12 papers · ranked by Valyu relevance
Xin Sun, Piotr Kulicki, Mirek Sopek, Peter Harremoës
This paper investigates the usage of logic and logic programming in the design of smart contracts. Our starting point is the logic-based programming language for smart contracts used in a recently proposed framework of quantum-secured blockchain, called Logicontract (LC). We then extend the logic used in LC by answer…
Alexandre Lemos, Inês Lynce, Pedro T. Monteiro
Background Boolean models of biological signalling-regulatory networks are increasingly used to formally describe and understand complex biological processes. These models may become inconsistent as new data become available and need to be repaired. In the past, the focus has been shed on the inference of (classes of)…
Günther Charwat, Wolfgang Dvořák, Sarah A. Gaggl, Johannes P. Wallner + 1 more
'Johannes P. Wallner' 'Stefan Woltran'] Within the last decade, abstract argumentation has emerged as a central field in Artificial Intelligence. Besides providing a core formalism for many advanced argumentation systems, abstract argumentation has also served to capture several non-monotonic logics and other AI…
Nico M. Franz, Chao Zhang, Joohyung Lee
We utilize an Answer Set Programming (ASP) approach to show that the principles of nomenclature are tractable in computational logic. To this end we design a hypothetical, 20 nomenclatural taxon use case with starting conditions that embody several overarching principles of the International Code of Zoological…
Louis Fippo Fitime, Olivier Roux, Carito Guziolowski, Loïc Paulevé
Background Numerous cellular differentiation processes can be captured using discrete qualitative models of biological regulatory networks. These models describe the temporal evolution of the state of the network subject to different competing transitions, potentially leading the system to different attractors. This…
Torsten Gross, Matthew Wongchenko, Yibing Yan, Nils Blüthgen
A major challenge in molecular and cellular biology is to map out the regulatory networks of cells. As regulatory interactions can typically not be directly observed experimentally, various computational methods have been proposed to disentangling direct and indirect effects. Most of these rely on assumptions that are…
Rémi Segretain, Sergiu Ivanov, Laurent Trilling, Nicolas Glade
Formal interaction networks are well suited for representing complex biological systems and have been used to model signalling pathways, gene regulatory networks, interaction within ecosystems, etc. In this paper, we introduce Sign Boolean Networks (SBNs), which are a uniform variant of Threshold Boolean Networks…
Carito Guziolowski, Santiago Videla, Federica Eduati, Sven Thiele + 3 more
'Thomas Cokelaer' 'Anne Siegel' 'Julio Saez-Rodriguez'] Vol. 29, No. 18, 2013, pp. 2320-2326 doi:10.1093/bioinformatics/btt393 The authors would like to note that the joint corresponding authors of btt393 Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming are Drs’ Anne…
Jing Xie, Qi Duan
Biological pathway analysis often requires identifying interventions that block reachability to an undesirable state, such as a disease-associated module, toxic byproduct, or adverse phenotype, while preserving reachability among essential biological functions. Motivated by this setting, we study the Reachability…
Bryan Glazer, Jonathan Lifferth, Carlos F. Lopez
Many important processes in biology, such as signaling and gene regulation, can be described using logic models. These logic models are typically built to behaviorally emulate experimentally observed phenotypes, which are assumed to be steady states of a biological system. Most models are built by hand and therefore…
Zhongtao Xie, Yisong Wang, Lei Yang, Renyan Feng
Circumscription is an important logic framework for representing and reasoning common-sense knowledge. With efficient implementations for circumscription, including circ2dlp and aspino, it has been widely used in model-based diagnosis and other domains. We propose a notion of minimal reduct for propositional…
Brian Hie, Salvatore Candido, Zeming Lin, Ori Kabeli + 4 more
Combining a basic set of building blocks into more complex forms is a universal design principle. Most protein designs have proceeded from a manual bottom-up approach using parts created by nature, but top-down design of proteins is fundamentally hard due to biological complexity. We demonstrate how the modularity and…