is then used as an input for the clustering algorithm. It is divided into three clusters that define the fuzzy rules. The so defined fuzzy model provides results that correspond to the expected system’s behaviour.
 
Conclusions:
In order to construct a fuzzy model of the MAPK signaling pathway, the phosphorylation modules are sequentially bound to form a cascade. Since the fuzzy rules were generated generically, only small modifications of the modules are needed besides the definition of systems initial conditions. Namely, additional fitting of the membership functions is needed. For this purpose, general optimization approaches such as genetic algorithms and simulated annealing are used. The proposed approach can be thus efficiently applied to the reconstruction of computational models from the experimental data.
 
References:
1. J. Bordon, Modeliranje enostavnih bioloških preklopnih sistemov z uporabo mehke logike in razširjenih Petrijevih mrež, PhD dissertation, Univerza v Ljubljani (2017).
2. M. Kochańczyk et al., Relaxation oscillations and hierarchy of feedbacks in MAPK signaling, Sci Rep 7 (2017) 38244.

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2006 - University of Ljubljana, Faculty of Medicine, Center for Functional Genomics and Bio-chips.