Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

A roadmap to integrate astrocytes into Systems Neuroscience.

Systems neuroscience is still mainly a neuronal field, despite the plethora of evidence supporting the fact that astrocytes modulate local neural circuits, networks, and complex behaviors. In this article, we sought to identify which types of studies are necessary to establish whether astrocytes, beyond their well-documented homeostatic and metabolic functions, perform computations implementing mathematical algorithms that sub-serve coding and higher-brain functions. First, we reviewed Systems-like studies that include astrocytes in order to identify computational operations that these cells may perform, using Ca2+ transients as their encoding language. The analysis suggests that astrocytes may carry out canonical computations in a time scale of subseconds to seconds in sensory processing, neuromodulation, brain state, memory formation, fear, and complex homeostatic reflexes. Next, we propose a list of actions to gain insight into the outstanding question of which variables are encoded by such computations. The application of statistical analyses based on machine learning, such as dimensionality reduction and decoding in the context of complex behaviors, combined with connectomics of astrocyte-neuronal circuits, is, in our view, fundamental undertakings. We also discuss technical and analytical approaches to study neuronal and astrocytic populations simultaneously, and the inclusion of astrocytes in advanced modeling of neural circuits, as well as in theories currently under exploration such as predictive coding and energy-efficient coding. Clarifying the relationship between astrocytic Ca2+ and brain coding may represent a leap forward toward novel approaches in the study of astrocytes in health and disease

Feedback Controlled Software Systems

Software systems generally suffer from a certain fragility in the face of disturbances such as bugs, unforeseen user input, unmodeled interactions with other software components, and so on. A single such disturbance can make the machine on which the software is executing hang or crash. We postulate that what is required to address this fragility is a general means of using feedback to stabilize these systems. In this paper we develop a preliminary dynamical systems model of an arbitrary iterative software process along with the conceptual framework for stabilizing it in the presence of disturbances. To keep the computational requirements of the controllers low, randomization and approximation are used. We describe our initial attempts to apply the model to a faulty list sorter, using feedback to improve its performance. Methods by which software robustness can be enhanced by distributing a task between nodes each of which are capable of selecting the best input to process are also examined, and the particular case of a sorting system consisting of a network of partial sorters, some of which may be buggy or even malicious, is examined

Information and Computation

In this chapter, concepts related to information and computation are reviewed in the context of human computation. A brief introduction to information theory and different types of computation is given. Two examples of human computation systems, online social networks and Wikipedia, are used to illustrate how these can be described and compared in terms of information and computation.Comment: 9 pages, 3 figures. Draft of a chapter to be published in Michelucci, P. (Ed.) Handbook of Human Computation, Springe

Amorphous Medium Language

Programming reliable behavior on a large mesh network composed of unreliable parts is difficult. Amorphous Medium Language addresses this problem by abstracting robustness and networking issues away from the programmer via language of geometric primitives and homeostasis maintenance.AML is designed to operate on a high diameter network composed of thousands to billions of nodes, and does not assume coordinate, naming, or routing services. Computational processes are distributed through geometric regions of the space approximated by the network and specify behavior in terms of homeostasis conditions and actions to betaken when homeostasis is violated.AML programs are compiled for local execution using previously developed amorphous computing primitives which provide robustness against ongoing failures and joins and localize the impact of changes in topology. I show some examples of how AML allows complex robust behavior to be expressed in simple programs and some preliminary results from simulation

Verification of logical consistency in robotic reasoning

Most autonomous robotic agents use logic inference to keep themselves to safe and permitted behaviour. Given a set of rules, it is important that the robot is able to establish the consistency between its rules, its perception-based beliefs, its planned actions and their consequences. This paper investigates how a robotic agent can use model checking to examine the consistency of its rules, beliefs and actions. A rule set is modelled by a Boolean evolution system with synchronous semantics, which can be translated into a labelled transition system (LTS). It is proven that stability and consistency can be formulated as computation tree logic (CTL) and linear temporal logic (LTL) properties. Two new algorithms are presented to perform realtime consistency and stability checks respectively. Their implementation provides us a computational tool, which can form the basis of efficient consistency checks on-board robots