The special theme of DCM 2009, co-located with ICALP 2009, concerned Computational Models From Nature, with a particular emphasis on computational models derived from physics and biology. The intention was to bring together different approaches - in a community with a strong foundational background as proffered by the ICALP attendees - to create inspirational cross-boundary exchanges, and to lead to innovative further research. Specifically DCM 2009 sought contributions in quantum computation and information, probabilistic models, chemical, biological and bio-inspired ones, including spatial models, growth models and models of self-assembly. Contributions putting to the test logical or algorithmic aspects of computing (e.g., continuous computing with dynamical systems, or solid state computing models) were also very much welcomed.
{"title":"Proceedings Fifth Workshop on Developments in Computational Models--Computational Models From Nature, DCM 2009, Rhodes, Greece, 11th July 2009","authors":"S. Cooper, V. Danos","doi":"10.4204/EPTCS.9","DOIUrl":"https://doi.org/10.4204/EPTCS.9","url":null,"abstract":"The special theme of DCM 2009, co-located with ICALP 2009, concerned Computational Models From Nature, with a particular emphasis on computational models derived from physics and biology. The intention was to bring together different approaches - in a community with a strong foundational background as proffered by the ICALP attendees - to create inspirational cross-boundary exchanges, and to lead to innovative further research. Specifically DCM 2009 sought contributions in quantum computation and information, probabilistic models, chemical, biological and bio-inspired ones, including spatial models, growth models and models of self-assembly. Contributions putting to the test logical or algorithmic aspects of computing (e.g., continuous computing with dynamical systems, or solid state computing models) were also very much welcomed.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"6 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2009-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74810449","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Random instances of constraint satisfaction problems such as k-SAT provide challenging benchmarks. If there are m constraints over n variables there is typically a large range of densities r=m/n where solutions are known to exist with probability close to one due to non-constructive arguments. However, no algorithms are known to find solutions efficiently with a non-vanishing probability at even much lower densities. This fact appears to be related to a phase transition in the set of all solutions. The goal of this extended abstract is to provide a perspective on this phenomenon, and on the computational challenge that it poses.
{"title":"Random Constraint Satisfaction Problems","authors":"A. Coja-Oghlan","doi":"10.4204/EPTCS.9.4","DOIUrl":"https://doi.org/10.4204/EPTCS.9.4","url":null,"abstract":"Random instances of constraint satisfaction problems such as k-SAT provide challenging benchmarks. If there are m constraints over n variables there is typically a large range of densities r=m/n where solutions are known to exist with probability close to one due to non-constructive arguments. However, no algorithms are known to find solutions efficiently with a non-vanishing probability at even much lower densities. This fact appears to be related to a phase transition in the set of all solutions. The goal of this extended abstract is to provide a perspective on this phenomenon, and on the computational challenge that it poses.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"5 1","pages":"32-37"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74116331","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We introduce a natural language interface for building stochastic p calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We give a formal semantics for this language and a translation algorithm into stochastic p calculus that delivers this semantics. We demonstrate the language on a model of Fcg receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic p calculus language, Microsoft Research’s SPiM, which can be used for simulation and analysis. 1 2
{"title":"An Intuitive Automated Modelling Interface for Systems Biology","authors":"Ozan Kahramanoğulları, L. Cardelli, E. Caron","doi":"10.4204/EPTCS.9.9","DOIUrl":"https://doi.org/10.4204/EPTCS.9.9","url":null,"abstract":"We introduce a natural language interface for building stochastic p calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and transformation. This language thus allows us to model biochemical systems modularly by describing their dynamics in a narrative-style language, while making amendments, refinements and extensions on the models easy. We give a formal semantics for this language and a translation algorithm into stochastic p calculus that delivers this semantics. We demonstrate the language on a model of Fcg receptor phosphorylation during phagocytosis. We provide a tool implementation of the translation into a stochastic p calculus language, Microsoft Research’s SPiM, which can be used for simulation and analysis. 1 2","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"4 1","pages":"73-86"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90324357","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and simulators for low level biochemical processes. Apart from simulation work, much of the efforts are directed to using mean field equations (equivalent to the equations of classical chemical kinetics) to address various problems (stability, robustness, sensitivity analysis, etc.). Rarely is the use of mean field equations questioned. This review will provide a brief overview of the situations when mean field equations fail and should not be used. These equations can be derived from the theory of diffusion controlled reactions, and emerge when assumption of perfect mixing is used.
