Distributed models in P-Systems architectures to reduce computation time

Membrane systems are computational equivalent to Turing machines. However, their distributed and massively parallel nature obtains polynomial solutions opposite to traditional non-polynomial ones. At this point, it is very important to develop dedicated hardware and software implementations exploiting those two membrane systems features. Dealing with distributed implementations of P systems, the bottleneck communication problem has arisen. When the number of membranes grows up, the network gets congested. The purpose of distributed architectures is to reach a compromise between the massively parallel character of the system and the needed evolution step time to transit from one configuration of the system to the next one, solving the bottleneck communication problem. The goal of this paper is twofold. Firstly, to survey in a systematic and uniform way the main results regarding the way membranes can be placed on processors in order to get a software/hardware simulation of P-Systems in a distributed environment. Secondly, we improve some results about the membrane dissolution problem, prove that it is connected, and discuss the possibility of simulating this property in the distributed model. All this yields an improvement in the system parallelism implementation since it gets an increment of the parallelism of the external communication among processors. Proposed ideas improve previous architectures to tackle the communication bottleneck problem, such as reduction of the total time of an evolution step, increase of the number of membranes that could run on a processor and reduction of the number of processors.

Impacts of projected maximum temperature extremes for C21 by an ensemble of regional climate models on cereal cropping systems in the Iberian Peninsula

Crops growing in the Iberian Peninsula may be subjected to damagingly high temperatures during the sensitive development periods of flowering and grain filling. Such episodes are considered important hazards and farmers may take insurance to offset their impact. Increases in value and frequency of maximum temperature have been observed in the Iberian Peninsula during the 20th century, and studies on climate change indicate the possibility of further increase by the end of the 21st century. Here, impacts of current and future high temperatures on cereal cropping systems of the Iberian Peninsula are evaluated, focusing on vulnerable development periods of winter and summer crops. Climate change scenarios obtained from an ensemble of ten Regional Climate Models (multimodel ensemble) combined with crop simulation models were used for this purpose and related uncertainty was estimated. Results reveal that higher extremes of maximum temperature represent a threat to summer-grown but not to winter-grown crops in the Iberian Peninsula. The study highlights the different vulnerability of crops in the two growing seasons and the need to account for changes in extreme temperatures in developing adaptations in cereal cropping systems. Finally, this work contributes to clarifying the causes of high-uncertainty impact projections from previous studies.

Reduced order adaptive models for systems of PDEs using POD

In this work we propose a method to accelerate time dependent numerical solvers of systems of PDEs that require a high cost in computational time and memory. The method is based on the combined use of such numerical solver with a proper orthogonal decomposition, from which we identify modes, a Galerkin projection (that provides a reduced system of equations) and the integration of the reduced system, studying the evolution of the modal amplitudes. We integrate the reduced model until our a priori error estimator indicates that our approximation in not accurate. At this point we use again our original numerical code in a short time interval to adapt the POD manifold and continue then with the integration of the reduced model. Application will be made to two model problems: the Ginzburg-Landau equation in transient chaos conditions and the two-dimensional pulsating cavity problem, which describes the motion of liquid in a box whose upper wall is moving back and forth in a quasi-periodic fashion. Finally, we will discuss a way of improving the performance of the method using experimental data or information from numerical simulations

NetCDF based data archiving system applied to ITER Fast Plant System Control prototype

EURATOM/CIEMAT and Technical University of Madrid (UPM) have been involved in the development of a FPSC [1] (Fast Plant System Control) prototype for ITER, based on PXIe (PCI eXtensions for Instrumentation). One of the main focuses of this project has been data acquisition and all the related issues, including scientific data archiving. Additionally, a new data archiving solution has been developed to demonstrate the obtainable performances and possible bottlenecks of scientific data archiving in Fast Plant System Control. The presented system implements a fault tolerant architecture over a GEthernet network where FPSC data are reliably archived on remote, while remaining accessible to be redistributed, within the duration of a pulse. The storing service is supported by a clustering solution to guaranty scalability, so that FPSC management and configuration may be simplified, and a unique view of all archived data provided. All the involved components have been integrated under EPICS [2] (Experimental Physics and Industrial Control System), implementing in each case the necessary extensions, state machines and configuration process variables. The prototyped solution is based on the NetCDF-4 [3] and [4] (Network Common Data Format) file format in order to incorporate important features, such as scientific data models support, huge size files management, platform independent codification, or single-writer/multiple-readers concurrency. In this contribution, a complete description of the above mentioned solution is presented, together with the most relevant results of the tests performed, while focusing in the benefits and limitations of the applied technologies.

