Minimalism, move and the Internal Subject Hypothesis (ISH)

If CHL is optimal, why should it use costly Move-based feature-checking when a local Merge-based option is available? Why should a 'lazy' CHL bother to activate feature-clusters like Tns, available on verbs, check that FCs and verbs match, and finally remove FCs to satisfy FIP? Why should it furthermore copy-move DPs into the specifiers of FCs, satisfy itself that features match, and then remove all the copies but one? In MG such analyses result from a view of simplicity that induces biuniqueness between properties and positions, forces categories to be represented by `chains', and therefore requires a polistratal grammar. In this primarily conceptual paper, I argue. following CG-HPSG work, that the ISH is conceptually misguided, that FCs are uneconomic computational artifacts, that Move/Attract is as redundant as its triggers, or the deletions it causes, and that dropping them yields a neater theory of CHL.Si CHL es un sistema óptimo, ¿por qué usa una comprobación costosa basada en futuros movimientos cuando una opción local basada en la fusión está disponible? ¿Por qué debería un hermano CHL “perezoso” molestarse en activar clústeres de funciones como Tns, disponerlo en verbos, comprobar que los FCs y los verbos coinciden, y finalmente borrar los FCs para satisfacer al FIP? Aún más, ¿por qué debería copiar los DPs en los especificadores de FCs, darse por satisfecho con que las características coincidan, para acto seguido borrar todas las copias excepto una? En MG estos análisis surgen a raíz de un enfoque de simplicidad que propicia la correspondencia entre propiedades y posiciones, fuerza a las categorías a ser representadas por cadenas, y en consecuencia requiere una gramática poliestratal. En este artículo principalmente conceptual, discuto estas cuestiones, siguiendo el trabajo CG-HPSG, que el ISH está mal orientado conceptualmente, así como que los FCs son artefactos computacionales poco económicos, que el Movimiento/Atracción es tan redundante y como sus desencadenantes, y las supresiones que causa, y que alejar esto produce una teoría más ordenada de CHL

Extending relational model transformations to better support the verification of increasingly autonomous systems

Over the past decade the capabilities of autonomous systems have been steadily increasing. Unmanned systems are moving from systems that are predominantly remotely operated, to systems that include a basic decision making capability. This is a trend that is expected to continue with autonomous systems making decisions in increasingly complex environments, based on more abstract, higher-level missions and goals. These changes have significant implications for how these systems should be designed and engineered. Indeed, as the goals and tasks these systems are to achieve become more abstract, and the environments they operate in become more complex, are current approaches to verification and validation sufficient? Domain Specific Modelling is a key technology for the verification of autonomous systems. Verifying these systems will ultimately involve understanding a significant number of domains. This includes goals/tasks, environments, systems functions and their associated performance. Relational Model Transformations provide a means to utilise, combine and check models for consistency across these domains. In this thesis an approach that utilises relational model transformation technologies for systems verification, Systems MDD, is presented along with the results of a series of trials conducted with an existing relational model transformation language (QVT-Relations). These trials identified a number of problems with existing model transformation languages, including poorly or loosely defined semantics, differing interpretations of specifications across different tools and the lack of a guarantee that a model transformation would generate a model that was compliant with its associated meta-model. To address these problems, two related solvers were developed to assist with realising the Systems MDD approach. The first solver, MMCS, is concerned with partial model completion, where a partial model is defined as a model that does not fully conform with its associated meta-model. It identifies appropriate modifications to be made to a partial model in order to bring it into full compliance. The second solver, TMPT, is a relational model transformation engine that prioritises target models. It considers multiple interpretations of a relational transformation specification, chooses an interpretation that results in a compliant target model (if one exists) and, optionally, maximises some other attribute associated with the model. A series of experiments were conducted that applied this to common transformation problems in the published literature

