Research

Articles

Other: Papers, Dissertations, Presentations, Posters, Reports, Course notes, Proposals

Bioinformatics

Transgenic mice expressing constitutive active MAPKAPK5 display gender-dependent differences in exploration and activity
November 2007 - Nancy Gerits, Werner Van Belle, Ugo Moens

Background: The mitogen-activated protein kinases, MAPKs for short, constitute cascades of signalling pathways involved in the regulation of several cellular processes that include cell proliferation, differentiation and motility. They also intervene in neurological processes like fear conditioning and memory. Since little remains known about the MAPK-Activated Protein Kinase, MAPKAPK5, we constructed the first MAPKAPK knockin mouse model, using a constitutive active variant of MAPKAPK5 and analysed the resulting mice for changes in anxiety-related behaviour. Methods: We performed primary SHIRPA observations during background breeding into the C57BL/6 background and assessed the behaviour of the background-bred animals on the elevated plus maze and in the light-dark test. Our results were analysed using Chi-square tests and homo- and heteroscedatic T-tests; Results: Female transgenic mice displayed increased amounts of head dips and open arm time on the maze, compared to littermate controls. In addition, they also explored further into the open arm on the elevated plus maze and were less active in the closed arm compared to littermate controls. Male transgenic mice displayed no differences in anxiety, but their locomotor activity increased compared to non-transgenic littermates; Conclusions: Our results revealed anxiety-related traits and locomotor differences between transgenic mice expressing constitutive active MAPKAPK5 and control littermates.

Confidence Intervals on Microarray Measurement of Differentially Expressed Genes: A Case Study on the effects of MK5, TAF4 and FKRP on the transcriptome
May 2007 - Werner Van Belle, Nancy Gerits, Kirsti Jakobsen, Vigdis Brox, Marijke Van Ghelue, Ugo Moens

To perform a quantitative analysis with gene-arrays, one must take into account inaccuracies (experimental variations, biological variations and other measurement errors) which are seldomly known. In this paper we investigated amplification and noise propagation related errors by measuring intensity dependent variations. Based on a set of control samples, we create confidence intervals on up and down regulations. We validated our method through a qPCR experiment and compared it to standard analysis methods (including loess normalization and filtering methods based on genetic variability). The results reveal that experimental variability and amplification related errors are a major concern that should be accounted for.

Adaptive contrast enhancement of two-dimensional electrophoretic protein gel images facilitates visualization, orientation and alignment
October 2006 - Werner Van Belle, Gry Sjøholt, Nina Ånensen, Kjell-Arild Høgda, Bjørn Tore Gjertsen

Two-dimensional polyacrylamide gel electrophoresis (2-DE) is a powerful technique to discriminate post-translationally modified protein isoforms. However, all steps of 2-DE preparation and gel-staining may introduce unwanted artefacts, including inconsistent variation of background intensity over the entire 2-DE gel image. Background intensity variations limit the accuracy of gel orientation, overlay alignment and spot detection methods. We present a compact and efficient denoising algorithm that adaptively enhances the image contrast and then, through thresholding and median filtering, removes the gray-scale range covering the background. Applicability of the algorithm is demonstrated on immuno-blots, isotope labeled gels, and protein stained gels. Validation is performed in contexts of i) automatic gel orientation based on Hough transformation, ii) overlay alignment based on cross correlation and iii) spot detection. In gel-stains with low background variability, e.g. Sypro Ruby, denoising will lower the spot detection sensitivity. In gel regions with high background levels denoising enhances spot detection. We propose that the denoising algorithm prepares images with high background for further automatic analysis, without requiring manual input on a gel-to-gel basis.