Innovative self management system for guided cardiac rehabilitation

This paper describes the design and development of a system for cardio rehabilitation of patients that suffered a myocardial infarction. The proposed solution focuses on exercise prescriptions and the encouragement of healthy behaviors. The innovative strategy of the design takes into account health promotion models to provide safe, assistive exercise training sessions, personalized feedbacks, and educational contents.

Image Segmentation Using Ant System-based Clustering Algorithm

Industrial applications of computer vision sometimes require detection of atypical objects that occur as small groups of pixels in digital images. These objects are difficult to single out because they are small and randomly distributed. In this work we propose an image segmentation method using the novel Ant System-based Clustering Algorithm (ASCA). ASCA models the foraging behaviour of ants, which move through the data space searching for high data-density regions, and leave pheromone trails on their path. The pheromone map is used to identify the exact number of clusters, and assign the pixels to these clusters using the pheromone gradient. We applied ASCA to detection of microcalcifications in digital mammograms and compared its performance with state-of-the-art clustering algorithms such as 1D Self-Organizing Map, k-Means, Fuzzy c-Means and Possibilistic Fuzzy c-Means. The main advantage of ASCA is that the number of clusters needs not to be known a priori. The experimental results show that ASCA is more efficient than the other algorithms in detecting small clusters of atypical data.

UPM system for the translation task

This paper describes the UPM system for translation task at the EMNLP 2011 workshop on statistical machine translation (http://www.statmt.org/wmt11/), and it has been used for both directions: Spanish-English and English-Spanish. This system is based on Moses with two new modules for pre and post processing the sentences. The main contribution is the method proposed (based on the similarity with the source language test set) for selecting the sentences for training the models and adjusting the weights. With system, we have obtained a 23.2 BLEU for Spanish-English and 21.7 BLEU for EnglishSpanish

Community Structure in Soil Porous System

Diffusion controls the gaseous transport process in soils when advective transport is almost null. Knowledge of the soil structure and pore connectivity are critical issues to understand and modelling soil aeration, sequestration or emission of greenhouse gasses, volatilization of volatile organic chemicals among other phenomena. In the last decades these issues increased our attention as scientist have realize that soil is one of the most complex materials on the earth, within which many biological, physical and chemical processes that support life and affect climate change take place. A quantitative and explicit characterization of soil structure is difficult because of the complexity of the pore space. This is the main reason why most theoretical approaches to soil porosity are idealizations to simplify this system. In this work, we proposed a more realistic attempt to capture the complexity of the system developing a model that considers the size and location of pores in order to relate them into a network. In the model we interpret porous soils as heterogeneous networks where pores are represented by nodes, characterized by their size and spatial location, and the links representing flows between them. In this work we perform an analysis of the community structure of porous media of soils represented as networks. For different real soils samples, modelled as heterogeneous complex networks, spatial communities of pores have been detected depending on the values of the parameters of the porous soil model used. These types of models are named as Heterogeneous Preferential Attachment (HPA). Developing an exhaustive analysis of the model, analytical solutions are obtained for the degree densities and degree distribution of the pore networks generated by the model in the thermodynamic limit and shown that the networks exhibit similar properties to those observed in other complex networks. With the aim to study in more detail topological properties of these networks, the presence of soil pore community structures is studied. The detection of communities of pores, as groups densely connected with only sparser connections between groups, could contribute to understand the mechanisms of the diffusion phenomena in soils.

