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.

Analytical Study of Typographical Errors in OPACS and Corrective Measures

The present study is an attempt to highlight the problem of typographical errors in OPACS. The errors made while typing catalogue entries as well as importing bibliographical records from other libraries exist unnoticed by librarians resulting the non-retrieval of available records and affecting the quality of OPACs. This paper follows previous research on the topic mainly by Jeffrey Beall and Terry Ballard. The word “management” was chosen from the list of likely to be misspelled words identified by previous research. It was found that the word is wrongly entered in several forms in local, national and international OPACs justifying the observations of Ballard that typos occur in almost everywhere. Though there are lots of corrective measures proposed and are in use, the study asserts the fact that human effort is needed to get rid of the problem. The paper is also an invitation to the library professionals and system designers to construct a strategy to solve the issue

Handling OOV Words in Phrase-Based Statistical Machine Translation for Malayalam

Statistical Machine Translation (SMT) is one of the potential applications in the field of Natural Language Processing. The translation process in SMT is carried out by acquiring translation rules automatically from the parallel corpora. However, for many language pairs (e.g. Malayalam- English), they are available only in very limited quantities. Therefore, for these language pairs a huge portion of phrases encountered at run-time will be unknown. This paper focuses on methods for handling such out-of-vocabulary (OOV) words in Malayalam that cannot be translated to English using conventional phrase-based statistical machine translation systems. The OOV words in the source sentence are pre-processed to obtain the root word and its suffix. Different inflected forms of the OOV root are generated and a match is looked up for the word variants in the phrase translation table of the translation model. A Vocabulary filter is used to choose the best among the translations of these word variants by finding the unigram count. A match for the OOV suffix is also looked up in the phrase entries and the target translations are filtered out. Structuring of the filtered phrases is done and SMT translation model is extended by adding OOV with its new phrase translations. By the results of the manual evaluation done it is observed that amount of OOV words in the input has been reduced considerably

Analytical Study of Typographical Errors in OPACS and Corrective Measures

The present study is an attempt to highlight the problem of typographical errors in OPACS. The errors made while typing catalogue entries as well as importing bibliographical records from other libraries exist unnoticed by librarians resulting the non-retrieval of available records and affecting the quality of OPACs. This paper follows previous research on the topic mainly by Jeffrey Beall and Terry Ballard. The word “management” was chosen from the list of likely to be misspelled words identified by previous research. It was found that the word is wrongly entered in several forms in local, national and international OPACs justifying the observations of Ballard that typos occur in almost everywhere. Though there are lots of corrective measures proposed and are in use, the study asserts the fact that human effort is needed to get rid of the problem. The paper is also an invitation to the library professionals and system designers to construct a strategy to solve the issue

Impact of ICT on Library and Information Science: Major Shifts and Practices in CUSAT Central Library

Information is knowledge, facts or data. For the purpose of enabling the users to assimilate information, it should be repacked. Knowledge becomes information when it is externalized i.e. put in to the process of communication. The effectiveness of communication technology depends how well it provides its clients with information rapidly, economically and authentically. A large number of ICT enabled services including OPAC; e-resources etc. are available in the university library. Studies have been done to find the impact of ICT on different sections of CUSAT library by observing the activities of different sections; discussions with colleagues and visitors; and analyzing the entries in the library records. The results of the studies are presented here in the form of a paper.