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Reynolds, Robert. "Gene Expression Data Analysis Using Fuzzy Logic." Fogler Library, University of Maine, 2001. http://www.library.umaine.edu/theses/pdf/REynoldsR2001.pdf.
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Moore, S. J. "The regulatory logic of Pax3 expression in the neural tube." Thesis, University College London (University of London), 2012. http://discovery.ucl.ac.uk/1370636/.
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The development of complex tissues is dependent on the specification and maintenance of distinct transcriptional identities within populations of equivalent progenitors. In the vertebrate neural tube, progenitor identity is specified by the spatially organised expression of transcription factors within the dorso-ventral (DV) axis of the tissue. A series of selective cross-repressive interactions between transcription factors expressed in adjacent domains forms the basis of a gene regulatory network (GRN), which acts to define and maintain the boundaries between progenitor populations. Pax3 is a key member of the neural tube GRN that is transcribed throughout the dorsal domains of the spinal cord and exhibits a ventral boundary of expression at the level of the sulcus limitans. The regulatory mechanisms that induce Pax3 transcription in neural progenitors and subsequently produce a sharp ventral boundary of gene expression are poorly understood. Using a genetic lineage tracing strategy in mice, we show that the position of the Pax3 expression domain is established within the neural plate and subsequently maintained throughout spinal cord development. Additionally, we demonstrate that V0 interneuron progenitors transiently express Pax3 during their early development. We employ a comparative genomics based approach to investigate the molecular basis of Pax3 transcription, revealing several novel enhancers associated with the locus. Functional dissection of an early central nervous system (CNS) specific enhancer supports the role of the Wnt signaling pathway in the induction of Pax3 transcription. Furthermore, we establish the function of direct transcriptional repression in the establishment of the Pax3 expression domain. Analysis of a second CNS specific enhancer reveals that Pax3 expression is dependent on autoregulation and Pax7 mediated positive feedback post-neurulation. Together, these data indicate that the temporal activity of two distinct enhancers underlies the regulatory logic of Pax3 expression in the neural tube.
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Selpi. "An inductive logic programming approach to learning which uORFs regulate gene expression." Thesis, Robert Gordon University, 2008. http://hdl.handle.net/10059/224.
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Some upstream open reading frames (uORFs) regulate gene expression (i.e. they are functional) and can play key roles in keeping organisms healthy. However, how uORFs are involved in gene regulation is not het fully understood. In order to get a complete view of how uORFs are involved in gene regulation, it is expected that a large number of functional uORFs are needed. Unfortunately , lab experiments to verify that uORFs are functional are expensive. In this thesis, for the first time, the use of inductive logic programming (ILP) is explored for the task of learning which uORFs regulate gene expression in the yeast Saccharomyces cerevisiae. This work is directed to help select sets of candidate functional uORFs for experimental studies. With limited background knowledge, ILP can generate hypotheses which make the search for novel functional uORFs 17 times more efficient than random sampling. Adding mRNA secondary structure to the background knowledge results in hypotheses with significantly increased performance. This work is the first machine learning work to study both uORFs and mRNA secondary structures in the context of gene regulation. Using a novel combination of knowledge about biological conservation, gene ontology annotations and genes' response to different conditions results in hypotheses that are simple, informative, have an estimated sensitivity of 81% and provide provisional insights into biological characteristics of functional uORFs. The hypotheses predict 299 further genes to have 450 novel functional uORFs. A comparison with a related study suggests that 8 of these predicted functional uORFs (from 8 genes) are strong candidates for experimental studies.
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Santos, Patrick John. "Facial Expression Cloning with Fuzzy Membership Functions." Thèse, Université d'Ottawa / University of Ottawa, 2013. http://hdl.handle.net/10393/26260.
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This thesis describes the development and experimental results of a system to explore cloning of facial expressions between dissimilar face models, so new faces can be animated using the animations from existing faces. The system described in this thesis uses fuzzy membership functions and subtractive clustering to represent faces and expressions in an intermediate space. This intermediate space allows expressions for face models with different resolutions to be compared. The algorithm is trained for each pair of faces using particle swarm optimization, which selects appropriate weights and radii to construct the intermediate space. These techniques allow the described system to be more flexible than previous systems, since it does not require prior knowledge of the underlying implementation of the face models to function.
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Shafiei, Mohammad. "Signification et Intentionnalité : une approche dialogique." Thesis, Paris 1, 2017. http://www.theses.fr/2017PA01H202.
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Ce travail contient une investigation sur la théorie phénoménologique de la signification. L'idée-clé du projet est d'expliquer la constitution de la signification au moyen des analyses de l'intentionnalité. Nous avons étudié différents actes intentionnels qui fonctionnent dans l'expression et dans la construction des significations. Nous avons étudié à cet égard, d'abord, l'acte d'expression primordiale, dans lequel le contenu d'une intuition est élevé au domaine de l'idéal, puis les actes de synthèse catégorielle, dans lesquels d'autres significations se constituent en absence de leur propre intuition. Nous avons puis étudié les effets de la théorie de la signification à la conception de la logique pure. En conséquence, nous avons discuté que la sémantique dialogique est un cadre adéquat, selon le phénoménologie, pour interpréter le raisonnement logique et pour expliquer la signification des constantes logiques. Nous avons également discuté la signification de certains connecteurs logiques, et leurs formalisations, en utilisant notre méthode phénoménologique-dialogique<br>This work contains an investigation on the phenomenological theory of meaning. The key idea of the project is to explain the constitution of the meaning by means of the analyses of the intentionality. We have investigated different intentional acts which are functioning in expression and in constructing the meanings. In this regard we have studied, first, the act of primordial expression, in which a content of an intuition is raised to the realm of the ideal, and then the acts of categorial synthesis, in which further meanings are constituted in the absence of their proper intuition. We have investigated the effects of the theory of meaning to the conception of pure logic. Dialogical semantic is shown to be an adequate framework to interpret logical reasoning and to explain the meaning of the logical constants as well. We have also discussed the meaning of some logical connectives, and their formalizations, using our phenomenologico-dialogical method
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Mutňanský, Filip. "Ověřování parametrických vlastností nad záznamy běhů programů." Master's thesis, Vysoké učení technické v Brně. Fakulta informačních technologií, 2020. http://www.nusl.cz/ntk/nusl-417229.
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The goal of this thesis is to implement a tool that based on user defined properties can verify sequences of events in the traces of the program, or the log file. Properties are defined in extended regular expressions. The tool is able to verify parametric properties. User can define relations between parameters of events. Input of this tool is the definition of properties and constraints of parameters. Output of the tool is the report of violated properties with its sequences of events that caused the error.
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Lecroisey, Loïc. "Les visages des sportifs : analyse des expressions faciales et des sous-rôles sociomoteurs par des observateurs selectionnés." Thesis, Sorbonne Paris Cité, 2017. http://www.theses.fr/2017USPCB096/document.
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Parlebas (1970) affirmait déjà, il y a plus de quarante ans, « l’affectivité est la clef des conduites motrices ». De nombreux travaux se sont concentrés sur la verbalisation des émotions en contexte sportif. A priori ou a posteriori, c’est le sportif qui détermine ce qu’il ressent. Est-il possible de proposer une approche qui viendrait s’adjoindre à celles existantes afin de s’intéresser aux émotions qui naissent durant l’action motrice? L’objet de ce travail porte sur la mise en œuvre d’une méthodologie d’observation qui permet de préserver le caractère écologique de l’émotion sportive. Nous l’envisageons à partir du décryptage des mimiques émotionnelles et des actions du joueur. À l’appui des travaux de Frijda et Tcherkassof (1997), Tcherkassof (2008), Parlebas (1999), Collard (2004), Oboeuf (2010) nous décryptons les émotions et les sous-rôles moteurs actualisés par le joueur en utilisant les expressions faciales et les tendances à l’action. Dans un premier temps, nous créons un test de reconnaissance des expressions faciales sportives. Nous le soumettons à des étudiants STAPS afin d’objectiver des capacités de décodage des visages. Nous constatons que la spécialité sportive a un impact sur la performance. Les résultats suggèrent que les spécialistes des activités de coopération sont de bons décodeurs. Les spécialistes de l’opposition « avec agressivité motrice limitée » sont assez bons. Les combattants sont de piètres décodeurs malgré qu’ils reconnaissent parfaitement la peur. Les spécialistes des activités psychomotrices sont plutôt mauvais mais peu en lien avec cette habileté de décodage. Dans un second temps, nous utilisons les excellents décodeurs sélectionnés grâce à notre test afin qu’ils analysent des vidéos de sportifs en action motrice. Grâce à une caméra embarquée, les visages de chaque joueur peuvent être recensés et analysés dans deux jeux sociomoteurs : la balle assise et l’ours et son gardien. Les observateurs formés et sélectionnés retranscrivent dans une grille d’analyse situationnelle les expressions faciales prototypiques d’une émotion et les sous-rôles sociomoteurs que le joueur actualise (Oboeuf, 2010). Cette grille est un ludogramme émotionnel (Parlebas, 1999). Les seconds types de résultats ainsi recueillis nous invitent à penser qu’il y a des émotions typiques de certaines actions. Lorsqu’elle précède un sous-rôle, la colère est celle de la frappe ou du tir puissant tandis que la peur est celle de l’esquive. Lorsqu’elle succède un replacement ou une interaction de marque favorable, la joie est un retour sur l’objectif du jeu et la douleur est consentie par le contrat ludique. En tant que processus, l’émotion permet au sportif de choisir la conduite motrice qu’il doit mettre en œuvre. En tant que résultat de l’action, l’émotion est une information sur l’atteinte du but du jeu. L’ensemble de nos résultats nous invite à valider cette méthodologie. Il sera désormais nécessaire de reproduire ce type d’étude dans de nombreux sports<br>More than forty years ago, Parlebas (1970) affirmed: « affectivity is the key to motor skill ». Many studies have concentrated on the verbalization of emotions in sports context? Before the game or after the game, the sportsman determines what he feels. Is it possible to suggest an approach that would come in line with existing ones in order to be interested in the emotions that arises during motor action? The aim of this work is to implement an observational methodology that preserves the ecological character of sport’s emotion. We consider it from the deciphering of the emotional mimics and the actions of the player. In support of the work of Frijda and Tcherkassof (1997), Tcherkassof (2008), Parlebas (1999), Collard (2004), Oboeuf (2010), we decrypt the emotions and the motor sub-role of player using facial expressions and tendency to action. As a first step, we create a test for recognition of sport’s facial expressions. We submit it to sport students in order to objectify capacities of decoding the faces. We see that the sporting specialty has an impact on performance. The results suggest that specialists in cooperative activities are good decoders. The opposition specialists "with limited motor aggressiveness" are quite good. The fighters are poor decoders despite they fully recognize the fear. Specialists in psychomotor activities are rather bad but not very much related to this skill of decoding. In a second step, we use the excellent decoders selected by our test so that they analyze videos of sportsmen in motor action. Thanks to an embedded camera, the faces of each player can be recorded and analyzed in two sociomotor games: the seated ball and the bear and his keeper. In a situational analysis grid, trained and selected observers retranscribe the prototypical facial expressions of an emotion and the sociomotor sub-roles that the player updates (Oboeuf, 2010). This grid is an emotional ludogram (Parlebas, 1999). The second type of results collected thought that method invite us to think that there are typical emotions inherent to certain actions. Before a sub-role, anger is related to powerful striking or shooting, while fear is interconnected with dodging. Following a replacement or a favorable brand interaction, the joy is a return on the game’s aim and the pain is consented by the play contract. As a process, the emotion allows the athlete to choose the driving behavior that he must implement. As a result of action, emotions are information about reaching the goal of the game. All of our results invite us to validate this methodology. It will now be necessary to repeat this type of study in many sports
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Rico-Fontalvo, Florentino Antonio. "A Decision Support Model for Personalized Cancer Treatment." Scholar Commons, 2014. https://scholarcommons.usf.edu/etd/5621.