Some past decision theory models for euro construction model codes and for road drainage in Spain, and modest hints with multi-criteria methods for agro and environmental assurance

The authors are from UPM and are relatively grouped, and all have intervened in different academic or real cases on the subject, at different times as being of different age. With precedent from E. Torroja and A. Páez in Madrid Spain Safety Probabilistic models for concrete about 1957, now in ICOSSAR conferences, author J.M. Antón involved since autumn 1967 for euro-steel construction in CECM produced a math model for independent load superposition reductions, and using it a load coefficient pattern for codes in Rome Feb. 1969, practically adopted for European constructions, giving in JCSS Lisbon Feb. 1974 suggestion of union for concrete-steel-al.. That model uses model for loads like Gumbel type I, for 50 years for one type of load, reduced to 1 year to be added to other independent loads, the sum set in Gumbel theories to 50 years return period, there are parallel models. A complete reliability system was produced, including non linear effects as from buckling, phenomena considered somehow in actual Construction Eurocodes produced from Model Codes. The system was considered by author in CEB in presence of Hydraulic effects from rivers, floods, sea, in reference with actual practice. When redacting a Road Drainage Norm in MOPU Spain an optimization model was realized by authors giving a way to determine the figure of Return Period, 10 to 50 years, for the cases of hydraulic flows to be considered in road drainage. Satisfactory examples were a stream in SE of Spain with Gumbel Type I model and a paper of Ven Te Chow with Mississippi in Keokuk using Gumbel type II, and the model can be modernized with more varied extreme laws. In fact in the MOPU drainage norm the redacting commission acted also as expert to set a table of return periods for elements of road drainage, in fact as a multi-criteria complex decision system. These precedent ideas were used e.g. in wide Codes, indicated in symposia or meetings, but not published in journals in English, and a condensate of contributions of authors is presented. The authors are somehow involved in optimization for hydraulic and agro planning, and give modest hints of intended applications in presence of agro and environment planning as a selection of the criteria and utility functions involved in bayesian, multi-criteria or mixed decision systems. Modest consideration is made of changing in climate, and on the production and commercial systems, and on others as social and financial.

A Multi-agent System for Emergency Decision Support

This paper describes the multi-agent organization of a computer system that was designed to assist operators in decision making in the presence of emergencies. The application was developed for the case of emergencies caused by river floods. It operates on real-time receiving data recorded by sensors (rainfall, water levels, flows, etc.) and applies multi-agent techniques to interpret the data, predict the future behavior and recommend control actions. The system includes an advanced knowledge based architecture with multiple symbolic representation with uncertainty models (bayesian networks). This system has been applied and validated at two particular sites in Spain (the Jucar basin and the South basin).

Hydrologic models for emergency decision support using Bayesian networks

In the presence of a river flood, operators in charge of control must take decisions based on imperfect and incomplete sources of information (e.g., data provided by a limited number sensors) and partial knowledge about the structure and behavior of the river basin. This is a case of reasoning about a complex dynamic system with uncertainty and real-time constraints where bayesian networks can be used to provide an effective support. In this paper we describe a solution with spatio-temporal bayesian networks to be used in a context of emergencies produced by river floods. In the paper we describe first a set of types of causal relations for hydrologic processes with spatial and temporal references to represent the dynamics of the river basin. Then we describe how this was included in a computer system called SAIDA to provide assistance to operators in charge of control in a river basin. Finally the paper shows experimental results about the performance of the model.

