http://hdl.handle.net/2268/85 Search this channel search http://orbi.ulg.ac.be/simple-search http://hdl.handle.net/2268/150651 Title: On the Relevance of Sophisticated Structural Annotations for Disulfide Connectivity Pattern Prediction <br/> <br/>Author, co-author: Becker, Julien; Maes, Francis; Wehenkel, Louis <br/> <br/>Abstract: Disulfide bridges strongly constrain the native structure of many proteins and predicting their formation is therefore a key sub-problem of protein structure and function inference. Most recently proposed approaches for this prediction problem adopt the following pipeline: first they enrich the primary sequence with structural annotations, second they apply a binary classifier to each candidate pair of cysteines to predict disulfide bonding probabilities and finally, they use a maximum weight graph matching algorithm to derive the predicted disulfide connectivity pattern of a protein. In this paper, we adopt this three step pipeline and propose an extensive study of the relevance of various structural annotations and feature encodings. In particular, we consider five kinds of structural annotations, among which three are novel in the context of disulfide bridge prediction. So as to be usable by machine learning algorithms, these annotations must be encoded into features. For this purpose, we propose four different feature encodings based on local windows and on different kinds of histograms. The combination of structural annotations with these possible encodings leads to a large number of possible feature functions. In order to identify a minimal subset of relevant feature functions among those, we propose an efficient and interpretable feature function selection scheme, designed so as to avoid any form of overfitting. We apply this scheme on top of three supervised learning algorithms: k-nearest neighbors, support vector machines and extremely randomized trees. Our results indicate that the use of only the PSSM (position-specific scoring matrix) together with the CSP (cysteine separation profile) are sufficient to construct a high performance disulfide pattern predictor and that extremely randomized trees reach a disulfide pattern prediction accuracy of on the benchmark dataset SPX+, which corresponds to +3.2% improvement over the state of the art. A web-application is available at http://m24.giga.ulg.ac.be:81/x3CysBridge​s. Mon, 17 Jun 2013 09:38:47 GMT http://hdl.handle.net/2268/150519 Title: An efficient algorithm to perform multiple testing in epistasis screening <br/> <br/>Author, co-author: Van Lishout, François; Mahachie John, Jestinah; Gusareva, Elena; Urrea, Victor; Cleynen, Isabelle; Theatre, Emilie; Charloteaux, Benoît; Calle, Malu Luz; Wehenkel, Louis; Van Steen, Kristel <br/> <br/>Abstract: Background: Research in epistasis or gene-gene interaction detection for human complex traits has grown over the last few years. It has been marked by promising methodological developments, improved translation efforts of statistical epistasis to biological epistasis and attempts to integrate different omics information sources into the epistasis screening to enhance power. The quest for gene-gene interactions poses severe multiple-testing problems. In this context, the maxT algorithm is one technique to control the false-positive rate. However, the memory needed by this algorithm rises linearly with the amount of hypothesis tests. Gene-gene interaction studies will require a memory proportional to the squared number of SNPs. A genome-wide epistasis search would therefore require terabytes of memory. Hence, cache problems are likely to occur, increasing the computation time. In this work we present a new version of maxT, requiring an amount of memory independent from the number of genetic effects to be investigated. This algorithm was implemented in C++ in our epistasis screening software MBMDR-3.0.3. We evaluate the new implementation in terms of memory efficiency and speed using simulated data. The software is illustrated on real-life data for Crohn's disease. Results: In the case of a binary (affected/unaffected) trait, the parallel workflow of MBMDR-3.0.3 analyzes all gene-gene interactions with a dataset of 100,000 SNPs typed on 1000 individuals within 4 days and 9 hours, using 999 permutations of the trait to assess statistical significance, on a cluster composed of 10 blades, containing each four Quad-Core AMD Opteron Processor 