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This work is motivated by the need of providing patients with a decision support system that facilitates the selection of the most appropriate treatment strategy in cancer treatment. Treatment options are currently subject to predetermined clinical pathways and medical expertise, but generally, do not consider the individual patient characteristics or preferences. Although genomic patient data are available, this information is rarely used in the clinical setting for real-life patient care. In the area of personalized medicine, the advancement in the fundamental understanding of cancer biology and clinical oncology can promote the prevention, detection, and treatment of cancer diseases.
The objectives of this research are twofold. 1) To develop a patient-centered decision support model that can determine the most appropriate cancer treatment strategy based on subjective medical decision criteria, and patient's characteristics concerning the treatment options available and desired clinical outcomes; and 2) to develop a methodology to organize and analyze gene expression data and validate its accuracy as a predictive model for patient's response to radiation therapy (tumor radiosensitivity).
The complexity and dimensionality of the data generated from gene expression microarrays requires advanced computational approaches. The microarray gene expression data processing and prediction model is built in four steps: response variable transformation to emphasize the lower and upper extremes (related to Radiosensitive and Radioresistant cell lines); dimensionality reduction to select candidate gene expression probesets; model development using a Random Forest algorithm; and validation of the model in two clinical cohorts for colorectal and esophagus cancer patients.
Subjective human decision-making plays a significant role in defining the treatment strategy. Thus, the decision model developed in this research uses language and mechanisms suitable for human interpretation and understanding through fuzzy sets and degree of membership. This treatment selection strategy is modeled using a fuzzy logic framework to account for the subjectivity associated to the medical strategy and the patient's characteristics and preferences. The decision model considers criteria associated to survival rate, adverse events and efficacy (measured by radiosensitivity) for treatment recommendation. Finally, a sensitive analysis evaluates the impact of introducing radiosensitivity in the decision-making process.
The intellectual merit of this research stems from the fact that it advances the science of decision-making by integrating concepts from the fields of artificial intelligence, medicine, biology and biostatistics to develop a decision aid approach that considers conflictive objectives and has a high practical value. The model focuses on criteria relevant to cancer treatment selection but it can be modified and extended to other scenarios beyond the healthcare environment.
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Schulthess, Pascal. "Thermodynamic modeling explains the regulation of CYP1A1 expression in the liver." Doctoral thesis, Humboldt-Universität zu Berlin, Lebenswissenschaftliche Fakultät, 2016. http://dx.doi.org/10.18452/17454.
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Die vorliegende Studie präsentiert eine Analyse der Integration der AhR und Wnt/beta-catenin Signalwege in den CYP1A1 Promotor sowie den regulatorischen Einfluss der Promotorlogik auf die Genexpression. Experimentell wurde diese Analyse mithilfe 29 mutagener Reporterkonstrukte des humanen CYP1A1 Promotors durchgeführt. Ein mathematisches Modell, welches eine Repräsentation des Crosstalks der Signaltransduktionswege mit einer statistisch mechanischen Beschreibung der kombinatorischen Promotorbelegung kombiniert, komplementierte den experimentellen Ansatz. Unter zusätzlicher Zuhilfenahme von gut kontrollierbaren synthetischen Promotorkonstrukten fand ich heraus, dass nur jenes Dioxin-responsive Element das sich am nächsten am Transkriptionsstartpunkt befindet, die Promotorbelegung an die RNA Polymerase kommuniziert. Außerdem beobachtete ich, dass Transkriptionsfaktoren alleine mit Transkriptionsfaktoren interagieren die mit benachbarten Bindestellen assoziieren, d.h. Interaktionen überbrücken keine größeren Entfernungen. Der Modellierungsansatz ermöglichte zudem die erfolgreiche Vorhersage einer UND-Gatter-ähnlichen Integration der beiden Signalwege in den Promotor. Für die genomische Architektur des CYP1A1 Promotors konnte ich die Signifikanz der Zielbindestelle des Wnt/beta-catenin Signalwegs innerhalb des cis-regulatorischen Region demonstrieren. Mithilfe des Modells fand ich heraus, dass diese Bindestelle am stärksten und vielfältigsten mit den restlichen Transkriptionsfaktoren interagiert. Zusätzliche konnte, im Vergleich zu dem alles-oder-nichts UND-Gatter der synthetischen Konstrukte, eine sehr viel graduellere Antwort auf die Integration der beiden Signalwege aufgezeigt werden. Abschließend wurde das physiologisch zu beobachtende Expressionsmuster von dem Modell vorhergesagt und experimentell validiert.<br>The study at hand presents an analysis of the integration of the AhR and the Wnt/beta-catenin signaling pathways into the CYP1A1 promoter as well as the regulatory influence of the promoter logic on gene expression. Experimentally, this analysis was conducted with the help of 29 mutant constructs of the human CYP1A1 promoter. I complemented this experimental approach with a set of mathematical models that combined a representation of the signaling crosstalk with a statistical mechanics description of the combinatorial promoter occupancy. With the help of well controllable synthetic promoter constructs I found that only the dioxin responsive element closest to the transcription start site communicates the promoter occupancy to the RNA polymerase. Furthermore, transcription factors only interact with transcription factors that associate with nearby binding sites, i.e., no long-distance binding was observed. The modeling approach subsequently enabled the successful prediction of an AND-gate-like integration of the two signaling pathways into the promoter. For the genomic architecture of the CYP1A1 promoter, I could demonstrate the importance of the Wnt/beta-catenin pathway target binding site within the cis-regulatory region. The model uncovered that this binding site is the strongest and most promiscuous interaction partner of the remaining transcription factors. In addition, a less switch-like response to the integration of the two signaling pathways as compared to the all-or-none AND-gate within the synthetic constructs could be demonstrated. And lastly, the physiological expression pattern in liver lobules could be successfully predicted by the model and experimentally verified.
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Bahsoun, Jean-Paul. "Expression de la synchronisation dans un module contrôlé par priorité : implantation et méthode de preuve." Toulouse 3, 1988. http://www.theses.fr/1988TOU30126.
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Le module controle par priorite (mcp) est un constructeur de type abstrait, avec un controleur local appele synchroniseur. Sa definition repose sur l'idee de base qu'il existe deux sortes de controles a effectuer pour acceder a un objet partage: les controles lies a l'etat intrinseque de l'objet et ceux provenant d'une politique d'utilisation de l'objet ou d'ordonnancement; ces deux types de controles sont separes dans le mcp
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Weidner, Thomas. "Probabilistic Logic, Probabilistic Regular Expressions, and Constraint Temporal Logic." Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-208732.
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The classic theorems of Büchi and Kleene state the expressive equivalence of finite automata to monadic second order logic and regular expressions, respectively. These fundamental results enjoy applications in nearly every field of theoretical computer science. Around the same time as Büchi and Kleene, Rabin investigated probabilistic finite automata. This equally well established model has applications ranging from natural language processing to probabilistic model checking.
Here, we give probabilistic extensions Büchi\\\'s theorem and Kleene\\\'s theorem to the probabilistic setting. We obtain a probabilistic MSO logic by adding an expected second order quantifier. In the scope of this quantifier, membership is determined by a Bernoulli process. This approach turns out to be universal and is applicable for finite and infinite words as well as for finite trees. In order to prove the expressive equivalence of this probabilistic MSO logic to probabilistic automata, we show a Nivat-theorem, which decomposes a recognisable function into a regular language, homomorphisms, and a probability measure.
For regular expressions, we build upon existing work to obtain probabilistic regular expressions on finite and infinite words. We show the expressive equivalence between these expressions and probabilistic Muller-automata. To handle Muller-acceptance conditions, we give a new construction from probabilistic regular expressions to Muller-automata. Concerning finite trees, we define probabilistic regular tree expressions using a new iteration operator, called infinity-iteration. Again, we show that these expressions are expressively equivalent to probabilistic tree automata.
