A review on probabilistic graphical models in evolutionary computation

Thanks to their inherent properties, probabilistic graphical models are one of the prime candidates for machine learning and decision making tasks especially in uncertain domains. Their capabilities, like representation, inference and learning, if used effectively, can greatly help to build intelligent systems that are able to act accordingly in different problem domains. Evolutionary algorithms is one such discipline that has employed probabilistic graphical models to improve the search for optimal solutions in complex problems. This paper shows how probabilistic graphical models have been used in evolutionary algorithms to improve their performance in solving complex problems. Specifically, we give a survey of probabilistic model building-based evolutionary algorithms, called estimation of distribution algorithms, and compare different methods for probabilistic modeling in these algorithms.

Gestión óptima de embalses en avenidas incorporando al concepto de incertidumbre : aplicación a embalses con central hidroeléctrica

Esta tesis realiza una contribución metodológica al problema de la gestión óptima de embalses hidroeléctricos durante eventos de avenidas, considerando un enfoque estocástico y multiobjetivo. Para ello se propone una metodología de evaluación de estrategias de laminación en un contexto probabilístico y multiobjetivo. Además se desarrolla un entorno dinámico de laminación en tiempo real con pronósticos que combina un modelo de optimización y algoritmos de simulación. Estas herramientas asisten a los gestores de las presas en la toma de decisión respecto de cuál es la operación más adecuada del embalse. Luego de una detallada revisión de la bibliografía, se observó que los trabajos en el ámbito de la gestión óptima de embalses en avenidas utilizan, en general, un número reducido de series de caudales o hidrogramas para caracterizar los posibles escenarios. Limitando el funcionamiento satisfactorio de un modelo determinado a situaciones hidrológicas similares. Por otra parte, la mayoría de estudios disponibles en este ámbito abordan el problema de la laminación en embalses multipropósito durante la temporada de avenidas, con varios meses de duración. Estas características difieren de la realidad de la gestión de embalses en España. Con los avances computacionales en materia de gestión de información en tiempo real, se observó una tendencia a la implementación de herramientas de operación en tiempo real con pronósticos para determinar la operación a corto plazo (involucrando el control de avenidas). La metodología de evaluación de estrategias propuesta en esta tesis se basa en determinar el comportamiento de éstas frente a un espectro de avenidas características de la solicitación hidrológica. Con ese fin, se combina un sistema de evaluación mediante indicadores y un entorno de generación estocástica de avenidas, obteniéndose un sistema implícitamente estocástico. El sistema de evaluación consta de tres etapas: caracterización, síntesis y comparación, a fin de poder manejar la compleja estructura de datos resultante y realizar la evaluación. En la primera etapa se definen variables de caracterización, vinculadas a los aspectos que se quieren evaluar (seguridad de la presa, control de inundaciones, generación de energía, etc.). Estas variables caracterizan el comportamiento del modelo para un aspecto y evento determinado. En la segunda etapa, la información de estas variables se sintetiza en un conjunto de indicadores, lo más reducido posible. Finalmente, la comparación se lleva a cabo a partir de la comparación de esos indicadores, bien sea mediante la agregación de dichos objetivos en un indicador único, o bien mediante la aplicación del criterio de dominancia de Pareto obteniéndose un conjunto de soluciones aptas. Esta metodología se aplicó para calibrar los parámetros de un modelo de optimización de embalse en laminación y su comparación con otra regla de operación, mediante el enfoque por agregación. Luego se amplió la metodología para evaluar y comparar reglas de operación existentes para el control de avenidas en embalses hidroeléctricos, utilizando el criterio de dominancia. La versatilidad de la metodología permite otras aplicaciones, tales como la determinación de niveles o volúmenes de seguridad, o la selección de las dimensiones del aliviadero entre varias alternativas. Por su parte, el entorno dinámico de laminación al presentar un enfoque combinado de optimización-simulación, permite aprovechar las ventajas de ambos tipos de modelos, facilitando la interacción con los operadores de las presas. Se mejoran los resultados respecto de los obtenidos con una regla de operación reactiva, aun cuando los pronósticos se desvían considerablemente del hidrograma real. Esto contribuye a reducir la tan mencionada brecha entre el desarrollo teórico y la aplicación práctica asociada a los modelos de gestión óptima de embalses. This thesis presents a methodological contribution to address the problem about how to operate a hydropower reservoir during floods in order to achieve an optimal management considering a multiobjective and stochastic approach. A methodology is proposed to assess the flood control strategies in a multiobjective and probabilistic framework. Additionally, a dynamic flood control environ was developed for real-time operation, including forecasts. This dynamic platform combines simulation and optimization models. These tools may assist to dam managers in the decision making process, regarding the most appropriate reservoir operation to be implemented. After a detailed review of the bibliography, it was observed that most of the existing studies in the sphere of flood control reservoir operation consider a reduce number of hydrographs to characterize the reservoir inflows. Consequently, the adequate functioning of a certain strategy may be limited to similar hydrologic scenarios. In the other hand, most of the works in this context tackle the problem of multipurpose flood control operation considering the entire flood season, lasting some months. These considerations differ from the real necessity in the Spanish context. The implementation of real-time reservoir operation is gaining popularity due to computational advances and improvements in real-time data management. The methodology proposed in this thesis for assessing the strategies is based on determining their behavior for a wide range of floods, which are representative of the hydrological forcing of the dam. An evaluation algorithm is combined with a stochastic flood generation system to obtain an implicit stochastic analysis framework. The evaluation system consists in three stages: characterizing, synthesizing and comparing, in order to handle the complex structure of results and, finally, conduct the evaluation process. In the first stage some characterization variables are defined. These variables should be related to the different aspects to be evaluated (such as dam safety, flood protection, hydropower, etc.). Each of these variables characterizes the behavior of a certain operating strategy for a given aspect and event. In the second stage this information is synthesized obtaining a reduced group of indicators or objective functions. Finally, the indicators are compared by means of an aggregated approach or by a dominance criterion approach. In the first case, a single optimum solution may be achieved. However in the second case, a set of good solutions is obtained. This methodology was applied for calibrating the parameters of a flood control model and to compare it with other operating policy, using an aggregated method. After that, the methodology was extent to assess and compared some existing hydropower reservoir flood control operation, considering the Pareto approach. The versatility of the method allows many other applications, such as determining the safety levels, defining the spillways characteristics, among others. The dynamic framework for flood control combines optimization and simulation models, exploiting the advantages of both techniques. This facilitates the interaction between dam operators and the model. Improvements are obtained applying this system when compared with a reactive operating policy, even if the forecasts deviate significantly from the observed hydrograph. This approach contributes to reduce the gap between the theoretical development in the field of reservoir management and its practical applications.