Proteomics of p53 in Diagnostics and Therapy of Acute Myeloid Leukemia
July 2006 - Nina Ånensen, Ingvild Haaland, Clive D'Santos, Werner Van Belle, Bjørn Tore Gjertsen

The anti-oncogene TP53 is frequently mutated in human cancer, but in hematological malignancies this is a rare feature. In acute myeloid leukemia (AML) more than 90% of the patients comprise wild type TP53 in their cancer cells, but if TP53 is mutated or deleted the disease is often found to be chemoresistant. In this review we define proteomics of the oncogene product p53 as the study of proteins in the p53 regulating signaling networks, as well as the protein study of members of the p53 family itself. Various messenger RNA splice forms as well as a multitude of posttranslational modifications give a high number of protein isoforms in the p53 family. Some of the proteomic techniques allow detection of various isoforms, such as two-dimensional gel electrophoresis in combination with tandem mass spectrometry (MS/MS) and this methodology may therefore increasingly be used as a diagnostic tool in human disease. We introduce the p53 protein as an illustration of the complexity of post-translational modifications that may affect one highly connected protein and discuss the possible impact in AML diagnostics if the p53 profile is reflecting cell stress and status of signal transduction systems of the malignancy

Correlation analysis of two-dimensional gel electrophoretic protein patterns and biological variables
April 2006 - Werner Van Belle, Nina Ånensen, Ingvild Haaland, Oystein Bruserud, Kjell-Arild Høgda, Bjørn Tore Gjertsen

Background) Two-dimensional gel electrophoresis (2DE) is a powerful technique to examine post-translational modifications of complexly modulated proteins. Currently, spot detection is a necessary step to assess relations between spots and biological variables. This often proves time consuming and difficult when working with non-perfect gels. We developed an analysis technique to measure correlation between 2DE images and biological variables on a pixel by pixel basis. After image alignment and normalization, the biological parameters and pixel values are replaced by their specific rank. These rank adjusted images and parameters are then put into a standard linear Pearson correlation and further tested for significance and variance. Results) We validated this technique on a set of simulated 2DE images, which revealed also correct working under the presence of normalization factors. This was followed by an analysis of p53 2DE immunoblots from cancer cells, known to have unique signaling networks. Since p53 is altered through these signaling networks, we expected to find correlations between the cancer type (acute lymphoblastic leukemia and acute myeloid leukemia) and the p53 profiles. A second correlation analysis revealed a more complex relation between the differentiation stage in acute myeloid leukemia and p53 protein isoforms. Conclusion) The presented analysis method measures relations between 2DE images and external variables without requiring spot detection, thereby enabling the exploration of biosignatures of complex signaling networks in biological systems.

Artefacts in the Mass Spectra Output from MALDI-TOF and MALDI-TOF/TOF Machines
April 2005 - Werner Van Belle, Olav Mjaavatten

MALDI-TOF mass spectrometry is a well known and widely used technique to fingerprint and sequence proteins. A carefull investigation of the mass spectra output from unnamed machines shows a number of artefacts produced by the machines themselves. Because these artefacts complicate a number of procedures we present a number of preliminary techniques we developed to get rid of most of the artefacts.

Computer Science

Ambient Actors as a Formalism for Ubiquitous and Mobile Computing
October 2006 - Werner Van Belle, Jessie Dedecker

Networks formed by the interconnection of mobile wireless devices are often called mobile ad-hoc networks. Such networks are highly volatile because communication partners can move in and out of range. This leads to unwanted interruptions of communication sessions, which in turn complicates the development of software that relies on a long term distributed state. Standard solutions seem inadequate because all too often they assume an inherent client server role or they assume a bound latency on communication sessions. One cannot make such assumptions in mobile ad-hoc networks. In order to resolve this matter a programming model must support the ability to pick up previous communication sessions; it must remember the devices/resources it has seen in the past; and it must provide a realistic approach towards concurrency, taking into account the limitations of a peer to peer ad-hoc network. This article presents the ambient actor model which extends the operational semantics of the actor model to capture the limitations posed by this novel paradigm

Actors for Mobile Ad-Hoc Networks (The Ambient Actor Model)
August 2004 - Jessie Dedecker, Werner Van Belle

Wireless communication has a limited communication range which introduces two major problems, currently not captured in distributed middleware. First, they are less reliable than their wired variants and secondly they are extremely dynamic. Both problems complicate the development of mobile software. In this paper we extend the operational semantics of the actor model to capture these two properties. We do this by adding a single new concept to the model: the mailbox. This paper provides a foundation for new implementations of the actor language and frameworks that are usable in the context of wireless network environments.

