Set-Theoretic Formalism for Treating Ligand-Target Datasets

Data on ligand–target (LT) interactions has played a growing role in drug research for several decades. Even though the amount of data has grown significantly in size and coverage during this period, most datasets remain difficult to analyze because of their extreme sparsity, as there is no activity data whatsoever for many LT pairs. Even within clusters of data there tends to be a lack of data completeness, making the analysis of LT datasets problematic. The current effort extends earlier works on the development of set-theoretic formalisms for treating thresholded LT datasets. Unlike many approaches that do not address pairs of unknown interaction, the current work specifically takes account of their presence in addition to that of active and inactive pairs. Because a given LT pair can be in any one of three states, the binary logic of classical set-theoretic methods does not strictly apply. The current work develops a formalism, based on ternary set-theoretic relations, for treating thresholded LT datasets. It also describes an extension of the concept of data completeness, which is typically applied to sets of ligands and targets, to the local data completeness of individual ligands and targets. The set-theoretic formalism is applied to the analysis of simple and joint polypharmacologies based on LT activity profiles, and it is shown that null pairs provide a means for determining bounds to these values. The methodology is applied to a dataset of protein kinase inhibitors as an illustration of the method. Although not dealt with here, work is currently underway on a more refined treatment of activity values that is based on increasing the number of activity classes.

Application three-valued logic in symmetric block encryption algorithms

The issues of limiting the use of binary logic for the further development of science engineering are discussed. The effectiveness of the use of the ternary number system at this stage in the development of information technologies is substantiated and shown. A method is proposed for increasing the informational entropy of plaintext by adding random data using ternary logic in the process of symmetric encryption. To reliably hide the added random data, the first transforming function is proposed to choose gamming with a key.

Fantasmorphoses and Hybrid Becomings of Identities

Deleuze and Guattari crafted the concept of “becoming” as a way of theorizing the rampant chimerization and polymorphism of identities in today's world. They used Kafka's work to show how the frequent use of metamorphosis in his stories prefigures this widespread phenomenon of hybridization of identities. The frequency of such hybrid becomings raises questions about the very foundations of modernity's subjective construct. Does this proliferation reflect new configurations of desiring activities, or is it the result of early interference in what Melanie Klein conceptualized as “primary confusion”? The author will use Klein's notion to show how, early in life, envy of the breast and primary confusion can blur the organization of binary logic essential to establishing the ability to judge and the activity of primal symbolization.

Catatan Awal tentang Logika Sentensial dan implikasinya dalam diskusi Manunggaling Kawula Gusti dan Trinitas

AbstrakDalam catatan awal ini kami mengajukan argumen bahwa konsep logikasentensial memuat kemungkinan betweenness/neitherness/ bothness yang tidakdikenal dalam logika biner Aristotelian. Kami mengusulkan bahwa konsep logikasentensial akan berguna untuk menjembatani dialog antara pendukung nondualisme seperti mistisisme kaum sufi dan para pendukung mazhab dualisme.Dalam konteks ini, kekristenan menawarkan kerangka berpikir bahwa hanyaYesuslah satu-satunya Sang Manunggaling Kawula Gusti yang sejati, sementarakita sebagai manusia dapat berperan sekaligus sebagai makhluk yang berbedadengan Sang Gusti, namun pada saat yang sama, umat percaya menyatu denganTuhan, meski bukan dengan konsep manunggalnya para sufi. Artinya, logikasentensial/ proposisional memungkinkan kita memahami bahwa manusiaserempak disatukan dengan Sang Khalik, namun pada saat yang sama tetapberbeda dengan Sang Khalik. Artinya non-dualisme dan dualisme pada saat yangsama. Tentunya diperlukan kajian yang lebih mendalam mengenai topik ini, yangakan kami tuliskan dalam artikel lain kemudian. AbstractIn this introductory exploration, we argue that the concept of sentential logiccontains a possibility of betweenness / neitherness / bothness unknown toAristotelian binary logic. We propose that the concept of sentential logic will beuseful for bridging the dialogue between supporters of non-dualism such as themysticism of the Sufis and the supporters of the dualism schools. In this context,Christianity offers a framework of thinking that only Jesus is the trueManunggaling Kawula Gusti, while we humans can simultaneously act ascreatures that are different from the Gusti (God), but at the same time, believersare one with God, although not the same with the concept of divine unity of theSufis. That is, sentential / propositional logic makes it possible that humans aresimultaneously united with the Creator, but at the same time remain differentfrom the Creator. It means non-dualism and dualism at the same time. For sure, amore in-depth exploration is required, and we plan to present it in another article.