Fighting tax evasion: a cellular automata approach

Estudio de la dinámica de una población donde los individuos son contribuyentes (pagadores de impuestos) o no mediante un autómata celular 2D

Probabilistic reasoning with a bayesian DNA device based on strand displacement

We present a computing model based on the DNA strand displacement technique which performs Bayesian inference. The model will take single stranded DNA as input data, representing the presence or absence of a specific molecular signal (evidence). The program logic encodes the prior probability of a disease and the conditional probability of a signal given the disease playing with a set of different DNA complexes and their ratios. When the input and program molecules interact, they release a different pair of single stranded DNA species whose relative proportion represents the application of Bayes? Law: the conditional probability of the disease given the signal. The models presented in this paper can empower the application of probabilistic reasoning in genetic diagnosis in vitro.

Uniform Distributed Pushdown Automata Systems.

We consider here uniform distributed pushdown automata systems (UDPAS), namely distributed pushdown automata systems having all components identical pushdown automata. We consider here just a single protocol for activating/deactivating components, namely a component stays active as long as it can perform moves, as well as two ways of accepting the input word: by empty stacks (all components have empty stacks) or by final states (all components are in final states), when the input word is completely read. We mainly investigate the computational power of UDPAS accepting by empty stacks and a few decidability and closure properties of the families of languages they define. Some directions for further work and open problems are also discussed.

