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This article is part of the supplement: Nineteenth Annual Computational Neuroscience Meeting: CNS*2010

Open Access Poster Presentation

Classifying functional and non-functional model neurons using the theory of rough sets

Tomasz G Smolinski* and Astrid A Prinz

Author Affiliations

Department of Biology, Emory University, Atlanta, GA 30322, USA

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BMC Neuroscience 2010, 11(Suppl 1):P157  doi:10.1186/1471-2202-11-S1-P157

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2202/11/S1/P157


Published:20 July 2010

© 2010 Smolinski and Prinz; licensee BioMed Central Ltd.

Poster Presentation

We explored a 12-dimensional parameter space of a 2-compartment model of the AB (anterior burster) neuron, which is one of the two cells that form the pacemaker kernel in the pyloric network in the lobster stomatogastric ganglion (STG). The computational exploration started with a hand-tuned AB model [1] and systematically varied maximal conductances of membrane currents to determine ranges and variation steps that could potentially produce physiologically realistic behavior. We varied the conductances for the following currents in the model: fast sodium INa and delayed-rectifier potassium IKd in the axon compartment, and delayed-rectifier IKd, calcium-dependent IKCa, transient potassium IA, transient ICaT and persistent ICaS calcium, persistent sodium INaP, and hyperpolarization-activated inward Ih in the some/neurite (S/N) compartment. To model the descending modulatory inputs, a voltage-gated inward current (such as the one activated by the neuropeptide proctolin) Iproc was added to the S/N compartment. Both compartments also contained the leak current IL.

Every parameter set representing an individual model neuron was simulated and analyzed in terms of its period, burst duration, spike and slow wave amplitude, number of spikes per burst, spike frequency, and after-hyperpolarization potential, as well as the model’s responses to neuromodulator deprivation and current injections. All of the above characteristics had to be within limits determined in physiological experiments performed on the AB cell, in order for a model to be classified as functional [2].

In addition to several other data mining and visualization techniques we have previously employed to analyze the parameter space of the “good” models [3], we propose to utilize the theory of rough sets (RS) to investigate the role and importance of the parameters in differentiating between the functional and non-functional models. One of the most useful aspects of the RS theory in these kinds of classification tasks is the concept of a reduct—the smallest possible subset of attributes (i.e., maximal conductances in our model) that preserves the classification accuracy of the full set of attributes [4]. There are usually several such reducts for a given problem, and by extracting the so-called core of the reducts (i.e., the attributes that all the discovered reducts have in common), one can estimate the relative importance of the attributes. For instance, based on the 10 reducts computed from our dataset, we can state that soma CaT, NaP, Kd, KCa, and Proc, are absolutely necessary for differentiation between the functional and non-functional models (they were included in all 10 reducts), the axon Na current is very important (utilized in 9 out of 10 reducts), while the leak currents (both in the soma and the axon) seem to be the least important (they were present in 6 and 7 of the reducts, respectively). Furthermore, based on reducts, one can easily generate IF-THEN rules that not only describe how the model’s proper behavior depends on its parameters, but also how those parameters (i.e., ionic currents) “cooperate” with one another to assure such activity. For example, one of the most trustworthy rules we discovered (confidence of 78%) describes the following relationship:

IF soma NaP∈[2.7μS÷6.4μS) AND soma KCa∈[3,000μS÷6,000μS) AND axon Na∈[300μS÷450μS)

THEN “functional AB model,”

where the values in parentheses represent the ranges for the corresponding maximum membrane conductances.

Acknowledgements

Support contributed by: Burroughs-Wellcome Fund CASI Award to AAP.

References

  1. Soto-Treviño , et al.: Computational model of electrically coupled, intrinsically distinct pacemaker neurons.

    J Neurophysiol 2005, 94:590-604. PubMed Abstract | Publisher Full Text | PubMed Central Full Text OpenURL

  2. Smolinski , et al.: Systematic selection of model parameter values matching biological behavior under different simulation scenarios.

    BMC Neuroscience 2008, 9(Suppl 1):53. BioMed Central Full Text OpenURL

  3. Smolinski , Prinz : Computational Intelligence in Modeling of Biological Neurons: A Case Study of an Invertebrate Pacemaker Neuron. In Proc International Joint Conference on Neural Networks. Atlanta, GA; 2009. OpenURL

  4. Pawlak : Rough sets.

    Int J Computer and Information Sci 1982, 11:341-356. Publisher Full Text OpenURL