The Failure of the Connectionless Model and the Vice Software Model
February 2004 - Werner Van Belle

We investigate a number of modularity problems that arise from using a connection-less software model. A connection-less approach leads naturally to an unmanaged use of direct references. This results in crucial software composition complications such as the inability to replace objects, difficulties to track outgoing messages, difficulties in writing glue-codehidden communication. As a solution to these problems, we present our connection oriented software model, Vice. Its reflective design makes that it surpasses existing architectures in its modularity, manageability and performance.

Actors for Pervasive Computing
June 2003 - Jessie Dedecker, Werner Van Belle, Wolfgang De Meuter

The position we defend in this paper is that asynchronous communication patterns are to be considered to be the main communication paradigm in pervasive applications and that the actor model, which relies on such a form of communication, needs extenstion to be practical useful.

Using Genetic Programming to Generate Protocol Adaptors for Interprocess Communication
March 2003 - Werner Van Belle, Tom Mens, Theo D'Hondt

As mobile devices become more powerful, interprocess communication becomes increasingly more important. Unfortunately, this larger freedom of mobility gives rise to unknown environments. In these environments, processes that want to communicate with each other will be unable to do so because of protocol conflicts. Although conflicting protocols can be remedied by using adaptors, the number of possible combinations of different protocols increases dramatically. Therefore we propose a technique to generate protocol adaptors automatically. This is realised by means of genetically engineered classifier systems that use Petri nets as a specification for the underlying protocols. This paper reports on an experiment that validates this approach.

Automatic Adaptor Generation by means of Genetic Algorithms
August 2002 - Werner Van Belle, Tom Mens, Theo D'Hondt

Mobile multi-agent systems can be seen as a basis for global peer-to-peer computing. This new computation paradigm becomes increasingly more important as mobile devices become more powerful. Unfortunately, an open internet environment is an excellent area for interface conflicts between agents that want to communicate with each other. Although conflicting interfaces can be remedied by using adaptors, the number of possible combinations of different interfaces increases dramatically. Therefore we propose a technique to generate interface adaptors automatically. This is achieved by means of genetically engineered classifier systems (a well-known genetic algorithm technique) that use Petri nets as a specification for the underlying interfaces. This paper reports on an experiment that validates this approach. For designers of mobile applications, our approach is an important step forward, since the task of the developer is shifted from the writing of adaptors to the specification of test scenarios.

An experiment in automatic Adaptor Generation by means of Genetic Algorithms / Ma2002
May 2002 - Werner Van Belle, Theo D'Hondt

Mobile multi agent systems can be seen as a basis for global peer to peer computing. Nevertheless such an open environment makes it difficult to write agents which can interface with other agents because it is an excellent area for interface conflicts. Conflicting interfaces can be remedied by using adaptors. It is possible to automatically generate those glue-adaptors by means of genetically engineered classifier systems, which use Petri-nets as a model for the underlying interfaces. This paper reports on an experiment that illustrates this approach.

An experiment in automatic Adaptor Generation by means of Genetic Algorithms / Aamas2002
April 2002 - Werner Van Belle, Theo D'Hondt

The Reflective Virtual Machine
June 2001 - Karsten Verelst, Werner Van Belle, Theo D'Hondt

We claim that current day reflective architectures do not offer sufficient functionality, and that new developments in computer science push us towards a stronger reflective model: reflective virtual machines. We have witnessed these shortcomings in the application domain of mobility. Strong mobility is very difficult to implement in today's programming languages, mainly because of the inability to capture the program's computational state. Therefore we propose a new reflective architecture, the reflective virtual machine, that offers sufficient support for applications in mobility. In this paper we will first describe the basic functionality a mobile agentplatform should offer. This shall be done using a solution to the malicious host problem as a case. After identifying these needs we will introduce an interpreter, the Reflective Virtual Machine, that offers sufficient reflection, so that mobile applications can be straightforwardly implemented.