Connexin-43 prevents hematopoietic stem cell senescence through transfer of reactive oxygen species to bone marrow stromal cells

Hematopoietic stem cell (HSC) aging has become a concern in chemotherapy of older patients. Humoral and paracrine signals from the bone marrow (BM) hematopoietic microenvironment (HM) control HSC activity during regenerative hematopoiesis. Connexin-43 (Cx43), a connexin constituent of gap junctions (GJs) is expressed in HSCs, down-regulated during differentiation, and postulated to be a self-renewal gene. Our studies, however, reveal that hematopoietic-specific Cx43 deficiency does not result in significant long-term competitive repopulation deficiency. Instead, hematopoietic Cx43 (H-Cx43) deficiency delays hematopoietic recovery after myeloablation with 5-fluorouracil (5-FU). 5-FU-treated H-Cx43-deficient HSC and progenitors (HSC/P) cells display decreased survival and fail to enter the cell cycle to proliferate. Cell cycle quiescence is associated with down-regulation of cyclin D1, up-regulation of the cyclin-dependent kinase inhibitors, p21cip1. and p16INK4a, and Forkhead transcriptional factor 1 (Foxo1), and activation of p38 mitogen-activated protein kinase (MAPK), indicating that H-Cx43-deficient HSCs are prone to senescence. The mechanism of increased senescence in H-Cx43-deficient HSC/P cells depends on their inability to transfer reactive oxygen species (ROS) to the HM, leading to accumulation of ROS within HSCs. In vivo antioxidant administration prevents the defective hematopoietic regeneration, as well as exogenous expression of Cx43 in HSC/P cells. Furthermore, ROS transfer from HSC/P cells to BM stromal cells is also rescued by reexpression of Cx43 in HSC/P. Finally, the deficiency of Cx43 in the HM phenocopies the hematopoietic defect in vivo. These results indicate that Cx43 exerts a protective role and regulates the HSC/P ROS content through ROS transfer to the HM, resulting in HSC protection during stress hematopoietic regeneration.

Dielectric behaviour of Hf-doped CaCu3Ti4O12 ceramics obtained by conventional synthesis and reactive sintering

CaCu3(Ti4xHfx)O12 ceramics (JC = 0.04, 0.1 and 0.2) were prepared by conventional synthesis (CS) and through reactive sintering (RS), in which synthesis and sintering of the material take place in one single step. The microstructure and the dielectric properties of Hf-doped CCTO (CCTOHf) have been studied by XRD, FE-SEM, AFM, Raman and impedance spectroscopy (IS) in order to correlate the structure, microstructure and the electrical properties. Samples prepared by reactive sintering show slightly higher dielectric constant than those prepared by conventional synthesis in the same way than the pure CCTO. Dielectric constant and dielectric losses decrease slightly increasing Hf content. For CCTOHf ceramics with x> 0.04 for CS and x> 0.1 for RS, a secondary phase HfTi04 appears. As expected, the reactive sintering processing method allows a higher incorporation of Hf in the CCTO lattice than the conventional synthesis one.

The Influence of Communication Range on Connectivity for Resilient Wireless Sensor Networks Using a Probabilistic Approach.

Wireless sensor networks (WSNs) consist of thousands of nodes that need to communicate with each other. However, it is possible that some nodes are isolated from other nodes due to limited communication range. This paper focuses on the influence of communication range on the probability that all nodes are connected under two conditions, respectively: (1) all nodes have the same communication range, and (2) communication range of each node is a random variable. In the former case, this work proves that, for 0menor queepsmenor quee^(-1) , if the probability of the network being connected is 0.36eps , by means of increasing communication range by constant C(eps) , the probability of network being connected is at least 1-eps. Explicit function C(eps) is given. It turns out that, once the network is connected, it also makes the WSNs resilient against nodes failure. In the latter case, this paper proposes that the network connection probability is modeled as Cox process. The change of network connection probability with respect to distribution parameters and resilience performance is presented. Finally, a method to decide the distribution parameters of node communication range in order to satisfy a given network connection probability is developed.

Efficient algorithms for dynamic probabilistic safety assessment. An application to convex damage domain.

