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.

Design and Development of an Adaptable Frame -Based System for Dravidian Language Processing

This work is aimed at building an adaptable frame-based system for processing Dravidian languages. There are about 17 languages in this family and they are spoken by the people of South India.Karaka relations are one of the most important features of Indian languages. They are the semabtuco-syntactic relations between verbs and other related constituents in a sentence. The karaka relations and surface case endings are analyzed for meaning extraction. This approach is comparable with the borad class of case based grammars.The efficiency of this approach is put into test in two applications. One is machine translation and the other is a natural language interface (NLI) for information retrieval from databases. The system mainly consists of a morphological analyzer, local word grouper, a parser for the source language and a sentence generator for the target language. This work make contributios like, it gives an elegant account of the relation between vibhakthi and karaka roles in Dravidian languages. This mapping is elegant and compact. The same basic thing also explains simple and complex sentence in these languages. This suggests that the solution is not just ad hoc but has a deeper underlying unity. This methodology could be extended to other free word order languages. Since the frame designed for meaning representation is general, they are adaptable to other languages coming in this group and to other applications.

Design Techniques for Sigmadelta based ADC for Wireless Applications

Analog-to digital Converters (ADC) have an important impact on the overall performance of signal processing system. This research is to explore efficient techniques for the design of sigma-delta ADC,specially for multi-standard wireless tranceivers. In particular, the aim is to develop novel models and algorithms to address this problem and to implement software tools which are avle to assist the designer's decisions in the system-level exploration phase. To this end, this thesis presents a framework of techniques to design sigma-delta analog to digital converters.A2-2-2 reconfigurable sigma-delta modulator is proposed which can meet the design specifications of the three wireless communication standards namely GSM,WCDMA and WLAN. A sigma-delta modulator design tool is developed using the Graphical User Interface Development Environment (GUIDE) In MATLAB.Genetic Algorithm(GA) based search method is introduced to find the optimum value of the scaling coefficients and to maximize the dynamic range in a sigma-delta modulator.

Design and development of an LED based fiber optic evanescent wave sensor for simultaneous detection of chromium and nitrite traces in water

The design and development of a cost-effective, simple, sensitive and portable LED based fiber optic evanescent wave sensor for simultaneously detecting trace amounts of chromium and nitrite in water are presented. In order to obtain the desired performance, the middle portions of two multimode plastic clad silica fibers are unclad and are used as the sensing elements in the two arms of the sensor. Each of the sensor arms is sourced by separate super bright green LEDs, which are modulated in a time-sharing manner and a single photo detector is employed for detecting these light signals. The performance and characteristics of this system clearly establish the usefulness of the technique for detecting very low concentrations of the dissolved contaminants.

Phenylethynylarene Based Donor-Acceptor Systems: Design, Synthesis and Photophysical Studies

This thesis Entitled phenylethynylarene based Donor-Acceptor systems:Desigh,Synthesis and Photophysical studies. A strategy for the design of donor-acceptor dyads, wherein decay of the charge separated (CS) state to low lying local triplet levels could possibly be prevented, is proposed. In order to examine this strategy, a linked donor-acceptor dyad BPEPPT with bis(phenylethYlly/)pyrene (BPEP) as the light absorber and acceptor and phenothiazine (PT) as donor was designed and photoinduced electron transfer in the dyad investigated. Absorption spectra of the dyad can be obtained by adding contributions due 10 the BPEP and PT moieties indicating that the constituents do not interact in the ground stale. Fluorescence of the BPEP moiety was efficiently quenched by the PT donor and this was attributed to electron lransfer from PT to BPEP. Picosecond transient absorption studies suggested formation of a charge separated state directly from the singlet excited state of BPEP. Nanosecond flash photolysis experiments gave long-ived transient absorptions assignable to PT radical cation and BPEP radical anion. These assignments were confirmed by oxygen quenching studies and secondary electron transfer experiments. Based on the available data, energy level diagram for BPEP-PT was constructed. The long lifetime of the charge separated state was attributed to the inverted region effects. The CS state did not undergo decay to low lying BPEP triplet indicating the success of our strategy