Modal Logic S5 Satisfiability in Answer Set Programming

Modal logic S5 has attracted significant attention and has led to several practical applications, owing to its simplified approach to dealing with nesting modal operators. Efficient implementations for evaluating satisfiability of S5 formulas commonly rely on Skolemisation to convert them into propositional logic formulas, essentially by introducing copies of propositional atoms for each set of interpretations (possible worlds). This approach is simple, but often results into large formulas that are too difficult to process, and therefore more parsimonious constructions are required. In this work, we propose to use Answer Set Programming for implementing such constructions, and in particular for identifying the propositional atoms that are relevant in every world by means of a reachability relation. The proposed encodings are designed to take advantage of other properties such as entailment relations of subformulas rooted by modal operators. An empirical assessment of the proposed encodings shows that the reachability relation is very effective and leads to comparable performance to a state-of-the-art S5 solver based on SAT, while entailment relations are possibly too expensive to reason about and may result in overhead.</p

Soames's argument 1 against strong two-dimensionalism

This paper criticizes Soames's main argument against a variant of two-dimensionalism that he calls strong two-dimensionalism. The idea of Soames's argument is to show that the strong two-dimensionalist's semantics for belief ascriptions delivers wrong semantic verdicts about certain complex modal sentences that contain both such ascriptions and claims about the truth of the ascribed beliefs. A closer look at the formal semantics underlying strong two-dimensionalism reveals that there are two feasible ways of specifying the truth conditions for claims of the latter sort. Only one of the two yields the problematic semantic verdicts, so strong two-dimensionalists can avoid Soames's argument by settling for the other wa

Étude de la coopération hôte-microbiote par des problèmes d'optimisation basés sur la complétion de réseaux métaboliques

Systems biology relies on computational biology to integrate knowledge and data, for a better understanding of organisms’ physiology. Challenges reside in the applicability of methods and tools to non-model organisms, for instance in marine biology. Sequencing advances and the growing importance of elucidating microbiotas’ roles, have led to an increased interest into these organisms. This thesis focuses on the modeling of the metabolism through networks, and of its functionality using graphs and constraints semantics. In particular, a first part presents work on gap-filling metabolic networks in the context of non-model organisms. A graph-based method is benchmarked and validated and a hybrid one is developed using Answer Set Programming (ASP) and linear programming. Such gap-filling is applied on algae and extended to decipher putative interactions between Ectocarpus siliculosus and a symbiotic bacterium. In this direction, the second part of the thesis aims at proposing formalisms and implementation of a tool for selecting and screening communities of interest within microbiotas. It enables to scale to large microbiotas and, with a two-step approach, to suggest symbionts that fit the desired objective. The modeling supports the computation of exchanges, and solving can cover the whole solution space. Applications are presented on the human gut microbiota and the selection of bacterial communities for a brown alga. Altogether, this thesis proposes modeling, software and biological applications using graph-based semantics to support the elaboration of hypotheses for elucidating the metabolism of organisms.La biologie des systèmes intègre données et connaissances par des méthodes bioinformatiques, afin de mieux appréhender la physiologie des organismes. Une problématique est l’applicabilité de ces techniques aux organismes non modèles, au centre de plus en plus d’études, grâce aux avancées de séquençage et à l’intérêt croissant de la recherche sur les microbiotes. Cette thèse s’intéresse à la modélisation du métabolisme par des réseaux, et de sa fonctionnalité par diverses sémantiques basées sur les graphes et les contraintes stoechiométriques. Une première partie présente des travaux sur la complétion de réseaux métaboliques pour les organismes non modèles. Une méthode basée sur les graphes est validée, et une seconde, hybride, est développée, en programmation par ensembles réponses (ASP). Ces complétions sont appliquées à des réseaux métaboliques d’algues en biologie marine, et étendues à la recherche de complémentarité métabolique entre Ectocarpus siliculosus et une bactérie symbiotique. En s’appuyant sur les méthodes de complétion, la seconde partie de la thèse vise à proposer et implémenter une sélection de communautés à l’échelle de grands microbiotes. Une approche en deux étapes permet de suggérer des symbiotes pour l’optimisation d’un objectif donné. Elle supporte la modélisation des échanges et couvre tout l’espace des solutions. Des applications sur le microbiote intestinal humain et la sélection de bactéries pour une algue brune sont présentées. Dans l’ensemble, cette thèse propose de modéliser, développer et appliquer des méthodes reposant sur des sémantiques de graphe pour élaborer des hypothèses sur le métabolisme des organismes