On a second track of our research we investigate Constraint LTL over multidimensional data words with data values from the infinite tree. Such LTL formulas are evaluated over infinite words, where every position possesses several data values from the infinite tree. Within Constraint LTL on can compare these values from different positions. We show that the model checking problem for this logic is PSPACE-complete via investigating the emptiness problem of Constraint Büchi automata.
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Boehm, Christian Reiner. "Gene expression control for synthetic patterning of bacterial populations and plants." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/267842.
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The development of shape in multicellular organisms has intrigued human minds for millenia. Empowered by modern genetic techniques, molecular biologists are now striving to not only dissect developmental processes, but to exploit their modularity for the design of custom living systems used in bioproduction, remediation, and regenerative medicine. Currently, our capacity to harness this potential is fundamentally limited by a lack of spatiotemporal control over gene expression in multicellular systems. While several synthetic genetic circuits for control of multicellular patterning have been reported, hierarchical induction of gene expression domains has received little attention from synthetic biologists, despite its fundamental role in biological self-organization. In this thesis, I introduce the first synthetic genetic system implementing population-based AND logic for programmed hierarchical patterning of bacterial populations of Escherichia coli, and address fundamental prerequisites for implementation of an analogous genetic circuit into the emergent multicellular plant model Marchantia polymorpha. In both model systems, I explore the use of bacteriophage T7 RNA polymerase as a gene expression engine to control synthetic patterning across populations of cells. In E. coli, I developed a ratiometric assay of bacteriophage T7 RNA polymerase activity, which I used to systematically characterize different intact and split enzyme variants. I utilized the best-performing variant to build a three-color patterning system responsive to two different homoserine lactones. I validated the AND gate-like behavior of this system both in cell suspension and in surface culture. Then, I used the synthetic circuit in a membrane-based spatial assay to demonstrate programmed hierarchical patterning of gene expression across bacterial populations. To prepare the adaption of bacteriophage T7 RNA polymerase-driven synthetic patterning from the prokaryote E. coli to the eukaryote M. polymorpha, I developed a toolbox of genetic elements for spatial gene expression control in the liverwort: I analyzed codon usage across the transcriptome of M. polymorpha, and used insights gained to design codon-optimized fluorescent reporters successfully expressed from its nuclear and chloroplast genomes. For targeting of bacteriophage T7 RNA polymerase to these cellular compartments, I functionally validated nuclear localization signals and chloroplast transit peptides. For spatiotemporal control of bacteriophage T7 RNA polymerase in M. polymorpha, I characterized spatially restricted and inducible promoters. For facilitated posttranscriptional processing of target transcripts, I functionally validated viral enhancer sequences in M. polymorpha. Taking advantage of this genetic toolbox, I introduced inducible nuclear-targeted bacteriophage T7 RNA polymerase into M. polymorpha. I showed implementation of the bacteriophage T7 RNA polymerase/PT7 expression system accompanied by hypermethylation of its target nuclear transgene. My observations suggest operation of efficient epigenetic gene silencing in M. polymorpha, and guide future efforts in chassis engineering of this multicellular plant model. Furthermore, my results encourage utilization of spatiotemporally controlled bacteriophage T7 RNA polymerase as a targeted silencing system for functional genomic studies and morphogenetic engineering in the liverwort. Taken together, the work presented enhances our capacity for spatiotemporal gene expression control in bacterial populations and plants, facilitating future efforts in synthetic morphogenesis for applications in synthetic biology and metabolic engineering.
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Lester, Nigel L. K. "Logic synthesis using Reed-Muller and SOP expressions." Thesis, University of Bristol, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.295060.
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Fallah, Farzan. "A new algorithm for factorization of logic expressions." Thesis, Massachusetts Institute of Technology, 1996. http://hdl.handle.net/1721.1/38822.
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Trefler, Richard Jay. "Expressive and efficient model checking /." Digital version accessible at:, 1999. http://wwwlib.umi.com/cr/utexas/main.
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Oral, Sabri Onur. "The minimization of multiple valued logic expressions using parallel processors." Thesis, Monterey, California. Naval Postgraduate School, 1991. http://hdl.handle.net/10945/26633.
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Young, Gareth. "Revenge : dialetheism and its expressive limitations." Thesis, University of Glasgow, 2015. http://theses.gla.ac.uk/6415/.
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This thesis is about dialetheism and the problem of revenge. More broadly, it is about truth and what the logical paradoxes tell us about the logical behaviour of truth. One of the driving forces behind the contemporary study of truth and paradox is the problem of revenge: that many, perhaps all, available theories of truth, give rise to further paradoxes, invoking central notions of those theories, which demonstrate that the theory cannot express those notions. This sort of expressive limitation, especially if it involves the very notion invoked to diagnose what goes wrong in paradoxical sentences, would normally be thought a decisive point against a given theory of the paradoxes, were it not for the fact that the problem is so pervasive that every currently available theory has, at some point, been argued to suffer from it. Dialetheism, the view that some contradictions are true, has often been thought to be the only view which has a reasonable chance of avoiding the problem. Indeed, the surge of interest in the view since the first publication of Priest’s In Contradiction, in 1987, defending dialetheism, is probably due in large part to the seeming immunity to the revenge problem that Priest’s view possesses. Its virtue, in respect of revenge, is that its ability to accept, without collapse into incoherence, contradictions, allows it to accept any further revenge paradoxes as merely giving more sound arguments for dialetheia (true contradictions). This thesis argues that this appearance of revenge-immunity is mistaken. Dialetheism, too, has its revenge problems. The seeming virtue of dialetheism, that it can accept the contradictions generated by revenge paradoxes without incoherence, also has its drawbacks. This is because dialetheists are not only able, but compelled to accept the contradictions arising from the semantic paradoxes. This means that contradictions can arise in certain areas where they are undesirable. In particular, there are notions which seem to require consistency in order to be expressible. If we can demonstrate, using revenge paradoxes, that, on dialetheism, predicates putatively representing these notions would have to behave inconsistently, then we can demonstrate that dialetheists cannot express the notions. There are many ways one might wish to carve up the different varieties of dialetheism available. I have separated the view into two broad kinds: metatheoretically paraconsistent dialetheism, on the one hand, and metatheoretically consistent dialetheism, on the other. This distinction decides to which variety of revenge problem the version of dialetheism in question is subject. I take each in turn, and argue that they are each subject to expressive limitations brought about by revenge paradox.
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Dalglish, Steven Jack William. "Least and Inflationary Fixed-Point Logics: A Comparison of Expressive Strength." The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1597163479372308.
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Weidner, Thomas [Verfasser], Manfred [Akademischer Betreuer] Droste, Manfred [Gutachter] Droste, and Benedikt [Gutachter] Bollig. "Probabilistic Logic, Probabilistic Regular Expressions, and Constraint Temporal Logic / Thomas Weidner ; Gutachter: Manfred Droste, Benedikt Bollig ; Betreuer: Manfred Droste." Leipzig : Universitätsbibliothek Leipzig, 2016. http://d-nb.info/1240627777/34.
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Moraes, Olinda Martins. "Logical relations in students' written expression." reponame:Repositório Institucional da UFSC, 2012. http://repositorio.ufsc.br/xmlui/handle/123456789/75147.
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Dissertação (mestrado) - Universidade Federal de Santa Catarina, Centro de Comunicação e Expressão, Programa de Pós-Graduação em Letras, Florianópolis, 1984.<br>Made available in DSpace on 2012-10-15T22:34:14Z (GMT). No. of bitstreams: 0Bitstream added on 2016-01-08T14:59:11Z : No. of bitstreams: 1
278071.pdf: 3744078 bytes, checksum: 2874a455e7a9b2dd5a697eae8053cf9f (MD5)
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Reynolds, Mark. "The expressive power of query languages based on logic programming." Thesis, Imperial College London, 1988. http://hdl.handle.net/10044/1/47227.
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Lehmann, Jens. "Learning OWL Class Expressions." Doctoral thesis, Universitätsbibliothek Leipzig, 2010. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-38351.
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With the advent of the Semantic Web and Semantic Technologies, ontologies have become one of the most prominent paradigms for knowledge representation and reasoning. The popular ontology language OWL, based on description logics, became a W3C recommendation in 2004 and a standard for modelling ontologies on the Web. In the meantime, many studies and applications using OWL have been reported in research and industrial environments, many of which go beyond Internet usage and employ the power of ontological modelling in other fields such as biology, medicine, software engineering, knowledge management, and cognitive systems.
However, recent progress in the field faces a lack of well-structured ontologies with large amounts of instance data due to the fact that engineering such ontologies requires a considerable investment of resources. Nowadays, knowledge bases often provide large volumes of data without sophisticated schemata. Hence, methods for automated schema acquisition and maintenance are sought. Schema acquisition is closely related to solving typical classification problems in machine learning, e.g. the detection of chemical compounds causing cancer. In this work, we investigate both, the underlying machine learning techniques and their application to knowledge acquisition in the Semantic Web.
In order to leverage machine-learning approaches for solving these tasks, it is required to develop methods and tools for learning concepts in description logics or, equivalently, class expressions in OWL. In this thesis, it is shown that methods from Inductive Logic Programming (ILP) are applicable to learning in description logic knowledge bases. The results provide foundations for the semi-automatic creation and maintenance of OWL ontologies, in particular in cases when extensional information (i.e. facts, instance data) is abundantly available, while corresponding intensional information (schema) is missing or not expressive enough to allow powerful reasoning over the ontology in a useful way. Such situations often occur when extracting knowledge from different sources, e.g. databases, or in collaborative knowledge engineering scenarios, e.g. using semantic wikis. It can be argued that being able to learn OWL class expressions is a step towards enriching OWL knowledge bases in order to enable powerful reasoning, consistency checking, and improved querying possibilities. In particular, plugins for OWL ontology editors based on learning methods are developed and evaluated in this work.
