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2015

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Articles 391 - 420 of 2105

Full-Text Articles in Computer Sciences

Should I Follow This Fault Localization Tool's Output? Automated Prediction Of Fault Localization Effectiveness, Tien-Duy B. Le, David Lo, Ferdian Thung Oct 2015

Should I Follow This Fault Localization Tool's Output? Automated Prediction Of Fault Localization Effectiveness, Tien-Duy B. Le, David Lo, Ferdian Thung

Research Collection School Of Computing and Information Systems

Debugging is a crucial yet expensive activity to improve the reliability of software systems. To reduce debugging cost, various fault localization tools have been proposed. A spectrum-based fault localization tool often outputs an ordered list of program elements sorted based on their likelihood to be the root cause of a set of failures (i.e., their suspiciousness scores). Despite the many studies on fault localization, unfortunately, however, for many bugs, the root causes are often low in the ordered list. This potentially causes developers to distrust fault localization tools. Recently, Parnin and Orso highlight in their user study that many debuggers …


Social Tag Relevance Estimation Via Ranking-Oriented Neighbour Voting, Chaoran Cui, Jialie Shen, Jun Ma, Tao Lian Oct 2015

Social Tag Relevance Estimation Via Ranking-Oriented Neighbour Voting, Chaoran Cui, Jialie Shen, Jun Ma, Tao Lian

Research Collection School Of Computing and Information Systems

User-generated tags associated with social images are frequently imprecise and incomplete. Therefore, a fundamental challenge in tag-based applications is the problem of tag relevance estimation, which concerns how to interpret and quantify the relevance of a tag with respect to the contents of an image. In this paper, we address the key problem from a new perspective of learning to rank, and develop a novel approach to facilitate tag relevance estimation to directly optimize the ranking performance of tag-based image search. A supervision step is introduced into the neighbour voting scheme, in which tag relevance is estimated by accumulating votes …


What Are The Characteristics Of High-Rated Apps? A Case Study On Free Android Applications, Tian Yuan, Meiyappan Nagappan, David Lo, Ahmed E. Hassan Oct 2015

What Are The Characteristics Of High-Rated Apps? A Case Study On Free Android Applications, Tian Yuan, Meiyappan Nagappan, David Lo, Ahmed E. Hassan

Research Collection School Of Computing and Information Systems

The tremendous rate of growth in the mobile app market over the past few years has attracted many developers to build mobile apps. However, while there is no shortage of stories of how lone developers have made great fortunes from their apps, the majority of developers are struggling to break even. For those struggling developers, knowing the “DNA” (i.e., characteristics) of high-rated apps is the first step towards successful development and evolution of their apps. In this paper, we investigate 28 factors along eight dimensions to understand how high-rated apps are different from low-rated apps. We also investigate what are …


Constrained Feature Selection For Localizing Faults, Tien-Duy B. Le, David Lo, Ming Li Oct 2015

Constrained Feature Selection For Localizing Faults, Tien-Duy B. Le, David Lo, Ming Li

Research Collection School Of Computing and Information Systems

Developers often take much time and effort to find buggy program elements. To help developers debug, many past studies have proposed spectrum-based fault localization techniques. These techniques compare and contrast correct and faulty execution traces and highlight suspicious program elements. In this work, we propose constrained feature selection algorithms that we use to localize faults. Feature selection algorithms are commonly used to identify important features that are helpful for a classification task. By mapping an execution trace to a classification instance and a program element to a feature, we can transform fault localization to the feature selection problem. Unfortunately, existing …


A Note On The Security Of Khl Scheme, Jian Weng, Yunlei Zhao, Deng, Robert H., Shengli Liu, Yanjiang Yang, Kouichi Sakurai Oct 2015

A Note On The Security Of Khl Scheme, Jian Weng, Yunlei Zhao, Deng, Robert H., Shengli Liu, Yanjiang Yang, Kouichi Sakurai

