Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

In the context of the emerging Semantic Web and the quest for a common logical framework underpinning its architecture, the relation of rule-based languages such as Answer Set Programming (ASP) and ontology languages such as the Web Ontology Language (OWL) has attracted a lot of attention in the literature over the past years. With its roots in Deductive Databases and Datalog though, ASP shares much more commonality with another Semantic Web standard, namely the Simple Protocol and RDF Query Language (...) (SPARQL). In this paper, we take the recent approval of the SPARQL1.1 standard by the World Wide Web consortium (W3C) as an opportunity to introduce this standard to the Logic Programming community by providing a translation of SPARQL1.1 into ASP. In this translation, we explain and highlight peculiarities of the new W3C standard. Along the way, we survey existing literature on foundations of SPARQL and SPARQL1.1, and also combinations of SPARQL with ontology and rules languages. Thereby, apart from providing the means to implement and support SPARQL natively within Logic Programming engines and particularly ASP engines, we hope to pave the way for further research on a common logical framework for Semantic Web languages, including query languages, from an ASP point of view. (shrink)

This work concerns itself with characterising the different types of contents that arise from uses of interrogative sentences, describing what meanings get associated with particular interrogative sentences, and explaining how these get put together compositionally on the basis of the meaning of their constituents, with particular attention to the meaning of interrogative phrases. ;Within most recent work in linguistic semantics, questions, the contents of query uses of interrogatives, have been analysed reductively as higher order propositional objects. The current work (...) argues against such an analysis. In its stead a view of questions is offered wherein these constitute the subclass of singular propositional entities, unresolved states-of-affairs , those that contain one or more argument roles of the propositional entity with whom no entity is associated. This view provides for an inherently richer notion of answerhood that is at the same time based on entities that are more plausibly available to cognitive agents engaged in querying. The need for a richer notion of answerhood is prompted by our demonstration that the class of answers to any given question--contents that can be conveyed by acceptable responses--has been considerably under-recognized in past work. An important gain made by the proposed approach is that it reveals and provides a simple account of systematic and cross-linguistically stable contrasts in the ability of a predicate to take an interrogative meaning as an argument. ;Our proposal for characterising the meaning of interrogative expressions argues that there exist three independent classes of uses which interrogative phrases can undergo, which we dub independent, dependent, and reprise uses. We argue extensively against an assumption common to most past work that interrogatives should be viewed as quantifiers on either syntactic or semantic grounds. We propose that dependent and reprise uses of interrogative expressions are each particular instances of use-types applicable to non-interrogative expressions. Dependent uses include bound variable anaphora as an instance. Reprise uses comprehend quotative uses of declarative sentences. We show how combining the general characteristics of each use type with the characterisation of independent interrogative uses we provide enables the defining conditions pertaining to these additional interrogative uses to be derived. This allows for a simple and comprehensive account of the available interrogative meanings. (shrink)

The notion of a “query” occurred in legal, medical, theological and scientific writings during the early modern period. Whereas the “questionary” (from c. 1400s) sought replies from within a doctrine (such as Galenic medicine), in the 1600s the query posed open-ended inquiries, seeking empirical information from travellers, explorers and others. During the 1660s in Britain, three versions of the query (and lists of queries) emerged. Distinctions need to be made between queries seeking information via observation and those (...) asking for experimentation, and between those aiming to keep theory to one side and those that framed theoretical conjectures. My examples are drawn from the work of the Royal Society of London (founded 1660) and from some of its leading members, especially Robert Boyle, Robert Hooke and Isaac Newton. (shrink)

LetA be any nonrecursive set. We define a hierarchy of sets (and a corresponding hierarchy of degrees) that are reducible toA based on bounding the number of queries toA that an oracle machine can make. WhenA is the halting problemK our hierarchy of sets interleaves with the difference hierarchy on the r.e. sets in a logarithmic way; this follows from a tradeoff between the number of parallel queries and the number of serial queries needed to compute a function with oracleK.

In this essay, I attempt to provide answers to the following four queries concerning the metaphysics of early human embryogenesis. (1) Following its first cellular fission, is it coherent to claim that one and only one of two “blastomeric” twins of a human zygote is identical with that zygote? (2) Following the fusion of two human pre-embryos, is it coherent to claim that one and only one pre-fusion pre-embryo is identical with that postfusion pre-embryo? (3) Does a live human being (...) come into existence only when its brain comes into existence? (4) At implantation, does a pre-embryo become a mere part of its mother? I argue that either if things have quidditative properties or if criterialism is false, then queries (1) and (2) can be answered in the affirmative; that in light of recent developments in theories of human death and in light of a more “functional” theory of brains, query (3) can be answered in the negative; and that plausible mereological principles require a negative answer to query (4). (shrink)