The developed algorithms are not restricted to ontology engineering and can handle other learning problems. Indeed, they lend themselves to generic use in machine learning in the same way as ILP systems do. The main difference, however, is the employed knowledge representation paradigm: ILP traditionally uses logic programs for knowledge representation, whereas this work rests on description logics and OWL. This difference is crucial when considering Semantic Web applications as target use cases, as such applications hinge centrally on the chosen knowledge representation format for knowledge interchange and integration. The work in this thesis can be understood as a broadening of the scope of research and applications of ILP methods. This goal is particularly important since the number of OWL-based systems is already increasing rapidly and can be expected to grow further in the future.
The thesis starts by establishing the necessary theoretical basis and continues with the specification of algorithms. It also contains their evaluation and, finally, presents a number of application scenarios. The research contributions of this work are threefold:
The first contribution is a complete analysis of desirable properties of refinement operators in description logics. Refinement operators are used to traverse the target search space and are, therefore, a crucial element in many learning algorithms. Their properties (completeness, weak completeness, properness, redundancy, infinity, minimality) indicate whether a refinement operator is suitable for being employed in a learning algorithm. The key research question is which of those properties can be combined. It is shown that there is no ideal, i.e. complete, proper, and finite, refinement operator for expressive description logics, which indicates that learning in description logics is a challenging machine learning task. A number of other new results for different property combinations are also proven. The need for these investigations has already been expressed in several articles prior to this PhD work. The theoretical limitations, which were shown as a result of these investigations, provide clear criteria for the design of refinement operators. In the analysis, as few assumptions as possible were made regarding the used description language.
The second contribution is the development of two refinement operators. The first operator supports a wide range of concept constructors and it is shown that it is complete and can be extended to a proper operator. It is the most expressive operator designed for a description language so far. The second operator uses the light-weight language EL and is weakly complete, proper, and finite. It is straightforward to extend it to an ideal operator, if required. It is the first published ideal refinement operator in description logics. While the two operators differ a lot in their technical details, they both use background knowledge efficiently.
The third contribution is the actual learning algorithms using the introduced operators. New redundancy elimination and infinity-handling techniques are introduced in these algorithms. According to the evaluation, the algorithms produce very readable solutions, while their accuracy is competitive with the state-of-the-art in machine learning. Several optimisations for achieving scalability of the introduced algorithms are described, including a knowledge base fragment selection approach, a dedicated reasoning procedure, and a stochastic coverage computation approach.
The research contributions are evaluated on benchmark problems and in use cases. Standard statistical measurements such as cross validation and significance tests show that the approaches are very competitive. Furthermore, the ontology engineering case study provides evidence that the described algorithms can solve the target problems in practice. A major outcome of the doctoral work is the DL-Learner framework. It provides the source code for all algorithms and examples as open-source and has been incorporated in other projects.
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Marpaung, Andreas. "TOWARD BUILDING A SOCIAL ROBOT WITH AN EMOTION-BASED INTERNAL CONTROL." Master's thesis, University of Central Florida, 2004. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/3901.
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In this thesis, we aim at modeling some aspects of the functional role of emotions on an autonomous embodied agent. We begin by describing our robotic prototype, Cherry--a robot with the task of being a tour guide and an office assistant for the Computer Science Department at the University of Central Florida. Cherry did not have a formal emotion representation of internal states, but did have the ability to express emotions through her multimodal interface. The thesis presents the results of a survey we performed via our social informatics approach where we found that: (1) the idea of having emotions in a robot was warmly accepted by Cherry's users, and (2) the intended users were pleased with our initial interface design and functionalities. Guided by these results, we transferred our previous code to a human-height and more robust robot--Petra, the PeopleBot™--where we began to build a formal emotion mechanism and representation for internal states to correspond to the external expressions of Cherry's interface. We describe our overall three-layered architecture, and propose the design of the sensory motor level (the first layer of the three-layered architecture) inspired by the Multilevel Process Theory of Emotion on one hand, and hybrid robotic architecture on the other hand. The sensory-motor level receives and processes incoming stimuli with fuzzy logic and produces emotion-like states without any further willful planning or learning. We will discuss how Petra has been equipped with sonar and vision for obstacle avoidance as well as vision for face recognition, which are used when she roams around the hallway to engage in social interactions with humans. We hope that the sensory motor level in Petra could serve as a foundation for further works in modeling the three-layered architecture of the Emotion State Generator.<br>M.S.<br>School of Computer Science<br>Engineering and Computer Science<br>Computer Science
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Kocurek, Alexander William. "What Can You Say? Measuring the Expressive Power of Languages." Thesis, University of California, Berkeley, 2018. http://pqdtopen.proquest.com/#viewpdf?dispub=10830321.
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<p> There are many different ways to talk about the world. Some ways of talking are more expressive than others—that is, they enable us to say more things about the world. But what exactly does this mean? When is one language able to express more about the world than another? In my dissertation, I systematically investigate different ways of answering this question and develop a formal theory of expressive power. In doing so, I show how these investigations help to clarify the role that expressive power plays within debates in metaphysics, logic, and the philosophy of language.</p><p> When we attempt to describe the world, we are trying to distinguish the way things are from all the many ways things could have been—in other words, we are trying to locate ourselves within a region of logical space. According to this picture, languages can be thought of as ways of carving logical space or, more formally, as maps from sentences to classes of models. For example, the language of first-order logic is just a mapping from first-order formulas to model-assignment pairs that satisfy those formulas. Almost all formal languages discussed in metaphysics and logic, as well as many of those discussed in natural language semantics, can be characterized in this way. </p><p> Using this picture of language, I analyze two different approaches to defining expressive power, each of which is motivated by different roles a language can play in a debate. One role a language can play is to divide and organize a shared conception of logical space. If two languages share the same conception of logical space (i.e., are defined over the same class of models), then one can compare the expressive power of these languages by comparing how finely they carve logical space. This is the approach commonly employed, for instance, in debates over tense and modality, such as the primitivism-reductionism debate.</p><p> But a second role languages can play in a debate is to advance a conception or theory of logical space itself. For example, consider the debate between perdurantism, which claims that objects persist through time by having temporal parts located throughout that time, and endurantism, which claims that objects persist through time by being wholly present at that time. A natural thought about this debate is that perdurantism and endurantism are simply alternative but equally good descriptions of the world rather than competing theories. Whenever the endurantist says, for instance, that an object is red at time <i> t</i>, the perdurantist can say that the object’s temporal part at <i>t</i> is red. On this view, one should conceive of perdurantism and endurantism not as theories picking out disjoint regions of logical space, but as theories offering alternative conceptions of logical space: one in which persistence through time is analogous to location in space and one in which it is not. A similar distinction applies to other metaphysical debates, such as the mereological debate between universalism and nihilism.</p><p> If two theories propose incommensurable conceptions of logical space, we can still compare their expressive power utilizing the notion of a translation, which acts as a correlation between points in logical space that preserves the language’s inferential connections. I build a formal theory of translation that explores different ways of making this notion precise. I then apply this theory to two metaphysical debates, viz., the debate over whether composite objects exist and the debate over how objects persist through time. This allows us to get a clearer picture of the sense in which these debates can be viewed as genuine.</p><p>
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Zhao, Yizheng. "Automated semantic forgetting for expressive description logics." Thesis, University of Manchester, 2018. https://www.research.manchester.ac.uk/portal/en/theses/automated-semantic-forgetting-for-expressive-description-logics(9d780243-e896-4007-b47a-dd713837011c).html.
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Ontologies, exploiting Description Logics (DLs) as the representational underpinning, provide a logic-based data model for knowledge processing thereby supporting intelligent reasoning of domain knowledge for various applications, most evidently for modern biomedical, life science and text mining applications. However, with their growing utilisation, not only has the number of available ontologies increased considerably, but they are also blowing up in size and becoming more complex to manage. Moreover, capturing domain knowledge in the form of ontologies is labour-intensive work which is expensive from an implementation perspective. There is a strong demand for techniques and automated tools for creating restricted views of ontologies while preserving complete information up to the restricted views. Forgetting is a non-standard reasoning technique which provides such a service by eliminating concept and role symbols from ontologies in a way such that all logical consequences are preserved up to the remaining signature. It has turned out to be very useful in ontology-based knowledge processing, as it allows users to focus on specific parts of (usually very large) ontologies for easy reuse, or to zoom in on (usually very complex) ontologies for in-depth analysis. Other uses of forgetting are information hiding, explanation generation, abduction, ontology debugging and repair, and computing logical differences between ontology versions. Despite its notable usefulness as described above, forgetting, on the other hand, is an inherently difficult problem --- it is much harder than standard reasoning (satisfiability testing) --- and very few logics are known to be complete for forgetting, there has been insufficient research on the topic and few forgetting tools are available. This thesis investigates practical methods for semantic forgetting in expressive description logics not considered before. In particular, we present a practical method for forgetting concept symbols from ontologies expressible in the description logic ALCOI, i.e. the basic ALC extended with nominals and inverse roles. Being based on a generalisation of a monotonicity property called Ackermann's Lemma, the method is the first and only approach to concept forgetting in description logics with nominals. We also present a practical method for forgetting role symbols from ontologies expressible in the description logic ALCOIH, i.e. ALCOI extended with role hierarchies, the universal role and role conjunction. The universal role and role conjunction enrich our target language, making it expressive enough to represent the forgetting solution which otherwise would have been lost. Being based on a non-trivial generalisation of Ackermann's Lemma, the method is the first and only approach so far that provides support for role forgetting in description logics with nominals. Both methods are goal-oriented and incremental. They are terminating, and are sound in the sense that the forgetting solutions are equivalent to the original ontologies up to (the interpretations of) the symbols that have been forgotten, possibly with (the interpretations of) the symbols that have been introduced. These two methods can be used as a unifying method for forgetting both concept and role symbols from ontologies expressible in the description logic ALCOIH. The method has been implemented in Java using the OWL API and the prototypical implementation, called FAME, has been evaluated on a corpus of real-world ontologies (in order to verify its practicality). Performance results have shown that FAME was successful (i.e., eliminated all specified concept and role symbols) in most of the test cases, and in most of these cases the elimination was done within a very short period of time.