Research Collection School Of Computing and Information Systems

A public key trace and revoke scheme combines the functionality of broadcast encryption with the capability of traitor tracing. In Asiacrypt 2003, Kim, Hwang and Lee proposed a public key trace and revoke scheme (referred to as KHL scheme), and gave the security proof to support that their scheme is z-resilient against adaptive chosen-ciphertext attacks, in which the adversary is allowed to adaptively issue decryption queries as well as adaptively corrupt up to z users. In the passed ten years, KHL scheme has been believed as one of the most efficient public key trace and revoke schemes with z-resilience against …


Extensible Authentication Protocol Vulnerabilities And Improvements, Akshay Baheti Oct 2015

Extensible Authentication Protocol Vulnerabilities And Improvements, Akshay Baheti

Master's Projects

Extensible Authentication Protocol(EAP) is a widely used security protocol for Wireless networks around the world. The project examines different security issues with the EAP based protocols, the family of security protocols for Wireless LAN. The project discovers an attack on the subscriber identity module(SIM) based extension of EAP. The attack is a Denial-of-Service attack that exploits the error handling mechanism in EAP protocols. The project further proposes countermeasures for detection and a defense against the discovered attack. The discovered attack can be prevented by changing the protocol to delay the processing of protocol error messages.


A Forecasting Tool For Predicting Australia's Domestic Airline Passenger Demand Using A Genetic Algorithm, Panarat Srisaeng, Glenn Baxter, Steven Richardson, Graham Wild Oct 2015

A Forecasting Tool For Predicting Australia's Domestic Airline Passenger Demand Using A Genetic Algorithm, Panarat Srisaeng, Glenn Baxter, Steven Richardson, Graham Wild

Research outputs 2014 to 2021

This study has proposed and empirically tested for the first time genetic algorithm optimization models for modelling Australia’s domestic airline passenger demand, as measured by enplaned passengers (GAPAXDE model) and revenue passenger kilometres performed (GARPKSDE model). Data was divided into training and testing datasets; 74 training datasets were used to estimate the weighting factors of the genetic algorithm models and 13 out-of-sample datasets were used for testing the robustness of the genetic algorithm models. The genetic algorithm parameters used in this study comprised population size (n): 200; the generation number: 1,000; and mutation rate: 0.01. The modelling results have shown …


Computational Approaches For Remote Monitoring Of Symptoms And Activities, Ferdaus Kawsar Oct 2015

Computational Approaches For Remote Monitoring Of Symptoms And Activities, Ferdaus Kawsar

Dissertations (1934 -)

We now have a unique phenomenon where significant computational power, storage, connectivity, and built-in sensors are carried by many people willingly as part of their life style; two billion people now use smart phones. Unique and innovative solutions using smart phones are motivated by rising health care cost in both the developed and developing worlds. In this work, development of a methodology for building a remote symptom monitoring system for rural people in developing countries has been explored. Design, development, deployment, and evaluation of e-ESAS is described. The system’s performance was studied by analyzing feedback from users. A smart phone …


Fraglight: Shedding Light On Broken Pointcuts In Evolving Aspect-Oriented Software, Raffi Khatchadourian, Awais Rashid, Hidehiko Masuhara, Takuya Watanabe Oct 2015

Fraglight: Shedding Light On Broken Pointcuts In Evolving Aspect-Oriented Software, Raffi Khatchadourian, Awais Rashid, Hidehiko Masuhara, Takuya Watanabe

Publications and Research

Pointcut fragility is a well-documented problem in Aspect-Oriented Programming; changes to the base code can lead to join points incorrectly falling in or out of the scope of pointcuts. Deciding which pointcuts have broken due to base-code changes is daunting, especially in large and complex systems. We demonstrate an automated tool called FRAGLIGHT that recommends a set of pointcuts that are likely to require modification due to a certain base-code change. The underlying approach is rooted in harnessing unique and arbitrarily deep structural commonality between program elements corresponding to join points selected by a pointcut in a particular software version. …


Automated Prediction Of Bug Report Priority Using Multi-Factor Analysis, Yuan Tian, David Lo, Chengnian Sun, Xin Xia Oct 2015

Automated Prediction Of Bug Report Priority Using Multi-Factor Analysis, Yuan Tian, David Lo, Chengnian Sun, Xin Xia

