Petri nets for modelling metabolic pathways: a survey

Abstract  In the last 15 years, several research efforts have been directed towards the representation and the analysis of metabolic
pathways by using Petri nets. The goal of this paper is twofold. First, we discuss how the knowledge about m…

Abstract  

In the last 15 years, several research efforts have been directed towards the representation and the analysis of metabolic
pathways by using Petri nets. The goal of this paper is twofold. First, we discuss how the knowledge about metabolic pathways
can be represented with Petri nets. We point out the main problems that arise in the construction of a Petri net model of
a metabolic pathway and we outline some solutions proposed in the literature. Second, we present a comprehensive review of
recent research on this topic, in order to assess the maturity of the field and the availability of a methodology for modelling
a metabolic pathway by a corresponding Petri net.

  • Content Type Journal Article
  • DOI 10.1007/s11047-010-9180-6
  • Authors
    • Paolo Baldan, Dipartimento di Matematica Pura e Applicata, Università di Padova, via Trieste 63, 35121 Padova, Italy
    • Nicoletta Cocco, Dipartimento di Informatica, Università Ca’ Foscari di Venezia, via Torino 155, 30172 Venezia Mestre, Italy
    • Andrea Marin, Dipartimento di Informatica, Università Ca’ Foscari di Venezia, via Torino 155, 30172 Venezia Mestre, Italy
    • Marta Simeoni, Dipartimento di Informatica, Università Ca’ Foscari di Venezia, via Torino 155, 30172 Venezia Mestre, Italy

Image annotation by incorporating word correlations into multi-class SVM

Abstract  Image annotation systems aim at automatically annotating images with semantic keywords. Machine learning approaches are often
used to develop these systems. In this paper, we propose an image annotation approach by incorporating wo…

Abstract  

Image annotation systems aim at automatically annotating images with semantic keywords. Machine learning approaches are often
used to develop these systems. In this paper, we propose an image annotation approach by incorporating word correlations into
multi-class support vector machine (SVM). At first, each image is segmented into five fixed-size blocks instead of time-consuming
object segmentation. Every keyword from training images is manually assigned to the corresponding block and word correlations
are computed by a co-occurrence matrix. Then, MPEG-7 visual descriptors are applied to these blocks to represent visual features
and the minimal-redundancy-maximum-relevance (mRMR) method is used to reduce the feature dimension. A block-feature-based
multi-class SVM classifier is trained for 80 semantic concepts. At last, the probabilistic outputs from SVM and the word correlations
are integrated to obtain the final annotation keywords. The experiments on Corel 5000 dataset demonstrate our approach is
effective and efficient.

  • Content Type Journal Article
  • Pages 1-11
  • DOI 10.1007/s00500-010-0558-2
  • Authors
    • Lei Zhang, Shandong University School of Computer Science and Technology Jinan China
    • Jun Ma, Shandong University School of Computer Science and Technology Jinan China

LSGA: combining level-sets and genetic algorithms for segmentation

Abstract  A novel technique is presented to combine genetic algorithms (GAs) with level-set functions to segment objects with known
shapes and variabilities on images. The individuals of the GA, also known as chromosomes consist of a sequenc…

Abstract  

A novel technique is presented to combine genetic algorithms (GAs) with level-set functions to segment objects with known
shapes and variabilities on images. The individuals of the GA, also known as chromosomes consist of a sequence of parameters of a level-set function. Each chromosome represents a unique segmenting contour. An initial
population of segmenting contours is generated based on the learned variation of the level-set parameters from training images.
Each segmenting contour (an individual) is evaluated for its fitness based on the texture of the region it encloses. The fittest
individuals are allowed to propagate to future generations of the GA run using selection, crossover and mutation. The GA thus
provides a framework for combining texture and shape features for segmentation. Level-set-based segmentation methods typically
perform gradient descent minimization on an energy function to deform a segmenting contour. The computational complexity of
computing derivatives increases as the number of terms increases in the energy function. In contrast, here the level-set-based
curve evolution/deformation is performed derivative-free using a genetic algorithm. The algorithm has been tested for segmenting
thermographic images of hands and for segmenting the prostate in pelvic CT and MRI images. In this paper we describe the former;
the latter is described in [11, 12]. The LSGA successfully segments entire hands on images in which hands are only partially visible. At the end of the paper
we report experimental evaluation of the performance of LSGA and compare it with algorithms using single features: the Gabor
wavelet based textural segmentation method [1, 9], and the level-set based segmentation algorithm of Chan and Vese [6].