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Koopmann, Patrick. "Practical uniform interpolation for expressive description logics." Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/practical-uniform-interpolation-for-expressive-description-logics(b04c6bc6-0877-488b-86d7-fa37ae99eeb6).html.
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The thesis investigates methods for uniform interpolation in expressive description logics. Description logics are formalisms commonly used to model ontologies. Ontologies store terminological information and are used in a wide range of applications, such as the semantic web, medicine, bio-informatics, software development, data bases and language processing. Uniform interpolation eliminates terms from an ontology such that logical entailments in the remaining language are preserved. The result, the uniform interpolant, is a restricted view of the ontology that can be used for a variety of tasks such as ontology analysis, ontology reuse, ontology evolution and information hiding. Uniform interpolation for description logics has only gained an interest in the research community in the last years, and theoretical results show that it is a hard problem requiring specialised reasoning approaches. We present a range of uniform interpolation methods that can deal with expressive description logics such as ALC and many of its extensions. For all these logics, these are the first methods that are able to compute uniform interpolants for all inputs. The methods are based a new family of saturation-based reasoning methods, which make it possible to eliminate symbols in a goal-oriented manner. The practicality of this approach is shown by an evaluation on realistic ontologies.
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Drobics, Mario. "Data analysis using fuzzy expressions /." Linz : Trauner, 2005. http://aleph.unisg.ch/hsgscan/hm00166742.pdf.
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Halaschek-Wiener, Franz Christian. "Expressive syndication on the web using a description logic-based approach." College Park, Md.: University of Maryland, 2007. http://hdl.handle.net/1903/7755.
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Thesis (Ph. D.) -- University of Maryland, College Park, 2007.<br>Thesis research directed by: Dept. of Computer Science. Title from t.p. of PDF. Includes bibliographical references. Published by UMI Dissertation Services, Ann Arbor, Mich. Also available in paper.
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Feng, Shiguang. "The Expressive Power, Satisfiability and Path Checking Problems of MTL and TPTL over Non-Monotonic Data Words." Doctoral thesis, Universitätsbibliothek Leipzig, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-208823.
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Recently, verification and analysis of data words have gained a lot of interest. Metric temporal logic (MTL) and timed propositional temporal logic (TPTL) are two extensions of Linear time temporal logic (LTL). In MTL, the temporal operator are indexed by a constraint interval. TPTL is a more powerful logic that is equipped with a freeze formalism. It uses register variables, which can be set to the current data value and later these register variables can be compared with the current data value. For monotonic data words, Alur and Henzinger proved that MTL and TPTL are equally expressive and the satisfiability problem is decidable. We study the expressive power, satisfiability problems and path checking problems for MLT and TPTL over all data words. We introduce Ehrenfeucht-Fraisse games for MTL and TPTL. Using the EF-game for MTL, we show that TPTL is strictly more expressive than MTL. Furthermore, we show that the MTL definability problem that whether a TPTL-formula is definable in MTL is not decidable. When restricting the number of register variables, we are able to show that TPTL with two register variables is strictly more expressive than TPTL with one register variable. For the satisfiability problem, we show that for MTL, the unary fragment of MTL and the pure fragment of MTL, SAT is not decidable. We prove the undecidability by reductions from the recurrent state problem and halting problem of two-counter machines. For the positive fragments of MTL and TPTL, we show that a positive formula is satisfiable if and only it is satisfied by a finite data word. Finitary SAT and infinitary SAT coincide for positive MTL and positive TPTL. Both of them are r.e.-complete. For existential TPTL and existential MTL, we show that SAT is NP-complete. We also investigate the complexity of path checking problems for TPTL and MTL over data words. These data words can be either finite or infinite periodic. For periodic words without data values, the complexity of LTL model checking belongs to the class AC^1(LogDCFL). For finite monotonic data words, the same complexity bound has been shown for MTL by Bundala and Ouaknine. We show that path checking for TPTL is PSPACE-complete, and for MTL is P-complete. If the number of register variables allowed is restricted, we obtain path checking for TPTL with only one register variable is P-complete over both infinite and finite data words; for TPTL with two register variables is PSPACE-complete over infinite data words. If the encoding of constraint numbers of the input TPTL-formula is in unary notation, we show that path checking for TPTL with a constant number of variables is P-complete over infinite unary encoded data words. Since the infinite data word produced by a deterministic one-counter machine is periodic, we can transfer all complexity results for the infinite periodic case to model checking over deterministic one-counter machines.
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Williams, Andre. "Stereotype Logit Models for High Dimensional Data." VCU Scholars Compass, 2010. http://scholarscompass.vcu.edu/etd/147.
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Gene expression studies are of growing importance in the field of medicine. In fact, subtypes within the same disease have been shown to have differing gene expression profiles (Golub et al., 1999). Often, researchers are interested in differentiating a disease by a categorical classification indicative of disease progression. For example, it may be of interest to identify genes that are associated with progression and to accurately predict the state of progression using gene expression data. One challenge when modeling microarray gene expression data is that there are more genes (variables) than there are observations. In addition, the genes usually demonstrate a complex variance-covariance structure. Therefore, modeling a categorical variable reflecting disease progression using gene expression data presents the need for methods capable of handling an ordinal outcome in the presence of a high dimensional covariate space. In this research we present a method that combines the stereotype regression model (Anderson, 1984) with an elastic net penalty (Friedman et al., 2010) as a method capable of modeling an ordinal outcome for high-throughput genomic datasets. Results from applying the proposed method to both simulated and gene expression data will be reported and the effectiveness of the proposed method compared to a univariable and heuristic approach will be discussed.
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Domin, Gesine, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, and Mario Mörl. "Applicability of a computational design approach for synthetic riboswitches." Universitätsbibliothek Leipzig, 2017. http://nbn-resolving.de/urn:nbn:de:bsz:15-qucosa-218007.
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Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer
structures not corresponding to the calculated MFE state.
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Lee, Hoon S. "A CAD tool for current-mode multiple-valued CMOS circuits." Thesis, Monterey, California. Naval Postgraduate School, 1988. http://hdl.handle.net/10945/22935.
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Approved for public release; distribution is unlimited<br>The contribution of this thesis is the development of a CAD (computer aided
design) tool for current mode multiple-valued logic (MVL) CMOS circuits. It is
only the second known MVL CAD tool and the first CAD tool for MVL CMOS.
The tool accepts a specification of the function to be realized by the user,
produces a minimal or near-minimal realization (if such a realization is possible),
and produces a layout of a programmable logic array (PLA) integrated circuit that
realizes the given function. The layout is in MAGIC format, suitable for submission
to a chip manufacturer. The CAD tool also allows the user to simulate the realized
function so that he/she can verify correctness of design.
The CAD tool is designed also to be an analysis tool for heuristic minimization
algorithms. As part of this thesis, a random function generator and statistics gathering
package were developed. In the present tool, two heuristics are provided and
the user can choose one or both. In the latter case, the better realization is output
to the user. The CAD tool is designed to be flexible, so that future improvements
can be made in the heuristic algorithms, as well as the layout generator. Thus,
the tool can be used to accommodate new technologies, for example, a voltage mode
CMOS PLA rather than the current mode CMOS currently implemented.<br>http://archive.org/details/cadtoolforcurren00leeh<br>Lieutenant, Republic of Korea Navy
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Magnago, Enrico. "Facing infinity in model checking expressive specification languages." Doctoral thesis, Università degli studi di Trento, 2022. https://hdl.handle.net/11572/356869.
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Society relies on increasingly complex software and hardware systems, hence techniques capable of proving that they behave as expected are of great and growing interest. Formal verification procedures employ mathematically sound reasoning to address this need.
This thesis proposes novel techniques for the verification and falsification of expressive specifications on timed and infinite-state systems. An expressive specification language allows the description of the intended behaviour of a system via compact formal statements written at an abstraction level that eases the review process. Falsifying a specification corresponds to identifying an execution of the system that violates the property (i.e. a witness). The capability of identifying witnesses is a key feature in the iterative refinement of the design of a system, since it provides a description of how a certain error can occur. The designer can analyse the witness and take correcting actions by refining either the description of the system or its specification.
The contribution of this thesis is twofold. First, we propose a semantics for Metric Temporal Logic that considers four different models of time (discrete, dense, super-discrete and super-dense). We reduce its verification problem to finding an infinite fair execution (witness) for an infinite-state system with discrete time. Second, we define a novel SMT-based algorithm to identify such witnesses. The algorithm employs a general representation of such executions that is both informative to the designer and provides sufficient structure to automate the search of a witness.
We apply the proposed techniques to benchmarks taken from software, infinite-state, timed and hybrid systems. The experimental results highlight that the proposed approaches compete and often outperform specific (application tailored) techniques currently used in the state of the art.
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Monmege, Benjamin. "Specification and verification of quantitative properties : expressions, logics, and automata." Thesis, Cachan, Ecole normale supérieure, 2013. http://www.theses.fr/2013DENS0039/document.
