Stacked regression ensemble for cancer class prediction

Design of a machine learning algorithm as a robust class predictor for various DNA microarray datasets is a challenging task, as the number of samples are very small as compared to the thousands of genes (feature set). For such datasets, a class prediction model could be very successful in classifying one type of dataset but may fail to perform in a similar fashion for other datasets. This paper presents a stacked regression ensemble (SRE) model for cancer class prediction. Results indicate that SRE has provided performance stability for various microarray datasets. The performance of SRE has been cross validated using the k-fold cross validation method (leave one out) technique for BRCA1, BRCA2 and sporadic classes for ovarian and breast cancer microarray datasets. The paper also presents comparative results of SRE with most commonly used SVM and GRNN. Empirical results confirmed that SRE has demonstrated better performance stability as compared to SVM and GRNN for the classification of assorted cancer data

A hybrid neural network based speech recognition system for pervasive environments

One of the major drawbacks to using speech as the input to any pervasive environment is the requirement to balance accuracy with the high processing overheads involved. This paper presents an Arabic speech recognition system (called UbiqRec), which address this issue by providing a natural and intuitive way of communicating within ubiquitous environments, while balancing processing time, memory and recognition accuracy. A hybrid approach has been used which incorporates spectrographic information, singular value decomposition, concurrent self-organizing maps (CSOM) and pitch contours for Arabic phoneme recognition. The approach employs separate self-organizing maps (SOM) for each Arabic phoneme joined in parallel to form a CSOM. The performance results confirm that with suitable preprocessing of data, including extraction of distinct power spectral densities (PSD) and singular value decomposition, the training time for CSOM was reduced by 89%. The empirical results also proved that overall recognition accuracy did not fall below 91%

How to Improve Postgenomic Knowledge Discovery Using Imputation

While microarrays make it feasible to rapidly investigate many complex biological problems, their multistep fabrication has the proclivity for error at every stage. The standard tactic has been to either ignore or regard erroneous gene readings as missing values, though this assumption can exert a major influence upon postgenomic knowledge discovery methods like gene selection and gene regulatory network (GRN) reconstruction. This has been the catalyst for a raft of new flexible imputation algorithms including local least square impute and the recent heuristic collateral missing value imputation, which exploit the biological transactional behaviour of functionally correlated genes to afford accurate missing value estimation. This paper examines the influence of missing value imputation techniques upon postgenomic knowledge inference methods with results for various algorithms consistently corroborating that instead of ignoring missing values, recycling microarray data by flexible and robust imputation can provide substantial performance benefits for subsequent downstream procedures

DLocalMotif: a discriminative approach for discovering local motifs in protein sequences

Motivation: Local motifs are patterns of DNA or protein sequences that occur within a sequence interval relative to a biologically defined anchor or landmark. Current protein motif discovery methods do not adequately consider such constraints to identify biologically significant motifs that are only weakly over-represented but spatially confined. Using negatives, i.e. sequences known to not contain a local motif, can further increase the specificity of their discovery

Performance of the gas gain monitoring system of the CMS RPC muon detector

The RPC muon detector of the CMS experiment at the LHC (CERN, Geneva, Switzerland) is equipped with a Gas Gain Monitoring (GGM) system. A report on the stability of the system during the 2011-2012 data taking run is given, as well as the observation of an effect which suggests a novel method for the monitoring of gas mixture composition.Comment: Presented at RPC2014, Beijing, China. Accepted for publication on JINS

A clustering based hybrid system for mass spectrometry data analysis

Recently, much attention has been given to the mass spectrometry (MS) technology based disease classification, diagnosis, and protein-based biomarker identification. Similar to microarray based investigation, proteomic data generated by such kind of high-throughput experiments are often with high feature-to-sample ratio. Moreover, biological information and pattern are compounded with data noise, redundancy and outliers. Thus, the development of algorithms and procedures for the analysis and interpretation of such kind of data is of paramount importance. In this paper, we propose a hybrid system for analyzing such high dimensional data. The proposed method uses the k-mean clustering algorithm based feature extraction and selection procedure to bridge the filter selection and wrapper selection methods. The potential informative mass/charge (m/z) markers selected by filters are subject to the k-mean clustering algorithm for correlation and redundancy reduction, and a multi-objective Genetic Algorithm selector is then employed to identify discriminative m/z markers generated by k-mean clustering algorithm. Experimental results obtained by using the proposed method indicate that it is suitable for m/z biomarker selection and MS based sample classification. <br /

A probabilistic model of nuclear import of proteins

Motivation: Nucleo-cytoplasmic trafficking of proteins is a core regulatory process that sustains the integrity of the nuclear space of eukaryotic cells via an interplay between numerous factors. Despite progress on experimentally characterizing a number of nuclear localization signals, their presence alone remains an unreliable indicator of actual translocation

Resistive plate chambers for 2013-2014 muon upgrade in CMS at LHC

During 2013 and 2014 (Long Shutdown LS1) the CMS experiment is upgrading the forward region installing a fourth layer of RPC detectors in order to complete and improve the muon system performances in the view ofthe foreseen high luminosity run ofLHC. The new two endcap disks consists of 144 double-gap RPC chambers assembled at three different production sites: CERN, Ghent (Belgium) and BARC (India). The chamber components as well as the final detectors are subjected to full series oftests established in parallel at all the production sites. All assembly and test operations have been engineered in order to standardize and improve detector production. In this work the complete chamber construction, quality control procedures and preliminary results will be detailed