_Querying Consent_ examines the ways in which the concept of consent is used to map and regulate sexual desire, gender relationships, global positions, technological interfaces, relationships of production and consumption, and literary and artistic interactions. From philosophy to literature, psychoanalysis to the art world, the contributors to _Querying Consent_ address the most uncomfortable questions about consent today. Grounded in theoretical explorations of the entanglement of consent and subjectivity across a range of textual, visual, multi- and digital media, _Querying Consent_ considers (...) the relationships between consent and agency before moving on to trace the concept’s outcomes through a range of investigations of the mutual implication of personhood and self-ownership. (shrink)

Robert Brandom’s normative-pragmatic theory is intended to represent the minimal set of practical abilities whose exhibition qualifies creatures as speaking a language. His model of a minimally discursive practice (MDP) is one in which participants, devoid of logical vocabulary, are only capable of making assertions and drawing inferences. This paper argues that Brandom’s purely assertional practices are not MDPs and that speech acts of asking questions (queries) must be included in any practice that counts as an MDP. The upshot of (...) the argument is support for the claim that the normative pragmatic analysis of assertions requires a corresponding analysis of queries and vice versa. (shrink)

In recent years large amounts of electronic texts have become available. While the first of these corpora had only a low level of annotation, the more recent ones are annotated with refined syntactic information. To make these rich annotations accessible for linguists, the development of query systems has become an important goal. One of the main difficulties in this task consists in the choice of the right query language, a language which at the same time should be powerful (...) enough to let users formulate the queries they want and which should be efficiently evaluable to keep query response times short. There is a widespread belief that such a query language does not exist. It is therefore the aim of this paper to show that there is indeed a powerful query language that can be efficiently evaluated. We propose the use of monadic second-order logic as a query language. We show that a query in this language can be evaluated in linear time in the size of a tree in the corpus. We also provide examples of complicated linguistic queries expressed in monadic second-order logic thereby demonstrating the high expressive power of the language. (shrink)

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Exploring the risks, ambiguities, and unstable conceptual worlds of contemporary thought, Crossover Queries brings together the wide-ranging writings, across twenty years, of one of our most important philosophers.Ranging from twentieth-century European philosophy—the thought of Heidegger, Foucault, Derrida, Levinas, Janicaud, and others—to novels and artworks, music and dance, from traditional Jewish thought to Jain andBuddhist metaphysics, Wyschogrod’s work opens radically new vistas while remaining mindful that the philosopher stands within and is responsible to a philosophical legacy conditioned by the negative.Rather than (...) point to a Hegelian dialectic of overcoming negation or to a postmetaphysical exhaustion, Wyschogrod treats negative moments as opening novel spaces for thought. She probes both the desire for God and an ethics grounded in the interests of the other person, seeing these as moments both of crossing over and of negation. Alert to the catastrophes that have marked our times, she exposes the underlying logical structures of nihilatory forces that have been exerted to exterminate whole peoples. Analyzing the negationsof biological research and cultural images of mechanized and robotic bodies, she shows how they contest the body as lived in ordinary experience.“Crossover Queries brings together important essays on a remarkable range of topics by one of our most insightful cultural critics. Commenting on philosophical and theological issues that have shaped the recent past as well as scientific and technological questions that will preoccupy us in the near future, Wyschogrod consistently alerts us to the urgency of problems whose importance few recognize. To avoid the challenge these essays pose is to avoid responsibility for a future that appears to be increasingly fragile.”—Mark C. Taylor, Columbia University. (shrink)

Querying the Medieval. Texts and the History of Practices in South Asia. Ronald Inden, Jonathan Walters, Daud Ali. Oxford University Press, New York 2000. 235 pp. £32.50. ISBN 0-19-512430-8.

We argue that a conflict between two conceptions of “quantity of matter” employed in a corollary to proposition 6 of Book III of the Principia illustrates a deeper conflict between Newton’s view of the nature of extended bodies and the concept of mass appropriate for the theoretical framework of the Principia. We trace Newton’s failure to recognize the conflict to the fact that he allowed for the justification of natural philosophical claims by two types of a posteriori, empiricist methodologies. Newton's (...) thoughts on these methodologies demonstrate that his natural philosophy continued to develop after the publication of the first edition of Principia and that De Grav should be understood as an early, and not necessarily representative, text. (shrink)

