An empirical evaluation of P system testing techniques

Abstract  This paper presents the existing techniques for P system testing and performs an empirical evaluation of their fault-detection
efficiency. The comparison is performed using mutation testing and, based on the results obtained, some …

Abstract  

This paper presents the existing techniques for P system testing and performs an empirical evaluation of their fault-detection
efficiency. The comparison is performed using mutation testing and, based on the results obtained, some improved testing methodologies
are proposed.

  • Content Type Journal Article
  • Pages 1-15
  • DOI 10.1007/s11047-010-9188-y
  • Authors
    • Raluca Lefticaru, University of Pitesti Department of Computer Science Str Targu din Vale 1 110040 Pitesti Romania
    • Marian Gheorghe, University of Pitesti Department of Computer Science Str Targu din Vale 1 110040 Pitesti Romania
    • Florentin Ipate, University of Pitesti Department of Computer Science Str Targu din Vale 1 110040 Pitesti Romania

Continuous-action reinforcement learning with fast policy search and adaptive basis function selection

Abstract  As an important approach to solving complex sequential decision problems, reinforcement learning (RL) has been widely studied
in the community of artificial intelligence and machine learning. However, the generalization ability of …

Abstract  

As an important approach to solving complex sequential decision problems, reinforcement learning (RL) has been widely studied
in the community of artificial intelligence and machine learning. However, the generalization ability of RL is still an open
problem and it is difficult for existing RL algorithms to solve Markov decision problems (MDPs) with both continuous state
and action spaces. In this paper, a novel RL approach with fast policy search and adaptive basis function selection, which
is called Continuous-action Approximate Policy Iteration (CAPI), is proposed for RL in MDPs with both continuous state and
action spaces. In CAPI, based on the value functions estimated by temporal-difference learning, a fast policy search technique
is suggested to search for optimal actions in continuous spaces, which is computationally efficient and easy to implement.
To improve the generalization ability and learning efficiency of CAPI, two adaptive basis function selection methods are developed
so that sparse approximation of value functions can be obtained efficiently both for linear function approximators and kernel
machines. Simulation results on benchmark learning control tasks with continuous state and action spaces show that the proposed
approach not only can converge to a near-optimal policy in a few iterations but also can obtain comparable or even better
performance than Sarsa-learning, and previous approximate policy iteration methods such as LSPI and KLSPI.

  • Content Type Journal Article
  • DOI 10.1007/s00500-010-0581-3
  • Authors
    • Xin Xu, National University of Defense Technology College of Mechatronics and Automation, Institute of Automation ChangSha Hunan 410073 People’s Republic of China
    • Chunming Liu, National University of Defense Technology College of Mechatronics and Automation, Institute of Automation ChangSha Hunan 410073 People’s Republic of China
    • Dewen Hu, National University of Defense Technology College of Mechatronics and Automation, Institute of Automation ChangSha Hunan 410073 People’s Republic of China

A computational modeling for real ecosystems based on P systems

Abstract  In this paper, a P systems based general framework for modeling ecosystems dynamics is presented. Particularly, ecosystems
are specified by means of multienvironment P systems composed of a finite number of environments, each of th…

Abstract  

In this paper, a P systems based general framework for modeling ecosystems dynamics is presented. Particularly, ecosystems
are specified by means of multienvironment P systems composed of a finite number of environments, each of them having an extended
P system with active membranes. The semantics is of a probabilistic type and it is implemented by assigning each rule of the
system a probabilistic constant which depends on the environment and the run time. As a case study, two real ecosystems are
described: scavenger birds in the Catalan Pyrenees and the zebra mussel (Dreissena Polymorpha) in Ribarroja reservoir (Spain).