2352 2.1 GHz. In the case of a continuous trait, a similar run takes 9 days. Our program found 14 SNP-SNP interactions with a multiple-testing corrected p-value of less than 0.05 on real-life Crohn's disease data. Conclusions: Our software is the first implementation of the MB-MDR methodology able to solve large-scale SNP-SNP interactions problems within a few days, without using much memory, while adequately controlling the type I error rates. A new implementation to reach genome-wide epistasis screening is under construction. In the context of Crohn's disease, MBMDR-3.0.3 could identify epistasis involving regions that are well known in the field and could be explained from a biological point of view. This demonstrates the power of our software to find relevant phenotype-genotype higher-order associations. Sat, 15 Jun 2013 03:00:09 GMT http://hdl.handle.net/2268/150147 Title: A HYDROGEN BOND INFLUENCES THE 5-HT1A/D4 SELECTIVITY OF WAY-100635 ANALOGUES: AN IN SILICO APPROACH <br/> <br/>Author, co-author: Dilly, Sébastien; Liégeois, Jean-François <br/> <br/>Abstract: WAY-100635 is widely used in vitro and in vivo as an antagonist of 5-HT1A receptors. In terms of pharmacological tools and pharmacological investigations, the ideal reference molecule would be highly selective for its target over other related and non-related targets. However WAY-100635 displays affinity for and activity at D4 dopamine receptors, and that "off-target" activity confounds its use in pharmacological studies, particularly when both receptors are present. In this context, we carried out various chemical modifications of the WAY-100635 structure in order to improve its 5-HT1A versus D4 selectivity. An important increase of selectivity was obtained when the basic side chain of WAY-100635 was replaced by a 4-phenylpiperazine or a 4-phenyl-1,2,3,6-tetrahydropyridine moiety. In contrast, the introduction of nitrogen atoms in the acyl group decreased the selectivity by reducing the affinity for 5-HT1A receptors, on the one hand, and enhancing the affinity for D4 receptors on the other hand. In order to explain the reduced 5-HT1A/D4 selectivity of aza-derivatives, the binding modes of the compounds were explored by docking analysis on homology models of the two receptors. It appears that the formation of an additional hydrogen bond within D4 receptors could be the key of the decreased selectivity. These results will be very helpful for developing molecules with an improved 5-HT1A/D4 selectivity. Tue, 11 Jun 2013 06:16:59 GMT http://hdl.handle.net/2268/150070 Title: A Site-Specific Grain Yield Response Surface : Computing the Identity Card of a Crop Under Different Nitrogen Management Scenarios <br/> <br/>Author, co-author: Dumont, Benjamin; Basso, Bruno; Leemans, Vincent; Destain, Jean-Pierre; Bodson, Bernard; Destain, Marie-France <br/> <br/>Abstract: At the parcel scale, crop models such as STICS are powerful tools to study the effects of variable inputs such as management practices (e.g. nitrogen (N) fertilization). In combination with a weather generator, we propose a general methodology that allows studying the yield variability linked to climate uncertainty, in order to assess the best practices in applying fertilizers. Our study highlights that, using the usual practice of Belgian farmers, namely applying three doses of 60kgN/ha, the yield’s distribution presents the highest degree of asymmetry. This implies the highest probability to achieve yields superior to the mean. The computed return time of expected yield shows that 9 years out of 10, a grain yield of 7.26 tons.ha-1 could at least be achieved. Mon, 10 Jun 2013 06:37:42 GMT http://hdl.handle.net/2268/149895 Title: Suivi diachronique de l’analyse de corpus partagés <br/> <br/>Author, co-author: Bénel, Aurélien; Lejeune, Christophe <br/> <br/>Abstract: Les anthropologues des sciences ont développé un mode d'inscription permettant le suivi de l'innovation qu'ils appellent "graphe socio-technique". Cette contribution présente les tentatives d'application de ce dispositif de visualisation au suivi de l'activité sur des plateformes informatiques. Elle soulève des difficultés à la fois techniques et méthodologiques. Thu, 06 Jun 2013 07:47:34 GMT http://hdl.handle.net/2268/149120 Title: Stratégies d'échantillonnage pour l'apprentissage par renforcement batch <br/> <br/>Author, co-author: Fonteneau, Raphaël; Murphy, Susan