MAREX: A general purpose hardware architecture for membrane computing

Membrane computing is an unconventional computing paradigm that has gained much attention in recent decades because of its massively parallel character and its usefulness to build models of complex systems. However, until now, there was no generic hardware implementation of P systems. Computational frameworks to execute P systems up to this day rely on the simulation of the parallel working mechanisms of P systems by inherently sequential algorithms. Such algorithms can then be implemented as is or can be parallelized, up to a certain point, to run on parallel computers. However, this is not as efficient as a dedicated parallel hardware implementation. There have been ad hoc implementations of particular P systems for parallel hardware, but they lack to be problem-generic or they are not scalable enough to implement large P systems. In this paper, a first intrinsically parallel hardware architecture to implement generic P system models is introduced. It is designed to be straightforwardly implemented in programmable logic circuits like FPGAs. The feasibility and correct execution of our architecture has been verified by means of a simulator, and several simulation results for different P system examples have been analysed to foresee the pros and cons of this design.Ministerio de Ciencia e Innovacion of Spain and the AEI/FEDER (EU) project TIN2017-89842-P (MABICAP)Ministerio de Ciencia e Innovacion of Spain and the AEI/FEDER (EU) project PID2019-110455GB-I00 (Par-HoT

Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures

The protein-folding problem has been extensively studied during the last fifty years. The understanding of the dynamics of global shape of a protein and the influence on its biological function can help us to discover new and more effective drugs to deal with diseases of pharmacological relevance. Different computational approaches have been developed by different researchers in order to foresee the threedimensional arrangement of atoms of proteins from their sequences. However, the computational complexity of this problem makes mandatory the search for new models, novel algorithmic strategies and hardware platforms that provide solutions in a reasonable time frame. We present in this revision work the past and last tendencies regarding protein folding simulations from both perspectives; hardware and software. Of particular interest to us are both the use of inexact solutions to this computationally hard problem as well as which hardware platforms have been used for running this kind of Soft Computing techniques.This work is jointly supported by the FundaciónSéneca (Agencia Regional de Ciencia y Tecnología, Región de Murcia) under grants 15290/PI/2010 and 18946/JLI/13, by the Spanish MEC and European Commission FEDER under grant with reference TEC2012-37945-C02-02 and TIN2012-31345, by the Nils Coordinated Mobility under grant 012-ABEL-CM-2014A, in part financed by the European Regional Development Fund (ERDF). We also thank NVIDIA for hardware donation within UCAM GPU educational and research centers.Ingeniería, Industria y Construcció

Herding as a Learning System with Edge-of-Chaos Dynamics

Herding defines a deterministic dynamical system at the edge of chaos. It generates a sequence of model states and parameters by alternating parameter perturbations with state maximizations, where the sequence of states can be interpreted as "samples" from an associated MRF model. Herding differs from maximum likelihood estimation in that the sequence of parameters does not converge to a fixed point and differs from an MCMC posterior sampling approach in that the sequence of states is generated deterministically. Herding may be interpreted as a"perturb and map" method where the parameter perturbations are generated using a deterministic nonlinear dynamical system rather than randomly from a Gumbel distribution. This chapter studies the distinct statistical characteristics of the herding algorithm and shows that the fast convergence rate of the controlled moments may be attributed to edge of chaos dynamics. The herding algorithm can also be generalized to models with latent variables and to a discriminative learning setting. The perceptron cycling theorem ensures that the fast moment matching property is preserved in the more general framework

Towards experimental P-systems using multivesicular liposomes

P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be experimentally produced through electroformation of dipalmitoylphosphatidylcholine (DOPC) films for use in ‘real’ P-systems. We first present the electroformation protocol and microscopic characterisation of incident liposomes towards estimating the size of computing elements, level of internal compartment recursion, fault tolerance and stability. Following, we demonstrate multiple routes towards embedding symbols, namely modification of swelling solutions, passive diffusion and microinjection. Finally, we discuss how computing devices based on P-systems can be produced and their current limitations

Dagstuhl Reports : Volume 1, Issue 2, February 2011

Online Privacy: Towards Informational Self-Determination on the Internet (Dagstuhl Perspectives Workshop 11061) : Simone Fischer-Hübner, Chris Hoofnagle, Kai Rannenberg, Michael Waidner, Ioannis Krontiris and Michael Marhöfer Self-Repairing Programs (Dagstuhl Seminar 11062) : Mauro Pezzé, Martin C. Rinard, Westley Weimer and Andreas Zeller Theory and Applications of Graph Searching Problems (Dagstuhl Seminar 11071) : Fedor V. Fomin, Pierre Fraigniaud, Stephan Kreutzer and Dimitrios M. Thilikos Combinatorial and Algorithmic Aspects of Sequence Processing (Dagstuhl Seminar 11081) : Maxime Crochemore, Lila Kari, Mehryar Mohri and Dirk Nowotka Packing and Scheduling Algorithms for Information and Communication Services (Dagstuhl Seminar 11091) Klaus Jansen, Claire Mathieu, Hadas Shachnai and Neal E. Youn