Localization of Light in Photonics Lattices for All-Optical Representation of Binaries

In this paper we present a novel conceptual method for all optical representation of binary numbers that could be used for all-optical binary logic components in optical digital computing, as well as for other applications. The new concept is based on effect of localization of light in specially designed binary photonics lattices whose central parts resemble the represented binaries, and the localizations occur due to breaking periodicities of the lattices. The proposed structures can be made with integrated photonics on-chip that are highly programmable and controllable. Most significantly, the working principle of the novel method doesn’t require nonlinear interaction between light and material, which is the most serious obstacle in the conventional method that uses optical transistors whose mechanism relies mainly on optical nonlinearity. We will discuss some technical challenges in developing the components.

Physics is Organized Around Transformations Connecting Contextures in a Polycontextural World

The rich body of physical theories defines the foundation of our understanding of the world. Its mathematical formulation is based on classical Aristotelian (binary) logic. In the philosophy of science the ambiguities, paradoxes, and the possibility of subjective interpretations of facts have challenged binary logic, leading, among other developments, to Gotthard Günther’s theory of polycontexturality (often also termed ’transclassical logic’). Günther’s theory explains how observers with subjective perception can become aware of their own subjectivity and provides means to describe contradicting or even paradox observations in a logically sound formalism. Here we summarize the formalism behind Günther’s theory and apply it to two well-known examples from physics where different observers operate in distinct and only locally valid logical systems. Using polycontextural logic we show how the emerging awareness of these limitations of logical systems entails the design of mathematical transformations, which then become an integral part of the theory. In our view, this approach offers a novel perspective on the structure of physical theories and, at the same time, emphasizes the relevance of the theory of polycontexturality in modern sciences.

The binary logic and the socialist city

The discussion between the followers of Howard’s garden city concept and supporters of the Fordian social city concept is considered on the basis of archival documents. The discussion took place in the 1920s and ended with the administrative suppression of one of the parties, which largely determined the ways of further development of the socialist urban planning. The article expresses the thesis that the opposing concepts were not antagonists at all. The development of architecture over the next hundred years has shown that both concepts are successfully developing, complementing each other.

Mainstream Psychology And The Gender Binary: Toward An Account Of Becoming "Non-Binary"

The gender binary haunts mainstream psychology’s history of medicalizing trans and gender nonconforming people, particularly its construction of their gender identities as psychopathological and in need of treatment for violating the binary logic of normative (cis) development. Drawing on interviews with 24 participants who identified as “non-binary,” this dissertation advances: 1) a genealogical analysis of the construction, interpretation, and administration of “transgenderism” (psychology’s parlance) which elucidates the discipline’s maintenance of the gender binary through said construction, interpretation, and administration; and (2) an account of “becoming” gendered (non-binary, in this case) as an alternative to the mainstream models of gender identity development. Becoming (a) shifts from the etiological “why” to the psychosocial “how” (as in, how to go about assembling oneself as non-binary; labels and pronouns are key); (b) eschews teleology (there is no end goal with regard to embodiment); (c) privileges gender self-determination; (d) attends to intersectionality; and (e) foregrounds intersubjectivity. The participants were largely concerned with asserting the validity of their gender identities as non-binary, which are routinely dismissed and invalidated, and this dissertation works toward undoing psychology’s own invalidating practices.