Notion Of Form Research Articles

Characterizing behavioural differentiation in gene regulatory networks with representation graphs.

We introduce the formal notion of representation graphs, encapsulating the state space structure of gene regulatory network models in a compact and concise form that highlights the most significant features of stable states and differentiation processes leading to distinct stability regions. The concept has been developed in the context of a hybrid system-based gene network modelling framework; however, we anticipate that it can also be adapted to other approaches of modelling gene networks in discrete terms. We describe a practical algorithm for representation graph computation as well as two case studies demonstrating their real-world application and utility. The first case study presents models for three phage viruses. It shows that the process of differentiation into lytic and lysogenic behavioural states for all these models is described by the same representation graph despite the distinctive underlying mechanisms for differentiation. The second case study shows the advantages of our approach for modelling the process of myeloid cell differentiation from a common progenitor into different cell types. Both case studies also demonstrate the potential of the representation graph approach for deriving and validating hypotheses about regulatory interactions that must be satisfied for biologically viable behaviours.

Singularity of AI?

This article presents a series of reflections on the so-called ‘singularity’ of Artificial Intelligence (AI). It begins with a meditation on Freud’s notion of the ‘Uncanny’ to help us understand the experience of interacting with the new AI. It then critically engages the formal notion of ‘the singularity’ by returning to the classical critique of artificial computing in Hubert Dreyfus, and suggests that ‘singularity’ should be understood rather in its effects within the context of a socio-cultural phenomenon which progressively disembodies the human being. Finally, in conversation with Dominique Janicaud and Emmanuel Falque, it begins to outline the contours of an alternative ‘philosophical-theological intelligence’: characterized by ambivalence, the ‘potentiality’ of rationality, and the finitude of our human condition that Christ came to fully embody and share with us, not so that we might escape it, but ‘undergo’ it in common together.

Optimal Transport and Generalized Ricci Flow

We prove results relating the theory of optimal transport and generalized Ricci flow. We define an adapted cost functional for measures using a solution of the associated dilaton flow. This determines a formal notion of geodesics in the space of measures, and we show geodesic convexity of an associated entropy functional. Finally, we show monotonicity of the cost along the backwards heat flow, and use this to give a new proof of the monotonicity of the energy functional along generalized Ricci flow.

The Theory of Gene Family Histories.

Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.e., the precise dating of evolutionary events relative to phylogenetic tree of the underlying species has remained a challenging topic despite their importance as a basis for detailed investigations into adaptation and functional evolution of individual members of the gene family. The identification of orthologs, moreover, is a particularly important subproblem of the more general setting considered here. In the last few years, an extensive body of mathematical results has appeared that tightly links orthology, a formal notion of best matches among genes, and horizontal gene transfer. The purpose of this chapter is to broadly outline some of the key mathematical insights and to discuss their implication for practical applications. In particular, we focus on tree-free methods, i.e., methods to infer orthology or horizontal gene transfer as well as gene trees, species trees, and reconciliations between them without using a priori knowledge of the underlying trees or statistical models for the inference of phylogenetic trees. Instead, the initial step aims to extract binary relations among genes.

Better Late than Never: On Epistemic Diagnosability of Discrete Event Systems

We investigate the diagnosability verification problem in the framework of discrete-event systems. Most of the existing works on this topic assume that faults are related to the internal behaviors of the system such as occurrences of particular events. In this work, motivated by information-flow security considerations, we model faults as some critical information leakages of the system to an intruder, which may have different observations from the system user. Specifically, we say that a fault occurs if the intruder knows that the system has passed by a secret state. We present a formal notion called epistemic diagnosability to capture whether or not the system user can always detect, based on its own observation, the critical information leakage to an intruder within a bounded delay. We show that this new notion subsumes the standard notion of event-based diagnosability. Furthermore, an effective algorithm is provided to verify this new notion.

