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We present and study an agent-based model of T-Cell cross-regulation in the adaptive immune system, which we apply to binary classification. Our method expands an existing analytical model of T-cell cross-regulation (Carneiro et al. in Immunol Rev 216(1):48-68, 2007) that was used to study the self-organizing dynamics of a single population of T-Cells in interaction with an idealized antigen presenting cell capable of presenting a single antigen. With agent-based modeling we are able to study the self-organizing dynamics of multiple populations of distinct T-cells which interact via antigen presenting cells that present hundreds of distinct antigens. Moreover, we show that such self-organizing dynamics can be guided to produce an effective binary classification of antigens, which is competitive with existing machine learning methods when applied to biomedical text classification. More specifically, here we test our model on a dataset of publicly available full-text biomedical articles provided by the BioCreative challenge (Krallinger in The biocreative ii. 5 challenge overview, p 19, 2009). We study the robustness of our models parameter configurations, and show that it leads to encouraging results comparable to state-of-the-art classifiers. Our results help us understand both T-cell cross-regulation as a general principle of guided self-organization, as well as its applicability to document classification. Therefore, we show that our bio-inspired algorithm is a promising novel method for biomedical article classification and for binary document classification in general.
In this paper, we begin by reviewing a certain number of mathematical challenges posed by the modelling of collective dynamics and self-organization. Then, we focus on two specific problems, first, the derivation of fluid equations from particle dyna
We review attempts that have been made towards understanding the computational properties and mechanisms of input-driven dynamical systems like RNNs, and reservoir computing networks in particular. We provide details on methods that have been develop
Self-regulation of living tissue as an example of self-organization phenomena in hierarchical systems of biological, ecological, and social nature is under consideration. The characteristic feature of these systems is the absence of any governing cen
Cytoskeletal networks form complex intracellular structures. Here we investigate a minimal model for filament-motor mixtures in which motors act as depolymerases and thereby regulate filament length. Combining agent-based simulations and hydrodynamic
Cross-Domain Recommendation (CDR) and Cross-System Recommendation (CSR) have been proposed to improve the recommendation accuracy in a target dataset (domain/system) with the help of a source one with relatively richer information. However, most exis