ECG Noise Removal using GA tuned Sign-Data Least Mean Square Algorithm

Adaptive filter is a primary method to filter Electrocardiogram (ECG), because it does not need the signal statistical characteristics. In this paper, an adaptive filtering technique for denoising the ECG based on Genetic Algorithm (GA) tuned Sign-Data Least Mean Square (SD-LMS) algorithm is proposed. This technique minimizes the mean-squared error between the primary input, which is a noisy ECG, and a reference input which can be either noise that is correlated in some way with the noise in the primary input or a signal that is correlated only with ECG in the primary input. Noise is used as the reference signal in this work. The algorithm was applied to the records from the MIT -BIH Arrhythmia database for removing the baseline wander and 60Hz power line interference. The proposed algorithm gave an average signal to noise ratio improvement of 10.75 dB for baseline wander and 24.26 dB for power line interference which is better than the previous reported works

Design and Development of data mining models for the predictions of manpower placement in the technical Domain

Data mining is one of the hottest research areas nowadays as it has got wide variety of applications in common man’s life to make the world a better place to live. It is all about finding interesting hidden patterns in a huge history data base. As an example, from a sales data base, one can find an interesting pattern like “people who buy magazines tend to buy news papers also” using data mining. Now in the sales point of view the advantage is that one can place these things together in the shop to increase sales. In this research work, data mining is effectively applied to a domain called placement chance prediction, since taking wise career decision is so crucial for anybody for sure. In India technical manpower analysis is carried out by an organization named National Technical Manpower Information System (NTMIS), established in 1983-84 by India's Ministry of Education & Culture. The NTMIS comprises of a lead centre in the IAMR, New Delhi, and 21 nodal centres located at different parts of the country. The Kerala State Nodal Centre is located at Cochin University of Science and Technology. In Nodal Centre, they collect placement information by sending postal questionnaire to passed out students on a regular basis. From this raw data available in the nodal centre, a history data base was prepared. Each record in this data base includes entrance rank ranges, reservation, Sector, Sex, and a particular engineering. From each such combination of attributes from the history data base of student records, corresponding placement chances is computed and stored in the history data base. From this data, various popular data mining models are built and tested. These models can be used to predict the most suitable branch for a particular new student with one of the above combination of criteria. Also a detailed performance comparison of the various data mining models is done.This research work proposes to use a combination of data mining models namely a hybrid stacking ensemble for better predictions. A strategy to predict the overall absorption rate for various branches as well as the time it takes for all the students of a particular branch to get placed etc are also proposed. Finally, this research work puts forward a new data mining algorithm namely C 4.5 * stat for numeric data sets which has been proved to have competent accuracy over standard benchmarking data sets called UCI data sets. It also proposes an optimization strategy called parameter tuning to improve the standard C 4.5 algorithm. As a summary this research work passes through all four dimensions for a typical data mining research work, namely application to a domain, development of classifier models, optimization and ensemble methods.

Mean Squared Residue Based Biclustering Algorithms for the Analysis of Gene Expression Data

