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In this study the effect of a roughness discontinuity caused by a pipeline cover layer in the sea bed is investigated. As a result of this non-uniform flow configuration, the environmental forces acting on the pipeline cover layer change. To investigate the effect of roughness discontinuities, a numerical model of the flow is made; thereby neglecting the effect of waves. This is done by making use of the flow solvers Delft3D-FL0W and CFX. The most important difference between these solvers is the hydrostatic pressure assumption in Delft3D-FL0W, while CFX solves the full 3D Navier Stokes equations. In order to create reliable simulations, both hydrostatic and non-hydrostatic calculations are performed and compared with experiments and calculations found in literature. These calculations deal with the transition from hydraulically smooth to hydraulically rough surfaces and vice versa. The phenomena of overshooting and undershooting of the wall/bed shear stress near the discontinuity and the development of a sub or 'internal' boundary layer, concluded from previous investigations, are calculated with Delft3D-FL0W as CFX as well. Modelling abrupt roughness discontinuities presents considerable difficulties with respect to the convergence to a grid independent solution in both Delft3D-FL0W as CFX, particularly in the smooth to rough case. The (equilibrium) wall function concept, strictly speaking only valid for uniform flow conditions, could be an important explanation for this problem Based on these test case calculations, the flow near an abrupt roughness increment caused by a pipeline cover layer of 10 m length is modelled with CFX. The model is used to make qualitative predictions of the flow and loads on the pipeline cover layer, but is not able to predict the exact loads. The different calculations lead to the consideration that both the instantaneous bed shear stress and its standard deviation increase near the roughness discontinuity. It is therefore concluded that the stones are under heavier attack in comparison to uniform flow conditions. For realistic situations, when the influence of the bed forms resulting from sediment transport are taken into account, these variations are probably small. It is suggested that these findings are verified experimentally and extended with investigation to the effect of waves and the influence on the problem of sediment transport.

Methods commonly used for speech and sign language recognition often rely on outputs of Hidden Markov Models (HMM) or Dynamic TimeWarping (DTW) for classification, which aremerely factorized observation likelihoods. Instead, we propose to use Statistical DTW (SDTW) only for warping, while classifying the synchronized features with either of two proposed discriminants. This hybrid approach is shown to outperform HMM and SDTW. However, we have found that combining likelihoods of multiple models in a second classification stage degrades performance of the proposed classifiers, while improving performance with HMM and SDTW. A proof-of-concept experiment, combining DFFM mappings of multiple SDTW models with SDTW likelihoods, shows that also for model-combining, hybrid classification can provide significant improvement over SDTW.

A method is proposed for filling in missing areas of degraded images through explicit structure reconstruction, followed by texture synthesis. The structure being reconstructed represents meaningful edges from the image, which are traced inside the artefact. The structure reconstruction step relies on different properties of the edges touching the artefact and of the areas between them, in order to sketch the missing edges within the artefact area. The texture synthesis step is based on Markov random fields and is constrained by the traced edges in order to preserve both the shape and the appearance of the various regions in the image. The novelty of our contribution concerns constraining the texture synthesis, which proves to give results superior to the original texture synthesis alone, or to the smoothness-preserving structure-based restoration.

To recognize speech, handwriting, or sign language, many hybrid approaches have been proposed that combine Dynamic Time Warping (DTW) or Hidden Markov Models (HMMs) with discriminative classifiers. However, all methods rely directly on the likelihood models of DTW/HMM. We hypothesize that time warping and classification should be separated because of conflicting likelihood modeling demands. To overcome these restrictions, we propose using Statistical DTW (SDTW) only for time warping, while classifying the warped features with a different method. Two novel statistical classifiers are proposed—Combined Discriminative Feature Detectors (CDFDs) and Quadratic Classification on DF Fisher Mapping (Q-DFFM)—both using a selection of discriminative features (DFs), and are shown to outperform HMM and SDTW. However, we have found that combining likelihoods of multiple models in a second classification stage degrades performance of the proposed classifiers, while improving performance with HMM and SDTW. A proof-of-concept experiment, combining DFFM mappings of multiple SDTW models with SDTW likelihoods, shows that, also for model-combining, hybrid classification can provide significant improvement over SDTW. Although recognition is mainly based on 3D hand motion features, these results can be expected to generalize to recognition with more detailed measurements such as hand/body pose and facial expression.

In recent years, more and more high-throughput data sources useful for protein complex prediction have become available (e.g., gene sequence, mRNA expression, and interactions). The integration of these different data sources can be challenging. Recently, it has been recognized that kernel-based classifiers are well suited for this task. However, the different kernels (data sources) are often combined using equal weights. Although several methods have been developed to optimize kernel weights, no large-scale example of an improvement in classifier performance has been shown yet. In this work, we employ an evolutionary algorithm to determine weights for a larger set of kernels by optimizing a criterion based on the area under the ROC curve. We show that setting the right kernel weights can indeed improve performance. We compare this to the existing kernel weight optimization methods (i.e., (regularized) optimization of the SVM criterion or aligning the kernel with an ideal kernel) and find that these do not result in a significant performance improvement and can even cause a decrease in performance. Results also show that an expert approach of assigning high weights to features with high individual performance is not necessarily the best strategy.

Comparative analysis of metabolic networks in multiple species yields important information on their evolution, and has great practical value in metabolic engineering, human disease analysis, drug design etc. In this work, we aim to systematically search for conserved pathways in two species, quantify their similarities, and focus on the variations between them

In recent work, attempts have been made to link the structure of biochemical networks to their complex dynamics. It was shown that structurally stable network motifs are enriched in such networks. In this work, we investigate to what extent these findings apply to metabolic networks. To this end, we extend a previously proposed method by changing the null model for determining motif enrichment, by using interaction types directly obtained from structural interaction matrices, by generating a distribution of partial derivatives of reaction rates and by simulating enzymatic regulation on metabolic networks. Our findings suggest that the conclusions drawn in previous work cannot be extended to metabolic networks, that is, structurally stable network motifs are not enriched in metabolic networks.