Design And Development Of A Named Entity Based Question Answering System For Malayalam Language

This is a Named Entity Based Question Answering System for Malayalam Language. Although a vast amount of information is available today in digital form, no effective information access mechanism exists to provide humans with convenient information access. Information Retrieval and Question Answering systems are the two mechanisms available now for information access. Information systems typically return a long list of documents in response to a user’s query which are to be skimmed by the user to determine whether they contain an answer. But a Question Answering System allows the user to state his/her information need as a natural language question and receives most appropriate answer in a word or a sentence or a paragraph. This system is based on Named Entity Tagging and Question Classification. Document tagging extracts useful information from the documents which will be used in finding the answer to the question. Question Classification extracts useful information from the question to determine the type of the question and the way in which the question is to be answered. Various Machine Learning methods are used to tag the documents. Rule-Based Approach is used for Question Classification. Malayalam belongs to the Dravidian family of languages and is one of the four major languages of this family. It is one of the 22 Scheduled Languages of India with official language status in the state of Kerala. It is spoken by 40 million people. Malayalam is a morphologically rich agglutinative language and relatively of free word order. Also Malayalam has a productive morphology that allows the creation of complex words which are often highly ambiguous. Document tagging tools such as Parts-of-Speech Tagger, Phrase Chunker, Named Entity Tagger, and Compound Word Splitter are developed as a part of this research work. No such tools were available for Malayalam language. Finite State Transducer, High Order Conditional Random Field, Artificial Immunity System Principles, and Support Vector Machines are the techniques used for the design of these document preprocessing tools. This research work describes how the Named Entity is used to represent the documents. Single sentence questions are used to test the system. Overall Precision and Recall obtained are 88.5% and 85.9% respectively. This work can be extended in several directions. The coverage of non-factoid questions can be increased and also it can be extended to include open domain applications. Reference Resolution and Word Sense Disambiguation techniques are suggested as the future enhancements

Design and Development of a Frame Based MT System for English-to-ISL

This paper presents the design and development of a frame based approach for speech to sign language machine translation system in the domain of railways and banking. This work aims to utilize the capability of Artificial intelligence for the improvement of physically challenged, deaf-mute people. Our work concentrates on the sign language used by the deaf community of Indian subcontinent which is called Indian Sign Language (ISL). Input to the system is the clerk’s speech and the output of this system is a 3D virtual human character playing the signs for the uttered phrases. The system builds up 3D animation from pre-recorded motion capture data. Our work proposes to build a Malayalam to ISL

Design of a Knowledge-Based Geographic Information System

A GIS has been designed with limited Functionalities; but with a novel approach in Aits design. The spatial data model adopted in the design of KBGIS is the unlinked vector model. Each map entity is encoded separately in vector fonn, without referencing any of its neighbouring entities. Spatial relations, in other words, are not encoded. This approach is adequate for routine analysis of geographic data represented on a planar map, and their display (Pages 105-106). Even though spatial relations are not encoded explicitly, they can be extracted through the specially designed queries. This work was undertaken as an experiment to study the feasibility of developing a GIS using a knowledge base in place of a relational database. The source of input spatial data was accurate sheet maps that were manually digitised. Each identifiable geographic primitive was represented as a distinct object, with its spatial properties and attributes defined. Composite spatial objects, made up of primitive objects, were formulated, based on production rules defining such compositions. The facts and rules were then organised into a production system, using OPS5

FEM based Virtual Prototyping and Design of Third Harmonic Excitation System for Low Voltage Brushless Alternators

