Process Calculi Abstractions for Biology

Several approaches have been proposed to model biological systems by means of the formal techniques and tools available in computer science. To mention just a few of them, some representations are inspired by Petri Nets theory, and some other by stochastic processes. A most recent approach consists in interpreting the living entities as terms of process calculi where the behavior of the represented systems can be inferred by applying syntax-driven rules. A comprehensive picture of the state of the art of the process calculi approach to biological modeling is still missing. This paper goes in the direction of providing such a picture by presenting a comparative survey of the process calculi that have been used and proposed to describe the behavior of living entities. This is the preliminary version of a paper that was published in Algorithmic Bioprocesses. The original publication is available at http://www.springer.com/computer/foundations/book/978-3-540-88868-

Cognitive computation using neural representations of time and space in the Laplace domain

Memory for the past makes use of a record of what happened when---a function over past time. Time cells in the hippocampus and temporal context cells in the entorhinal cortex both code for events as a function of past time, but with very different receptive fields. Time cells in the hippocampus can be understood as a compressed estimate of events as a function of the past. Temporal context cells in the entorhinal cortex can be understood as the Laplace transform of that function, respectively. Other functional cell types in the hippocampus and related regions, including border cells, place cells, trajectory coding, splitter cells, can be understood as coding for functions over space or past movements or their Laplace transforms. More abstract quantities, like distance in an abstract conceptual space or numerosity could also be mapped onto populations of neurons coding for the Laplace transform of functions over those variables. Quantitative cognitive models of memory and evidence accumulation can also be specified in this framework allowing constraints from both behavior and neurophysiology. More generally, the computational power of the Laplace domain could be important for efficiently implementing data-independent operators, which could serve as a basis for neural models of a very broad range of cognitive computations.First author draf

The Lost Art of Mathematical Modelling

We provide a critique of mathematical biology in light of rapid developments in modern machine learning. We argue that out of the three modelling activities -- (1) formulating models; (2) analysing models; and (3) fitting or comparing models to data -- inherent to mathematical biology, researchers currently focus too much on activity (2) at the cost of (1). This trend, we propose, can be reversed by realising that any given biological phenomena can be modelled in an infinite number of different ways, through the adoption of an open/pluralistic approach. We explain the open approach using fish locomotion as a case study and illustrate some of the pitfalls -- universalism, creating models of models, etc. -- that hinder mathematical biology. We then ask how we might rediscover a lost art: that of creative mathematical modelling. This article is dedicated to the memory of Edmund Crampin

06031 Abstracts Collection -- Organic Computing -- Controlled Emergence

Organic Computing has emerged recently as a challenging vision for future information processing systems, based on the insight that we will soon be surrounded by large collections of autonomous systems equipped with sensors and actuators to be aware of their environment, to communicate freely, and to organize themselves in order to perform the actions and services required. Organic Computing Systems will adapt dynamically to the current conditions of its environment, they will be self-organizing, self-configuring, self-healing, self-protecting, self-explaining, and context-aware. From 15.01.06 to 20.01.06, the Dagstuhl Seminar 06031 ``Organic Computing -- Controlled Emergence\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. The seminar was characterized by the very constructive search for common ground between engineering and natural sciences, between informatics on the one hand and biology, neuroscience, and chemistry on the other. The common denominator was the objective to build practically usable self-organizing and emergent systems or their components. An indicator for the practical orientation of the seminar was the large number of OC application systems, envisioned or already under implementation, such as the Internet, robotics, wireless sensor networks, traffic control, computer vision, organic systems on chip, an adaptive and self-organizing room with intelligent sensors or reconfigurable guiding systems for smart office buildings. The application orientation was also apparent by the large number of methods and tools presented during the seminar, which might be used as building blocks for OC systems, such as an evolutionary design methodology, OC architectures, especially several implementations of observer/controller structures, measures and measurement tools for emergence and complexity, assertion-based methods to control self-organization, wrappings, a software methodology to build reflective systems, and components for OC middleware. Organic Computing is clearly oriented towards applications but is augmented at the same time by more theoretical bio-inspired and nature-inspired work, such as chemical computing, theory of complex systems and non-linear dynamics, control mechanisms in insect swarms, homeostatic mechanisms in the brain, a quantitative approach to robustness, abstraction and instantiation as a central metaphor for understanding complex systems. Compared to its beginnings, Organic Computing is coming of age. The OC vision is increasingly padded with meaningful applications and usable tools, but the path towards full OC systems is still complex. There is progress in a more scientific understanding of emergent processes. In the future, we must understand more clearly how to open the configuration space of technical systems for on-line modification. Finally, we must make sure that the human user remains in full control while allowing the systems to optimize

An Integrated Qualitative and Quantitative Biochemical Model Learning Framework Using Evolutionary Strategy and Simulated Annealing

The authors would like to thank the support on this research by the CRISP Project (Combinatorial Responses In Stress Pathways) funded by the BBSRC (BB/F00513X/1) under the Systems Approaches to Biological Research (SABR) Initiative.Peer reviewedPublisher PD

Contractive Autoencoding for Hierarchical Temporal Memory and Sparse Distributed Representation Binding

Hierarchical Temporal Memory is a brain inspired memory prediction framework modeled after the uniform structure and connectivity of pyramidal neurons found in the human neocortex. Similar to the neocortex, Hierarchical Temporal Memory processes spatiotemporal information for anomaly detection and prediction. A critical component in the Hierarchical Temporal Memory algorithm is the Spatial Pooler, which is responsible for processing feedforward data into sparse distributed representations. This study addresses three fundamental research questions for Hierarchical Temporal Memory algorithms. What are the metrics for understanding the semantic content of sparse distributed representations? The semantic content and relationships between representations was visualized with uniqueness matrices and dimensionality reduction techniques. How can spatial semantic information in images be encoded into binary representations for the Hierarchical Temporal Memory\u27s Spatial Pooler? A Contractive Autoencoder was exploited to create binary representations containing spatial information from image data. The uniqueness matrix shows that the Contractive Autoencoder encodes spatial information with strong spatial semantic relationships. The final question is how can vector operations of sparse distributed representations be enhanced to produce separable representations? A binding operation that results in a novel vector was implemented as a circular bit shift between two binary vectors. Binding of labeled sparse distributed representations was shown to create separable representations, but more robust representations are limited by vector density

Grammar-Based Set-Theoretic Formalization of Emergence in Complex Systems

Master'sMASTER OF SCIENC