The Bradleyan Regress, Non-Relational Realism, and the Quinean Semantic Strategy

Non-Relational Realism is a popular solution to the Bradleyan regress of facts or truths. It denies that there is a relational universal of exemplification; for an object a to exemplify a universal F-ness, on this view, is not for a relation to subsist between a and F-ness. An influential objection to Non-Relational Realism is that it is unacceptably obscure. The author argues that Non-Relational Realism can be understood as a selective application of satisfaction semantics to predicates like ‘exemplify’, and that so understood, it is not obscure. This kind of selective use of satisfaction semantics may be feasible in other contexts as a means of making theories more parsimonious

Propositional Anaphora: The case of embedded polar responses in Dutch and English

This dissertation investigates the embedded polar response paradigms of Dutch, English and to some extent of German. These are responses that involve an agent, a propositional attitude verb and an anaphor, such as the affirmative response ‘I think so’ to a question like ‘Did John feed the dog?’ (cf. Sailor 2012). In such responses, anaphors, like ‘so’, have been argued to refer to the proposition introduced in the preceding questions (see, e.g., Cushing 1972; Cornish 1992; Asher 1993; Needham 2012; Krifka 2013; Snider 2017). Unlike anaphors in for instance the nominal domain, propositional anaphors have not been studied extensively, with the exceptions of Cushing (1972); Webber (1991); Cornish (1992); Asher (1993); Hegarty et al. (2002), Snider (2017), Pasquereau (2018, 2022) and recent studies of response particles ‘yes’ and ‘no’ (see, e.g., Krifka, 2013; Brasoveanu et al., 2013; Roelofsen and Farkas, 2015; Claus et al., 2017; Goodhue and Wagner, 2018). The present work aims to fill this gap from the perspective of embedded polar responses. Note that the English embedded polar response paradigm consists of responses like ‘I think so’, ‘I think’ (using a null proform), or ‘I think not’ in combination with the predicate ‘think’. The response ‘I think it’ is considered infelicitous. In combination with, e.g., ‘doubt’, one can only response ‘I doubt it’ in response to a question, whereas ‘I doubt so’ or ‘I doubt’ would be infelicitous responses. This pattern raises the question why there are multiple embedded polar responses in the first place and why they are restricted to certain predicates. Furthermore, it raises the question if embedded polar response paradigms in other languages are similar. To shed light on these questions, the present dissertation investigates responses in Dutch, English and to some extent in German. One of the main conclusions of this dissertation is that there is no uniform class of anaphoric items used in embedded polar responses. I show that these anaphors, like ‘it’, ‘so’, or the null proform, are very different from one another in terms of their semantic contribution and their pragmatic role in their paradigms. Despite these differences, there are also similarities between the different responses considered and the different languages under consideration. This dissertation considers two categories: Type I and Type II responses. This dissertation first argues that the category of Type I responses consists of responses involving items like Dutch polar ‘van’ and English ‘so’. It argues that these responses signal that the proposition under reference has not been settled yet - because either the speaker is uncertain about it his/herself or other interlocutors disagree about the status of the proposition. As a consequence, both polar ‘van’ and ‘so’ cannot generally occur with factive predicates. Note that polar ‘van’ and ‘so’ signal their Type I meanings in different ways. Chapter 3 argues that the ‘uncertainty’ signaled by polar ‘van’ is due to the similative meaning hardwired into its semantics. In contrast, Chapter 4 argues that ‘so’ bears a presupposition with respect to the common ground status of its referent. More specifically, Chapter 4 argues that ‘so’ presupposes that its referent is still under discussion, i.e. on the Table in terms of Farkas and Bruce (2009), thereby building on Needham’s (2012) account. In addition, this dissertation shows that ‘so’ is in fact an adverb. These two properties set ‘so’ apart from the other anaphors considered in this thesis, although this anphor is often considered an exemplary propositional anaphor. In the first part of this dissertation we thus saw that embedded polar responses with polar ‘van’ and ‘so’ thus have rather similar functions, but a very different underlying semantics and pragmatics. This dissertation argues that the second category, Type II responses, consists of embedded polar responses that lack a presupposition or implication that signals uncertainty or non-settledness. This dissertation