Optimal cardinal contests

We study the design of crowdsourcing contests in settings where the outputs of the contestants are quantifiable, for example, a data science challenge. This setting is in contrast to those where the output is only qualitative and cannot be objectively quantified, for example, when the goal of the contest is to design a logo. The literature on crowdsourcing contests focuses largely on ordinal contests, where contestants' outputs are ranked by the designer and awards are based on relative ranks. Such contests are ideally suited for the latter setting, where output is qualitative. For our setting (quantitative output), it is possible to design cardinal contests, where awards could be based on the actual outputs and not on their ranking alone—thus, the family of cardinal contests includes the family of ordinal contests. We study the problem of designing an optimal cardinal contest. We use mechanism design theory to derive an optimal cardinal mechanism and provide a convenient implementation—a decreasing reward‐meter mechanism—of the optimal contest. We establish the practicality of our mechanism by showing that it is “Obviously Strategy‐Proof,” a recently introduced formal notion of simplicity in the literature. We also compare the optimal cardinal contest with the most popular ordinal contest—namely, the Winner‐Takes‐All (WTA) contest, along several metrics. In particular, the optimal cardinal mechanism delivers a superior expected best output, whereas the WTA contest yields a greater expected contestant welfare. Furthermore, under a sufficiently large budget, the contest designer's expected net‐benefit is higher under the optimal cardinal mechanism than that under the WTA contest, regardless of the number of contestants in the two mechanisms. Our numerical analysis suggests that, for the contest designer, the average improvement provided by the optimal cardinal mechanism over the WTA contest is about 23%. For a given number of contestants, the benefit of the optimal cardinal mechanism is especially appreciable for projects where the ratio of the designer's utility to agents' cost‐of‐effort falls within a wide practical range. For projects where this ratio is very high, the expected profit of the best WTA contest is reasonably close to that of the optimal cardinal mechanism.

Are Large Cardinal Axioms Restrictive?

Abstract The independence phenomenon in set theory, while pervasive, can be partially addressed through the use of large cardinal axioms. A commonly assumed idea is that large cardinal axioms are species of maximality principles. In this paper I question this claim. I show that there is a kind of maximality (namely absoluteness) on which large cardinal axioms come out as restrictive relative to a formal notion of restrictiveness. Within this framework, I argue that large cardinal axioms can still play many of their usual foundational roles.

Jeffrey imaging revisited

Abstract In ‘The logic of partial supposition’ (Analysis vol. 81), Benjamin Eva and Stephan Hartmann investigate partial imaging, a credence-revision method which combines the partiality familiar from Jeffrey Conditioning(The Logic of Decision, 1983) with the formal notion of imaging familiar from Lewis’s ‘Causal decision theory’ (1981). They argue that because partial imaging is non-monotonic, it ‘fail[s] to provide a plausible account of the norms of partial subjunctive suppositions’. In this note, I present a notion of partial imaging that does satisfy monotonicity, and discuss some of the applications and ramifications. The account frames conditioning as a form of imaging, and rejects Gärdenfors’s principle of linearity in ‘Imaging and conditionalization’ (1982).

Engaging with readers: Students’ metalinguistic understanding of the use of pronouns in building reader-writer relationships

Students’ metalinguistic understanding of the written academic argument is important both to increase writer independence and inform writing instruction. This article draws on a study which investigated undergraduate students’ metalinguistic understanding of the metadiscourse features in their own written arguments. The specific focus of the paper is to determine what metalinguistic understanding students express about the use of pronouns in written argument as engagement or stance markers to build a relationship with the reader. The analysis indicates many students believed the use of reader pronouns were inappropriate in written argument, often because this was what they had been taught. Students’ metalinguistic understanding was shaped more by notions of formality and objectivity than by understanding of how pronouns play a role in reader engagement. The article argues that greater emphasis on the function of pronouns rather than the form, drawing on metadiscourse theory, and on generating metalinguistic understanding of the differing ways that pronouns function in written argument might better support writers in agentic linguistic decision-making.