The editorial introduces issue 21.1 of Technoetic Arts via a critical reflection on the artificial intelligence hype (AI hype) that emerged in 2022. Tracing the history of the critique of Large Language Models, the editorial underscores that there are substantial ethical challenges related to bias in the training data, copyright issues, as well as ecological challenges which the technology industry has consistently downplayed over the years. -/- The editorial highlights the distinction between the current AI technology’s reliance on extensive pre-existing (...) human-generated data for pattern recognition and the performative process inherent in art practice. Patterns of creative output can be replicated without a thorough understanding of underlying concepts. In contrast, the performative process of art practice, as explored through the conceptual frameworks of creativity by Noam Chomsky, Charles Sanders Peirce, and Roger T. Ames and with reference to an earlier publication of the editorial’s author, creates concepts and continually ‘strives to extend itself towards the unknown.’ -/- Following this introductory section, the editorial provides an overview of the ten articles featured in this issue of Technoetic Arts. The first four texts engage with emerging technologies from various perspectives in art and design. The subsequent six articles, part of a special section titled 'Perspectives from Chandigarh,' reflect a quest for meaningful existence within colonial, patriarchal, and biopolitical structures that frame everyday practices of exclusion and oppression. (shrink)

Large databases of linguistic annotations are used for testing linguistic hypotheses and for training language processing models. These linguistic annotations are often syntactic or prosodic in nature, and have a hierarchical structure. Query languages are used to select particular structures of interest, or to project out large slices of a corpus for external analysis. Existing languages suffer from a variety of problems in the areas of expressiveness, efficiency, and naturalness for linguistic query. We describe the domain of linguistic (...) trees and discuss the expressive requirements for a query language. Then we present a language that can express a wide range of queries over these trees, and show that the language is first-order complete over trees. (shrink)

This paper concerns the paraconsistent logic LPQ⊃,F and an application of it in the area of relational database theory. The notions of a relational database, a query applicable to a relational database, and a consistent answer to a query with respect to a possibly inconsistent relational database are considered from the perspective of this logic. This perspective enables among other things the definition of a consistent answer to a query with respect to a possibly inconsistent database without (...) resort to database repairs. In an earlier paper, LPQ⊃,F is presented with a sequent-style natural deduction proof system. In this paper, a sequent calculus proof system is presented instead because such proof systems are generally considered more suitable as the basis of proof search procedures than natural deduction proof systems and proof search procedures can serve as the core of algorithms for computing consistent answers to queries. (shrink)

As argued above, if we examine each "form of knowledge" within a modern historical context, it seems that we can see a sequentially transformational and coincident historical line that links the material, then the institutional, and then the cultural, while maintaining the sequential development of the linked trends from beginning to end. Even a summary of Lin Yusheng's hypothesis is a continuation of the "mind's" function orientation. This framework, however, must still answer the following question: In the process whereby "forms (...) of knowledge" become intimately connected with transformational events or time sequencing, do they appear in the form of a totalitarian theoretical model, or do they exert their influence in the form of the dispersed role of a discourse? More concretely, in the case of China: When the traditional "forms of knowledge" of modern Chinese intellectuals—for example, the methodology and behavior within the "thought discourses" of the Confucian School—faced the challenge of the West, did they use "a comprehensive theory" to undertake self-adjustment? Michel Foucault raised a query about the role of totalitarian discourse in saying: "At the beginning of any research I expressed a query about these long-established ‘unified’ models. Traditionally, according to these ‘unified’ models we differentiate infinite, repetitive and fecund territories within the discourse. Must we necessarily, on these ‘unities’ which actually are not unities, pile up yet another even more obscure and even more controversial ‘unitary’ model?". (shrink)

Call a set A n-correctable if every set Turing reducible to A via a Turing machine that on any input makes at most n queries is Turing reducible to A via a Turing machine that on any input makes at most n-queries and on any input halts no matter what answers are given to its queries. We show that if a c.e. set A is n-correctable for some n ≥ 2, then it is n-correctable for all n. We show that (...) this is the optimal such result by constructing a c.e. set that is 1-correctable but not 2-correctable. The former result is obtained by examining the logical closure properties of c.e. sets that are 2-correctable. (shrink)

It is commonly assumed that personalization technologies used by Google for the purpose of tailoring search results for individual users create filter bubbles, which reinforce users’ political views. Surprisingly, empirical evidence for a personalization-induced filter bubble has not been forthcoming. Here, we investigate whether filter bubbles may result instead from a searcher’s choice of search queries. In the first experiment, participants rated the left-right leaning of 48 queries (search strings), 6 for each of 8 topics (abortion, benefits, climate change, sex (...) equality, immigration, nuclear family, Islam, and taxation). An independent sample of participants were then asked to select one of these queries for each of the 8 topics. With the exception of the topic of Islam, participants were significantly more likely to select a query corresponding to their own political leaning, compared to other queries, explaining between 12% and 39% of the variance. A second experiment investigated the effect of the political leaning of the same queries on the overall political leaning of Search Engine Result Pages (SERPs) in Google Search. The top six results of each SERP were rated collectively by a third group of participants, explaining 36.3% of the variance across all 48 search terms (p < .00001). That is, (1) participants in our experiments tended to select own-side search queries, and (2) using those queries tended to yield own-side search results when using the Google search engine. Our results are consistent with the notion of a self-imposed filter bubble in which query selection plays a salient role. (shrink)