shows that this category involves embedded polar responses containing for instance weak pronouns, like ‘het’ or ‘it’, or the null proform. As a consequence, these kinds of responses compete with Type I responses. Whenever a speaker wishes to express that the proposition under reference is not yet settled, s/he will choose a Type I response over a Type II response. That is, an English speaker would prefer a response involving ‘so’ over a response involving a null proform in such a scenario. The Dutch counterpart would involve polar ‘van’ instead of ‘het’. Furthermore, Chapters 5 and Chapter 6 argue that there are differences between English and German, on the one hand, and Dutch, on the other, where it comes to Type II responses. Both English and German are able to form embedded polar responses with predicates like ‘think’ or ‘guess’ and the null complement anaphor (NCA) and are unable to form such responses with weak pronouns. For Dutch, this works the other way around: Dutch can form embedded polar responses with, e.g., ‘denken’ (think) and ‘het’ (it), but not with an NCA. Moreover, English and German may use propositional attitude verbs in combination with the negative adverbs ‘nicht’ and ‘not’ in embedded polar responses, whereas Dutch cannot. Chapter 5 shows that such responses with negative operators are most parsimoniously analyzed as involving NCA, just like their non-negative counterparts. On the basis of the languages under consideration this dissertation argues there seems to exist a correlation between (i) being able to form embedded polar responses with NCA and a negative adverb and (ii) being unable to form one with a weak pronoun and a predicate like think. Chapter 6 investigates Dutch embedded polar responses with weak pronouns in more detail. The main question of this chapter is why Dutch features such responses whereas English does not. Chapter 6 argues that this is the case, because ‘het’ is the phonologically weakest proform available in Dutch. Dutch does not feature an NCA. The competitors of ‘het’ are, e.g., the phonologically heavier demonstratives ‘dat’ (= that) and ‘dit’ (= this). These proforms, on their turn, compete with one another in terms of proxomity. Since the demonstratives are phonologically heavier than the weak proform, they are dispreferred for embedded polar responses, which target the most salient proposition in the discourse at the moment of answering. In addition, ‘het’ competes with polar ‘van’. As mentioned above, polar ‘van’ is chosen over ‘het’ if the speaker wishes to express a more subjective meaning. There are thus different types of competition at play: Competition in terms of subjectivity, phonological strength and proximity. The same competition applies to the Dutch forms. This dissertation shows that we cannot simply compare the licensing of one propositional anaphor with another without taking into consideration the individual meanings and uses of these proforms. In discussing different kinds of responses across languages, this dissertation also provides insight into the different discourse moves that constitute answers to polar questions. It shows that responses with for instance polar ‘van’ in Dutch or ‘so’ in English convey more and different information than those with for instance ‘het’ in Dutch or NCA in English. The former bear more information than just the information that the proposition under reference is compatible or not with the attitude holder’s information state, as they also provide information on the unsettledness or uncertainty of the proposition under reference. In addition, the present work sheds more light on propositional attitude verbs. It shows that Anand and Hacquard’s (2008, 2013) distinction between doxastic and assertive predicates is highly relevant when considering embedded polar responses (cf. Scheffler 2008) and that these predicates behave differently when occurring with different items in embedded polar responses. We saw that the use of polar ‘van’ in Dutch and ‘so’ in English is more flexible than that of other anaphors. Again, this can be attributed to the ‘special’ meaning of these anaphors and their evidential uses. This illustrates once more that the items used in embedded polar responses are not a uniform set

Bioinformatics for comparative cell biology

For hundreds of years biologists have studied the naturally occurring diversity in plant and animal species. The invention of the electron microscope in the rst half of the 1900's reveled that cells also can be incredible complex (and often stunningly beautiful). However, despite the fact that the eld of cell biology has existed for over 100 years we still lack a formal understanding of how cells evolve: It is unclear what the extents are in cell and organelle morphology, if and how diversity might be constrained, and how organelles change morphologically over time.(...