Step forward to map fully parallel energy efficient cortical columns on field programmable gate arrays

This study presents energy and area-efficient hardware architectures to map fully parallel cortical columns on reconfigurable platform - field programmable gate arrays (FPGAs). An area-efficient architecture is proposed at the system level and benchmarked with a speech recognition application. Owing to the spatio-temporal nature of spiking neurons it is more suitable to map such architectures on FPGAs where signals can be represented in binary form and communication can be performed through the use of spikes. The viability of implementing multiple recurrent neural reservoirs is demonstrated with a novel multiplier-less reconfigurable architectures and a design strategy is devised for its implementation

Formal Verification of P Systems

Membrane systems, also known as P systems, constitute an innovative computational paradigm inspired by the structure and dynamics of the living cell. A P system consists of a hierarchical arrangement of compartments and a finite set of multiset rewriting and communication rules, which operate in a maximally parallel manner. The organic vision of concurrent dynamics captured by membrane systems stands in antithesis with conventional formal modelling methods which focus on algebraic descriptions of distributed systems. As a consequence, verifying such models in a mathematically rigorous way is often elusive and indeed counter-intuitive when considering established approaches, which generally require sequential process representations or highly abstract theoretical frameworks. The prevalent investigations with this objective in the field of membrane computing are ambivalent and inconclusive in the wider application scope of P systems. In this thesis we directly address the formal verification of membrane systems by means of model checking. A fundamental distinction between the agnostic perspective on parallelism, advocated by process calculi, and P systems' emblematic maximally parallel execution strategy is identified. On this basis, we establish that an intuitional translation to traditional process models is inadequate for the purpose of formal verification, due to a state space growth disparity. The observation is essential for this research project: on one hand it implies the feasibility of model checking P systems, and on the other hand it underlines the suitability of this formal verification technique in the context of membrane computing. Model checking entails an exhaustive state space exploration and does not derive inferences based on the independent instructions comprising a state transition. In this respect, we define a new sequential modelling strategy which is optimal for membrane systems and targets the SPIN formal verification tool. We introduce elementary P systems, a distributed computational model which subsumes the feature diversity of the membrane computing paradigm and distils its functional vocabulary. A suite of supporting software tools which gravitate around this formalism has also been developed, comprising of 1. the eps modelling language for elementary P systems; 2. a parser for the eps specification; 3. a model simulator and 4. a translation tool which targets the Promela specification of the SPIN model checker. The formal verification approach proposed in this thesis is progressively demonstrated in four heterogeneous case studies, featuring 1. a parallel algorithm applicable to a structured model; 2. a linear time solution to an NP-complete problem; 3. an innovative implementation of the Dining Philosophers scenario (a synchronisation problem) using an elementary P system and 4. a quantitative analysis of a simple random process implemented without the support of a probabilistic model

WISM 2005 : web information systems modeling

Modern Web Information Systems (WIS) need to satisfy a large number of requirements coming from different WIS stakeholders. Modeling WIS by focusing at one design aspect at-a-time helps the implementation of these requirements. During the last years several model-driven methodologies have been proposed to support the WIS design. Strategic modeling is usually the first step in WIS design. It is a very general characterization of WIS which answers questions like: what is the purpose of the WIS?, which are the WIS users?, what functionality is provided by the WIS?, what is the content of the WIS?, what is the layout and atmosphere of the presentations provided by the WIS?, etc. It is only after answering the above questions at a high abstract level that the designer can proceed with the detailed specifications of the WIS. Data integration is one of the most important characteristics of WIS. Some examples of domains in which data integration is present are: public services and bioinformatics. WIS need to support user interfaces that make a lot of data coming from different sources available to the user in a transparent way. The Semantic Web technologies seem to facilitate the data integration problem on the Web by providing the necessary languages to describe the data semantics. Very often the Web user browses pages that he will like to view again at a later time. The present browsing history mechanisms included in Web browsers proved to be insufficient for an adequate retrieval of already seen information. A semantical organization of the previously visited pages can improve the process of retrieving previously seen data. There is an increasing demand to make WIS personalizable so that these systems better deal with the user interests. WIS design methodologies do propose adaptation techniques in order to realize WIS personalization. Despite the fact that some of these adaptation techniques are very similar (or even the same) in different methodologies, the notations to specify WIS personalization aspects are quite different. By defining a reference model for specifying WIS personalization one could improve the reuse of the personalization specifications and also enable a seamless translation between different specific personalization specifications. The above issues are some of the topics that are tackled in the workshop papers. We hope that we did raise the readers’ interest so that they will have a close look at the papers and possibly contribute to the fascinating and challenging area of WIS modeling