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ϵ-Semantics computations on biological systems

A. Casagrande, T. Dreossi, J. Fabriková, C. Piazza
2014 Information and Computation  
This paper extends the classical reachability algorithm based on these semantics.  ...  Moreover, it reduces the computation of two specific -semantics to the decidability of a first-order theory and suggests how to decrease the complexity of the involved formulae.  ...  These optimizations will be exploited in the analysis of two real biological cases, demonstrating the fact the -semantics represent a valid tool in the the study of biological systems.  ... 
doi:10.1016/j.ic.2014.01.011 fatcat:lrvms3ieqrdlfkswsgbknshywq

A conversation with Professor Jianzhong Li

Jianzhong Li
2012 SIGKDD Explorations  
IEEE Transactions on Parallel and Distributed Systems, Parallel and Distributed Database, SIGMOD, VLDB, ICDE, INFOCOM, ICDCS.  ...  His current research interests include database management systems, data warehousing, data mining, and wireless sensor networks.  ...  uncertain graph data under the expected semantics based on expected support.  ... 
doi:10.1145/2207243.2207258 fatcat:xflqiph5o5bnxaybhs22sfdy3i

Hybrid Automata and ε-Analysis on a Neural Oscillator

Alberto Casagrande, Tommaso Dreossi, Carla Piazza
2012 Electronic Proceedings in Theoretical Computer Science  
Finally, we focus on approximations via epsilon-semantics, proving how these can be computed in practice.  ...  Our construction points out that in this case the standard techniques, based on replacing sigmoids with step functions, is not satisfactory.  ...  As noticed in [3] , especially in the study of biological systems, such ability may result misleading.  ... 
doi:10.4204/eptcs.92.5 fatcat:q2pjw65trnfrzlc3xgy2jq4fha

UTP and Sustainability [chapter]

Yifeng Chen, Jeff W. Sanders
2010 Lecture Notes in Computer Science  
University development projects, which complement the curriculum development projects by aiming to strengthen all aspects of computer science teaching in universities in developing countries, 5.  ...  To do so it analyses the nature of UTP, focusing primarily on unification, and makes suggestions to expand its use.  ...  • machine learning • quantum computation • game-theoretic semantics • hardware systemsbiologically-inspired systems.  ... 
doi:10.1007/978-3-642-16690-7_2 fatcat:2rls3o2y7fhwjdueirysdh4nvy

Bisimulations in calculi modelling membranes

Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Angelo Troina
2008 Formal Aspects of Computing  
In this paper we show how semantics based on labelled transition systems and bisimulations can be defined for two formalisms for the description of biological systems, both capable of describing membrane  ...  Bisimulations are well-established behavioural equivalences that are widely used to study properties of computer science systems.  ...  Acknowledgments This research has been partially supported by MiUR PRIN 2006 Project "Biologically Inspired Systems and Calculi and their Applications (BISCA)".  ... 
doi:10.1007/s00165-008-0071-x fatcat:5yrobr5vhjb3vdd2ayofly2roi

On attribute context free grammar derived from Brix2 database to describe protein's fragment assembly

Prof. Dr. Nabeel Hashem Kaghed
2013 IOSR Journal of Engineering  
) and facilitate handling it in terms of (addition, deletion, and modification), and be a solid basis to any current or future method to deal with folding proteins in dry lab(computational methods).  ...  Building blocks to secondary structure elements is founded by data mining method, these rules were given in format of formal language grammar in order to increase the ability to understand these steps (semantic  ...  Also, someone can said that the ACF-Grammar it a good describing method and can be implemented on complex biological systems like protein folding process.  ... 
doi:10.9790/3021-031224651 fatcat:vqhxdaf22vadpcwvb6vc7hbxhm

Delayed Continuous-Time Markov Chains for Genetic Regulatory Circuits [chapter]

Călin C. Guet, Ashutosh Gupta, Thomas A. Henzinger, Maria Mateescu, Ali Sezgin
2012 Lecture Notes in Computer Science  
We use our formalism to model genetic regulatory circuits (biological systems where delayed events are common) and report on the results of our numerical algorithm as run on a cluster.  ...  Our algorithm effectively decomposes the computation into two stages: a pure CTMC governs event initiations while a deterministic process guarantees lower bounds on event completion times.  ...  Consequently, the observed behavior of the system is crucially dependent on the presence of delays, a well known phenomenon in biological systems [5, 9, 11] .  ... 
doi:10.1007/978-3-642-31424-7_24 fatcat:sp3wwho55rbxxbvsroiw43z7wq

The energy cost of protein messages lead to a new protein information law [article]

Robersy Sanchez, Ricardo Grau
2005 arXiv   pre-print
considering the energy cost of messages carried by proteins as proportional to their information content we found experimental proof that proteins from all living organisms tend to have their estimated semantic  ...  Our results suggest the existence of a continuous optimization process that living organisms had to face, in which a compromise between biological functionality, economic feasibility and the survival requirements  ...  The semantic content of protein message is estimated on a new point of view of the genetic information system as a Boolean information system.  ... 
arXiv:q-bio/0512025v1 fatcat:toi42cosmjaljfyze3k7roz7re