The design of nuclear power plant has to follow a number of regulations aimed at limiting the risks inherent in this type of installation. The goal is to prevent and to limit the consequences of any possible incident that might threaten the public or the environment. To verify that the safety requirements are met a safety assessment process is followed. Safety analysis is as key component of a safety assessment, which incorporates both probabilistic and deterministic approaches. The deterministic approach attempts to ensure that the various situations, and in particular accidents, that are considered to be plausible, have been taken into account, and that the monitoring systems and engineered safety and safeguard systems will be capable of ensuring the safety goals. On the other hand, probabilistic safety analysis tries to demonstrate that the safety requirements are met for potential accidents both within and beyond the design basis, thus identifying vulnerabilities not necessarily accessible through deterministic safety analysis alone. Probabilistic safety assessment (PSA) methodology is widely used in the nuclear industry and is especially effective in comprehensive assessment of the measures needed to prevent accidents with small probability but severe consequences. Still, the trend towards a risk informed regulation (RIR) demanded a more extended use of risk assessment techniques with a significant need to further extend PSA’s scope and quality. Here is where the theory of stimulated dynamics (TSD) intervenes, as it is the mathematical foundation of the integrated safety assessment (ISA) methodology developed by the CSN(Consejo de Seguridad Nuclear) branch of Modelling and Simulation (MOSI). Such methodology attempts to extend classical PSA including accident dynamic analysis, an assessment of the damage associated to the transients and a computation of the damage frequency. The application of this ISA methodology requires a computational framework called SCAIS (Simulation Code System for Integrated Safety Assessment). SCAIS provides accident dynamic analysis support through simulation of nuclear accident sequences and operating procedures. Furthermore, it includes probabilistic quantification of fault trees and sequences; and integration and statistic treatment of risk metrics. SCAIS comprehensively implies an intensive use of code coupling techniques to join typical thermal hydraulic analysis, severe accident and probability calculation codes. The integration of accident simulation in the risk assessment process and thus requiring the use of complex nuclear plant models is what makes it so powerful, yet at the cost of an enormous increase in complexity. As the complexity of the process is primarily focused on such accident simulation codes, the question of whether it is possible to reduce the number of required simulation arises, which will be the focus of the present work. This document presents the work done on the investigation of more efficient techniques applied to the process of risk assessment inside the mentioned ISA methodology. Therefore such techniques will have the primary goal of decreasing the number of simulation needed for an adequate estimation of the damage probability. As the methodology and tools are relatively recent, there is not much work done inside this line of investigation, making it a quite difficult but necessary task, and because of time limitations the scope of the work had to be reduced. Therefore, some assumptions were made to work in simplified scenarios best suited for an initial approximation to the problem. The following section tries to explain in detail the process followed to design and test the developed techniques. Then, the next section introduces the general concepts and formulae of the TSD theory which are at the core of the risk assessment process. Afterwards a description of the simulation framework requirements and design is given. Followed by an introduction to the developed techniques, giving full detail of its mathematical background and its procedures. Later, the test case used is described and result from the application of the techniques is shown. Finally the conclusions are presented and future lines of work are exposed.

Probabilistic Analysis of Tunnel Liners

The use of probabilistic methods to analyse reliability of structures is being applied to a variety of engineering problems due to the possibility of establishing the failure probability on rational grounds. In this paper we present the application of classical reliability theory to analyse the safety of underground tunnels.

