1,721,072 research outputs found
Systems Biology: Models and Logics
No full textThe field of system biology focuses on creating a finely detailed picture of biological mechanisms. Recently, the need has arisen for more and more sophisticated and mathematically well founded computational tools capable of analyzing the models that are and will be at the core of system biology. Such computational models should be implemented in software packages faithfully while exploiting the potential trade-offs among usability, accuracy, and scalability dealing with large amounts of data. The aim of this talk is that of introducing some emerging problems and proposed solutions in this context
Is Hyper-extensionality Preservable Under Deletions of Graph Elements?
Full text linkAny hereditarily finite set S can be represented as a finite pointed graph –dubbed membership graph– whose nodes denote elements of the transitive closure of {S} and whose edges model the membership relation. Membership graphs must be hyper-extensional, that is pairwise distinct nodes are not bisimilar and (uniquely) represent hereditarily finite sets.
We will see that the removal of even a single node or edge from a membership graph can cause “collapses” of different nodes and, therefore, the loss of hyper-extensionality of the graph itself. With the intent of gaining a deeper understanding on the class of hyper-extensional hereditarily finite sets, this paper investigates whether pointed hyper-extensional graphs always contain either a node or an edge whose removal does not disrupt the hyper-extensionality property
The Subgraph Bisimulation Problem
No full textWe study the complexity of the Subgraph Bisimulation Problem, which relates to Graph Bisimulation as Subgraph Isomorphism relates to Graph Isomorphism, and we prove its NP-Completeness. Our analysis is motivated by its applications to semistructured databases
Unwinding biological systems
Full text linkUnwinding conditions have been fruitfully exploited in Information Flow Security to define persistent security properties. In this paper we investigate their meaning and possible uses in the analysis of biological systems. In particular, we elaborate on the notion of robustness and propose some instances of unwinding over the process algebra Bio-PEPA and over hybrid automata. We exploit such instances to analyse two case-studies: Neurospora crassa circadian system and Influenza kinetics models. © 2015 Elsevier B.V
Rank and simulation: the well-founded case
Full text linkWe consider the algorithmic problem of computing the maximal simulation preorder (and quotient) on acyclic labelled graphs. The acyclicity allows to exploit an inner structure on the set of nodes, that can be processed in stages according to a set-theoretic notion of rank. This idea, previously used for bisimulation computation, on the one hand improves on the performances of the ensuing procedure and, on the other hand, gives to the solution an orderly iterative flavour making the algorithmic idea more explicit. The computational complexity achieved is good as we obtain the best performing algorithm for simulation computation on acyclic graphs, in both time and space. © The Author, 2013. Published by Oxford University Press. All rights reserved
- …