Is Message Sending Good enough for Distributed Systems ? Communication and synchronisation revisited
June 2001 - Werner Van Belle, Karsten Verelst, Kristof Van Buggenhout, Theo D'Hondt

This position paper looks at current day distributed object systems. In most of these systems we see a basic building primitive which offers us the needed distribution capabilities. Most of the time this is a synchronous or asynchronous message send. We argue that this is not good enough for distributed systems. Choosing the 'message-send' as primitive operation creates too many problems and creates the illusion that writing distributed programs is as easy as 'calling an object'. This is not true. In this paper we would like to present our ideas about this and hope to provoke some discussion about them.

Experiences in Mobile Computing: The CBorg Mobile Multi-Agent System
March 2001 - Werner Van Belle, Johan Fabry, Karsten Verelst, Theo D'Hondt

This paper reports on our experiences in the field of mobile components. In the past 4 years we developed a mobile component system, which allowed us to experiment with code mobility in distributed systems. These experiments have given us a unique opportunity to study two major issues in mobile component systems. The first issue is how to develop and provide a robust mobile component architecture. The second issue is how to write code in these kinds of systems. This paper discusses our experience in both of the above.

The CBorg Mobile Multi-Agent System
October 2000 - Werner Van Belle, Karsten Verelst, Theo D'Hondt

This paper describes the design behind an experimental mobile multi agent system we have built over the past 4 years. The architecture itself is called Cborg. The objective was to create an architecture which can be easily used to implement intelligent autonomous agents in a wide area network.

Towards a unified terminology for component-based development
June 2000 - Stefan Van Baelen, David Urting, Werner Van Belle, Viviane Jonckers, Tom Holvoet, Yolande Berbers, Karel De Vlaminck

Component-oriented programming and component-based development have become rather mature software development approaches in the last years, with both quite good conceptual and technological support. In spite of this rapid growth, the concepts used when talking about components are not always well-defined and can lead to misconception, misunderstanding and confusion. Although the general, abstract definition of a component, as defined at WCOP96: A software component is a unit of composition with contractually specified interfaces and explicit context dependencies only. A software component can be deployed independently and is subject to composition by third parties. is widely accepted, a lot of confusion can arise when characteristics of components are described.

Agent mobility and Reification of Computational State
June 2000 - Werner Van Belle, Theo D'Hondt

This paper describes an experiment with mobility in multi-agent systems. The setting is a virtual machine that supports reification of the computational state of a running process. The objective is to investigate how this feature facilitates telescripting and to speculate on how languages like Java should evolve to include the resulting notion of strong migration.

Communication & Synchronization in Mobile Multi-Agent Systems, CSP Revisited
March 2000 - Karsten Verelst, Werner Van Belle, Theo D'Hondt

We have created a communication model by extending an imperative language with 4 simple communication primitives. It turns out that these four primitives are very versatile and cover a large portion of existing communication protocols such as CSP and Actor systems. Our communication model offers both synchronous and asynchronous communication in an easy-to-use communication model. This is achieved by extending an imperative language with 4 communication primitives. Because we desire asynchronous means of communication, our main communication primitives, send and receive, both work asynchronous. We have also included a sync-primitive that synchronizes two processes, and thus synchronous communication can be simulated. The fourth primitive, newagent, is used to create new agents. In this document we first introduce these communication primitives with the help of some examples. Next we give an example that demonstrates the use of our communication model. This example already gives a hint of the great expressive power of our communication language and in the last part of this document we show that our communication model can simulate the behaviour of more well-known protocols, such as CSP, Pi-calculus, actor-systems, RMI and others.

Location Transparent Routing in Mobile Agent Systems - Merging Name Lookups with Routing
December 1999 - Werner Van Belle, Karsten Verelst, Theo D'Hondt

Telecommunication systems these days are moving from static wide area component structures towards highly dynamic mobile infrastructures. This shift requires new algorithms to interconnect these mobile entities/components and route messages between them. In this paper we describe a naming and routing algorithm which can be used in fine-grained mobile component systems. As a case we use a homogenous environment of mobile multi-agent systems, which executes agents as they pass by.

