Save analysis of your results

Over the last few years, the increasing interest in machine learning has resulted in the design and development of several competitive learners. Usually, the performance of these methods is evaluated by comparing the new techniques to state-of-the-art methods over a collection of real-world problems.
In early days, these comparisons followed no standard, and qualitative arguments […]

Over the last few years, the increasing interest in machine learning has resulted in the design and development of several competitive learners. Usually, the performance of these methods is evaluated by comparing the new techniques to state-of-the-art methods over a collection of real-world problems.

In early days, these comparisons followed no standard, and qualitative arguments where used to extract conclusions from the results. Although these types of analyses enabled highlighting key points about the results, they also depended, to a certain extent, on the eyes of the beholder. Therefore, the need for finding a saver framework to analyze the results arose. With these, several researchers started drawing a methodology based on statistical tests. In the last three years, the first papers appeared on that topic. One of the first contributions can be found in the paper “Statistical Comparisons of Classifiers over Multiple Data Sets” by Janez Demsar. Later on, several authors extended this first efforts to build a save environment for results analysis.

And even more recently, Francisco Herrera and his research group gathered all these efforts and made a tutorial which is available here. The tutorial explains how different tests work and draws different ways to take when applying a statistical analysis to your results.

There is no thirteen

Some days ago I noticed that there is no button thirteen in the control panel of the elevator of my building. The owner, the architect, or someone else should be superstitious. Because of that, an ad hoc control panel was made and the displayer programming was adjusted to jump from 12 to 14. Nevertheless, despite […]

Some days ago I noticed that there is no button thirteen in the control panel of the elevator of my building. The owner, the architect, or someone else should be superstitious. Because of that, an ad hoc control panel was made and the displayer programming was adjusted to jump from 12 to 14. Nevertheless, despite these precautions, the 13th floor still exists.

It is fun to see how numbers, black cats, broken mirrors, stairs, salt, and so on, all of them quotidian elements, turn into malignant for some people, and how curios folkloric remedies survive and new appear to dodge the evil or protect from it.

I am not superstitious but I admit that it is a charming way to contribute to make up mystic stories and, at the same time, keep in mind pieces of our history, which are the origin and the real explanation of these superstitions.

I encourage you to provide your comments about a superstition and its origin.

Control panel of the elevator

Panel control of the elevator

SIGEVOlution Volume 3, Issue 3, is now available

I’m a little late with this post because I couldn’t reach the blog from China (where I was for the 2009 World Summit on Genetic and Evolutionary Computation). Aside from the web access issues it was an interesting conference and I had a great visit in China more generally. I’m now in Tokyo where I’ll visit GPEM associate editor Hitoshi Iba tomorrow, and the only web challenge appears to be in getting Blogger’s menus to appear in English rather than Japanese… but I’ve managed.
Anyway, in the interim I have received mail from Pier Luca Lanzi informing me that the latest issue of SIGEVOlution, the SIGEVO newsletter, has just been released. It is available from http://www.sigevolution.org and features:
  • An Interview with John H. Holland with an introduction by Lashon Booker
  • It’s Not Junk! by Clare Bates Congdon, H. Rex Gaskins, Gerardo M. Nava & Carolyn Mattingly
  • Car racing @ CIG-2008
  • GECCO-2009 competitions
  • New issues of journals
  • Calls & calendar
Don’t be confused by the “Autumn 2008” cover date. It is indeed a new issue that just came out in June, 2009, but the volume/date correspondence has slipped (and will probably be adjusted soon).
I’m a little late with this post because I couldn’t reach the blog from China (where I was for the 2009 World Summit on Genetic and Evolutionary Computation). Aside from the web access issues it was an interesting conference and I had a great visit in China more generally. I’m now in Tokyo where I’ll visit GPEM associate editor Hitoshi Iba tomorrow, and the only web challenge appears to be in getting Blogger’s menus to appear in English rather than Japanese… but I’ve managed.
Anyway, in the interim I have received mail from Pier Luca Lanzi informing me that the latest issue of SIGEVOlution, the SIGEVO newsletter, has just been released. It is available from http://www.sigevolution.org and features:
  • An Interview with John H. Holland with an introduction by Lashon Booker
  • It’s Not Junk! by Clare Bates Congdon, H. Rex Gaskins, Gerardo M. Nava & Carolyn Mattingly
  • Car racing @ CIG-2008
  • GECCO-2009 competitions
  • New issues of journals
  • Calls & calendar
Don’t be confused by the “Autumn 2008” cover date. It is indeed a new issue that just came out in June, 2009, but the volume/date correspondence has slipped (and will probably be adjusted soon).