The Privilege of Art

The Privilege of Art

CONDITIONALITY OF NOTION “COMPLEXITY” IN TERMINOLOGY OF CONTEMPORARY ARCHITECTURAL FORM-GENERATION

Problem statement. As a starting point, the article takes the need for constant revision of basic architectural categories and notions, caused by events associated with the emergence in the 1990s − digital non-linear architecture. As the culmination of the postmodern period, digital architecture continues to enrich its paradigm with a focus on complexity of architectural forms. However, based on the current complexity sciences achievements, digital architecture takes complexity with understanding not encountered previously in architectural design theory. The equivocality of notion definition of «complexity» is accepted as a research problem. The purpose of the article. The purpose of the research is to define notion of «complexity» in the context of contemporary architectural form-generation. Methods. The method of semantic analysis was chosen as the main one. Conclusion. The relationship between the notions of form and complexity is revealed, based on a historical analysis of the notion definitions of «form». The term definition of «architectural form» is given through the connection of form and content, that reviles the key aspects of contemporary architectural form content. Changes in the content of notion definitions of «complexity» are analyzed from the design methodology standpoint and general scientific methods. The meaning of complexity is revealed at three levels of form perception: morphological, symbolic and phenomenological levels. The conditionality of necessity and emergence causes of complexity in contemporary architectural forms as a result of changes in the society value orientations is considered. Examples of the gradual implementation of principles and the influence of complexity science upon the architecture theory are given. Taking into account the considered features of complexity understanding and ideas about complex objects taken from complexity theories, a notion definition that does not cause difficulties in application of «complexity» is formulated. Conclusions with nuances of application and characteristics of the obtained definition are given. The possibilities for the further implementation of relevant systemic ideas about city and urban environment that capable to introduce architecture to a new scientific world picture are determined.

Philosophie der Bionik: Das Komponieren von bio-robotischen Formen

AbstractIn this paper, I explore how bio-hybrid forms can be created and combined starting from organic forms. The thesis put forward is epistemological: the combinatorial practice of bionics, biomimetics, biorobotics, and all design strategies inspired by nature is not based on a kind of biomimetic inspiration, i. e., on a kind of imitation of nature, but on a practice of translation.To develop this thesis, I focus on the practices of contemporary biorobotics, first examining the practice of translating natural forms into technical artefacts as developed by Raoul Heinrich Francé at the beginning of the 20th century, secondly, analysing the production of robots capable of replicating complex locomotion systems and, finally, investigating the interaction between robots and living organisms (fish). In the last part of the paper, I reflect on the philosophical payoff and broader conditions of possibility for this translational practice. I discuss when and to what extent a translation of biological forms into biotechnical ones is acceptable and point out the notion of form that underlies this practice. Moreover, I draw attention to the need to philosophically investigate what happens between different domains of knowledge – and especially between science and technology. This article is thus an invitation to philosophers to develop a philosophy in the interstices of knowledge production.

The Toral Rank Conjecture and variants of equivariant formality

An action of a compact Lie group is called equivariantly formal, if the Leray–Serre spectral sequence of its Borel fibration degenerates at the E2-term. This term is as prominent as it is restrictive.In this article, also motivated by the lack of junction between the notion of equivariant formality and the concept of formality of spaces (surging from rational homotopy theory) we suggest two new variations of equivariant formality: “MOD-formal actions” and “actions of formal core”.We investigate and characterize these new terms in many different ways involving various tools from rational homotopy theory, Hirsch–Brown models, A∞-algebras, etc., and, in particular, we provide different applications ranging from actions on symplectic manifolds and rationally elliptic spaces to manifolds of non-negative sectional curvature.A major motivation for the new definitions was that an almost free action of a torus Tn↷X possessing any of the two new properties satisfies the toral rank conjecture, i.e. dim⁡H⁎(X;Q)≥2n. This generalizes and proves the toral rank conjecture for actions with formal orbit spaces.

Introduction to Brian H. Bix, Svein Eng, and Giorgio Ridolfi on Alf Ross

Introduction to Brian H. Bix, Svein Eng, and Giorgio Ridolfi on Alf Ross

Going round in squares: Theory-based measurement requires a theory of measurement

In their article on theory-based measurement, Borgstede and Eggert (2023) argue that a substantive formal psychological theory that is capable of predicting expected measurement outcomes for the theoretical objects of measurement it posits to exist is both necessary and sufficient for psychological measurement. They reveal that measurement in psychology mostly concerns the estimation of latent variables and compares unfavorably to the development of measurement in the history of physics. They, however, fail to include a comparison with the great advances in theory-based measurement achieved in modern physics. In this commentary, I describe how measurement is formalized in classical physics and examine what would be required to formalize the physical measurement of psychological phenomena. I conclude that, without an examination of the theoretical assumptions underlying current measurement procedures and a formal notion of psychological measurement, it is unlikely that psychological science will be able to generate the substantive theories suggested by Borgstede and Eggert.

A comprehensive account of the burden of persuasion in abstract argumentation

AbstractIn this paper, we provide a formal framework for modeling the burden of persuasion in legal reasoning. The framework is based on abstract argumentation, a frequently studied method of non-monotonic reasoning, and can be applied to different argumentation semantics; it supports burdens of persuasion with arbitrary many levels, and allows for the placement of a burden of persuasion on any subset of an argumentation framework’s arguments. Our framework can be considered an extension of related works that raise questions on how burdens of persuasion should be handled in some conflict scenarios that can be modeled with abstract argumentation. An open source software implementation of the introduced formal notions is available as an extension of an argumentation reasoning library. A theoretical analysis shows that our approach can be generalized to a novel method for the preference-based selection of extensions from argumentation frameworks.

