Structurally robust biological networks

Background: The molecular circuitry of living organisms performs remarkably robust regulatory tasks, despite the often intrinsic variability of its components. A large body of research has in fact highlighted that robustness is often a structural property of biological systems. However, there are few systematic methods to mathematically model and describe structural robustness. With a few exceptions, numerical studies are often the preferred approach to this type of investigation. Results: In this paper, we propose a framework to analyze robust stability of equilibria in biological networks. We employ Lyapunov and invariant sets theory, focusing on the structure of ordinary differential equation models. Without resorting to extensive numerical simulations, often necessary to explore the behavior of a model in its parameter space, we provide rigorous proofs of robust stability of known bio-molecular networks. Our results are in line with existing literature. Conclusions: The impact of our results is twofold: on the one hand, we highlight that classical and simple control theory methods are extremely useful to characterize the behavior of biological networks analytically. On the other hand, we are able to demonstrate that some biological networks are robust thanks to their structure and some qualitative properties of the interactions, regardless of the specific values of their parameters

Evolutionary robotics and neuroscience

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Dengue disease, basic reproduction number and control

Dengue is one of the major international public health concerns. Although progress is underway, developing a vaccine against the disease is challenging. Thus, the main approach to fight the disease is vector control. A model for the transmission of Dengue disease is presented. It consists of eight mutually exclusive compartments representing the human and vector dynamics. It also includes a control parameter (insecticide) in order to fight the mosquito. The model presents three possible equilibria: two disease-free equilibria (DFE) and another endemic equilibrium. It has been proved that a DFE is locally asymptotically stable, whenever a certain epidemiological threshold, known as the basic reproduction number, is less than one. We show that if we apply a minimum level of insecticide, it is possible to maintain the basic reproduction number below unity. A case study, using data of the outbreak that occurred in 2009 in Cape Verde, is presented.Comment: This is a preprint of a paper whose final and definitive form has appeared in International Journal of Computer Mathematics (2011), DOI: 10.1080/00207160.2011.55454

Mathematical modeling of Zika disease in pregnant women and newborns with microcephaly in Brazil

We propose a new mathematical model for the spread of Zika virus. Special attention is paid to the transmission of microcephaly. Numerical simulations show the accuracy of the model with respect to the Zika outbreak occurred in Brazil.Comment: This is a preprint of a paper whose final and definite form is with 'Mathematical Methods in the Applied Sciences', ISSN 0170-4214. Submitted Aug 10, 2017; Revised Nov 13, 2017; accepted for publication Nov 14, 201

Completeness of Lyapunov Abstraction

In this work, we continue our study on discrete abstractions of dynamical systems. To this end, we use a family of partitioning functions to generate an abstraction. The intersection of sub-level sets of the partitioning functions defines cells, which are regarded as discrete objects. The union of cells makes up the state space of the dynamical systems. Our construction gives rise to a combinatorial object - a timed automaton. We examine sound and complete abstractions. An abstraction is said to be sound when the flow of the time automata covers the flow lines of the dynamical systems. If the dynamics of the dynamical system and the time automaton are equivalent, the abstraction is complete. The commonly accepted paradigm for partitioning functions is that they ought to be transversal to the studied vector field. We show that there is no complete partitioning with transversal functions, even for particular dynamical systems whose critical sets are isolated critical points. Therefore, we allow the directional derivative along the vector field to be non-positive in this work. This considerably complicates the abstraction technique. For understanding dynamical systems, it is vital to study stable and unstable manifolds and their intersections. These objects appear naturally in this work. Indeed, we show that for an abstraction to be complete, the set of critical points of an abstraction function shall contain either the stable or unstable manifold of the dynamical system.Comment: In Proceedings HAS 2013, arXiv:1308.490

Guaranteeing Convergence of Iterative Skewed Voting Algorithms for Image Segmentation

In this paper we provide rigorous proof for the convergence of an iterative voting-based image segmentation algorithm called Active Masks. Active Masks (AM) was proposed to solve the challenging task of delineating punctate patterns of cells from fluorescence microscope images. Each iteration of AM consists of a linear convolution composed with a nonlinear thresholding; what makes this process special in our case is the presence of additive terms whose role is to "skew" the voting when prior information is available. In real-world implementation, the AM algorithm always converges to a fixed point. We study the behavior of AM rigorously and present a proof of this convergence. The key idea is to formulate AM as a generalized (parallel) majority cellular automaton, adapting proof techniques from discrete dynamical systems

Towards integrated neural-symbolic systems for human-level AI: Two research programs helping to bridge the gaps

After a human-level AI-oriented overview of the status quo in neural-symbolic integration, two research programs aiming at overcoming long-standing challenges in the field are suggested to the community: The first program targets a better understanding of foundational differences and relationships on the level of computational complexity between symbolic and subsymbolic computation and representation, potentially providing explanations for the empirical differences between the paradigms in application scenarios and a foothold for subsequent attempts at overcoming these. The second program suggests a new approach and computational architecture for the cognitively-inspired anchoring of an agent's learning, knowledge formation, and higher reasoning abilities in real-world interactions through a closed neural-symbolic acting/sensing-processing-reasoning cycle, potentially providing new foundations for future agent architectures, multi-agent systems, robotics, and cognitive systems and facilitating a deeper understanding of the development and interaction in human-technological settings