Approximate Relational Reasoning for Probabilistic Programs

La seguridad verificada es una metodología para demostrar propiedades de seguridad de los sistemas informáticos que se destaca por las altas garantías de corrección que provee. Los sistemas informáticos se modelan como programas probabilísticos y para probar que verifican una determinada propiedad de seguridad se utilizan técnicas rigurosas basadas en modelos matemáticos de los programas. En particular, la seguridad verificada promueve el uso de demostradores de teoremas interactivos o automáticos para construir demostraciones completamente formales cuya corrección es certificada mecánicamente (por ordenador). La seguridad verificada demostró ser una técnica muy efectiva para razonar sobre diversas nociones de seguridad en el área de criptografía. Sin embargo, no ha podido cubrir un importante conjunto de nociones de seguridad “aproximada”. La característica distintiva de estas nociones de seguridad es que se expresan como una condición de “similitud” entre las distribuciones de salida de dos programas probabilísticos y esta similitud se cuantifica usando alguna noción de distancia entre distribuciones de probabilidad. Este conjunto incluye destacadas nociones de seguridad de diversas áreas como la minería de datos privados, el análisis de flujo de información y la criptografía. Ejemplos representativos de estas nociones de seguridad son la indiferenciabilidad, que permite reemplazar un componente idealizado de un sistema por una implementación concreta (sin alterar significativamente sus propiedades de seguridad), o la privacidad diferencial, una noción de privacidad que ha recibido mucha atención en los últimos años y tiene como objetivo evitar la publicación datos confidenciales en la minería de datos. La falta de técnicas rigurosas que permitan verificar formalmente este tipo de propiedades constituye un notable problema abierto que tiene que ser abordado. En esta tesis introducimos varias lógicas de programa quantitativas para razonar sobre esta clase de propiedades de seguridad. Nuestra principal contribución teórica es una versión quantitativa de una lógica de Hoare relacional para programas probabilísticos. Las pruebas de correción de estas lógicas son completamente formalizadas en el asistente de pruebas Coq. Desarrollamos, además, una herramienta para razonar sobre propiedades de programas a través de estas lógicas extendiendo CertiCrypt, un framework para verificar pruebas de criptografía en Coq. Confirmamos la efectividad y aplicabilidad de nuestra metodología construyendo pruebas certificadas por ordendor de varios sistemas cuyo análisis estaba fuera del alcance de la seguridad verificada. Esto incluye, entre otros, una meta-construcción para diseñar funciones de hash “seguras” sobre curvas elípticas y algoritmos diferencialmente privados para varios problemas de optimización combinatoria de la literatura reciente. ABSTRACT The verified security methodology is an emerging approach to build high assurance proofs about security properties of computer systems. Computer systems are modeled as probabilistic programs and one relies on rigorous program semantics techniques to prove that they comply with a given security goal. In particular, it advocates the use of interactive theorem provers or automated provers to build fully formal machine-checked versions of these security proofs. The verified security methodology has proved successful in modeling and reasoning about several standard security notions in the area of cryptography. However, it has fallen short of covering an important class of approximate, quantitative security notions. The distinguishing characteristic of this class of security notions is that they are stated as a “similarity” condition between the output distributions of two probabilistic programs, and this similarity is quantified using some notion of distance between probability distributions. This class comprises prominent security notions from multiple areas such as private data analysis, information flow analysis and cryptography. These include, for instance, indifferentiability, which enables securely replacing an idealized component of system with a concrete implementation, and differential privacy, a notion of privacy-preserving data mining that has received a great deal of attention in the last few years. The lack of rigorous techniques for verifying these properties is thus an important problem that needs to be addressed. In this dissertation we introduce several quantitative program logics to reason about this class of security notions. Our main theoretical contribution is, in particular, a quantitative variant of a full-fledged relational Hoare logic for probabilistic programs. The soundness of these logics is fully formalized in the Coq proof-assistant and tool support is also available through an extension of CertiCrypt, a framework to verify cryptographic proofs in Coq. We validate the applicability of our approach by building fully machine-checked proofs for several systems that were out of the reach of the verified security methodology. These comprise, among others, a construction to build “safe” hash functions into elliptic curves and differentially private algorithms for several combinatorial optimization problems from the recent literature.

Probabilistic analysis of water availability for agriculture and associated crop net margins.

Rising water demands are difficult to meet in many regions of the world. In consequence, under meteorological adverse conditions, big economic losses in agriculture can take place. This paper aims to analyze the variability of water shortage in an irrigation district and the effect on farmer?s income. A probabilistic analysis of water availability for agriculture in the irrigation district is performed, through a supply-system simulation approach, considering stochastically generated series of stream-flows. Net margins associated to crop production are as well estimated depending on final water allocations. Net margins are calculated considering either single-crop farming, either a polyculture system. In a polyculture system, crop distribution and water redistribution are calculated through an optimization approach using the General Algebraic Modeling System (GAMS) for several scenarios of irrigation water availability. Expected net margins are obtained by crop and for the optimal crop and water distribution. The maximum expected margins are obtained for the optimal crop combination, followed by the alfalfa monoculture, maize, rice, wheat and finally barley. Water is distributed as follows, from biggest to smallest allocation: rice, alfalfa, maize, wheat and barley.

