Adaptive imputation of missing values for incomplete pattern classification

In classification of incomplete pattern, the missing values can either play a crucial role in the class determination, or have only little influence (or eventually none) on the classification results according to the context. We propose a credal classification method for incomplete pattern with adaptive imputation of missing values based on belief function theory. At first, we try to classify the object (incomplete pattern) based only on the available attribute values. As underlying principle, we assume that the missing information is not crucial for the classification if a specific class for the object can be found using only the available information. In this case, the object is committed to this particular class. However, if the object cannot be classified without ambiguity, it means that the missing values play a main role for achieving an accurate classification. In this case, the missing values will be imputed based on the K-nearest neighbor (K-NN) and self-organizing map (SOM) techniques, and the edited pattern with the imputation is then classified. The (original or edited) pattern is respectively classified according to each training class, and the classification results represented by basic belief assignments are fused with proper combination rules for making the credal classification. The object is allowed to belong with different masses of belief to the specific classes and meta-classes (which are particular disjunctions of several single classes). The credal classification captures well the uncertainty and imprecision of classification, and reduces effectively the rate of misclassifications thanks to the introduction of meta-classes. The effectiveness of the proposed method with respect to other classical methods is demonstrated based on several experiments using artificial and real data sets

Heterologous expression screens in Nicotiana benthamiana identify a candidate effector of the wheat Yellow Rust Pathogen that associates with processing bodies

Rust fungal pathogens of wheat (Triticum spp.) affect crop yields worldwide. The molecular mechanisms underlying the virulence of these pathogens remain elusive, due to the limited availability of suitable molecular genetic research tools. Notably, the inability to perform high-throughput analyses of candidate virulence proteins (also known as effectors) impairs progress. We previously established a pipeline for the fast-forward screens of rust fungal candidate effectors in the model plant Nicotiana benthamiana. This pipeline involves selecting candidate effectors in silico and performing cell biology and protein-protein interaction assays in planta to gain insight into the putative functions of candidate effectors. In this study, we used this pipeline to identify and characterize sixteen candidate effectors from the wheat yellow rust fungal pathogen Puccinia striiformis f sp tritici. Nine candidate effectors targeted a specific plant subcellular compartment or protein complex, providing valuable information on their putative functions in plant cells. One candidate effector, PST02549, accumulated in processing bodies (P-bodies), protein complexes involved in mRNA decapping, degradation, and storage. PST02549 also associates with the P-body-resident ENHANCER OF mRNA DECAPPING PROTEIN 4 (EDC4) from N. benthamiana and wheat. We propose that P-bodies are a novel plant cell compartment targeted by pathogen effectors

Profound effect of profiling platform and normalization strategy on detection of differentially expressed microRNAs

Adequate normalization minimizes the effects of systematic technical variations and is a prerequisite for getting meaningful biological changes. However, there is inconsistency about miRNA normalization performances and recommendations. Thus, we investigated the impact of seven different normalization methods (reference gene index, global geometric mean, quantile, invariant selection, loess, loessM, and generalized procrustes analysis) on intra- and inter-platform performance of two distinct and commonly used miRNA profiling platforms. We included data from miRNA profiling analyses derived from a hybridization-based platform (Agilent Technologies) and an RT-qPCR platform (Applied Biosystems). Furthermore, we validated a subset of miRNAs by individual RT-qPCR assays. Our analyses incorporated data from the effect of differentiation and tumor necrosis factor alpha treatment on primary human skeletal muscle cells and a murine skeletal muscle cell line. Distinct normalization methods differed in their impact on (i) standard deviations, (ii) the area under the receiver operating characteristic (ROC) curve, (iii) the similarity of differential expression. Loess, loessM, and quantile analysis were most effective in minimizing standard deviations on the Agilent and TLDA platform. Moreover, loess, loessM, invariant selection and generalized procrustes analysis increased the area under the ROC curve, a measure for the statistical performance of a test. The Jaccard index revealed that inter-platform concordance of differential expression tended to be increased by loess, loessM, quantile, and GPA normalization of AGL and TLDA data as well as RGI normalization of TLDA data. We recommend the application of loess, or loessM, and GPA normalization for miRNA Agilent arrays and qPCR cards as these normalization approaches showed to (i) effectively reduce standard deviations, (ii) increase sensitivity and accuracy of differential miRNA expression detection as well as (iii) increase inter-platform concordance. Results showed the successful adoption of loessM and generalized procrustes analysis to one-color miRNA profiling experiments

Minimization of DDoS false alarm rate in Network Security; Refining fusion through correlation

Intrusion Detection Systems are designed to monitor a network environment and generate alerts whenever abnormal activities are detected. However, the number of these alerts can be very large making their evaluation a difficult task for a security analyst. Alert management techniques reduce alert volume significantly and potentially improve detection performance of an Intrusion Detection System. This thesis work presents a framework to improve the effectiveness and efficiency of an Intrusion Detection System by significantly reducing the false positive alerts and increasing the ability to spot an actual intrusion for Distributed Denial of Service attacks. Proposed sensor fusion technique addresses the issues relating the optimality of decision-making through correlation in multiple sensors framework. The fusion process is based on combining belief through Dempster Shafer rule of combination along with associating belief with each type of alert and combining them by using Subjective Logic based on Jøsang theory. Moreover, the reliability factor for any Intrusion Detection System is also addressed accordingly in order to minimize the chance of false diagnose of the final network state. A considerable number of simulations are conducted in order to determine the optimal performance of the proposed prototype