Afasias e construção de sentido: estudo com foco em história em quadrinhos

ABSTRACT Purpose to observe , in the language of aphasic adult subjects, the constitution of meanings, considering the enunciative (re)organization in reading and writing. Methods qualitative research with applied and exploratory methods and a perspective of enunciative analysis on language, using the notions of form and meaning as analytical base. From an activity performed by three subjects with aphasia (Bir, Cr and Aul), members of the Interdisciplinary Coexistence Group (GIC), formed by participants with and without aphasia, which constituted of (re)organizing the panels (frames) of a comic strip, in order to constitute meaning - since the reading/writing of texts are skills that are commonly affected in aphasia. Results the chronic time category shows itself to be fundamental for the elaboration of the narratives of the subjects with aphasia, however they found different ways of sustaining meanings, but always linked to experiences arising from the relationship between man and world. Conclusion the narratives were organized/constructed by the participants, having the images as a base (formal base) - since the ability to read verbal texts is impaired. Bir, Cr and Aul used chronic time as an organizational axis of their narratives and their comic strips show that these subjects with aphasia promote reading and writing when considering enunciative bias of language analysis.

Not All Computational Methods Are Effective Methods

An effective method is a computational method that might, in principle, be executed by a human. In this paper, I argue that there are methods for computing that are not effective methods. The examples I consider are taken primarily from quantum computing, but these are only meant to be illustrative of a much wider class. Quantum inference and quantum parallelism involve steps that might be implemented in multiple physical systems, but cannot be implemented, or at least not at will, by an idealised human. Recognising that not all computational methods are effective methods is important for at least two reasons. First, it is needed to correctly state the results of Turing and other founders of computation theory. Turing is sometimes said to have offered a replacement for the informal notion of an effective method with the formal notion of a Turing machine. I argue that such a view only holds under limited circumstances. Second, not distinguishing between computational methods and effective methods can lead to mistakes when quantifying over the class of all possible computational methods. Such quantification is common in philosophy of mind in the context of thought experiments that explore the limits of computational functionalism. I argue that these ‘homuncular’ thought experiments should not be treated as valid.

Investment Decisions under Almost Complete Causal Ignorance

This article investigates investment decision making under conditions of almost complete causal ignorance. Using two basic notions of causal dependence, probabilistic and counterfactual dependence, as building blocks, a formal notion of causal distance is presented that gives decision makers the ability to quantitatively assess the proximity that different causal graphs have to each other. The latter are directed acyclic graphs that can also be used to represent causal relations among economic events. Once the causal distance of each graph in a set of causal graphs is determined, it is possible to select the graph with the shortest total distance to the other graphs. This in turn allows decision makers to select a course of action that will be beneficial regardless of the particular set of causal relations that is actually driving observed economic events. The article describes how causal distance values can be used formally within an optimization to facilitate portfolio construction.

An argumentative approach for handling inconsistency in prioritized Datalog ± ontologies

Prioritized Datalog ± is a well-studied formalism for modelling ontological knowledge and data, and has a success story in many applications in the (Semantic) Web and in other domains. Since the information content on the Web is both inherently context-dependent and frequently updated, the occurrence of a logical inconsistency is often inevitable. This phenomenon has led the research community to develop various types of inconsistency-tolerant semantics over the last few decades. Although the study of query answering under inconsistency-tolerant semantics is well-understood, the problem of explaining query answering under such semantics took considerably less attention, especially in the scenario where the facts are prioritized. In this paper, we aim to fill this gap. More specifically, we use Dung’s abstract argumentation framework to address the problem of explaining inconsistency-tolerant query answering in Datalog ± KB where facts are prioritized, or preordered. We clarify the relationship between preferred repair semantics and various notions of extensions for argumentation frameworks. The strength of such argumentation-based approach is the explainability; users can more easily understand why different points of views are conflicting and why the query answer is entailed (or not) under different semantics. To this end we introduce the formal notion of a dialogical explanation, and show how it can be used to both explain showing why query results hold and not hold according to the known semantics in inconsistent Datalog ± knowledge bases.