{"title":"Diffusion Controlled Reactions, Fluctuation Dominated Kinetics, and Living Cell Biochemistry","authors":"Z. Konkoli","doi":"10.4204/EPTCS.9.11","DOIUrl":"https://doi.org/10.4204/EPTCS.9.11","url":null,"abstract":"In recent years considerable portion of the computer science community has focused its attention on understanding living cell biochemistry and efforts to understand such complication reaction environment have spread over wide front, ranging from systems biology approaches, through network analysis (motif identification) towards developing language and simulators for low level biochemical processes. Apart from simulation work, much of the efforts are directed to using mean field equations (equivalent to the equations of classical chemical kinetics) to address various problems (stability, robustness, sensitivity analysis, etc.). Rarely is the use of mean field equations questioned. This review will provide a brief overview of the situations when mean field equations fail and should not be used. These equations can be derived from the theory of diffusion controlled reactions, and emerge when assumption of perfect mixing is used.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"14 1","pages":"98-107"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73503845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
There are both benefits and drawbacks to creativity. In a social group it is not necessary for all members to be creative to benefit from creativity; some merely imitate or enjoy the fruits of others' creative efforts. What proportion should be creative? This paper contains a very preliminary investigation of this question carried out using a computer model of cultural evolution referred to as EVOC (for EVOlution of Culture). EVOC is composed of neural network based agents that evolve fitter ideas for actions by (1) inventing new ideas through modification of existing ones, and (2) imitating neighbors' ideas. The ideal proportion with respect to fitness of ideas occurs when thirty to forty percent of the individuals is creative. When creators are inventing 50% of iterations or less, mean fitness of actions in the society is a positive function of the ratio of creators to imitators; otherwise mean fitness of actions starts to drop when the ratio of creators to imitators exceeds approximately 30%. For all levels or creativity, the diversity of ideas in a population is positively correlated with the ratio of creative agents.
{"title":"How Creative Should Creators Be To Optimize the Evolution of Ideas? A Computational Model","authors":"S. Leijnen, L. Gabora","doi":"10.4204/EPTCS.9.12","DOIUrl":"https://doi.org/10.4204/EPTCS.9.12","url":null,"abstract":"There are both benefits and drawbacks to creativity. In a social group it is not necessary for all members to be creative to benefit from creativity; some merely imitate or enjoy the fruits of others' creative efforts. What proportion should be creative? This paper contains a very preliminary investigation of this question carried out using a computer model of cultural evolution referred to as EVOC (for EVOlution of Culture). EVOC is composed of neural network based agents that evolve fitter ideas for actions by (1) inventing new ideas through modification of existing ones, and (2) imitating neighbors' ideas. The ideal proportion with respect to fitness of ideas occurs when thirty to forty percent of the individuals is creative. When creators are inventing 50% of iterations or less, mean fitness of actions in the society is a positive function of the ratio of creators to imitators; otherwise mean fitness of actions starts to drop when the ratio of creators to imitators exceeds approximately 30%. For all levels or creativity, the diversity of ideas in a population is positively correlated with the ratio of creative agents.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"24 1","pages":"108-119"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81321290","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Recursive analysis was introduced by A. Turing [1936], A. Grzegorczyk [1955], and D. Lacombe [1955]. It is based on a discrete mechanical framework that can be used to model computation over the real numbers. In this context the computational complexity of real functions defined over compact domains has been extensively studied. However, much less have been done for other kinds of real functions. This article is divided into two main parts. The first part investigates polynomial time computability of rational functions and the role of continuity in such computation. On the one hand this is interesting for its own sake. On the other hand it provides insights into polynomial time computability of real functions for the latter, in the sense of recursive analysis, is modeled as approximations of rational computations. The main conclusion of this part is that continuity does not play any role in the efficiency of computing rational functions. The second part defines polynomial time computability of arbitrary real functions, characterizes it, and compares it with the corresponding notion over rational functions. Assuming continuity, the main conclusion is that there is a conceptual difference between polynomial time computation over the rationals and the reals manifested by the fact that there are polynomial time computable rational functions whose extensions to the reals are not polynomial time computable and vice versa.
