14 papers · ranked by Valyu relevance
Hope Kean, Alexander Fung, Paris Jaggers, Jason Chen + 6 more
Humans are endowed with a powerful capacity for both inductive and deductive logical thought: we easily form generalizations based on a few examples and draw conclusions from known premises. Humans also arguably have the most sophisticated communication system in the animal kingdom: natural language allows us to…
Hope Kean, Alexander Fung, Paris Jaggers, Jason Chen + 6 more
Humans are endowed with a powerful capacity for both inductive and deductive logical thought: we easily form generalizations based on a few examples and draw conclusions from known premises. Humans also arguably have the most sophisticated communication system in the animal kingdom: natural language allows us to…
Yun-Fei Liu, Marina Bedny
Programming is a cornerstone of modern society, yet its cognitive and neural basis remains poorly understood. In this study, we test the hypothesis that programming “recycles” pre-existing neural mechanisms and representations in fronto-parietal reasoning networks. Using fMRI, we scanned programming-naïve…
Martha Takane, Saúl Bernal-González, Jesús Mauro-Moreno, Gustavo García-López + 2 more
Regulated biological networks are commonly represented as logical diagrams, in which the exact interactions between the elements remain out of sight. Here we propose a new type of excitation-inhibition graph based on Boolean logic, which we name “logical directed graph or simply, logical digraph of the biological…
Yuxiang Yao, Dong Liu, Zheting Zhang, Chengchen Zhao + 1 more
Complex biosystems exhibit ordered, functional, self-organized features. How-ever, a universal framework for exploring their logical paradigms and dynamic characteristics remains lacking. Here we describe BioLogical, a user-friendly R package, designed for analyzing properties of biosystems. We demonstrate its…
Difei Tang, Natasa Miskov-Zivanov
In computational modeling, Bounded Linear Temporal Logic (BLTL) is a valuable formalism for describing and verifying the temporal behavior of biological systems. However, translating natural language (NL) descriptions of system behaviors into accurate BLTL properties remains a labor-intensive task, requiring deep…
Arturo Tozzi
The origin of life is a complex scientific problem demanding interdisciplinary approaches. We propose a Linear Logic (LL)-based computational framework to formally evaluate the feasibility of early biochemical pathways across competing abiogenesis scenarios. Unlike classical logic, LL explicitly tracks resource…
Arturo Tozzi
T cell activation results from the integration of multiple concurrent signals, including antigen engagement through the T cell receptor (TCR), co-stimulatory cues and inhibitory modulation. While traditional computational models often rely on Boolean logic to describe immune decision-making, these binary…
Luna Xingyu Li, Yue Zhang, Boris Aguilar, Tazein Shah + 2 more
Logical gene regulatory network (GRN) models provide interpretable, mechanistic representations of cellular regulation and are widely used in systems biology. However, most existing models remain incomplete, context-specific, and difficult to extend to comprehensive GRNs, limiting their broader applicability to tasks…
Panagiotis Mougkogiannis, Andrew Adamatzky
Proteinoid are thermal proteins which swell into microspheres in aqueous solution. Ensembles of proteinoids produce electrical spiking activity similar to that of neurons. We introduce a novel method for implementing logical gates in the ensembles of proteinoid microspheres using chronoamperometry. Chronoamperometry is…
Luna Xingyu Li, Carissa Bleker, Sylvain Soliman, Laurence Calzone + 13 more
Logical models are widely used to study regulatory and signaling systems, yet their reuse, annotation, and exchange across tools remain challenging. Although SBML Level 3 Qualitative Models (SBML-qual) provides a standard representation, its XML-based syntax is difficult to inspect and edit directly. Here we introduce…
Difei Tang, Natasa Miskov-Zivanov
Translating natural language biological discoveries into formal temporal logic specifications for model verification demands expertise most experimentalists lack. Bounded Linear Temporal Logic (BLTL), which attaches explicit time bounds to temporal operators, is well suited for capturing biological dynamics. However…
Timothy J. Rudge, Gonzalo Vidal
Bio-computation is the implementation of computational operations using biological substrates, such as cells engineered with synthetic genetic circuits. These genetic circuits can be composed of DNA parts with specific functions, such as promoters that initiate transcription, ribosome binding sites that initiate…
Lucas Y. Tian, Kedar U. Garzón, Adam G. Rouse, Mark A. G. Eldridge + 4 more
At the core of intelligence is proficiency in solving new problems, including those that differ dramatically from problems seen before. Problem-solving, in turn, depends on goal-directed generation of novel thoughts and behaviors^1^, which has been proposed to rely on internal representations of discrete units, or…