A Type System for Required/Excluded Elements in CLS

Mariangiola Dezani-Ciancaglini, Paola Giannini, Angelo Troina
2009 Electronic Proceedings in Theoretical Computer Science  
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules.  ...  As an example, we model a toy system where the repellency of a certain element is captured by our type system and forbids another element to exit a compartment.  ...  This has become one of the main motivations for the application of Computer Science formalisms to the description of biological systems [15] .  ... 
doi:10.4204/eptcs.9.5 fatcat:r6tj2itb6vb2zcf2j3pdu7wvo4

Typed stochastic semantics for the calculus of looping sequences

Livio Bioglio, Mariangiola Dezani-Ciancaglini, Paola Giannini, Angelo Troina
2012 Theoretical Computer Science  
In this paper, we propose an operational semantics for this calculus that considers the types of the species to derive the stochastic evolution of the system.  ...  The stochastic calculus of looping sequences is a quantitative term rewrite formalism suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities  ...  P-Systems [29] are a biologically inspired computational model. Later on, through the introduction of ad-hoc features, they have been applied to describe and analyse biological systems [30, 31] .  ... 
doi:10.1016/j.tcs.2011.12.062 fatcat:eitl3vp7wranbobx6tgvcnn7ly

Integrating and Ranking Uncertain Scientific Data

Landon Detwiler, Wolfgang Gatterbauer, Brent Louie, Dan Suciu, Peter Tarczy-Hornoch
2009 Proceedings / International Conference on Data Engineering  
The BioRank project investigates formalisms for modeling uncertainties of scientific data in a mediator-based data integration system.  ...  Much can be learned in biology by integrating known information with biological similarity functions and confidence values of experimental results.  ...  The fact that our system can evaluate probabilistic queries of a possible world semantics, however, in considerably less than a 100 msec and within 1-2 orders of magnitude of deterministic ones, is a positive  ... 
doi:10.1109/icde.2009.209 dblp:conf/icde/DetwilerGLST09 fatcat:lvx3uur4dbc3lnlichykzs2iva

A Type System for a Stochastic CLS

Mariangiola Dezani-Ciancaglini, Paola Giannini, Angelo Troina
2009 Electronic Proceedings in Theoretical Computer Science  
We propose a type system for this calculus that models how the presence of positive and negative catalysers can modify these speeds.  ...  The Stochastic Calculus of Looping Sequences is suitable to describe the evolution of microbiological systems, taking into account the speed of the described activities.  ...  Others, such as P-Systems [21] , have been proposed as biologically inspired computational models and have been later applied to the description of biological systems.  ... 
doi:10.4204/eptcs.11.6 fatcat:u5jlhbibybfubpbnb7nezvccd4

SNPranker 2.0: a gene-centric data mining tool for diseases associated SNP prioritization in GWAS

Ivan Merelli, Andrea Calabria, Paolo Cozzi, Federica Viti, Ettore Mosca, Luciano Milanesi
2013 BMC Bioinformatics  
and (3) on the SNP scoring function, which computes SNP scores using parameters and weights set by users.  ...  This system can be employed to design custom genotyping chips for disease-oriented studies and to re-score GWAS results.  ...  The fitness is calculated first by filtering scores with a threshold T ε defined as T ε = εσ i (w) (3) where ε is computed with steps of 0.1 starting from 0.1 to 1.0 and then by evaluating the sensitivity  ... 
doi:10.1186/1471-2105-14-s1-s9 pmid:23369106 pmcid:PMC3548692 fatcat:kfxzfdreeffupehj6b4otwaalq

Spatial Calculus of Looping Sequences

Roberto Barbuti, Andrea Maggiolo–Schettini, Paolo Milazzo, Giovanni Pardini
2009 Electronical Notes in Theoretical Computer Science  
It is based on term rewriting, hence a CLS model is composed of a term, which describes the biological system, and a set of rewrite rules, modeling its evolution.  ...  Other approaches dealing with spatial aspects, that have been used for describing biological systems, include cellular automata [31] [32] [33] , and models based on differential equations, such as those  ...  A cellular automaton is a discrete dynamical system and a computational formalism based on a finite grid of ''cells'' (no relation with biological cells), where cells can be in one of a finite set of different  ... 
doi:10.1016/j.entcs.2009.02.003 fatcat:qmaaodbokfa7hh3uyiizqdoxba

Spatial Calculus of Looping Sequences

Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini
2011 Theoretical Computer Science  
It is based on term rewriting, hence a CLS model is composed of a term, which describes the biological system, and a set of rewrite rules, modeling its evolution.  ...  Other approaches dealing with spatial aspects, that have been used for describing biological systems, include cellular automata [31] [32] [33] , and models based on differential equations, such as those  ...  A cellular automaton is a discrete dynamical system and a computational formalism based on a finite grid of ''cells'' (no relation with biological cells), where cells can be in one of a finite set of different  ... 
doi:10.1016/j.tcs.2011.01.020 fatcat:pv3avqb5yncovfybqacz2ctysi
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