A.; Wehenkel, Louis; Ernst, Damien <br/> <br/>Abstract: Cet article présente deux stratégies d’échantillonnage dans le contexte de l’apprentissage par renforcement en mode “batch”. La première stratégie repose sur l’idée que les expériences susceptibles de mener à une modification de la politique de décision courante sont particulièrement informatives. Etant donné a priori un algorithme d’inférence de politiques de décision ainsi qu’un modèle prédictif du système, une expérience est réalisée si, étant donné le modèle prédictif, cette expérience mène à l’apprentissage d’une politique de décision différente. La deuxième stratégie exploite des résultats récemment publiés pour calculer des bornes sur le retour des politiques de décision de manière à sélectionner des expériences améliorant la précision des bornes afin de discriminer les politiques non-optimales. Ces deux stratégies sont illustrées sur des problèmes élémentaires et les résultats obtenus sont prometteurs.; We propose two strategies for experiment selection in the context of batch mode reinforcement learning. The first strategy is based on the idea that the most interesting experiments to carry out at some stage are those that are the most liable to falsify the current hypothesis about the optimal control policy. We cast this idea in a context where a policy learning algorithm and a model identification method are given a priori. The second strategy exploits recently published methods for computing bounds on the return of control policies from a set of trajectories in order to sample the state-action space so as to be able to discriminate between optimal and non-optimal policies. Both strategies are experimentally validated, showing promising results. Thu, 23 May 2013 19:03:03 GMT http://hdl.handle.net/2268/148453 Title: Meta-learning of Exploration/Exploitation Strategies: The Multi-Armed Bandit Case <br/> <br/>Author, co-author: Maes, Francis; Wehenkel, Louis; Ernst, Damien <br/> <br/>Abstract: The exploration/exploitation (E/E) dilemma arises naturally in many subfields of Science. Multi-armed bandit problems formalize this dilemma in its canonical form. Most current research in this field focuses on generic solutions that can be applied to a wide range of problems. However, in practice, it is often the case that a form of prior information is available about the specific class of target problems. Prior knowledge is rarely used in current solutions due to the lack of a systematic approach to incorporate it into the E/E strategy. To address a specific class of E/E problems, we propose to proceed in three steps: (i) model prior knowledge in the form of a probability distribution over the target class of E/E problems; (ii) choose a large hypothesis space of candidate E/E strategies; and (iii), solve an optimization problem to find a candidate E/E strategy of maximal average performance over a sample of problems drawn from the prior distribution. We illustrate this meta-learning approach with two different hypothesis spaces: one where E/E strategies are numerically parameterized and another where E/E strategies are represented as small symbolic formulas. We propose appropriate optimization algorithms for both cases. Our experiments, with two-armed “Bernoulli” bandit problems and various playing budgets, show that the metalearnt E/E strategies outperform generic strategies of the literature (UCB1, UCB1-T UNED, UCB-V, KL-UCB and epsilon-GREEDY); they also evaluate the robustness of the learnt E/E strategies, by tests carried out on arms whose rewards follow a truncated Gaussian distribution. Tue, 14 May 2013 11:09:10 GMT http://hdl.handle.net/2268/147763 Title: A First Measurement Look at the Deployment and Evolution of the Locator/ID Separation Protocol <br/> <br/>Author, co-author: Saucez, Damien; Iannone, Luigi; Donnet, Benoît <br/> <br/>Abstract: During the last decade, we have seen the rise of discussions regarding the emergence of a Future Internet. One of the proposed approaches leverages on the separation of the identifier and the locator roles of IP addresses, leading to the LISP (Locator/Identifier Separation Protocol) protocol, currently under development at the IETF (Internet Engineering Task Force). Up to now, researches made on LISP have been rather theoretical, i.e., based on simulations/emulations often using Internet traffic traces. There is no work in the literature attempting to assess the state of its