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La vérification automatique est aujourd'hui devenue un domaine central de recherche en informatique. Depuis plus de 25 ans, une riche théorie a été développée menant à de nombreux outils, à la fois académiques et industriels, permettant la vérification de propriétés booléennes - celles qui peuvent être soit vraies soit fausses. Les besoins actuels évoluent vers une analyse plus fine, c'est-à-dire plus quantitative. L'extension des techniques de vérification aux domaines quantitatifs a débuté depuis 15 ans avec les systèmes probabilistes. Cependant, de nombreuses autres propriétés quantitatives existent, telles que la durée de vie d'un équipement, la consommation énergétique d'une application, la fiabilité d'un programme, ou le nombre de résultats d'une requête dans une base de données. Exprimer ces propriétés requiert de nouveaux langages de spécification, ainsi que des algorithmes vérifiant ces propriétés sur une structure donnée. Cette thèse a pour objectif l'étude de plusieurs formalismes permettant de spécifier de telles propriétés, qu'ils soient dénotationnels - expressions régulières, logiques monadiques ou logiques temporelles - ou davantage opérationnels, comme des automates pondérés, éventuellement étendus avec des jetons. Un premier objectif de ce manuscript est l'étude de résultats d'expressivité comparant ces formalismes. En particulier, on donne des traductions efficaces des formalismes dénotationnels vers celui opérationnel. Ces objets, ainsi que les résultats associés, sont présentés dans un cadre unifié de structures de graphes. Ils peuvent, entre autres, s'appliquer aux mots et arbres finis, aux mots emboîtés (nested words), aux images ou aux traces de Mazurkiewicz. Par conséquent, la vérification de propriétés quantitatives de traces de programmes (potentiellement récursifs, ou concurrents), les requêtes sur des documents XML (modélisant par exemple des bases de données), ou le traitement des langues naturelles sont des applications possibles. On s'intéresse ensuite aux questions algorithmiques que soulèvent naturellement ces résultats, tels que l'évaluation, la satisfaction et le model checking. En particulier, on étudie la décidabilité et la complexité de certains de ces problèmes, en fonction du semi-anneau sous-jacent et des structures considérées (mots, arbres...). Finalement, on considère des restrictions intéressantes des formalismes précédents. Certaines permettent d'étendre l'ensemble des semi-anneau sur lesquels on peut spécifier des propriétés quantitatives. Une autre est dédiée à l'étude du cas spécial de spécifications probabilistes : on étudie en particulier des fragments syntaxiques de nos formalismes génériques de spécification générant uniquement des comportements probabilistes<br>Automatic verification has nowadays become a central domain of investigation in computer science. Over 25 years, a rich theory has been developed leading to numerous tools, both in academics and industry, allowing the verification of Boolean properties - those that can be either true or false. Current needs evolve to a finer analysis, a more quantitative one. Extension of verification techniques to quantitative domains has begun 15 years ago with probabilistic systems. However, many other quantitative properties are of interest, such as the lifespan of an equipment, energy consumption of an application, the reliability of a program, or the number of results matching a database query. Expressing these properties requires new specification languages, as well as algorithms checking these properties over a given structure. This thesis aims at investigating several formalisms, equipped with weights, able to specify such properties: denotational ones - like regular expressions, first-order logic with transitive closure, or temporal logics - or more operational ones, like navigating automata, possibly extended with pebbles. A first objective of this thesis is to study expressiveness results comparing these formalisms. In particular, we give efficient translations from denotational formalisms to the operational one. These objects, and the associated results, are presented in a unified framework of graph structures. This permits to handle finite words and trees, nested words, pictures or Mazurkiewicz traces, as special cases. Therefore, possible applications are the verification of quantitative properties of traces of programs (possibly recursive, or concurrent), querying of XML documents (modeling databases for example), or natural language processing. Second, we tackle some of the algorithmic questions that naturally arise in this context, like evaluation, satisfiability and model checking. In particular, we study some decidability and complexity results of these problems depending on the underlying semiring and the structures under consideration (words, trees...). Finally, we consider some interesting restrictions of the previous formalisms. Some permit to extend the class of semirings on which we may specify quantitative properties. Another is dedicated to the special case of probabilistic specifications: in particular, we study syntactic fragments of our generic specification formalisms generating only probabilistic behaviors
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Monmège, Benjamin. "Specification and verification of quantitative properties : expressions, logics, and automata." Phd thesis, École normale supérieure de Cachan - ENS Cachan, 2013. http://tel.archives-ouvertes.fr/tel-00957763.
Full textAbstract:
Automatic verification has nowadays become a central domain of investigation in computer science. Over 25 years, a rich theory has been developed leading to numerous tools, both in academics and industry, allowing the verification of Boolean properties - those that can be either true or false. Current needs evolve to a finer analysis, a more quantitative one. Extension of verification techniques to quantitative domains has begun 15 years ago with probabilistic systems. However, many other quantitative properties are of interest, such as the lifespan of an equipment, energy consumption of an application, the reliability of a program, or the number of results matching a database query. Expressing these properties requires new specification languages, as well as algorithms checking these properties over a given structure. This thesis aims at investigating several formalisms, equipped with weights, able to specify such properties: denotational ones - like regular expressions, first-order logic with transitive closure, or temporal logics - or more operational ones, like navigating automata, possibly extended with pebbles. A first objective of this thesis is to study expressiveness results comparing these formalisms. In particular, we give efficient translations from denotational formalisms to the operational one. These objects, and the associated results, are presented in a unified framework of graph structures. This permits to handle finite words and trees, nested words, pictures or Mazurkiewicz traces, as special cases. Therefore, possible applications are the verification of quantitative properties of traces of programs (possibly recursive, or concurrent), querying of XML documents (modeling databases for example), or natural language processing. Second, we tackle some of the algorithmic questions that naturally arise in this context, like evaluation, satisfiability and model checking. In particular, we study some decidability and complexity results of these problems depending on the underlying semiring and the structures under consideration (words, trees...). Finally, we consider some interesting restrictions of the previous formalisms. Some permit to extend the class of semirings on which we may specify quantitative properties. Another is dedicated to the special case of probabilistic specifications: in particular, we study syntactic fragments of our generic specification formalisms generating only probabilistic behaviors.
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Ren, Yuan. "Tractable reasoning with quality guarantee for expressive description logics." Thesis, University of Aberdeen, 2014. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=217884.
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DL-based ontologies have been widely used as knowledge infrastructures in knowledge management systems and on the Semantic Web. The development of efficient, sound and complete reasoning technologies has been a central topic in DL research. Recently, the paradigm shift from professional to novice users, and from standalone and static to inter-linked and dynamic applications raises new challenges: Can users build and evolve ontologies, both static and dynamic, with features provided by expressive DLs, while still enjoying e cient reasoning as in tractable DLs, without worrying too much about the quality (soundness and completeness) of results? To answer these challenges, this thesis investigates the problem of tractable and quality-guaranteed reasoning for ontologies in expressive DLs. The thesis develops syntactic approximation, a consequence-based reasoning procedure with worst-case PTime complexity, theoretically sound and empirically high-recall results, for ontologies constructed in DLs more expressive than any tractable DL. The thesis shows that a set of semantic completeness-guarantee conditions can be identifed to efficiently check if such a procedure is complete. Many ontologies tested in the thesis, including difficult ones for an off-the-shelf reasoner, satisfy such conditions. Furthermore, the thesis presents a stream reasoning mechanism to update reasoning results on dynamic ontologies without complete re-computation. Such a mechanism implements the Delete-and-Re-derive strategy with a truth maintenance system, and can help to reduce unnecessary over-deletion and re-derivation in stream reasoning and to improve its efficiency. As a whole, the thesis develops a worst-case tractable, guaranteed sound, conditionally complete and empirically high-recall reasoning solution for both static and dynamic ontologies in expressive DLs. Some techniques presented in the thesis can also be used to improve the performance and/or completeness of other existing reasoning solutions. The results can further be generalised and extended to support a wider range of knowledge representation formalisms, especially when a consequence-based algorithm is available.
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Mansutti, Alessio. "Reasoning with separation logics : complexity, expressive power, proof systems." Electronic Thesis or Diss., université Paris-Saclay, 2020. http://www.theses.fr/2020UPASG050.
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Cette thèse propose une étude approfondie de problèmes de décision classiques, tels que la satisfaisabilité et la validité pour des logiques de séparation, langages d'assertion bien connus développés pour la vérification de programmes avec structures dynamiques. La première partie de la thèse s'intéresse à la notion d'accessibilité pour les logiques de séparation. Notre motivation est double: d'une part, il s'agit de comprendre les frontières de la décidabilité de fragments de la logique de séparation du premier ordre connue pour être indécidable; d'autre part l'intention est de concevoir une logique de séparation aussi expressive que possible qui contienne des prédicats d'accessibilité, et dont le problème de satisfaisabilité soit décidable avec une complexité algorithmique relativement modeste (PSpace).Dans la seconde partie de la thèse, nous tirons profit des techniques développées dans la première partie pour définir une axiomatisation à la Hilbert de logiques de séparation et d'autres logiques spatiales. En particulier, nous définissons le premier calcul interne correct et complet pour la logique de séparation sans quantification. En utilisant la même approche, nous définissons une axiomatisation pour une logique modale enrichie d'un opérateur de composition issu d'une logique des ambients, formalisme logique dédié à la vérification de systèmes distribués. Les deux systèmes de preuves mettent en lumière des relations intéressantes entre les logiques de séparation et les logiques des ambients.Dans la troisième partie de la thèse, nous approfondissons encore davantage les relations entre les logiques de séparation et les logiques des ambients. Des similarités et des différences sont établies en termes de pouvoir d'expression et de complexité algorithmique, en comparant la conjonction séparante des logiques de séparation avec l'opérateur de composition des logiques des ambients. Afin de mener à bien nos comparaisons, nous nous plaçons dans une cadre uniforme issu de la logique modale, ce qui permet de partir d'une base commune pour étudier ces deux logiques<br>This thesis proposes an in-depth study of classical decision problems, such as satisfiability and validity, for separation logics: well-known assertion languages developed to verify heap-manipulating programs. The first part of the thesis focus on the notion of reachability in separation logics. Our motivation is twofold: on one side, we want to understand the decidability frontier for fragments of the otherwise undecidable first-order separation logic; on the other side, we want to devise a very expressive separation logic featuring reachability predicates, whose satisfiability problem is decidable with a relatively low complexity (PSpace).In the second part, we take advantage of some of the techniques developed in the first part of the thesis in order to design Hilbert-style axiomatisations for separation logics and other spatial logics. In particular, we introduce the first sound and complete internal proof system for quantified-free separation logic and, by relying on the same technique, we design an axiomatisation for a modal logic enriched with the composition operator from ambient logic (a logic to verify distributed systems). The two proof systems reveal interesting connections between separation logics and ambient logics.In the third part of the thesis, we dig deep in the connections between separation logics and ambient logics, and find surprising similarities and differences, in terms of expressive power and computational complexity, between the separating conjunction of separation logic and the composition operator of ambient logic. In order to carry out our comparison, we devise a suitable framework based on modal logic, which gives us a common ground to study the two logics
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Place, Thomas. "Decidable characterizations for tree logics." Phd thesis, École normale supérieure de Cachan - ENS Cachan, 2010. http://tel.archives-ouvertes.fr/tel-00744954.
