Every normal logic program has a 2-valued semantics: theory, extensions, applications, implementations

Trabalho apresentado no âmbito do Doutoramento em Informática, como requisito parcial para obtenção do grau de Doutor em Informática

Pathway Semantics: An Algebraic Data Driven Algorithm to Generate Hypotheses about Molecular Patterns Underlying Disease Progression

The overarching goal of the Pathway Semantics Algorithm (PSA) is to improve the in silico identification of clinically useful hypotheses about molecular patterns in disease progression. By framing biomedical questions within a variety of matrix representations, PSA has the flexibility to analyze combined quantitative and qualitative data over a wide range of stratifications. The resulting hypothetical answers can then move to in vitro and in vivo verification, research assay optimization, clinical validation, and commercialization. Herein PSA is shown to generate novel hypotheses about the significant biological pathways in two disease domains: shock / trauma and hemophilia A, and validated experimentally in the latter. The PSA matrix algebra approach identified differential molecular patterns in biological networks over time and outcome that would not be easily found through direct assays, literature or database searches. In this dissertation, Chapter 1 provides a broad overview of the background and motivation for the study, followed by Chapter 2 with a literature review of relevant computational methods. Chapters 3 and 4 describe PSA for node and edge analysis respectively, and apply the method to disease progression in shock / trauma. Chapter 5 demonstrates the application of PSA to hemophilia A and the validation with experimental results. The work is summarized in Chapter 6, followed by extensive references and an Appendix with additional material.

Semantics of logic programs with explicit negation

After a historical introduction, the bulk of the thesis concerns the study of a declarative semantics for logic programs. The main original contributions are: ² WFSX (Well–Founded Semantics with eXplicit negation), a new semantics for logic programs with explicit negation (i.e. extended logic programs), which compares favourably in its properties with other extant semantics. ² A generic characterization schema that facilitates comparisons among a diversity of semantics of extended logic programs, including WFSX. ² An autoepistemic and a default logic corresponding to WFSX, which solve existing problems of the classical approaches to autoepistemic and default logics, and clarify the meaning of explicit negation in logic programs. ² A framework for defining a spectrum of semantics of extended logic programs based on the abduction of negative hypotheses. This framework allows for the characterization of different levels of scepticism/credulity, consensuality, and argumentation. One of the semantics of abduction coincides with WFSX. ² O–semantics, a semantics that uniquely adds more CWA hypotheses to WFSX. The techniques used for doing so are applicable as well to the well–founded semantics of normal logic programs. ² By introducing explicit negation into logic programs contradiction may appear. I present two approaches for dealing with contradiction, and show their equivalence. One of the approaches consists in avoiding contradiction, and is based on restrictions in the adoption of abductive hypotheses. The other approach consists in removing contradiction, and is based in a transformation of contradictory programs into noncontradictory ones, guided by the reasons for contradiction.

An algorithmic approach to estimating the minimal number of periodic points for smooth self-maps of simply-connected manifolds

For a given self-map f of M, a closed smooth connected and simply-connected manifold of dimension m ≥ 4, we provide an algorithm for estimating the values of the topological invariant Dm r [f], which equals the minimal number of r-periodic points in the smooth homotopy class of f. Our results are based on the combinatorial scheme for computing Dm r [f] introduced by G. Graff and J. Jezierski [J. Fixed Point Theory Appl. 13 (2013), 63–84]. An open-source implementation of the algorithm programmed in C++ is publicly available at http://www.pawelpilarczyk.com/combtop/.

Contractive metrics for a Boltzmann equation for granular gases: diffusive equilibriaThe Patterson-Sullivan embedding and minimal volume entropy for outer space

We quantify the long-time behavior of a system of (partially) inelastic particles in a stochastic thermostat by means of the contractivity of a suitable metric in the set of probability measures. Existence, uniqueness, boundedness of moments and regularity of a steady state are derived from this basic property. The solutions of the kinetic model are proved to converge exponentially as t→ ∞ to this diffusive equilibrium in this distance metrizing the weak convergence of measures. Then, we prove a uniform bound in time on Sobolev norms of the solution, provided the initial data has a finite norm in the corresponding Sobolev space. These results are then combined, using interpolation inequalities, to obtain exponential convergence to the diffusive equilibrium in the strong L¹-norm, as well as various Sobolev norms.