deployment and how this has evolved in recent years. This paper aims at bridging this gap by presenting a first measurement study on the existing worldwide LISP network (lisp4.net). Early results indicate that there is a steady growth of the LISP network but also that network manageability might receive a higher priority than performance in a large scale deployment. Thu, 02 May 2013 07:33:47 GMT http://hdl.handle.net/2268/145692 Title: Robust stress intensity factors evaluation for 3D cracks with X-FEM <br/> <br/>Author, co-author: Minnebo, Hans; Béchet, Eric; Moës, Nicolas Wed, 27 Mar 2013 20:12:36 GMT http://hdl.handle.net/2268/145691 Title: Explicit dynamics with X-FEM to handle complex geometries <br/> <br/>Author, co-author: Moes, Nicolas; Rozycki, P.; Béchet, Eric Wed, 27 Mar 2013 20:11:15 GMT http://hdl.handle.net/2268/145260 Title: Internet Topology Discovery <br/> <br/>Author, co-author: Donnet, Benoît <br/> <br/>Abstract: Since the nineties, the Internet has seen an impressive growth, in terms of users, intermediate systems (such as routers), autonomous systems, or applications. In parallel to this growth, the research community has been looking for obtaining and modeling the Internet topology, i.e., how the various elements of the network interconnect between themselves. An impressive amount of work has been done regarding how to collect data and how to analyse and model it. This chapter reviews main approaches for gathering Internet topology data. We first focus on hop limited probing, i.e., traceroute-like probing. We review large-scale tracerouting projects and discuss traceroute limitations and how they are mitigated by new techniques or extensions. Hop limited probing can reveal an IP interface vision of the Internet. We next focus on techniques for aggregating several IP interfaces of a given router into a single identifier. This leads to a router level vision of the topology. The aggregation can be done through a process called alias resolution. We also review a technique based on IGMP probing that silently collect all multicast interfaces of a router into a single probe. We next refine the router level topology by adding subnet information. We finish this chapter by discussing the AS level topology, in particular the relationships between ASes and the induced hierarchy. Fri, 22 Mar 2013 07:15:33 GMT http://hdl.handle.net/2268/145217 Title: PRIM related correlations <br/> <br/>Author, co-author: Mathéi, Axel Thu, 21 Mar 2013 11:32:04 GMT http://hdl.handle.net/2268/144646 Title: On the Number of Abelian Bordered Words <br/> <br/>Author, co-author: Rampersad, Narad; Rigo, Michel; Salimov, Pavel <br/> <br/>Abstract: In the literature, many bijections between (labeled) Motzkin paths and various other combinatorial objects are studied. We consider abelian (un)bordered words and show the connection with irreducible symmetric Motzkin paths and paths in Z not returning to the origin. This study can be extended to abelian unbordered words over an arbitrary alphabet and we derive expressions to compute the number of these words. In particular, over a 3-letter alphabet, the connection with paths in the triangular lattice is made. Finally, we study the lengths of the abelian unbordered factors occurring in the Thue--Morse word. Tue, 12 Mar 2013 18:12:02 GMT http://hdl.handle.net/2268/144561 Title: Extremely Randomized Trees and Random Subwindows for Image Classification, Annotation, and Retrieval <br/> <br/>Author, co-author: Marée, Raphaël; Wehenkel, Louis; Geurts, Pierre <br/> <br/>Abstract: We present a unified framework involving the extraction of random subwindows within images and the induction of ensembles of extremely randomized trees. We discuss the specialization of this framework for solving several general problems in computer vision, ranging from image classification and segmentation to content-based image retrieval and interest point detection. The methods are illustrated on various applications and datasets from the biomedical domain Tue, 12 Mar 2013 08:43:52 GMT http://hdl.handle.net/2268/143553 Title: Travaux Pratiques de Télédétection Spatiale <br/> <br/>Author, co-author: Denis, Antoine <br/> <br/>Abstract: Notes de travaux pratiques d'initiation à la télédétection spatiale. Le logiciel principalement utilisé dans ces travaux est ENVI de la firme Exelis. Les autres logiciels sont WINDIP, ViewSpecPro et Google Earth. Les exercices