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In this thesis we investigate the expressive power of several logics over finite trees. In particular we want to understand precisely the expressive power of first-order logic over finite trees. Because we study many logics, we proceed by comparison to a logic that subsumes them all and serves as a yardstick: monadic second-order logic. Each logic we consider is a fragment of monadic second-order logic. MSO is linked to the theory of formal languages. To each logical formula corresponds a tree language, which is the language of trees satisfying this formula. Furthermore, given a logic we can associate a class of tree languages: the class of languages definable by a formula of this logic. In the setting of finite trees MSO corresponds exactly to the class of regular tree languages. Given a logic, we actually look for a decidable characterization of the class of languages defined in this logic. By decidable characterization, we mean an algorithm for solving the following problem: given as input a finite tree automaton, decide if the recognized language belongs to the class in question. We will actually obtain our decidable characterizations by exhibiting for each class a set of closure properties such that a language is in the class under investigation if and only if it satisfies these closure properties. Each such closure property is then shown to be decidable. Stating and proving such closure properties usually yields a solid understanding of the expressive power of the corresponding logic. The main open problem in this research area is to obtain a decidable characterization for the class of tree languages that are definable in first-order logic. We provide decidable characterizations for several fragments of FO. First we provide three decidable characterizations for classes of regular languages of trees of bounded rank. The first class we consider is the class of languages definable in the temporal logic EF+F^-1. It essentially navigates the trees using two modalities for moving to a descendant node or an ancestor node. The second class we consider is the class of trees of bounded rank definable using one quantifier alternation. The last class, is the class of languages definable using a boolean combination of existential first order formulas. In the setting of forests, we investigate the class of languages definable in first-order logic using only two variables and two prediactes corresponding respectively to the ancestor and following sibling relations. We provide a characterization for this logic. The last class for which we provide a decidable characterization is the class of locally testable language (LT). A language L is in LT if membership in L depends only on the presence or absence of neighborhoods of a certain fixed size in the tree. We define notions of LT for both unranked trees and trees of bounded rank by adapting the definition of neighborhood to each setting. Then we provide a decidable characterization for both notions of LT.
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Nicolai, Carlo. "Truth, deflationism and the ontology of expressions : an axiomatic study." Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:a87eb43c-9657-4f13-b962-b18e04cff2e6.
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Philosophical enquiry on the notion of truth has traditionally involved the identification of a class of objects to which truth is ascribed. At the same time, formal investigations are often required when the notion of truth is at issue: semantic paradoxes force in fact philosophers to shape their arguments in a precise way. Objects of truth, in formal context, are always reduced to other, more manageable objects that mimic their structural properties such as numbers or sets. This form of reduction renders the distinction between linguistic or syntactic objects, to which truth is usually applied, and their mathematical counterparts opaque, at least from the point of view of the theory of truth. In informal metatheoretic discussion, in fact, they are clearly different entities. In this thesis we focus on an alternative way of constructing axiomatic theories of truth in which syntactic objects and mathematical objects belong to different universes. A brief introduction tries to situate the proposed theories in the context of different investigations on axiomatic truth. Chapter 2 is devoted to the discussion of historical and more theoretical motivations behind the proposed alternative. Chapter 3 will present the syntactic koinè spoken by our theories. Morphological categories of the object language and logical concepts concerning the object theory will be formalised in a recent axiomatisation of hereditarily finite sets. In Chapter 4 we finally introduce theories of truth with a built-in syntactic theory and examine some of their consequences. We briefly focus on disquotational truth, then consider compositional axioms for truth. Chapter 5 investigates a possible application of the setting just introduced: a realisation of the all-present interaction, in metamathematical practice, between informal metatheoretic claims and their (suitably chosen) coded counterparts. In the final chapter, after a brief characterisation of the key doctrines of the delflationary conception of truth, we evaluate the impact that the theories of truth studied in this work can have on the debate on the so-called conservativeness argument, which tries to match the alleged insubstantiality of the notion of truth, advocated by deflationists, with the deductive power of deflationary acceptable theories of truth.
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Montmerle, Martin. "The connectivity logic of cannabinoid type-1 expressing interneurones in the mouse visual cortex." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066493/document.
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La perception sensorielle dépend d'une interaction constante entre plusieurs zones corticales. Typiquement, pour chaque sens il y a une zone primaire qui reçoit directement des informations sensorielles du thalamus et une zone secondaire qui associe cette information avec des centres cognitifs plus élaborés (information descendante). Pourtant, les propriétés synaptiques et les microcircuits impliqués dans ces différents processus ne sont toujours pas élucidés. Nous savons que le récepteur cannabinoïde de type 1 (CB1) est exprimé à un plus grand niveau dans les cortex sensoriels secondaires. Ce récepteur est principalement exprimé par des cellules paniers inhibitrices qui expriment aussi le peptide cholecystokinin (CCK). En utilisant des enregistrements entre des paires d'IN CCK/CB1 et NP dans la couche 2/3 (C2/3) des centres visuels primaires (V1) et secondaires (V2) de souris adultes, nous avons demontré que dans le V1 les IN CCK projettent quasiment exclusivement dans leur propre couche, tandis que dans le V2 ils projettent aussi dans la couche 4 (C4). Malgré cette difference morphologique, ces IN avaient les mêmes signatures électrophysiologiques, suggérant qu'il s'agisse bien d'un type cellulaire homogène. En revanche, les connections synaptiques avec les NP étaient nettement plus petites et non fiable dans la C2/3 de V2. Cette différence disparut avec l'application d'un antagoniste de CB1, suggérant que ce récepteur médie une inhibition tonique qui est spécifique à une zone et couche corticale. Cette étude montre ainsi qu'il existe des microcircuits inhibiteurs particuliers dans les aires primaires et secondaires visuelles<br>During sensory processing, the correct subjective representation and interpretation of the external world is accomplished by a constant bi-directional communication between primary and secondary sensory cortices. Yet, the specific microcircuit players involved in these distinct cortical areas are still poorly characterized. After finding that the cannabinoid receptor (CB1) is more widely expressed in secondary than in primary sensory areas, we asked whether the neurons expressing CB1 had different properties in the two areas. CB1 is mainly expressed in large inhibitory basket cells that target the soma of other neurons. Using whole-cell patch clamping in acute brain slices from adult mice, we found that in layer 2/3 of the primary visual area of mice (V1), CB1+ interneurons exerted strong and reliable inhibition onto pyramidal cells, in contrast with the small and unreliable inhibition in secondary visual area (V2). Interestingly, pharmacological blocking of CB1Rs in V2 led to a potentiation of inhibition, while in V1 this effect was not observed, suggesting that CB1 interneurons in V2 are ‘doped’ by tonically or constitutively activated receptors. Differences in CB1 mediated plasticity also support this hypothesis. In V2, CB1+ interneurons projected their axons both within their cortical layer and to deeper layers, while in V1 these projections were principally intralaminar. Strikingly, infra laminar connections in V2 shared synaptic characteristics with those of L2/3 in V1. This study therefore suggests that different visual areas exhibit differential CB1-mediated modulation of perisomatic inhibition onto layer 2/3 and 4 principal neurons
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Bueno-Soler, Juliana 1976. "Multimodalidades anodicas e catodicas : a negação controlada em logicas multimodais e seu poder expressivo." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/280387.
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Orientador: Itala Maria Loffredo D'Ottaviano<br>Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Filosofia e Ciencias Humanas<br>Made available in DSpace on 2018-09-11T21:14:41Z (GMT). No. of bitstreams: 1
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Previous issue date: 2009<br>Resumo: O presente trabalho tem por objetivo investigar o papel da negação no âmbito das modalidades, de forma a poder esclarecer até que ponto a negação pode ser atenuada, controlada ou mesmo totalmente eliminada em favor da melhor expressabilidade lógica de certas teorias, asserções ou raciocínios que sofrem os efeitos da negação. Contudo, atenuar ou eliminar a negação tem um alto preço: métodos tradicionais em lógica podem deixar de ser válidos e certos resultados, como teoremas de completude para sistemas lógicos, podem ser derrogados. Do ponto de vista formal, a questão central que investigamos aqui e até que ponto tais métodos podem ser restabelecidos. Com tal finalidade, iniciamos nosso estudo a partir do que denominamos sistemas anódicos" (sem negação) e, a posteriori, introduzimos gradativamente o elemento catódico" (negações, com diversas gradações e diferentes características) nos sistemas modais por meio de combinações com certas lógicas paraconsistentes, as chamadas lógicas da inconsistência formal (LFIs). Todos os sistemas tratados são semanticamente caracterizados por semânticas de mundos possíveis; resultados de incompletude são também obtidos e discutidos. Obtemos ainda semânticas modais de traduções possíveis para diversos desses sistemas. Avançamos na direção das multimodalidades, investigando os assim chamados sistemas multimodais anódicos e catódicos. Finalmente, procuramos avaliar criticamente o alcance e o interesse dos resultados obtidos na direção da racionalidade sensível à negação.<br>Abstract: The present work aims to investigate the role of negations in the scope of modalities and in the reasoning expressed by modalities. The investigation starts from what we call anodic" systems (without any form of negation) and gradually reaches the cathodic" elements, where negations are introduced by means of combining modal logics with certain paraconsistent logics known as logics of formal inconsistency (LFIs). We obtain completeness results for all treated systems, and also show that certain incompleteness results can be obtained. The class of the investigated systems includes all normal modal logics that are extended by means of the schema Gk;l;m;n due to E. J. Lemmon and D. Scott combined with LFIs. We also tackle the question of obtaining modal possible-translations semantics for these systems. Analogous results are analyzed in the scope of multimodalities, where anodic as much as cathodic logics are studied. Finally, we advance a critical evaluation of the reach and scope of all the results obtained to what concerns expressibility of reasoning considered to be sensible to negation. We also critically assess the obtained results in contrast with problems of rationality that are sensible to negation.<br>Doutorado<br>Doutor em Filosofia
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Domin, Gesine, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, and Mario Mörl. "Applicability of a computational design approach for synthetic riboswitches." Oxford University Press, 2016. https://ul.qucosa.de/id/qucosa%3A15259.