  • Content Type Journal Article
  • DOI 10.1007/s12065-010-0036-x
  • Authors
    • Payel Ghosh, Portland State University Department of ECE Portland OR USA
    • Melanie Mitchell, Portland State University Department of ECE Portland OR USA
    • Judith Gold, Temple University Department of Public Health Philadelphia PA USA

Petri net representation of multi-valued logical regulatory graphs

Abstract  Relying on a convenient logical representation of regulatory networks, we propose a generic method to qualitatively model
regulatory interactions in the standard elementary and coloured Petri net frameworks. Logical functions gover…

Abstract  

Relying on a convenient logical representation of regulatory networks, we propose a generic method to qualitatively model
regulatory interactions in the standard elementary and coloured Petri net frameworks. Logical functions governing the behaviours
of the components of logical regulatory graphs are efficiently represented by Multivalued Decision Diagrams, which are also
at the basis of the translation of logical models in terms of Petri nets. We further delineate a simple strategy to sort trajectories
through the introduction of priority classes (in the logical framework) or priority functions (in the Petri net framework).
We also focus on qualitative behaviours such as multistationarity or sustained oscillations, identified as specific structures
in state transition graphs (for logical models) or in marking graphs (in Petri nets). Regulatory circuits are known to be
at the origin of such properties. In this respect, we present a method that allows to determine the functionality contexts
of regulatory circuits, i.e. constraints on external regulator states enabling the corresponding dynamical properties. Finally,
this approach is illustrated through an application to the modelling of a regulatory network controlling T lymphocyte activation
and differentiation.

  • Content Type Journal Article
  • Pages 727-750
  • DOI 10.1007/s11047-010-9178-0
  • Authors
    • C. Chaouiya, Instituto Gulbenkian de Ciência, Oeiras, Portugal
    • A. Naldi, INSERM U928—TAGC, Marseille, France
    • E. Remy, Institut de Mathématiques de Luminy, Marseille, France
    • D. Thieffry, INSERM U928—TAGC, Marseille, France

Variable precision rough set model over two universes and its properties

Abstract  The extension of rough set model is an important research direction in the rough set theory. In this paper, based on the rough
set model over two universes, we firstly propose the variable precision rough set model (VPRS-model) ove…

Abstract  

The extension of rough set model is an important research direction in the rough set theory. In this paper, based on the rough
set model over two universes, we firstly propose the variable precision rough set model (VPRS-model) over two universes using
the inclsion degree. Meantime, the concepts of the reverse lower and upper approximation operators are presented. Afterwards,
the properties of the approximation operators are studied. Finally, the approximation operators with two parameters are introduced
as a generalization of the VPRS-model over two universes, and the related conclusions are discussed.

  • Content Type Journal Article
  • Pages 1-11
  • DOI 10.1007/s00500-010-0562-6
  • Authors
    • Yonghong Shen, Tianshui Normal University School of Mathematics and Statistics Tianshui 741001 People’s Republic of China
    • Faxing Wang, Tongda College of Nanjing University of Posts and Telecommunications Nanjing 210046 People’s Republic of China

Not your grandmother’s genetic algorithm!

The video of David E. Goldberg’s talk on genetic algorithms entitled Not your Grandmother’s Genetic Algorithm is available on youtube.com. The talk covers topics from the simple genetic algorithm to advanced estimation of distribution algorithms, scalability theory of genetic algorithms and practical solutions to noisy problems of over one billion variables. An amazing lecture, and […]

The video of David E. Goldberg’s talk on genetic algorithms entitled Not your Grandmother’s Genetic Algorithm is available on youtube.com. The talk covers topics from the simple genetic algorithm to advanced estimation of distribution algorithms, scalability theory of genetic algorithms and practical solutions to noisy problems of over one billion variables. An amazing lecture, and a must-see for anyone interested in evolutionary computation and stochastic optimization.

The links to the videos: Part 1, part 2, part 3.

The embeds follow

On aggregation in multiset-based self-assembly of graphs

Abstract  We continue the formal study of multiset-based self-assembly. The process of self-assembly of graphs, where iteratively new
nodes are attached to a given graph, is guided by rules operating on nodes labelled by multisets. In this w…

Abstract  

We continue the formal study of multiset-based self-assembly. The process of self-assembly of graphs, where iteratively new
nodes are attached to a given graph, is guided by rules operating on nodes labelled by multisets. In this way, the multisets
and rules model connection points (such as “sticky ends”) and complementarity/affinity between connection points, respectively.
We identify three natural ways (individual, free, and collective) to attach (aggregate) new nodes to the graph, and study
the generative power of the corresponding self-assembly systems. For example, it turns out that individual aggregation can
be simulated by free or collective aggregation. However, we demonstrate that, for a fixed set of connection points, collective
aggregation is rather restrictive. We also give a number of results that are independent of the way that aggregation is performed.