concernent, par ordre d'importance: la classification supervisée d'une image haute résolution (observation, correction géométrique, identification des zones d'entrainement et caractérisation statistique des échantillons, classification, validation), l'analyse diachronique de 2 images basses résolution, l'analyse temporelle d'une série d'images basses résolution (profil NDVI), création de néo-canaux (NDVI, Tasseled cap, ACP) la visualisation 3D, l'analyse de données (image et ponctuelle) hyperspectrales, la découverte de Google Earth, la recherche d'images satellites sur le web,... Thu, 21 Feb 2013 19:22:26 GMT http://hdl.handle.net/2268/143530 Title: Optimal discovery with probabilistic expert advice: finite time analysis and macroscopic optimality <br/> <br/>Author, co-author: Bubeck, Sébastien; Ernst, Damien; Garivier, Aurélien <br/> <br/>Abstract: We consider an original problem that arises from the issue of security analysis of a power system and that we name optimal discovery with probabilistic expert advice. We address it with an algorithm based on the optimistic paradigm and on the Good-Turing missing mass estimator. We prove two different regret bounds on the performance of this algorithm under weak assumptions on the probabilistic experts. Under more restrictive hypotheses, we also prove a macroscopic optimality result, comparing the algorithm both with an oracle strategy and with uniform sampling. Finally, we provide numerical experiments illustrating these theoretical findings. Thu, 21 Feb 2013 15:36:29 GMT http://hdl.handle.net/2268/143530 Title: Optimal discovery with probabilistic expert advice: finite time analysis and macroscopic optimality <br/> <br/>Author, co-author: Bubeck, Sébastien; Ernst, Damien; Garivier, Aurélien <br/> <br/>Abstract: We consider an original problem that arises from the issue of security analysis of a power system and that we name optimal discovery with probabilistic expert advice. We address it with an algorithm based on the optimistic paradigm and on the Good-Turing missing mass estimator. We prove two different regret bounds on the performance of this algorithm under weak assumptions on the probabilistic experts. Under more restrictive hypotheses, we also prove a macroscopic optimality result, comparing the algorithm both with an oracle strategy and with uniform sampling. Finally, we provide numerical experiments illustrating these theoretical findings. Thu, 21 Feb 2013 15:36:29 GMT http://hdl.handle.net/2268/142763 Title: A Learning Procedure for Sampling Semantically Different Valid Expressions <br/> <br/>Author, co-author: Lupien St-Pierre, David; Maes, Francis; Ernst, Damien; Louveaux, Quentin Tue, 12 Feb 2013 09:14:18 GMT http://hdl.handle.net/2268/142672 Title: Survival analysis: finding relevant epistatic SNP pairs using Model- Based Multifactor Dimensionality Reduction <br/> <br/>Author, co-author: Van Lishout, François; Vens, Céline; Urrea, Victor; Calle, M. Luz; Wehenkel, Louis; Van Steen, Kristel <br/> <br/>Abstract: Analyzing the combined effects of genes (and/or environmental factors) on the development of complex diseases is quite challenging, both from the statistical and computational perspective, even using a relatively small number of genetic and non-genetic exposures. Several data-mining methods have been proposed for interaction analysis, among them, the Multifactor Dimensionality Reduction Method (MDR). Model-Based Multifactor Dimensionality Reduction (MB-MDR), a relatively new dimensionality reduction technique, is able to unify the best of both nonparametric and parametric worlds, and has proven its utility in a variety of theoretical and practical settings. Until now, MB-MDR software has only accommodated traits that are measured on a binary or interval scale. Time-to-event data could therefore not be analyzed with the MB-MDR methodology. MB-MDR-3.0.0 overcomes this shortcoming of earlier versions. We show the added value of MB-MDR for censored traits by comparing the implemented strategies with more classical methods such as those based on a parametric regression paradigm. The simulation results are supplemented with an application to real-life data. Sun, 10 Feb 2013 04:02:58 GMT http://hdl.handle.net/2268/142449 Title: Sparse Summarization of Robotic Grasp Data <br/> <br/>Author, co-author: Hjelm, Martin; Ek, Carl Henrik; Detry, Renaud; Kjellström, Hedvig; Kragic, Danica Thu, 07 Feb 2013 11:49:39 GMT