Probabilistic reasoning with an enzyme-driven DNA device

We present a biomolecular probabilistic model driven by the action of a DNA toolbox made of a set of DNA templates and enzymes that is able to perform Bayesian inference. The model will take single-stranded DNA as input data, representing the presence or absence of a specific molecular signal (the evidence). The program logic uses different DNA templates and their relative concentration ratios to encode the prior probability of a disease and the conditional probability of a signal given the disease. When the input and program molecules interact, an enzyme-driven cascade of reactions (DNA polymerase extension, nicking and degradation) is triggered, producing a different pair of single-stranded DNA species. Once the system reaches equilibrium, the ratio between the output species will represent the application of Bayes? law: the conditional probability of the disease given the signal. In other words, a qualitative diagnosis plus a quantitative degree of belief in that diagno- sis. Thanks to the inherent amplification capability of this DNA toolbox, the resulting system will be able to to scale up (with longer cascades and thus more input signals) a Bayesian biosensor that we designed previously.

Probabilistic meta-analysis of risk from the exposure to Hg in artisanal gold mining communities in Colombia

Colombia is one of the largest per capita mercury polluters in the world as a consequence of its artisanal gold mining activities. The severity of this problem in terms of potential health effects was evaluated by means of a probabilistic risk assessment carried out in the twelve departments (or provinces) in Colombia with the largest gold production. The two exposure pathways included in the risk assessment were inhalation of elemental Hg vapors and ingestion of fish contaminated with methyl mercury. Exposure parameters for the adult population (especially rates of fish consumption) were obtained from nation-wide surveys and concentrations of Hg in air and of methyl-mercury in fish were gathered from previous scientific studies. Fish consumption varied between departments and ranged from 0 to 0.3 kg d?1. Average concentrations of total mercury in fish (70 data) ranged from 0.026 to 3.3 lg g?1. A total of 550 individual measurements of Hg in workshop air (ranging from menor queDL to 1 mg m?3) and 261 measurements of Hg in outdoor air (ranging from menor queDL to 0.652 mg m?3) were used to generate the probability distributions used as concentration terms in the calculation of risk. All but two of the distributions of Hazard Quotients (HQ) associated with ingestion of Hg-contaminated fish for the twelve regions evaluated presented median values higher than the threshold value of 1 and the 95th percentiles ranged from 4 to 90. In the case of exposure to Hg vapors, minimum values of HQ for the general population exceeded 1 in all the towns included in this study, and the HQs for miner-smelters burning the amalgam is two orders of magnitude higher, reaching values of 200 for the 95th percentile. Even acknowledging the conservative assumptions included in the risk assessment and the uncertainties associated with it, its results clearly reveal the exorbitant levels of risk endured not only by miner-smelters but also by the general population of artisanal gold mining communities in Colombia.

Probabilistic approach for longitudinal ventilation system design in fire situations

The main objective of ventilation systems in tunnels is to reach the highest possible safety level both in service and fire situation; being the fire one, the most relevant when designing the system. When designing a longitudinal ventilation system, the methodology to evaluate the capacity of the system is similar both in service and fire situation, with the exception of the chimney effect and the phenomena of thermal transfer which is responsible or the changes in the density of the air. When facing the dimensioning task for longitudinal ventilated tunnels, although similar methodologies are used in different countries, specific hypothesis (aerodynamic, thermal properties, traffic) even if discussed in the literature or current practice, are not usually detailed in the regulations or recommendations. The aim of this paper is to propose a probabilistic approach to the problem which would allow the designer, and the tunnel owner, to understand the uncertainty and sensibility adopted in the results and, eventually, identify possible ways of optimizing the ventilation solution to be adopted.