  • Content Type Journal Article
  • Pages 1-22
  • DOI 10.1007/s11047-010-9183-3
  • Authors
    • Francesco Bernardini, Leiden University Leiden Institute of Advanced Computer Science Leiden The Netherlands
    • Robert Brijder, Leiden University Leiden Institute of Advanced Computer Science Leiden The Netherlands
    • Matteo Cavaliere, Centre for Computational and Systems Biology (CoSBi) The Microsoft Research-University of Trento Trento Italy
    • Giuditta Franco, University of Verona Department of Computer Science Strada Le Grazie 15 37134 Verona Italy
    • Hendrik Jan Hoogeboom, Leiden University Leiden Institute of Advanced Computer Science Leiden The Netherlands
    • Grzegorz Rozenberg, Leiden University Leiden Institute of Advanced Computer Science Leiden The Netherlands

Optimization by Building and Using Probabilistic Models (OBUPM-2010) Workshop

The workshop Optimization by Building and Using Probabilistic Models (OBUPM-2010) will take place at the Genetic and Evolutionary Computation Conference (GECCO-2010) in Portland, OR. OBUPM-2010 is organized by Mark Hauschild and Martin Pelikan.
We look forward to seeing you there and invite submission of papers for the workshop. The deadline for paper submission is March 25, […]

The workshop Optimization by Building and Using Probabilistic Models (OBUPM-2010) will take place at the Genetic and Evolutionary Computation Conference (GECCO-2010) in Portland, OR. OBUPM-2010 is organized by Mark Hauschild and Martin Pelikan.

We look forward to seeing you there and invite submission of papers for the workshop. The deadline for paper submission is March 25, 2010. Please check the website of OBUPM-2010 for more detailed information.

A modified hybrid method of spatial credibilistic clustering and particle swarm optimization

Abstract  Hybrid methods of spatial credibilistic clustering and particle swarm optimization (SCCPSO) (Wen et al. in Int J Fuzzy Syst
10:174–184, 2008) are validated to be effective, and produce better results than other common method…

Abstract  

Hybrid methods of spatial credibilistic clustering and particle swarm optimization (SCCPSO) (Wen et al. in Int J Fuzzy Syst
10:174–184, 2008) are validated to be effective, and produce better results than other common methods. In this paper, SCCPSO is further investigated
and a modified SCCPSO is put forward by discussing the membership functions and presenting a pre-selection method based on
proving an evaluation criterion on the clustering results. The analysis of computational complexity demonstrates the feasibility
of the modified SCCPSO. Experiments verify the discussion on the membership functions, the correctness of the evaluation criterion,
as well as the effectiveness of the pre-selection method and the modified SCCPSO.

  • Content Type Journal Article
  • Pages 1-11
  • DOI 10.1007/s00500-010-0553-7
  • Authors
    • Peihan Wen, Tsinghua University Department of Industrial Engineering Beijing 100084 China
    • Jian Zhou, Tsinghua University Department of Industrial Engineering Beijing 100084 China
    • Li Zheng, Tsinghua University Department of Industrial Engineering Beijing 100084 China

Entropy-type classification maximum likelihood algorithms for mixture models

Abstract  Mixtures of distributions are popularly used as probability models for analyzing grouped data. Classification maximum likelihood
(CML) is an important maximum likelihood approach to clustering with mixture models. Yang et al. exten…

Abstract  

Mixtures of distributions are popularly used as probability models for analyzing grouped data. Classification maximum likelihood
(CML) is an important maximum likelihood approach to clustering with mixture models. Yang et al. extended CML to fuzzy CML.
Although fuzzy CML presents better results than CML, it is always affected by the fuzziness index parameter. In this paper,
we consider fuzzy CML with an entropy-regularization term to create an entropy-type CML algorithm. The proposed entropy-type
CML is a parameter-free algorithm for mixture models. Some numerical and real-data comparisons show that the proposed method
provides better results than some existing methods.

  • Content Type Journal Article
  • Pages 1-9
  • DOI 10.1007/s00500-010-0560-8
  • Authors
    • Chien-Yo Lai, Chung Yuan Christian University Department of Applied Mathematics Chung-Li 32023 Taiwan
    • Miin-Shen Yang, Chung Yuan Christian University Department of Applied Mathematics Chung-Li 32023 Taiwan