Equipped with the ultimate query answering system, computers would finally be in a position to address all our information needs in a natural way. In this paper, we describe how Language and Computing nv (L&C), a developer of ontology-based natural language understanding systems for the healthcare domain, is working towards the ultimate Question Answering (QA) System for healthcare workers. L&C’s company strategy in this area is to design in a step-by-step fashion the essential components of such a system, each (...) component being designed to solve some one part of the total problem and at the same time reflect well-defined needs on the prat of our customers. We compare our strategy with the research roadmap proposed by the Question Answering Committee of the National Institute of Standards and Technology (NIST), paying special attention to the role of ontology. (shrink)

This paper addresses the problem of querying several databases considered as a whole. Assuming that the different databases share a common data description language, the problem that arises is to consistently answer queries even if the database contents are contradictory. The main contribution of this paper is the specification of a query-evaluator for answering closed and open general queries addressed to several databases and for providing explanations about the results. For doing so, we first specify a query-evaluator, in (...) logic, which assumes that the databases are propositional ones and do not contain disjunctions. Then we extend it to first-order databases defined by an extensional part and an intensional part. We also show that the query-evaluator corresponds to a majority merging of the databases. (shrink)

To solve the highly counterintuitive paradox of confirmation represented by the statement, “A pair of red shoes confirms that all ravens are black,” Hempel employed a strategy that retained the equivalence condition but abandoned Nicod’s irrelevance condition. However, his use of the equivalence condition is fairly ad hoc, raising doubts about its applicability to this problem. Furthermore, applying the irrelevance condition from Nicod’s criterion does not necessarily lead to paradoxes, nor does discarding it prevent the emergence of paradoxes. Hempel’s approach (...) fails to adequately resolve the paradox. (shrink)

Kurt Godel’s “Incompleteness Theorem” is generally seen as one of the three main achievements of modern logic in philosophy. However, in this article, three fundamental flaws in the theorem will be exposed about its concept, judgment and reasoning parts by analyzing the setting of the theorem, the process of demonstration and the extension of its conclusions. Thus through the analysis of the essence significance of the theorem, I think the theorem should be classified as "liar paradox" or something like that. (...) Therefore, the theorem is not reliable and then the content of the theorem itself is questionable. At the same time, please note, the root of the problem exposed in Godel's “Incompleteness Theorem” is a typical example o f existing loopholes in traditional logic. (shrink)

in evolutionary theorizing,, marilyn fischer carefully unpacks and analyzes the language in Democracy and Social Ethics, looking at both the final published text as well as Addams's earlier essays and talks that were eventually incorporated into the book. By researching authors that Addams either quotes or relied on, Fischer is able to excavate many layers of historical intellectual meaning and, in doing so, gives us a different picture of Addams than the one I'm familiar with. It's not a picture of (...) Addams that is always flattering. Fischer's unpacking of these early texts shines a light on the sometimes-racist evolutionary thinking of that time. She is doing, as she says, a "close textual analysis" within the... (shrink)

In this paper I ask whether either theology or religious practice actually contribute to ethical theory or ethical practice. I rehearse well-known Humean arguments that they do not. I then reflect on the idea from Professor O’Donovan’s paper that it is virtuous for us to entertain hopes for redemption or for fulfilment and suggest that a careful weighing of these words may indicate otherwise.

3 Please specify whether it is Meaney (2001a or 2001b) throughout the article. 4 Please provide location of the publisher for reference Ariew (2006). 5 Please update the following reference: Griffiths et al. (submitted); Jones..

Around 1950, B.A. Trakhtenbrot proved an important undecidability result (known, by a pure accident, as \Trakhtenbrot's theorem"): there is no algorithm to decide, given a rst-order sentence, whether the sentence is satis able in some nite model. The result is in fact true even if we restrict ourselves to languages that has only one binary relation Tra63]. It is hardly conceivable that at that time Prof. Trakhtenbrot expected his result to in uence the development of the theory of relational databases (...) query languages, but it did. This perhaps is not surprising in view of the following two facts: 1) The theory of relational databases is strongly rooted in logic and can easily be abstracted to make it a branch of mathematical logic. 2) The main interest in the theory of relational databases is in nite relations. In the rst section we explain those two points in more detail. Then, in section 2 of the present paper, we discuss the question: \What constitutes a reasonable query to a database?" The discussion naturally leads to a certain class of queries, known as the \domain independent" queries, as an ideal query language. At this point Trakhtenbrot's theorem appears as a major obstacle, since it easily implies that this ideal class is undecidable. Real query languages cannot be allowed to have this property. Section 3 outlines then several possible ways to circumvent this di culty. The following section explains the.. (shrink)

I aim to develop a tool for comparing theories of vagueness, using Structured Query Language. Relevant SQL snippets will be used throughout.