The Patterson-Sullivan embedding and minimal volume entropy for outer space

"Vegeu el resum a l'inici del document del fitxer adjunt."

Minimal truncations of supersingular p-divisible groups

"Vegeu el resum a l'inici del document del fitxer adjunt."

Minimal lenght elements of Thompson's groups F(p)

We describe a method for determining the minimal length of elements in the generalized Thompson's groups F(p). We compute the length of an element by constructing a tree pair diagram for the element, classifying the nodes of the tree and summing associated weights from the pairs of node classifications. We use this method to effectively find minimal length representatives of an element.

Minimal invasive surgery for coronoid fracture: technical note.

Operative treatment of coronoid fracture often requires a large dissection of soft tissue, resulting in elbow stiffness and functional limitation. The authors present a minimal invasive, safe technique, useful in the case of isolated coronoid fracture associated with elbow dislocation. This technique does not require soft tissue dissection and allows an early unlimited resumption of sports activities.

"MIATA"-minimal information about T cell assays.

Immunotherapy, especially therapeutic vaccination, has a great deal of potential in the treatment of cancer and certain infectious diseases such as HIV (Allison et al., 2006; Fauci et al., 2008; Feldmann and Steinman, 2005). Numerous vaccine candidates have been tested in patients with a variety of tumor types and chronic viral diseases. Often, the best way to assess the clinical potential of these vaccines is to monitor the induced T cell response, and yet there are currently no standards for reporting these results. This letter is an effort to address this problem.

El desastre quotidià i la disciplina repressora, respostes a la geometria minimal

La proposta de tesi pren com a punt de partida les respostes artístiques i teòriques dutes a terme a partir dels anys seixanta contra un context de coneixement tradicional fonamentalment racionalista, que segueix la tradició lògica de la modernitat i que troba el seu reflex i aplicació social en l’ordre espaial i per extensió, en la geometria. Un cop descrites les nocions que d’aquesta modernitat han estat aplicades a l’art dels anys 50 i 60, es mostra com les crítiques de determinats filòsofs i artistes han anat conformant un corpus teòric i artístic que ha implicat un intent d’enderrocament d’aquest sistema tradicional de coneixement, interpretació, lectura i atorgament de sentit a les obres artístiques. Aquests són: M.Foucault, J.Derrida, R. Smithson, R. Serra, R. Morris, Mona Hatoum, Imi Knoebel o Tacita Dean, entre d’altres. Seguidament es presenta un anàlisi més profund i detallat d’aquelles respostes artístiques més paradigmàtiques, tant al sistema de pensament tradicional com a l’ordre espaial que aquest conseqüentment implica. Aquestes crítiques s’organitzen en dues parts antagòniques: l’una és “L’adveniment del caos”, i l’altra és la “Crítica de l’ordre”. Els artistes són: L. Bourgeois, E.Hesse, A.Mendieta i P.Halley. En una tercera part, es descriu com aquest inici deconstructor del paradigma de coneixement tradicional iniciat als anys seixanta es desenvolupa durant els següents vint anys tenint en aquest cas com a fonament teòric les crítiques de R.Krauss, J. Baudrillard, P.Virilio, i com artistes els arquitectes P. Eienmann i F. Gehri, entre d’altres. La conclusió fonamental d’aquests apartats intenta posar de manifest la subversió o infracció de la geometria com a contenidora dels conceptes de la modernitat: raó i ordre moral. Finalment, en una quarta part s’inclou el propi projecte artístic que representa l’experimentació i praxi de les conclusions teòriques d’aquesta tesi.

Synergistic epistasis and alternative hypotheses.

Inbreeding generally results in deleterious shifts in mean fitness. If the fitness response to increasing inbreeding coefficient is non-linear, this suggests a contribution of epistasis to inbreeding depression. In a cross-breeding experiment, Salathe & Ebert (2003. J. Evol. Biol. 16: 976-985) tested and found the presence of this non-linearity in Daphnia magna. They argue that epistatic interactions cause this non-linearity. We argue here that their experimental protocol does not allow disentangling the effect of synergistic epistasis from two alternative hypotheses, namely hybrid vigour and statistical non-independence of data.