Oscillatory genetic circuits: new designs and mathematical models

Introduction and motivation: A wide variety of organisms have developed in-ternal biomolecular clocks in order to adapt to cyclic changes of the environment. Clock operation involves genetic networks. These genetic networks have to be mod¬eled in order to understand the underlying mechanism of oscillations and to design new synthetic cellular clocks. This doctoral thesis has resulted in two contributions to the fields of genetic clocks and systems and synthetic biology, generally. The first contribution is a new genetic circuit model that exhibits an oscillatory behav¬ior through catalytic RNA molecules. The second and major contribution is a new genetic circuit model demonstrating that a repressor molecule acting on the positive feedback of a self-activating gene produces reliable oscillations. First contribution: A new model of a synthetic genetic oscillator based on a typical two-gene motif with one positive and one negative feedback loop is pre¬sented. The originality is that the repressor is a catalytic RNA molecule rather than a protein or a non-catalytic RNA molecule. This catalytic RNA is a ribozyme that acts post-transcriptionally by binding to and cleaving target mRNA molecules. This genetic clock involves just two genes, a mRNA and an activator protein, apart from the ribozyme. Parameter values that produce a circadian period in both determin¬istic and stochastic simulations have been chosen as an example of clock operation. The effects of the stochastic fluctuations are quantified by a period histogram and autocorrelation function. The conclusion is that catalytic RNA molecules can act as repressor proteins and simplify the design of genetic oscillators. Second and major contribution: It is demonstrated that a self-activating gene in conjunction with a simple negative interaction can easily produce robust matically validated. This model is comprised of two clearly distinct parts. The first is a positive feedback created by a protein that binds to the promoter of its own gene and activates the transcription. The second is a negative interaction in which a repressor molecule prevents this protein from binding to its promoter. A stochastic study shows that the system is robust to noise. A deterministic study identifies that the oscillator dynamics are mainly driven by two types of biomolecules: the protein, and the complex formed by the repressor and this protein. The main conclusion of this study is that a simple and usual negative interaction, such as degradation, se¬questration or inhibition, acting on the positive transcriptional feedback of a single gene is a sufficient condition to produce reliable oscillations. One gene is enough and the positive transcriptional feedback signal does not need to activate a second repressor gene. At the genetic level, this means that an explicit negative feedback loop is not necessary. Unlike many genetic oscillators, this model needs neither cooperative binding reactions nor the formation of protein multimers. Applications and future research directions: Recently, RNA molecules have been found to play many new catalytic roles. The first oscillatory genetic model proposed in this thesis uses ribozymes as repressor molecules. This could provide new synthetic biology design principles and a better understanding of cel¬lular clocks regulated by RNA molecules. The second genetic model proposed here involves only a repression acting on a self-activating gene and produces robust oscil¬lations. Unlike current two-gene oscillators, this model surprisingly does not require a second repressor gene. This result could help to clarify the design principles of cellular clocks and constitute a new efficient tool for engineering synthetic genetic oscillators. Possible follow-on research directions are: validate models in vivo and in vitro, research the potential of second model as a genetic memory, investigate new genetic oscillators regulated by non-coding RNAs and design a biosensor of positive feedbacks in genetic networks based on the operation of the second model Resumen Introduccion y motivacion: Una amplia variedad de organismos han desarro-llado relojes biomoleculares internos con el fin de adaptarse a los cambios ciclicos del entorno. El funcionamiento de estos relojes involucra redes geneticas. El mo delado de estas redes geneticas es esencial tanto para entender los mecanismos que producen las oscilaciones como para diseiiar nuevos circuitos sinteticos en celulas. Esta tesis doctoral ha dado lugar a dos contribuciones dentro de los campos de los circuitos geneticos en particular, y biologia de sistemas y sintetica en general. La primera contribucion es un nuevo modelo de circuito genetico que muestra un comportamiento oscilatorio usando moleculas de ARN cataliticas. La segunda y principal contribucion es un nuevo modelo de circuito genetico que demuestra que una molecula represora actuando sobre el lazo de un gen auto-activado produce oscilaciones robustas. Primera contribucion: Es un nuevo modelo de oscilador genetico sintetico basado en una tipica red genetica compuesta por dos genes con dos lazos de retroa-limentacion, uno positivo y otro negativo. La novedad de este modelo es que el represor es una molecula de ARN catalftica, en lugar de una protefna o una molecula de ARN no-catalitica. Este ARN catalitico es una ribozima que actua despues de la transcription genetica uniendose y cortando moleculas de ARN mensajero (ARNm). Este reloj genetico involucra solo dos genes, un ARNm y una proteina activadora, aparte de la ribozima. Como ejemplo de funcionamiento, se han escogido valores de los parametros que producen oscilaciones con periodo circadiano (24 horas) tanto en simulaciones deterministas como estocasticas. El efecto de las fluctuaciones es-tocasticas ha sido cuantificado mediante un histograma del periodo y la función de auto-correlacion. La conclusion es que las moleculas de ARN con propiedades cataliticas pueden jugar el misnio papel que las protemas represoras, y por lo tanto, simplificar el diseno de los osciladores geneticos. Segunda y principal contribucion: Es un nuevo modelo de oscilador genetico que demuestra que un gen auto-activado junto con una simple interaction negativa puede producir oscilaciones robustas. Este modelo ha sido estudiado y validado matematicamente. El modelo esta compuesto de dos partes bien diferenciadas. La primera parte es un lazo de retroalimentacion positiva creado por una proteina que se une al promotor de su propio gen activando la transcription. La segunda parte es una interaction negativa en la que una molecula represora evita la union de la proteina con el promotor. Un estudio estocastico muestra que el sistema es robusto al ruido. Un estudio determinista muestra que la dinamica del sistema es debida principalmente a dos tipos de biomoleculas: la proteina, y el complejo formado por el represor y esta proteina. La conclusion principal de este estudio es que una simple y usual interaction negativa, tal como una degradation, un secuestro o una inhibition, actuando sobre el lazo de retroalimentacion positiva de un solo gen es una condition suficiente para producir oscilaciones robustas. Un gen es suficiente y el lazo de retroalimentacion positiva no necesita activar a un segundo gen represor, tal y como ocurre en los relojes actuales con dos genes. Esto significa que a nivel genetico un lazo de retroalimentacion negativa no es necesario de forma explicita. Ademas, este modelo no necesita reacciones cooperativas ni la formation de multimeros proteicos, al contrario que en muchos osciladores geneticos. Aplicaciones y futuras lineas de investigacion: En los liltimos anos, se han descubierto muchas moleculas de ARN con capacidad catalitica. El primer modelo de oscilador genetico propuesto en esta tesis usa ribozimas como moleculas repre¬soras. Esto podria proporcionar nuevos principios de diseno en biologia sintetica y una mejor comprension de los relojes celulares regulados por moleculas de ARN. El segundo modelo de oscilador genetico propuesto aqui involucra solo una represion actuando sobre un gen auto-activado y produce oscilaciones robustas. Sorprendente-mente, un segundo gen represor no es necesario al contrario que en los bien conocidos osciladores con dos genes. Este resultado podria ayudar a clarificar los principios de diseno de los relojes celulares naturales y constituir una nueva y eficiente he-rramienta para crear osciladores geneticos sinteticos. Algunas de las futuras lineas de investigation abiertas tras esta tesis son: (1) la validation in vivo e in vitro de ambos modelos, (2) el estudio del potential del segundo modelo como circuito base para la construction de una memoria genetica, (3) el estudio de nuevos osciladores geneticos regulados por ARN no codificante y, por ultimo, (4) el rediseno del se¬gundo modelo de oscilador genetico para su uso como biosensor capaz de detectar genes auto-activados en redes geneticas.