{"title":"Characterizing Polynomial Time Computability of Rational and Real Functions","authors":"W. Gomaa","doi":"10.4204/EPTCS.9.7","DOIUrl":"https://doi.org/10.4204/EPTCS.9.7","url":null,"abstract":"Recursive analysis was introduced by A. Turing [1936], A. Grzegorczyk [1955], and D. Lacombe [1955]. It is based on a discrete mechanical framework that can be used to model computation over the real numbers. In this context the computational complexity of real functions defined over compact domains has been extensively studied. However, much less have been done for other kinds of real functions. This article is divided into two main parts. The first part investigates polynomial time computability of rational functions and the role of continuity in such computation. On the one hand this is interesting for its own sake. On the other hand it provides insights into polynomial time computability of real functions for the latter, in the sense of recursive analysis, is modeled as approximations of rational computations. The main conclusion of this part is that continuity does not play any role in the efficiency of computing rational functions. The second part defines polynomial time computability of arbitrary real functions, characterizes it, and compares it with the corresponding notion over rational functions. Assuming continuity, the main conclusion is that there is a conceptual difference between polynomial time computation over the rationals and the reals manifested by the fact that there are polynomial time computable rational functions whose extensions to the reals are not polynomial time computable and vice versa.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"129 1","pages":"54-64"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75690471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a characterization of the class of circular languages generated by circular splicing systems is still an open problem. In this paper we solve this problem for complete systems, which are special finite circular splicing systems. We show that a circular language L is generated by a complete system if and only if the set Lin(L) of all words corresponding to L is a pure unitary language generated by a set closed under the conjugacy relation. The class of pure unitary languages was introduced by A. Ehrenfeucht, D. Haussler, G. Rozenberg in 1983, as a subclass of the class of context-free languages, together with a characterization of regular pure unitary languages by means of a decidable property. As a direct consequence, we characterize (regular) circular languages generated by complete systems. We can also decide whether the language generated by a complete system is regular. Finally, we point out that complete systems have the same computational power as finite simple systems, an easy type of circular splicing system defined in the literature from the very beginning, when only one rule is allowed. From our results on complete systems, it follows that finite simple systems generate a class of context-free languages containing non-regular languages, showing the incorrectness of a longstanding result on simple systems.
圆形剪接系统是圆形词的生成机制的正式模型，灵感来自圆形DNA的重组行为。一些未解决的问题与这种系统的计算能力有关，并且寻找由循环拼接系统生成的循环语言类的特征仍然是一个开放的问题。本文针对完全系统，即特殊的有限圆拼接系统，解决了这一问题。我们证明了一个循环语言L是由一个完备系统生成的，当且仅当L对应的所有词的集合Lin(L)是由一个共轭关系下封闭的集合生成的纯酉语言。纯酉型语言是a . Ehrenfeucht, D. Haussler, G. Rozenberg在1983年提出的，作为上下文无关语言的子类，并通过可决性对正则纯酉型语言进行了表征。作为直接的结果，我们描述了由完整系统生成的(规则)循环语言。我们还可以判断一个完整系统生成的语言是否规则。最后，我们指出，当只允许一个规则时，完整系统具有与有限简单系统相同的计算能力，有限简单系统是一种简单的圆形拼接系统，从一开始就在文献中定义。从我们在完整系统上的结果来看，有限简单系统产生了一类包含非规则语言的上下文无关语言，这表明了简单系统上长期结果的不正确性。
{"title":"Circular Languages Generated by Complete Splicing Systems and Pure Unitary Languages","authors":"P. Bonizzoni, C. Felice, Rosalba Zizza","doi":"10.4204/EPTCS.9.3","DOIUrl":"https://doi.org/10.4204/EPTCS.9.3","url":null,"abstract":"Circular splicing systems are a formal model of a generative mechanism of circular words, inspired by a recombinant behaviour of circular DNA. Some unanswered questions are related to the computational power of such systems, and finding a characterization of the class of circular languages generated by circular splicing systems is still an open problem. In this paper we solve this problem for complete systems, which are special finite circular splicing systems. We show that a circular language L is generated by a complete system if and only if the set Lin(L) of all words corresponding to L is a pure unitary language generated by a set closed under the conjugacy relation. The class of pure unitary languages was introduced by A. Ehrenfeucht, D. Haussler, G. Rozenberg in 1983, as a subclass of the class of context-free languages, together with a characterization of regular pure unitary languages by means of a decidable property. As a direct consequence, we characterize (regular) circular languages generated by complete systems. We can also decide whether the language generated by a complete system is regular. Finally, we point out that complete systems have the same computational power as finite simple systems, an easy type of circular splicing system defined in the literature from the very beginning, when only one rule is allowed. From our results on complete systems, it follows that finite simple systems generate a class of context-free languages containing non-regular languages, showing the incorrectness of a longstanding result on simple systems.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"62 1","pages":"22-31"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85679923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a gradual increase in agent and rule resolution, evolve into more detailed descriptions.