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Riboswitches have gained attention as tools for synthetic biology, since they enable researchers to reprogram cells to sense and respond to exogenous molecules. In vitro evolutionary approaches produced numerous RNA aptamers that bind such small ligands, but their conversion into functional riboswitches remains difficult. We previously developed a computational approach for the design of synthetic theophylline riboswitches based on secondary structure prediction. These riboswitches have been constructed to regulate ligand dependent transcription termination in Escherichia coli. Here, we test the usability of this design strategy by applying the approach to tetracycline and streptomycin aptamers. The resulting tetracycline riboswitches exhibit robust regulatory properties in vivo. Tandem fusions of these riboswitches with theophylline riboswitches represent logic gates responding to two different input signals. In contrast, the conversion of the streptomycin aptamer into functional riboswitches appears to be difficult. Investigations of the underlying aptamer secondary structure revealed differences between in silico prediction and structure probing. We conclude that only aptamers adopting the minimal free energy (MFE) structure are suitable targets for construction of synthetic riboswitches with design approaches based on equilibrium thermodynamics of RNA structures. Further improvements in the design strategy are required to implement aptamer
structures not corresponding to the calculated MFE state.
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Tjernström, Mikael, and Linus Werner. "Värdering, Grafik och Logik : En kvantitativ studie av svensk nyhetsgrafik." Thesis, Mid Sweden University, Department of Information Technology and Media, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:miun:diva-11109.
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<p>News graphics as a part of journalism is something that’s constantly developing along with the news. That’s what we believed when we started this paper including its study. And we still believe the same, now that we’re done.News graphics itself is fairly common in Swedish newspapers, it can be seen every day in almost any major newspaper and is perfect for describing an event like the pollution of the sea over many years or just simply point out on a map where a city is located.This is one of the reasons to why we wrote this; another reason is that there’s almost nothing else written on the subject in northern Europe. It’s an empty space in media science, which is waiting to be explored.In our study we have examined four Swedish newspapers; Dagens Nyheter, Svenska Dagbladet, Aftonbladet and Expressen over the month of November 2009, a total of 120 newspapers. We have looked at the news graphics in each paper’s news and economics section to examine if news graphics are affected by media logics and news value.The results of the study are quantified and what we did was that we converted the main theories of media logics and news valuing to suit our purpose – describing news graphics in the same way as the theories is used for describing the produced news.Our results indicate that news graphics are mostly used to describe crime, economics, politics and news regarding the environment. We also divided news graphics into different categories: maps, graphs and charts, illustrations and combinations of some of the three previously mentioned. The two most commonly used types of news graphics in our study are maps followed by graphs and charts.Our results also indicate that news graphics is highly affected by media logic seeing media logic as how we write and present news in newspapers i.e. personalization. But still, news graphics is not nearly as affected by media logic and news valuing as news articles in general.A conclusion is that the morning papers (Dagens Nyheter and Svenska Dagbladet) had a higher amount of news graphic overall than the tabloids Aftonbladet and Expressen. But the news graphics in the tabloids was more affected by media logic in many ways.</p>
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Bedhiafi, Walid. "Sciences de l'information pour l'étude des systèmes biologiques (exemple du vieillissement du système immunitaire)." Electronic Thesis or Diss., Paris 6, 2017. https://accesdistant.sorbonne-universite.fr/login?url=https://theses-intra.sorbonne-universite.fr/2017PA066139.pdf.
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Le laboratoire i3 et le laboratoire LGIPH, utilisent des approches à haut débit pour l’étude du système immunitaire et ces disfonctionnements. Des limites ont été observées quant à l’utilisation des approches classiques pour l’annotation des signatures d’expression des gènes. L’objectif principal a été de développer une approche d’annotation pour répondre à ce besoin. L’approche que nous avons développée est une approche basée sur la contextualisation des gènes et de leurs produits puis sur la modélisation des voies biologiques pour la production de bases de connaissances pour l’étude de l’expression des gènes. Nous définissons ici un contexte d’expression des gènes comme suit : population cellulaire+compartiment anatomique+état pathologique. Pour connaitre ces contextes, nous avons opté pour la fouille de la littérature et nous avons développé un package Python, qui permet d’annoter les textes automatiquement en fonction de trois ontologies choisies en fonction de notre définition du contexte. Nous montrons ici que notre package a des performances meilleures que un outil de référence. Nous avons l’avons utilisé pour le criblage d’un corpus sur le vieillissement du système immunitaire dont on présente ici les résultats. Pour la modélisation des voies biologiques nous avons développé en collaboration avec le LIPAH une méthode de modélisation basée sur un algorithme génétique qui permet de combiner les résultats de mesure de la proximité sémantique sur la base des annotations des gènes et les données d’interactions. Nous avons réussis retrouver des réseaux de références avec un taux d’erreur de 0,47<br>High-throughput experimental approaches for gene expression study involve several processing steps for the quantification, the annotation and interpretation of the results. The i3 lab and the LGIPH, applies these approaches in various experimental setups. However, limitations have been observed when using conventional approaches for annotating gene expression signatures. The main objective of this thesis was to develop an alternative annotation approach to overcome this problem. The approach we have developed is based on the contextualization of genes and their products, and then biological pathways modeling to produce a knowledge base for the study of gene expression. We define a gene expression context as follows: cell population+ anatomical compartment+ pathological condition. For the production of gene contexts, we have opted for the massive screening of literature. We have developed a Python package, which allows annotating the texts according to three ontologies chosen according to our definition of the context. We show here that it ensures better performance for text annotation the reference tool. We used our package to screen an aging immune system text corpus. The results are presented here. To model the biological pathways we have developed, in collaboration with the LIPAH lab a modeling method based on a genetic algorithm that allows combining the results semantics proximity using the Biological Process ontology and the interactions data from db-string. We were able to find networks with an error rate of 0.47
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Cohn, Paulo Gomide. "Programação em logica, prolog e restriçõs : poder de expressão v.s. eficiencia." [s.n.], 1991. http://repositorio.unicamp.br/jspui/handle/REPOSIP/275869.
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Orientadores: Antonio E. Costa Pereira, Tomasz Kowaltowski<br>Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Matematica Estatistica e Ciencia da Computação<br>Made available in DSpace on 2018-07-13T23:56:33Z (GMT). No. of bitstreams: 1
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Previous issue date: 1991<br>Resumo: Apresenta-se inicialmente uma introdução à programação em lógica através de uma abordagem evolutiva. Começando de um sistema formal de primeira ordem bastante complexo, descreve-se o conceito de prova de teoremas e sua automação. A partir daí apresenta-se a idéia de eficiência da prova. Os principais avanços obtidos durante o século XX nesta área são apontados, dando-se ênfase ao princípio de resolução de Robinson. Ao restringir a linguagem do sistema formal às sentenças de Horn, obtem-se uma grande melhora da eficiência do mecanismo de prova, preservando razoável poder de expressão. Alguns problemas relativos à expressividade da linguagem são apontados assim como formas em que têm sido abordados na atualidade. Uma delas é a programação por restrições. Na segunda parte do trabalho é apresentada a implementação de um interpretador/sistema de execução para a linguagem Prolog. A partir de uma especificação breve, de alto nivel, são introduzidos, incrementalmente, os detalhes de implementação de nivel mais baixo (estruturas de dados, controle de execução) até se obter um programa puramente procedimental escrito numa linguagem convencional (C). Finalmente, os conceitos de programação por restrições mencionados no inicio do trabalho são apresentados de forma mais detalhada para que se possa ter uma visão mais clara do seu funcionamento na prática. Assim, adotando uma abordagem semelhante à utilizada para descrever o compilador Prolog, é apresentado um interpretador de alto nivel para programas de restrições e, após alguns refinamentos, é obtido um conjunto de instruções que pode ser implementado numa linguagem de programação convencional.<br>Abstract: An introduction to logic programming is initially presented by means of an evolutionary approach. Starting with a fairly complex first order formal system, the concepts of theorem proving and its automatization are described. From there the idea of proof efficiency is presented. The most significant advances obtained during the 20th century in this area are pointed out emphasizing Robinson's resolution principle. Restraining the formal system's language to Horn sentences, a major improvement of the proof mechanism is obtained, preserving reasonable expressive power. Some problems related to language expressiveness and the ways in which they have been recently approached are shown. One of these approaches is constraint programming. In the second part of the work, the implementation of an interpreter/runtime system for the Prolog language is shown. From a brief, high-level specification, lower-level implementation details (data structures, execution control) are introduced until a purely procedural program written in a conventional language (C) is obtained. Finally, the contraint programming concepts mentioned in the first part are presented in a more detailed form in order to allow for a clearer vision of how it works in practice. Thus, by means of an approach similar to that used to describe the Prolog compiler, a high-level interpreter for constraint programs is presented and, after some refinements, an instruction set that may be implemented in a conventional programming language is obtained.<br>Mestrado<br>Mestre em Ciência da Computação
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Steigmiller, Andreas [Verfasser]. "Optimisation of tableau-based reasoning systems for expressive description logics / Andreas Steigmiller." Ulm : Universität Ulm, 2016. http://d-nb.info/1104840219/34.
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Wang, Xiaoting. "Functional and expression analysis of the novel angiogenic regulator GPR124 /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Kufleitner, Manfred. "Logical fragments for Mazurkiewicz traces expressive power and algebraic characterizations /." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-27812.
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Shi, Jing. "Biostatistics and bioinformatics methods for analysis of pathways and gene expression /." May be available electronically:, 2007. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Adler, Adam Shultz. "Mechanisms of large-scale gene expression programs in cancer and aging /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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