  • Content Type Journal Article
  • Pages 1-15
  • DOI 10.1007/s11047-010-9191-3
  • Authors
    • Mónica Cardona, University of Lleida Department of Mathematics Av. Alcalde Rovira Roure, 191 25198 Lleida Spain
    • M. Angels Colomer, University of Lleida Department of Mathematics Av. Alcalde Rovira Roure, 191 25198 Lleida Spain
    • Antoni Margalida, Bearded Vulture Study & Protection Group Adpo. 43 25520 El Pont de Suert (Lleida) Spain
    • Antoni Palau, Dirección de Medio Ambiente y Desarrollo Sostenible Endesa Spain
    • Ignacio Pérez-Hurtado, University of Sevilla Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence Avda. Reina Mercedes s/n 41012 Sevilla Spain
    • Mario J. Pérez-Jiménez, University of Sevilla Research Group on Natural Computing, Department of Computer Science and Artificial Intelligence Avda. Reina Mercedes s/n 41012 Sevilla Spain
    • Delfí Sanuy, University of Lleida Department of Animal Production Av. Alcalde Rovira Roure, 191 25198 Lleida Spain

A dynamic game of coalition formation under ambiguity

Abstract  In a previous paper, we generalized to the mixed strategy case the γ model of coalition formation (introduced by Hart and
Kurz in Econometrica 51(4):1047–1064, 1983) for situations in which players have ambiguous expectations ab…

Abstract  

In a previous paper, we generalized to the mixed strategy case the γ model of coalition formation (introduced by Hart and
Kurz in Econometrica 51(4):1047–1064, 1983) for situations in which players have ambiguous expectations about the formation of the coalitions in which they are not
involved; then we analyzed the corresponding evolutionary games. In this paper, we embody into the model rationality of the
players; it follows that allowing for mixed strategies makes it impossible to construct unequivocally a von Neumann–Morgestein
expected utility function coherent (in the sense of de Finetti B in Sul Significato Soggettivo della Probabilità, Fundamenta Mathematicae, T, vol XVIII, pp
298–329, 1931) to every strategy profile. We find out that if the multiplicity of coherent beliefs problem is approached by considering
“ambiguity loving” players then existence results for classical static equilibria can be obtained in this model. Moreover,
we provide conditions for the game to be dynamically playable and we find how the coalition structure beliefs might evolve
coherently (according) to the evolution of the strategies.

  • Content Type Journal Article
  • DOI 10.1007/s00500-010-0573-3
  • Authors
    • Giuseppe De Marco, Università di Napoli Parthenope Dipartimento di Statistica e Matematica per la Ricerca Economica Via Medina 40 80133 Naples Italy
    • Maria Romaniello, Seconda Università di Napoli Dipartimento di Strategie Aziendali e Metodologie Quantitative Corso Gran Priorato di Malta 81043 Capua Italy

Automatic summarisation and annotation of microarray data

Abstract  The study of biological processes within cells is based on the measurement of the activity of different molecules, in particular
genes and proteins whose activities are strictly related. The activity of genes is measured through a …

Abstract  

The study of biological processes within cells is based on the measurement of the activity of different molecules, in particular
genes and proteins whose activities are strictly related. The activity of genes is measured through a systematic investigation
carried out by microarrays. Such technology enables the investigation of all the genes of an organism in a single experiment,
encoding meaningful biological information. Nevertheless, the preprocessing of raw microarray data needs automatic tools that
standardise such phase in order to: (a) avoiding errors in analysis phases, and (b) making comparable the results of different
laboratories. The preprocessing problem is as much relevant as considering results obtained from analysis platforms of different
vendors. Nevertheless, there is currently a lack of tools that allow to manage and preprocess multivendor dataset. This paper
presents a software platform (called GSAT, General-purpose Summarisation and Annotation Tool) able to manage and preprocess
microarray data. The GSAT allows the summarisation, normalisation and annotation of multivendor microarray data, using web
services technology. First experiments and results on Affymetrix data samples are also discussed. GSAT is available online
at http://bioingegneria.unicz.it/m-cs as a standalone application or as a plugin of the TMEV microarray data analysis platform.