A Petri net representation of Bayesian message flows: importance of Bayesian networks for biological applications

Abstract  This article combines Bayes’ theorem with flows of probabilities, flows of evidences (likelihoods), and fundamental concepts
for learning Bayesian networks as biological models from data. There is a huge amount of biological appl…

Abstract  

This article combines Bayes’ theorem with flows of probabilities, flows of evidences (likelihoods), and fundamental concepts
for learning Bayesian networks as biological models from data. There is a huge amount of biological applications of Bayesian
networks. For example in the fields of protein modeling, pathway modeling, gene expression analysis, DNA sequence analysis,
protein–protein interaction, or protein–DNA interaction. Usually, the Bayesian networks have to be learned (statistically
constructed) from array data. Then they are considered as an executable and analyzable model of the data source. To improve
that, this work introduces a Petri net representation for the propagation of probabilities and likelihoods in Bayesian networks.
The reason for doing so is to exploit the structural and dynamic properties of Petri nets for increasing the transparency
of propagation processes. Consequently the novel Petri nets are called “probability propagation nets”. By means of examples
it is shown that the understanding of the Bayesian propagation algorithm is improved. This is of particular importance for
an exact visualization of biological systems by Bayesian networks.

  • Content Type Journal Article
  • Pages 683-709
  • DOI 10.1007/s11047-009-9142-z
  • Authors
    • Kurt Lautenbach, Institut für Softwaretechnik, Universität Koblenz-Landau, Universitätsstr. 1, 56070 Koblenz, Germany
    • Alexander Pinl, Institut für Softwaretechnik, Universität Koblenz-Landau, Universitätsstr. 1, 56070 Koblenz, Germany

Stochastic Petri net models of Ca2+ signaling complexes and their analysis

Abstract  Mathematical models of Ca2+ release sites derived from Markov chain models of intracellular Ca2+ channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic Ca2+ excitability (i.e., puffs a…

Abstract  

Mathematical models of Ca2+ release sites derived from Markov chain models of intracellular Ca2+ channels exhibit collective gating reminiscent of the experimentally observed phenomenon of stochastic Ca2+ excitability (i.e., puffs and sparks). Ca2+ release site models are composed of a number of individual channel models whose dynamic behavior depends on the local Ca2+ concentration which is influenced by the state of all channels. We consider this application area to illustrate how stochastic
Petri nets and in particular stochastic activity networks can be used to model dynamical phenomena in cell biology. We highlight
how state-sharing composition operations as supported by the Möbius framework can represent both mean-field and spatial coupling
assumptions in a natural manner. We investigate how state-of-the-art techniques for the numerical and simulative analysis
of Markov chains associated with stochastic Petri nets scale when modeling Ca2+ signaling complexes of physiological size and complexity.

  • Content Type Journal Article
  • Pages 1045-1075
  • DOI 10.1007/s11047-009-9143-y
  • Authors
    • Ruth Lamprecht, Department of Computer Science, College of William and Mary, Williamsburg, VA 23187, USA
    • Gregory D. Smith, Department of Applied Sciences, College of William and Mary, Williamsburg, VA 23187, USA
    • Peter Kemper, Department of Computer Science, College of William and Mary, Williamsburg, VA 23187, USA

The mysterious world of the quantum physics

Three weeks ago I read the post Prof. Cirac interviewed about quantum physics and theory information, where you can find the link to the video of the Cirac’s interview by […]

Three weeks ago I read the post Prof. Cirac interviewed about quantum physics and theory information, where you can find the link to the video of the Cirac’s interview by a Catalan TV. It is amazing how Prof. Cirac introduces some basics of the quantum physics by using easy words and a couple of dices. Basically, he explains the existence of two worlds: the macroscopic world (the real-world, as we know it) and the microscopic world (the world of tiny things, such as the particles). The quantum physics lives in the latter; a tailored world governed by its own laws which open the doors to parallel universes that allow paradoxical phenomena. The interest of the interview was the development of quantum computers and a revealing cryptography method to transmit information in an indecipherable way. How to ensure the reliability of such a secured transmission? Because there is no transmission by a channel, information just appears in the right place at the right moment.

This nice introduction helped me to follow the exciting talk Quantum computer compilers, performed by Prof. Al Aho, a computer science celebrity and one of the authors of the AWK programming language and of the so-called Dragon Book, Compilers: Principles, techniques, and tools.

The talk focused on the following six questions:

1. Why is there so much excitement about quantum computing?
2. How is a quantum computer different from a classical computer?
3. What is a good programming model for a quantum computer?
4. What would make a good quantum programming language?
5. What are the issues in making quantum computer compilers?
6. When are we likely to see scalable quantum computers?

Prof. Aho presented, with a clear explanation and a touch of humor, the fascinating field of the quantum computers by describing how “computation is just a particle dancing around others”, enumerating the four postulates of the quantum mechanics, mentioning that quantum teleportation is information transmission based on changes that take place instantly, envisaging programming without copy operation… However, despite the wonders of the quantum computers, it seems that we should wait a little bit more for being able to solve NP-hard problem.

Finally, take a glance at The Blog of Scott Aaronson. This is an unusual and interesting blog about this topic.