Reinforcement Learning as a Routing Technique for Mobile Multi Agent Systems
June 1998 - Werner Van Belle

Nowadays, a number of mobile multi agent systems are designed and implemented at a variety of research labs. Most of these systems suffer from a major problem: location transparency. Most systems do not implement this, and the few of them which do are not robust towards changes in the network topology and/or absolutely imperformant in wide area networks. In this paper we present a naming scheme and a location transparent routing algorithm, based upon reinforced Q learning, which is robust and performant.

Prototype Based agents for the Web
September 1997 - Wolfgang De Meuter, Kris De Volder, Werner Van Belle, Tom Tourwe, Theo D'Hondt

Signal Processing

An Adaptive Filter for the Correct Localization of Subimages: FFT based Subimage Localization Requires Image Normalization to work properly
October 2007 - Werner Van Belle

How to find subimages with the fast fourier transform ? It is well documented how Fourier transforms can speed up image alignment. The cross-correlation of an image can be calculated as the inverse Fourier transform of the inproduct of the Fourier transform of the first image and the conjugated Fourier transform of the second image. However, when one tries to extend this useful relation to locate subimages in larger images we find that it no longer performs properly. In this document we describe a fast normalization method that makes it possible to use the standard Fourier based cross-correlation technique for subimage localization. The technique relies on a low pass filtering followed by an adaptive contrast enhancement.

Correlation between the inproduct and the sum of absolute differences is -0.8485 for uniform sampled signals on [-1:1]
November 2006 - Werner Van Belle

While investigating relations between various comparators and the inproduct we found that the inproduct correlates strongly towards the absolute difference when the domain from which the values are taken come from a uniform distribution on [-1:1]. This useful relation might help to speed up block comparison in content databases and can be used as a valuable tool to estimate the inproduct based on the absolute difference and vice versa

Antenna Finding and Interpolation/Extrapolation of Signal Strength
November 2006 - Werner Van Belle

This article investigates the possibility to determine the position of a WiFi antenna by sampling the environment using a standard wireless card. The method is based on a search algorithm (simulated annealing) in a renormalized antenna model. The article further documents a sample acquisition phase in which a static wireless card measured the local environment. This might allow the integration of various oscillatory phenomena into the model.

Dj-ing under Linux with Bpmdj
October 2006 - Werner Van Belle

BpmDj provides the digital DJ with QT based tools to analyze, manage and play mp3/ogg songs. The program annotates all songs with psychoacoustic properties, including tempo, sound color, echo/delay information, rhythm information and composition information. The program relies on mplayer, ogg123 and/or mpg123 to decode songs while output is send through alsa or oss drivers. This article demonstrates beatmixing (how a DJ can superimpose two songs during longer times) and automixing (how BpmDj can mix music for you). It further sheds some light on the psychoacoustic properties used and a feature called beatgraphs.

Observations on spectrum and spectrum histograms in BpmDj
September 2005 - Werner Van Belle

BpmDj Is a program for DJ's. It helps to select songs and play them. To achieve this the program relies on a number of signal processing techniques. One of the available techniques compares song spectra. Both a standard spectrum analysis is performed as well as a distribution analysis ('echo' characteristics). In this short article we describe how this property is calculated and how it is further used in song comparison. We also present a short analysis of the structure of the space using correlation techniques.

BPM Measurement of Digital Audio by Means of Beat Graphs & Ray Shooting
October 2004 - Werner Van Belle

In this paper we present a) a novel audio visualization technique, called beat-graphs and b) a fully automatic algorithm to measure the mean tempo of a song with a very high accuracy. The algorithm itself is an easy implementable offline search algorithm that looks for the tempo that best describes the song. For every investigated tempo, it steps through the song and compares the similarity of consecutive pieces of information (bass drum, a hi-hat, ...). Its accuracy is two times higher than other fully automatic techniques, including Fourier analysis, envelope-spectrum analysis and autocorrelation.

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