  • Content Type Journal Article
  • DOI 10.1007/s00500-010-0600-4
  • Authors
    • Pietro H. Guzzi, University Magna Graecia Bioinformatics Laboratory, Department of Experimental Medicine and Clinic 88100 Catanzaro Italy
    • Maria Teresa Di Martino, T. Campanella Cancer Center, University Magna Graecia Medical Oncology Unit 88100 Catanzaro Italy
    • Giuseppe Tradigo, University Magna Graecia Bioinformatics Laboratory, Department of Experimental Medicine and Clinic 88100 Catanzaro Italy
    • Pierangelo Veltri, University Magna Graecia Bioinformatics Laboratory, Department of Experimental Medicine and Clinic 88100 Catanzaro Italy
    • Pierfrancesco Tassone, T. Campanella Cancer Center, University Magna Graecia Medical Oncology Unit 88100 Catanzaro Italy
    • Pierosandro Tagliaferri, T. Campanella Cancer Center, University Magna Graecia Medical Oncology Unit 88100 Catanzaro Italy
    • Mario Cannataro, University Magna Graecia Bioinformatics Laboratory, Department of Experimental Medicine and Clinic 88100 Catanzaro Italy

Automata theory based on lattice-ordered semirings

Abstract  In this paper, definitions of

K
automata,

K
regular languages,

K
regular expressions and

K
regular grammars based on lattice-ordered semirings are given. It is shown that

K
NFA is equivalent to

K
DFA under some finit…

Abstract  

In this paper, definitions of

K

automata,

K

regular languages,

K

regular expressions and

K

regular grammars based on lattice-ordered semirings are given. It is shown that

K

NFA is equivalent to

K

DFA under some finite condition, the Pump Lemma holds if

K

is finite, and

Ke

NFA is equivalent to

K

NFA. Further, it is verified that the concatenation of

K

regular languages remains a

K

regular language. Similar to classical cases and automata theory based on lattice-ordered monoids, it is also found that

K

NFA,

K

regular expressions and

K

regular grammars are equivalent to each other when

K

is a complete lattice.

  • Content Type Journal Article
  • DOI 10.1007/s00500-010-0565-3
  • Authors
    • Xian Lu, AMSS Institute of Mathematics, Academia Sinica Beijing 100190 People’s Republic of China
    • Yun Shang, AMSS Institute of Mathematics, Academia Sinica Beijing 100190 People’s Republic of China
    • Ruqian Lu, AMSS Institute of Mathematics, Academia Sinica Beijing 100190 People’s Republic of China

P systems with active membranes: trading time for space

Abstract  We consider recognizer P systems having three polarizations associated to the membranes, and we show that they are able to
solve the PSPACE-complete problem Quantified 3SAT when working in polynomial space and exponential time. The…

Abstract  

We consider recognizer P systems having three polarizations associated to the membranes, and we show that they are able to
solve the PSPACE-complete problem Quantified 3SAT when working in polynomial space and exponential time. The solution is uniform (all the instances of a fixed size are solved
by the same P system) and uses only communication rules: evolution rules, as well as membrane division and dissolution rules,
are not used. Our result shows that, as it happens with Turing machines, this model of P systems can solve in exponential
time and polynomial space problems that cannot be solved in polynomial time, unless P = SPACE.

  • Content Type Journal Article
  • Pages 1-16
  • DOI 10.1007/s11047-010-9189-x
  • Authors
    • Antonio E. Porreca, Università degli Studi di Milano-Bicocca Dipartimento di Informatica, Sistemistica e Comunicazione Viale Sarca 336/14 20126 Milan Italy
    • Alberto Leporati, Università degli Studi di Milano-Bicocca Dipartimento di Informatica, Sistemistica e Comunicazione Viale Sarca 336/14 20126 Milan Italy
    • Giancarlo Mauri, Università degli Studi di Milano-Bicocca Dipartimento di Informatica, Sistemistica e Comunicazione Viale Sarca 336/14 20126 Milan Italy
    • Claudio Zandron, Università degli Studi di Milano-Bicocca Dipartimento di Informatica, Sistemistica e Comunicazione Viale Sarca 336/14 20126 Milan Italy