The mysterious world of the quantum physics

Three weeks ago I read the post Prof. Cirac interviewed about quantum physics and theory information, where you can find the link to the video of the Cirac’s interview by a Catalan TV. It is amazing how Prof. Cirac introduces some basics of the quantum physics by using easy words and a couple of dices. […]

Three weeks ago I read the post Prof. Cirac interviewed about quantum physics and theory information, where you can find the link to the video of the Cirac’s interview by a Catalan TV. It is amazing how Prof. Cirac introduces some basics of the quantum physics by using easy words and a couple of dices. Basically, he explains the existence of two worlds: the macroscopic world (the real-world, as we know it) and the microscopic world (the world of tiny things, such as the particles). The quantum physics lives in the latter; a tailored world governed by its own laws which open the doors to parallel universes that allow paradoxical phenomena. The interest of the interview was the development of quantum computers and a revealing cryptography method to transmit information in an indecipherable way. How to ensure the reliability of such a secured transmission? Because there is no transmission by a channel, information just appears in the right place at the right moment.

This nice introduction helped me to follow the exciting talk Quantum computer compilers, performed by Prof. Al Aho, a computer science celebrity and one of the authors of the AWK programming language and of the so-called Dragon Book, Compilers: Principles, techniques, and tools.

The talk focused on the following six questions:

1. Why is there so much excitement about quantum computing?
2. How is a quantum computer different from a classical computer?
3. What is a good programming model for a quantum computer?
4. What would make a good quantum programming language?
5. What are the issues in making quantum computer compilers?
6. When are we likely to see scalable quantum computers?

Prof. Aho presented, with a clear explanation and a touch of humor, the fascinating field of the quantum computers by describing how “computation is just a particle dancing around others”, enumerating the four postulates of the quantum mechanics, mentioning that quantum teleportation is information transmission based on changes that take place instantly, envisaging programming without copy operation… However, despite the wonders of the quantum computers, it seems that we should wait a little bit more for being able to solve NP-hard problem.

Finally, take a glance at The Blog of Scott Aaronson. This is an unusual and interesting blog about this topic.

Structure versus function: a topological perspective on immune networks

Abstract  Many recent advances have been made in understanding the functional implications of the global topological properties of biological
networks through the application of complex network theory, particularly in the area of small-world…

Abstract  Many recent advances have been made in understanding the functional implications of the global topological properties of biological
networks through the application of complex network theory, particularly in the area of small-world and scale-free topologies.
Computational studies which attempt to understand the structure–function relationship usually proceed by defining a representation
of cells and an affinity measure to describe their interactions. We show that this necessarily restricts the topology of the
networks that can arise—furthermore, we show that although simple topologies can be produced via representation and affinity
measures common in the literature, it is unclear how to select measures which result in complex topologies, for example, exhibiting
scale-free functionality. In this paper, we introduce the concept of the potential network as a method in which abstract network topologies can be directly studied, bypassing any definition of shape-space and affinity
function. We illustrate the benefit of the approach by studying the evolution of idiotypic networks on a selection of scale-free
and regular topologies, finding that a key immunological property—tolerance—is promoted by bi-partite and heterogeneous topologies.
The approach, however, is applicable to the study of any network and thus has implications for both immunology and artificial
immune systems.

  • Content Type Journal Article
  • DOI 10.1007/s11047-009-9138-8
  • Authors
    • Emma Hart, Edinburgh Napier University Edinburgh Scotland, UK
    • Hugues Bersini, IRIDIA, Universite de Bruxelles Bruxelles Belgium
    • Francisco Santos, IRIDIA, Universite de Bruxelles Bruxelles Belgium

New issue of SIGEVOlution available now

The new issue of SIGEVOlution is now available for you to download from http://www.sigevolution.org. For me, the main highlight of the issue is the interview with John H. Holland with an introduction by Lashon Booker.

The new issue of SIGEVOlution is now available for you to download from http://www.sigevolution.org. For me, the main highlight of the issue is the interview with John H. Holland with an introduction by Lashon Booker.

SIGEVOlution Volume 3, Issue 3, Out Now!

The new issue of SIGEVOlution is now available for you to download from:
http://www.sigevolution.org

The issue features:

An Interview with John H. Holland with an introduction by Lashon Booker
It’s Not Junk! by Clare Bates Congdon, H. Rex Gaskins, Gerardo M. Nava & Carolyn Mattingly
car racing @ CIG-2008
GECCO-2009 competitions
new issues of journals
calls & calendar

Related Posts

The new issue of SIGEVOlution is now available for you to download from:
http://www.sigevolution.org

The issue features:

  • An Interview with John H. Holland with an introduction by Lashon Booker
  • It’s Not Junk! by Clare Bates Congdon, H. Rex Gaskins, Gerardo M. Nava & Carolyn Mattingly
  • car racing @ CIG-2008
  • GECCO-2009 competitions
  • new issues of journals
  • calls & calendar