Using ecological niche models to support tree species selection for forest restoration planning in largely deforested regions

Species selection for forest restoration is often supported by expert knowledge on local distribution patterns of native tree species. This approach is not applicable to largely deforested regions unless enough data on pre-human tree species distribution is available. In such regions, ecological niche models may provide essential information to support species selection in the framework of forest restoration planning. In this study we used ecological niche models to predict habitat suitability for native tree species in "Tierra de Campos" region, an almost totally deforested area of the Duero Basin (Spain). Previously available models provide habitat suitability predictions for dominant native tree species, but including non-dominant tree species in the forest restoration planning may be desirable to promote biodiversity, specially in largely deforested areas were near seed sources are not expected. We used the Forest Map of Spain as species occurrence data source to maximize the number of modeled tree species. Penalized logistic regression was used to train models using climate and lithological predictors. Using model predictions a set of tools were developed to support species selection in forest restoration planning. Model predictions were used to build ordered lists of suitable species for each cell of the study area. The suitable species lists were summarized drawing maps that showed the two most suitable species for each cell. Additionally, potential distribution maps of the suitable species for the study area were drawn. For a scenario with two dominant species, the models predicted a mixed forest (Quercus ilex and a coniferous tree species) for almost one half of the study area. According to the models, 22 non-dominant native tree species are suitable for the study area, with up to six suitable species per cell. The model predictions pointed to Crataegus monogyna, Juniperus communis, J.oxycedrus and J.phoenicea as the most suitable non-dominant native tree species in the study area. Our results encourage further use of ecological niche models for forest restoration planning in largely deforested regions.

Service needs forecasting: an approach for the automotive industry using analogies with medical ER management models.

During the past years, the industry has shifted position and moved towards “the luxury universe” whose customers are demanding, treating individuals as unique and valued customer for the business, offering vehicles produced with the state of the art technologies and implementing the highest finishing standards. Due to the competitive level in the market, car makers enable processes which equalizes customer services to E.R. management, being dealt with the maximum urgency that allows the comparison between both, car workshops and emergency rooms, where workshop bays or ramps will be equal to emergency boxes and skilled technicians are equivalent to the health care specialist, who will carry out tests and checks prior to afford any final operation, keeping the “patient” under control before it is back to normal utilization. This paper establishes a valid model for the automotive industry to estimate customer service demand forecasting under variable demand conditions using analogies with patient demand models used for the medical ER.

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.

Auto-Emergencia de Comunicación Sintáctica en Entornos Estáticos y Dinámicos para Grupos de Robots mediante Evolución Gramatical y Aprendizaje por Refuerzo