Computational Biology is the research are that contributes to the analysis of biological data through the development of algorithms which will address significant research problems.The data from molecular biology includes DNA,RNA ,Protein and Gene expression data.Gene Expression Data provides the expression level of genes under different conditions.Gene expression is the process of transcribing the DNA sequence of a gene into mRNA sequences which in turn are later translated into proteins.The number of copies of mRNA produced is called the expression level of a gene.Gene expression data is organized in the form of a matrix. Rows in the matrix represent genes and columns in the matrix represent experimental conditions.Experimental conditions can be different tissue types or time points.Entries in the gene expression matrix are real values.Through the analysis of gene expression data it is possible to determine the behavioral patterns of genes such as similarity of their behavior,nature of their interaction,their respective contribution to the same pathways and so on. Similar expression patterns are exhibited by the genes participating in the same biological process.These patterns have immense relevance and application in bioinformatics and clinical research.Theses patterns are used in the medical domain for aid in more accurate diagnosis,prognosis,treatment planning.drug discovery and protein network analysis.To identify various patterns from gene expression data,data mining techniques are essential.Clustering is an important data mining technique for the analysis of gene expression data.To overcome the problems associated with clustering,biclustering is introduced.Biclustering refers to simultaneous clustering of both rows and columns of a data matrix. Clustering is a global whereas biclustering is a local model.Discovering local expression patterns is essential for identfying many genetic pathways that are not apparent otherwise.It is therefore necessary to move beyond the clustering paradigm towards developing approaches which are capable of discovering local patterns in gene expression data.A biclusters is a submatrix of the gene expression data matrix.The rows and columns in the submatrix need not be contiguous as in the gene expression data matrix.Biclusters are not disjoint.Computation of biclusters is costly because one will have to consider all the combinations of columans and rows in order to find out all the biclusters.The search space for the biclustering problem is 2 m+n where m and n are the number of genes and conditions respectively.Usually m+n is more than 3000.The biclustering problem is NP-hard.Biclustering is a powerful analytical tool for the biologist.The research reported in this thesis addresses the problem of biclustering.Ten algorithms are developed for the identification of coherent biclusters from gene expression data.All these algorithms are making use of a measure called mean squared residue to search for biclusters.The objective here is to identify the biclusters of maximum size with the mean squared residue lower than a given threshold. All these algorithms begin the search from tightly coregulated submatrices called the seeds.These seeds are generated by K-Means clustering algorithm.The algorithms developed can be classified as constraint based,greedy and metaheuristic.Constarint based algorithms uses one or more of the various constaints namely the MSR threshold and the MSR difference threshold.The greedy approach makes a locally optimal choice at each stage with the objective of finding the global optimum.In metaheuristic approaches particle Swarm Optimization(PSO) and variants of Greedy Randomized Adaptive Search Procedure(GRASP) are used for the identification of biclusters.These algorithms are implemented on the Yeast and Lymphoma datasets.Biologically relevant and statistically significant biclusters are identified by all these algorithms which are validated by Gene Ontology database.All these algorithms are compared with some other biclustering algorithms.Algorithms developed in this work overcome some of the problems associated with the already existing algorithms.With the help of some of the algorithms which are developed in this work biclusters with very high row variance,which is higher than the row variance of any other algorithm using mean squared residue, are identified from both Yeast and Lymphoma data sets.Such biclusters which make significant change in the expression level are highly relevant biologically.

Modelling and Analysis of Recurrent Event Data with Multiple Causes

This thesis Entitled “modelling and analysis of recurrent event data with multiple causes.Survival data is a term used for describing data that measures the time to occurrence of an event.In survival studies, the time to occurrence of an event is generally referred to as lifetime.Recurrent event data are commonly encountered in longitudinal studies when individuals are followed to observe the repeated occurrences of certain events. In many practical situations, individuals under study are exposed to the failure due to more than one causes and the eventual failure can be attributed to exactly one of these causes.The proposed model was useful in real life situations to study the effect of covariates on recurrences of certain events due to different causes.In Chapter 3, an additive hazards model for gap time distributions of recurrent event data with multiple causes was introduced. The parameter estimation and asymptotic properties were discussed .In Chapter 4, a shared frailty model for the analysis of bivariate competing risks data was presented and the estimation procedures for shared gamma frailty model, without covariates and with covariates, using EM algorithm were discussed. In Chapter 6, two nonparametric estimators for bivariate survivor function of paired recurrent event data were developed. The asymptotic properties of the estimators were studied. The proposed estimators were applied to a real life data set. Simulation studies were carried out to find the efficiency of the proposed estimators.

“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.

A Data Mining Approach for the Identification of Adverse Drug Events (ADE) resulting from Drug-Drug Interactions (DDI) to improve pharmacovigilance

In the current study, epidemiology study is done by means of literature survey in groups identified to be at higher potential for DDIs as well as in other cases to explore patterns of DDIs and the factors affecting them. The structure of the FDA Adverse Event Reporting System (FAERS) database is studied and analyzed in detail to identify issues and challenges in data mining the drug-drug interactions. The necessary pre-processing algorithms are developed based on the analysis and the Apriori algorithm is modified to suit the process. Finally, the modules are integrated into a tool to identify DDIs. The results are compared using standard drug interaction database for validation. 31% of the associations obtained were identified to be new and the match with existing interactions was 69%. This match clearly indicates the validity of the methodology and its applicability to similar databases. Formulation of the results using the generic names expanded the relevance of the results to a global scale. The global applicability helps the health care professionals worldwide to observe caution during various stages of drug administration thus considerably enhancing pharmacovigilance