Motivation: Cells receive a wide variety of environmental signals, which are often processed combinatorially to generate specific genetic responses. Changes in transcript levels, as observed across different environmental conditions, can, to a large extent, be attributed to changes in the activity of transcription factors (TFs). However, in unraveling these transcription regulation networks, the actual environmental signals are often not incorporated into the model, simply because they have not been measured. The unquantified heterogeneity of the environmental parameters across microarray experiments frustrates regulatory network inference. Results: We propose an inference algorithm that models the influence of environmental parameters on gene expression. The approach is based on a yeast microarray compendium of chemostat steady-state experiments. Chemostat cultivation enables the accurate control and measurement of many of the key cultivation parameters, such as nutrient concentrations, growth rate and temperature. The observed transcript levels are explained by inferring the activity of TFs in response to combinations of cultivation parameters. The interplay between activated enhancers and repressors that bind a gene promoter determine the possible up- or downregulation of the gene. The model is translated into a linear integer optimization problem. The resulting regulatory network identifies the combinatorial effects of environmental parameters on TF activity and gene expression.

Background. The availability of large collections of microarray datasets (compendia), or knowledge about grouping of genes into pathways (gene sets), is typically not exploited when training predictors of disease outcome. These can be useful since a compendium increases the number of samples, while gene sets reduce the size of the feature space. This should be favorable from a machine learning perspective and result in more robust predictors. Methodology. We extracted modules of regulated genes from gene sets, and compendia. Through supervised analysis, we constructed predictors which employ modules predictive of breast cancer outcome. To validate these predictors we applied them to independent data, from the same institution (intra-dataset), and other institutions (inter-dataset). Conclusions. We show that modules derived from single breast cancer datasets achieve better performance on the validation data compared to gene-based predictors. We also show that there is a trend in compendium specificity and predictive performance: modules derived from a single breast cancer dataset, and a breast cancer specific compendium perform better compared to those derived from a human cancer compendium. Additionally, the module-based predictor provides a much richer insight into the underlying biology. Frequently selected gene sets are associated with processes such as cell cycle, E2F regulation, DNA damage response, proteasome and glycolysis. We analyzed two modules related to cell cycle, and the OCT1 transcription factor, respectively. On an individual basis, these modules provide a significant separation in survival subgroups on the training and independent validation data.

We introduce personalization on Tribler, a peer-to-peer (P2P) television system. Personalization allows users to browse programs much more efficiently according to their taste. It also enables to build social networks that can improve the performance of current P2P systems considerably, by increasing content availability, trust and the realization of proper incentives to exchange content. This paper presents a novel scheme, called BuddyCast, that builds such a social network for a user by exchanging user interest profiles using exploitation and exploration principles. Additionally, we show how the interest of a user in TV programs can be predicted from the zapping behavior by the introduced user-item relevance models, thereby avoiding the explicit rating of TV programs. Further, we present how the social network of a user can be used to realize a truly distributed recommendation of TV programs. Finally, we demonstrate a novel user interface for the personalized peer-to-peer television system that encompasses a personalized tag-based navigation to browse the available distributed content. The user interface also visualizes the social network of a user, thereby increasing community feeling which increases trust amongst users and within available content and creates incentives of to exchange content within the community.

Tumor formation is in part driven by DNA copy number alterations (CNAs), which can be measured using microarray-based Comparative Genomic Hybridization (aCGH). Multiexperiment analysis of aCGH data from tumors allows discovery of recurrent CNAs that are potentially causal to cancer development. Until now, multiexperiment aCGH data analysis has been dependent on discretization of measurement data to a gain, loss or no-change state. Valuable biological information is lost when a heterogeneous system such as a solid tumor is reduced to these states. We have developed a new approach which inputs nondiscretized aCGH data to identify regions that are significantly aberrant across an entire tumor set. Our method is based on kernel regression and accounts for the strength of a probe’s signal, its local genomic environment and the signal distribution across multiple tumors. In an analysis of 89 human breast tumors, our method showed enrichment for known cancer genes in the detected regions and identified aberrations that are strongly associated with breast cancer subtypes and clinical parameters. Furthermore, we identified 18 recurrent aberrant regions in a new dataset of 19 p53-deficient mouse mammary tumors. These regions, combined with gene expression microarray data, point to known cancer genes and novel candidate cancer genes.

Collaborative filtering is concerned with making recommendations about items to users. Most formulations of the problem are specifically designed for predicting user ratings, assuming past data of explicit user ratings is available. However, in practice we may only have implicit evidence of user preference; and furthermore, a better view of the task is of generating a top-N list of items that the user is most likely to like. In this regard, we argue that collaborative filtering can be directly cast as a relevance ranking problem. We begin with the classic Probability Ranking Principle of information retrieval, proposing a probabilistic item ranking framework. In the framework, we derive two different ranking models, showing that despite their common origin, different factorizations reflect two distinctive ways to approach item ranking. For the model estimations, we limit our discussions to implicit user preference data, and adopt an approximation method introduced in the classic text retrieval model (i.e. the Okapi BM25 formula) to effectively decouple frequency counts and presence/absence counts in the preference data. Furthermore, we extend the basic formula by proposing the Bayesian inference to estimate the probability of relevance (and non-relevance), which largely alleviates the data sparsity problem. Apart from a theoretical contribution, our experiments on real data sets demonstrate that the proposed methods perform significantly better than other strong baselines.