Some methodological issues in the design of CIAO - A generic, parallel concurrent constraint system

We informally discuss several issues related to the parallel execution of logic programming systems and concurrent logic programming systems, and their generalization to constraint programming. We propose a new view of these systems, based on a particular definition of parallelism. We argüe that, under this view, a large number of the actual systems and models can be explained through the application, at different levéis of granularity, of only a few basic principies: determinism, non-failure, independence (also referred to as stability), granularity, etc. Also, and based on the convergence of concepts that this view brings, we sketch a model for the implementation of several parallel constraint logic programming source languages and models based on a common, generic abstract machine and an intermedíate kernel language.

Towards resource usage analysis of miniZinc models

We present a method for the static resource usage analysis of MiniZinc models. The analysis can infer upper bounds on the usage that a MiniZinc model will make of some resources such as the number of constraints of a given type (equality, disequality, global constraints, etc.), the number of variables (search variables or temporary variables), or the size of the expressions before calling the solver. These bounds are obtained from the models independently of the concrete input data (the instance data) and are in general functions of sizes of such data. In our approach, MiniZinc models are translated into Ciao programs which are then analysed by the CiaoPP system. CiaoPP includes a parametric analysis framework for resource usage in which the user can define resources and express the resource usage of library procedures (and certain program construets) by means of a language of assertions. We present the approach and report on a preliminary implementation, which shows the feasibility of the approach, and provides encouraging results.

Some methodological issues in the design of CIAO, a generic, parallel concurrent constraint system

We informally discuss several issues related to the parallel execution of logic programming systems and concurrent logic programming systems, and their generalization to constraint programming. We propose a new view of these systems, based on a particular definition of parallelism. We argüe that, under this view, a large number of the actual systems and models can be explained through the application, at different levéis of granularity, of only a few basic principies: determinism, non-failure, independence (also referred to as stability), granularity, etc. Also, and based on the convergence of concepts that this view brings, we sketch a model for the implementation of several parallel constraint logic programming source languages and models based on a common, generic abstract machine and an intermedíate kernel language.