Biclustering Gene Expression Data using MSR Difference Threshold

Biclustering is simultaneous clustering of both rows and columns of a data matrix. A measure called Mean Squared Residue (MSR) is used to simultaneously evaluate the coherence of rows and columns within a submatrix. In this paper a novel algorithm is developed for biclustering gene expression data using the newly introduced concept of MSR difference threshold. In the first step high quality bicluster seeds are generated using K-Means clustering algorithm. Then more genes and conditions (node) are added to the bicluster. Before adding a node the MSR X of the bicluster is calculated. After adding the node again the MSR Y is calculated. The added node is deleted if Y minus X is greater than MSR difference threshold or if Y is greater than MSR threshold which depends on the dataset. The MSR difference threshold is different for gene list and condition list and it depends on the dataset also. Proper values should be identified through experimentation in order to obtain biclusters of high quality. The results obtained on bench mark dataset clearly indicate that this algorithm is better than many of the existing biclustering algorithms

A Novel Decision Tree Algorithm for Numeric Datasets - C 4.5*Stat

Decision trees are very powerful tools for classification in data mining tasks that involves different types of attributes. When coming to handling numeric data sets, usually they are converted first to categorical types and then classified using information gain concepts. Information gain is a very popular and useful concept which tells you, whether any benefit occurs after splitting with a given attribute as far as information content is concerned. But this process is computationally intensive for large data sets. Also popular decision tree algorithms like ID3 cannot handle numeric data sets. This paper proposes statistical variance as an alternative to information gain as well as statistical mean to split attributes in completely numerical data sets. The new algorithm has been proved to be competent with respect to its information gain counterpart C4.5 and competent with many existing decision tree algorithms against the standard UCI benchmarking datasets using the ANOVA test in statistics. The specific advantages of this proposed new algorithm are that it avoids the computational overhead of information gain computation for large data sets with many attributes, as well as it avoids the conversion to categorical data from huge numeric data sets which also is a time consuming task. So as a summary, huge numeric datasets can be directly submitted to this algorithm without any attribute mappings or information gain computations. It also blends the two closely related fields statistics and data mining

Development of Hierarchical Clustering Techniques for Gridded Data from Mixed Data Sequences

Knowledge discovery in databases is the non-trivial process of identifying valid, novel potentially useful and ultimately understandable patterns from data. The term Data mining refers to the process which does the exploratory analysis on the data and builds some model on the data. To infer patterns from data, data mining involves different approaches like association rule mining, classification techniques or clustering techniques. Among the many data mining techniques, clustering plays a major role, since it helps to group the related data for assessing properties and drawing conclusions. Most of the clustering algorithms act on a dataset with uniform format, since the similarity or dissimilarity between the data points is a significant factor in finding out the clusters. If a dataset consists of mixed attributes, i.e. a combination of numerical and categorical variables, a preferred approach is to convert different formats into a uniform format. The research study explores the various techniques to convert the mixed data sets to a numerical equivalent, so as to make it equipped for applying the statistical and similar algorithms. The results of clustering mixed category data after conversion to numeric data type have been demonstrated using a crime data set. The thesis also proposes an extension to the well known algorithm for handling mixed data types, to deal with data sets having only categorical data. The proposed conversion has been validated on a data set corresponding to breast cancer. Moreover, another issue with the clustering process is the visualization of output. Different geometric techniques like scatter plot, or projection plots are available, but none of the techniques display the result projecting the whole database but rather demonstrate attribute-pair wise analysis

A Compiler Integrated Assistance for Optimum Data Allocation in Banked Memory Embedded Processors

Bank switching in embedded processors having partitioned memory architecture results in code size as well as run time overhead. An algorithm and its application to assist the compiler in eliminating the redundant bank switching codes introduced and deciding the optimum data allocation to banked memory is presented in this work. A relation matrix formed for the memory bank state transition corresponding to each bank selection instruction is used for the detection of redundant codes. Data allocation to memory is done by considering all possible permutation of memory banks and combination of data. The compiler output corresponding to each data mapping scheme is subjected to a static machine code analysis which identifies the one with minimum number of bank switching codes. Even though the method is compiler independent, the algorithm utilizes certain architectural features of the target processor. A prototype based on PIC 16F87X microcontrollers is described. This method scales well into larger number of memory blocks and other architectures so that high performance compilers can integrate this technique for efficient code generation. The technique is illustrated with an example