La idea de dotar a un grupo de robots o agentes artificiales de un lenguaje ha sido objeto de intenso estudio en las ultimas décadas. Como no podía ser de otra forma los primeros intentos se enfocaron hacia el estudio de la emergencia de vocabularios compartidos convencionalmente por el grupo de robots. Las ventajas que puede ofrecer un léxico común son evidentes, como también lo es que un lenguaje con una estructura más compleja, en la que se pudieran combinar palabras, sería todavía más beneficioso. Surgen así algunas propuestas enfocadas hacia la emergencia de un lenguaje consensuado que muestre una estructura sintáctica similar al lenguaje humano, entre las que se encuentra este trabajo. Tomar el lenguaje humano como modelo supone adoptar algunas de las hipótesis y teorías que disciplinas como la filosofía, la psicología o la lingüística entre otras se han encargado de proponer. Según estas aproximaciones teóricas el lenguaje presenta una doble dimension formal y funcional. En base a su dimensión formal parece claro que el lenguaje sigue unas reglas, por lo que el uso de una gramática se ha considerado esencial para su representación, pero también porque las gramáticas son un dispositivo muy sencillo y potente que permite generar fácilmente estructuras simbólicas. En cuanto a la dimension funcional se ha tenido en cuenta la teoría quizá más influyente de los últimos tiempos, que no es otra que la Teoría de los Actos del Habla. Esta teoría se basa en la idea de Wittgenstein por la que el significado reside en el uso del lenguaje, hasta el punto de que éste se entiende como una manera de actuar y de comportarse, en definitiva como una forma de vida. Teniendo presentes estas premisas en esta tesis se pretende experimentar con modelos computacionales que permitan a un grupo de robots alcanzar un lenguaje común de manera autónoma, simplemente mediante interacciones individuales entre los robots, en forma de juegos de lenguaje. Para ello se proponen tres modelos distintos de lenguaje: • Un modelo basado en gramáticas probabilísticas y aprendizaje por refuerzo en el que las interacciones y el uso del lenguaje son claves para su emergencia y que emplea una gramática generativa estática y diseñada de antemano. Este modelo se aplica a dos grupos distintos: uno formado exclusivamente por robots y otro que combina robots y un humano, de manera que en este segundo caso se plantea un aprendizaje supervisado por humanos. • Un modelo basado en evolución gramatical que permite estudiar no solo el consenso sintáctico, sino también cuestiones relativas a la génesis del lenguaje y que emplea una gramática universal a partir de la cual los robots pueden evolucionar por sí mismos la gramática más apropiada según la situación lingüística que traten en cada momento. • Un modelo basado en evolución gramatical y aprendizaje por refuerzo que toma aspectos de los anteriores y amplia las posibilidades de los robots al permitir desarrollar un lenguaje que se adapta a situaciones lingüísticas dinámicas que pueden cambiar en el tiempo y también posibilita la imposición de restricciones de orden muy frecuentes en las estructuras sintácticas complejas. Todos los modelos implican un planteamiento descentralizado y auto-organizado, de manera que ninguno de los robots es el dueño del lenguaje y todos deben cooperar y colaborar de forma coordinada para lograr el consenso sintáctico. En cada caso se plantean experimentos que tienen como objetivo validar los modelos propuestos, tanto en lo relativo al éxito en la emergencia del lenguaje como en lo relacionado con cuestiones paralelas de importancia, como la interacción hombre-máquina o la propia génesis del lenguaje. ABSTRACT The idea of giving a language to a group of robots or artificial agents has been the subject of intense study in recent decades. The first attempts have focused on the development and emergence of a conventionally shared vocabulary. The advantages that can provide a common vocabulary are evident and therefore a more complex language that combines words would be even more beneficial. Thus some proposals are put forward towards the emergence of a consensual language with a sintactical structure in similar terms to the human language. This work follows this trend. Taking the human language as a model means taking some of the assumptions and theories that disciplines such as philosophy, psychology or linguistics among others have provided. According to these theoretical positions language has a double formal and functional dimension. Based on its formal dimension it seems clear that language follows rules, so that the use of a grammar has been considered essential for representation, but also because grammars are a very simple and powerful device that easily generates these symbolic structures. As for the functional dimension perhaps the most influential theory of recent times, the Theory of Speech Acts has been taken into account. This theory is based on the Wittgenstein’s idea about that the meaning lies in the use of language, to the extent that it is understood as a way of acting and behaving. Having into account these issues this work implements some computational models in order to test if they allow a group of robots to reach in an autonomous way a shared language by means of individual interaction among them, that is by means of language games. Specifically, three different models of language for robots are proposed: • A reinforcement learning based model in which interactions and language use are key to its emergence. This model uses a static probabilistic generative grammar which is designed beforehand. The model is applied to two different groups: one formed exclusively by robots and other combining robots and a human. Therefore, in the second case the learning process is supervised by the human. • A model based on grammatical evolution that allows us to study not only the syntactic consensus, but also the very genesis of language. This model uses a universal grammar that allows robots to evolve for themselves the most appropriate grammar according to the current linguistic situation they deal with. • A model based on grammatical evolution and reinforcement learning that takes aspects of the previous models and increases their possibilities. This model allows robots to develop a language in order to adapt to dynamic language situations that can change over time and also allows the imposition of syntactical order restrictions which are very common in complex syntactic structures. All models involve a decentralized and self-organized approach so that none of the robots is the language’s owner and everyone must cooperate and work together in a coordinated manner to achieve syntactic consensus. In each case experiments are presented in order to validate the proposed models, both in terms of success about the emergence of language and it relates to the study of important parallel issues, such as human-computer interaction or the very genesis of language.

System failure prediction through rare-events elastic-net logistic regression

Predicting failures in a distributed system based on previous events through logistic regression is a standard approach in literature. This technique is not reliable, though, in two situations: in the prediction of rare events, which do not appear in enough proportion for the algorithm to capture, and in environments where there are too many variables, as logistic regression tends to overfit on this situations; while manually selecting a subset of variables to create the model is error- prone. On this paper, we solve an industrial research case that presented this situation with a combination of elastic net logistic regression, a method that allows us to automatically select useful variables, a process of cross-validation on top of it and the application of a rare events prediction technique to reduce computation time. This process provides two layers of cross- validation that automatically obtain the optimal model complexity and the optimal mode l parameters values, while ensuring even rare events will be correctly predicted with a low amount of training instances. We tested this method against real industrial data, obtaining a total of 60 out of 80 possible models with a 90% average model accuracy.