Salient pole brushless alternators coupled to IC engines are extensively used as stand-by power supply units for meeting in- dustrial power demands. Design of such generators demands high power to weight ratio, high e ciency and low cost per KVA out- put. Moreover, the performance characteristics of such machines like voltage regulation and short circuit ratio (SCR) are critical when these machines are put into parallel operation and alterna- tors for critical applications like defence and aerospace demand very low harmonic content in the output voltage. While designing such alternators, accurate prediction of machine characteristics, including total harmonic distortion (THD) is essential to mini- mize development cost and time. Total harmonic distortion in the output voltage of alternators should be as low as possible especially when powering very sophis- ticated and critical applications. The output voltage waveform of a practical AC generator is replica of the space distribution of the ux density in the air gap and several factors such as shape of the rotor pole face, core saturation, slotting and style of coil disposition make the realization of a sinusoidal air gap ux wave impossible. These ux harmonics introduce undesirable e ects on the alternator performance like high neutral current due to triplen harmonics, voltage distortion, noise, vibration, excessive heating and also extra losses resulting in poor e ciency, which in turn necessitate de-rating of the machine especially when connected to non-linear loads. As an important control unit of brushless alternator, the excitation system and its dynamic performance has a direct impact on alternator's stability and reliability. The thesis explores design and implementation of an excitation i system utilizing third harmonic ux in the air gap of brushless al- ternators, using an additional auxiliary winding, wound for 1=3rd pole pitch, embedded into the stator slots and electrically iso- lated from the main winding. In the third harmonic excitation system, the combined e ect of two auxiliary windings, one with 2=3rd pitch and another third harmonic winding with 1=3rd pitch, are used to ensure good voltage regulation without an electronic automatic voltage regulator (AVR) and also reduces the total harmonic content in the output voltage, cost e ectively. The design of the third harmonic winding by analytic methods demands accurate calculation of third harmonic ux density in the air gap of the machine. However, precise estimation of the amplitude of third harmonic ux in the air gap of a machine by conventional design procedures is di cult due to complex geome- try of the machine and non-linear characteristics of the magnetic materials. As such, prediction of the eld parameters by conven- tional design methods is unreliable and hence virtual prototyping of the machine is done to enable accurate design of the third har- monic excitation system. In the design and development cycle of electrical machines, it is recognized that the use of analytical and experimental methods followed by expensive and in exible prototyping is time consum- ing and no longer cost e ective. Due to advancements in com- putational capabilities over recent years, nite element method (FEM) based virtual prototyping has become an attractive al- ternative to well established semi-analytical and empirical design methods as well as to the still popular trial and error approach followed by the costly and time consuming prototyping. Hence, by virtually prototyping the alternator using FEM, the important performance characteristics of the machine are predicted. Design of third harmonic excitation system is done with the help of results obtained from virtual prototype of the machine. Third harmonic excitation (THE) system is implemented in a 45 KVA ii experimental machine and experiments are conducted to validate the simulation results. Simulation and experimental results show that by utilizing third harmonic ux in the air gap of the ma- chine for excitation purposes during loaded conditions, triplen harmonic content in the output phase voltage is signi cantly re- duced. The prototype machine with third harmonic excitation system designed and developed based on FEM analysis proved to be economical due to its simplicity and has the added advan- tage of reduced harmonics in the output phase voltage.

Design and Development of Fiber Grating Based Chemical and Bio-Sensors

International School of Photonics

Design and Development of Spectral Signature Based Chipless RFID Tags

The main objective of this thesis is to design and develop spectral signature based chipless RFID tags Multiresonators are essential component of spectral signature based chipless tags. To enhance the data coding capacity in spectral signature based tags require large number of resonances in a limited bandwidth. The frequency of the resonators have to be close to each other. To achieve this condition, the quality factor of each resonance needs to be high. The thesis discusses about various types of multiresonators, their practical implementation and how they can be used in design. Encoding of data into spectral domain is another challenge in chipless tag design. Here, the technique used is the presence or absence encoding technique. The presence of a resonance is used to encode Logic 1 and absence of a speci c resonance is used to encode Logic 0. Di erent types of multiresonators such as open stub multiresonators, coupled bunch hairpin resonators and shorted slot ground ring resonator are proposed in this thesis.