Python LCS Implementations (XCS, UCS, MCS) for SNP Environment

Urbanowicz_XCS_2009

Urbanowicz_UCS_2009

Urbanowicz_MCS_2009

The above .zip files contain open source python implementations of existing LCS algorithms (XCS, UCS, MCS) written/modified to accommodate SNP gene association studies. These are the implementations used in the following paper published in the proceeding of GECCO 2009:

R.J. Urbanowicz, J.H Moore. The Application of Michigan-Style Learning Classifier
Systems to Address Genetic Heterogeneity and Epistasis
in Association Studies. GECCO 2010

Spatial P systems

Abstract  We present Spatial P systems, a variant of P systems which embodies the concept of space and position inside a membrane. Objects
in membranes are associated with positions. Rules specify, in the usual way, the objects which are con…

Abstract  

We present Spatial P systems, a variant of P systems which embodies the concept of space and position inside a membrane. Objects
in membranes are associated with positions. Rules specify, in the usual way, the objects which are consumed and the ones which
are produced; in addition, they can specify the positions of the produced objects. Objects belong to two different sets: the
set of ordinary objects and the set of mutually exclusive objects. Every position inside a membrane can accommodate an arbitrary number of ordinary objects, but at most one mutually
exclusive object. We prove that Spatial P systems are universal even if only non-cooperating rules are allowed. We also show
how Spatial P systems can be used to model the evolution of populations in presence of geographical separations.

  • Content Type Journal Article
  • Pages 1-14
  • DOI 10.1007/s11047-010-9187-z
  • Authors
    • Roberto Barbuti, Università di Pisa Dipartimento di Informatica Largo Pontecorvo 3 56127 Pisa Italy
    • Andrea Maggiolo-Schettini, Università di Pisa Dipartimento di Informatica Largo Pontecorvo 3 56127 Pisa Italy
    • Paolo Milazzo, Università di Pisa Dipartimento di Informatica Largo Pontecorvo 3 56127 Pisa Italy
    • Giovanni Pardini, Università di Pisa Dipartimento di Informatica Largo Pontecorvo 3 56127 Pisa Italy
    • Luca Tesei, Università di Camerino School of Science and Technology Via Madonna delle Carceri 9 62032 Camerino MC Italy

An improved multi-agent genetic algorithm for numerical optimization

Abstract  Multi-agent genetic algorithm (MAGA) is a good algorithm for global numerical optimization. It exploited the known characteristics
of some benchmark functions to achieve outstanding results. But for some novel composition functions…

Abstract  

Multi-agent genetic algorithm (MAGA) is a good algorithm for global numerical optimization. It exploited the known characteristics
of some benchmark functions to achieve outstanding results. But for some novel composition functions, the performance of the
MAGA significantly deteriorates when the relative positions of the variables at the global optimal point are shifted with
respect to the search ranges. To this question, an improved multi-agent genetic algorithm for numerical optimization (IMAGA)
is proposed. IMAGA make use of the agent evolutionary framework, and constructs heuristic search and a hybrid crossover strategy
to complete the competition and cooperation of agents, a convex mutation operator and some local search to achieve the self-learning
characteristic. Using the theorem of Markov chain, the improved multi-agent genetic algorithm is proved to be convergent.
Experiments are conducted on some benchmark functions and composition functions. The results demonstrate good performance
of the IMAGA in solving complicated composition functions compared with some existing algorithms.

  • Content Type Journal Article
  • Pages 1-20
  • DOI 10.1007/s11047-010-9192-2
  • Authors
    • Xiaoying Pan, Xi’an University of Posts and Telecommunications School of Computer Science and Technology Xi’an 710121 China
    • Licheng Jiao, Institute of Intelligent Information Processing, Xidian University Key Laboratory of Intelligent Perception and Image Understanding of Ministry of Education of China Xi’an 710071 China
    • Fang Liu, Xidian University School of Computer Science and Engineering Xi’an 710071 China