{"title":"Rule-based Modelling and Tunable Resolution","authors":"Russell Harmer","doi":"10.4204/EPTCS.9.8","DOIUrl":"https://doi.org/10.4204/EPTCS.9.8","url":null,"abstract":"We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a gradual increase in agent and rule resolution, evolve into more detailed descriptions.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"18 1","pages":"65-72"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84327833","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect to some biological properties deriving from the requirement of certain elements, and the repellency of others. 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.
{"title":"A Type System for Required/Excluded Elements in CLS","authors":"M. Dezani-Ciancaglini, P. Giannini, Angelo Troina","doi":"10.4204/EPTCS.9.5","DOIUrl":"https://doi.org/10.4204/EPTCS.9.5","url":null,"abstract":"The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. We enrich this calculus with a type discipline to guarantee the soundness of reduction rules with respect to some biological properties deriving from the requirement of certain elements, and the repellency of others. 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.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"3 1","pages":"38-48"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79106471","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
We apply to locally finite partially ordered sets a construction which associates a complete latticeto a given poset; the elements of the lattice are the closed subsets of a closure operator, definedstarting from the concurrency relation. We show that, if the partially ordered set satisfies a propertyof local density, i.e.: N-density, then the associated lattice is also orthomodular. We then consideroccurrence nets, introduced by C.A. Petri as models of concurrent computations, and define a familyof subsets of the elements of an occurrence net; we call those subsets causally closed because theycan be seen as subprocesses of the whole net which are, intuitively, closed with respect to the forwardand backward local state changes. We show that, when the net is K-dense, the causally closed setscoincide with the closed sets induced by the closure operator defined starting from the concurrencyrelation. K-density is a property of partially ordered sets introduced by Petri, on the basis of formeraxiomatizations of special relativity theory.
{"title":"Orthomodular Lattices Induced by the Concurrency Relation","authors":"L. Bernardinello, L. Pomello, S. Rombolà","doi":"10.4204/EPTCS.9.2","DOIUrl":"https://doi.org/10.4204/EPTCS.9.2","url":null,"abstract":"We apply to locally finite partially ordered sets a construction which associates a complete latticeto a given poset; the elements of the lattice are the closed subsets of a closure operator, definedstarting from the concurrency relation. We show that, if the partially ordered set satisfies a propertyof local density, i.e.: N-density, then the associated lattice is also orthomodular. We then consideroccurrence nets, introduced by C.A. Petri as models of concurrent computations, and define a familyof subsets of the elements of an occurrence net; we call those subsets causally closed because theycan be seen as subprocesses of the whole net which are, intuitively, closed with respect to the forwardand backward local state changes. We show that, when the net is K-dense, the causally closed setscoincide with the closed sets induced by the closure operator defined starting from the concurrencyrelation. K-density is a property of partially ordered sets introduced by Petri, on the basis of formeraxiomatizations of special relativity theory.","PeriodicalId":88470,"journal":{"name":"Dialogues in cardiovascular medicine : DCM","volume":"47 1","pages":"12-21"},"PeriodicalIF":0.0,"publicationDate":"2009-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80986066","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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