Research Collection School Of Computing and Information Systems

Bugs are prevalent. To improve software quality, developers often allow users to report bugs that they found using a bug tracking system such as Bugzilla. Users would specify among other things, a description of the bug, the component that is affected by the bug, and the severity of the bug. Based on this information, bug triagers would then assign a priority level to the reported bug. As resources are limited, bug reports would be investigated based on their priority levels. This priority assignment process however is a manual one. Could we do better? In this paper, we propose an automated …


Scheduled Approximation For Personalized Pagerank With Utility-Based Hub Selection, Fanwei Zhu, Yuan Fang, Kevin Chen-Chuan Chang, Jing Ying Oct 2015

Scheduled Approximation For Personalized Pagerank With Utility-Based Hub Selection, Fanwei Zhu, Yuan Fang, Kevin Chen-Chuan Chang, Jing Ying

Research Collection School Of Computing and Information Systems

As Personalized PageRank has been widely leveraged for ranking on a graph, the efficient computation of Personalized PageRank Vector (PPV) becomes a prominent issue. In this paper, we propose FastPPV, an approximate PPV computation algorithm that is incremental and accuracy-aware. Our approach hinges on a novel paradigm of scheduled approximation: the computation is partitioned and scheduled for processing in an “organized” way, such that we can gradually improve our PPV estimation in an incremental manner and quantify the accuracy of our approximation at query time. Guided by this principle, we develop an efficient hub-based realization, where we adopt the metric …


Detect Rumors Using Time Series Of Social Context Information On Microblogging Websites, Jing Ma, Wei Gao, Zhongyu Wei, Yueming Lu, Kam-Fai Wong Oct 2015

Detect Rumors Using Time Series Of Social Context Information On Microblogging Websites, Jing Ma, Wei Gao, Zhongyu Wei, Yueming Lu, Kam-Fai Wong

Research Collection School Of Computing and Information Systems

Automatically identifying rumors from online social media especially microblogging websites is an important research issue. Most of existing work for rumor detection focuses on modeling features related to microblog contents, users and propagation patterns, but ignore the importance of the variation of these social context features during the message propagation over time. In this study, we propose a novel approach to capture the temporal characteristics of these features based on the time series of rumor's lifecycle, for which time series modeling technique is applied to incorporate various social context information. Our experiments using the events in two microblog datasets confirm …


Social Signal Processing For Real-Time Situational Understanding: A Vision And Approach, Kasthuri Jeyarajah, Shuchao Yao, Raghava Muthuraju, Archan Misra, Geeth De Mel, Julie Skipper, Tarek Abdelzaher, Michael Kolodny Oct 2015

Social Signal Processing For Real-Time Situational Understanding: A Vision And Approach, Kasthuri Jeyarajah, Shuchao Yao, Raghava Muthuraju, Archan Misra, Geeth De Mel, Julie Skipper, Tarek Abdelzaher, Michael Kolodny

Research Collection School Of Computing and Information Systems

The US Army Research Laboratory (ARL) and the Air Force Research Laboratory (AFRL) have established a collaborative research enterprise referred to as the Situational Understanding Research Institute (SURI). The goal is to develop an information processing framework to help the military obtain real-time situational awareness of physical events by harnessing the combined power of multiple sensing sources to obtain insights about events and their evolution. It is envisioned that one could use such information to predict behaviors of groups, be they local transient groups (e.g., protests) or widespread, networked groups, and thus enable proactive prevention of nefarious activities. This paper …


On Robust Image Spam Filtering Via Comprehensive Visual Modeling, Jialie Shen, Deng, Robert H., Zhiyong Cheng, Liqiang Nie, Shuicheng Yan Oct 2015

On Robust Image Spam Filtering Via Comprehensive Visual Modeling, Jialie Shen, Deng, Robert H., Zhiyong Cheng, Liqiang Nie, Shuicheng Yan

Research Collection School Of Computing and Information Systems

The Internet has brought about fundamental changes in the way peoples generate and exchange media information. Over the last decade, unsolicited message images (image spams) have become one of the most serious problems for Internet service providers (ISPs), business firms and general end users. In this paper, we report a novel system called RoBoTs (Robust BoosTrap based spam detector) to support accurate and robust image spam filtering. The system is developed based on multiple visual properties extracted from different levels of granularity, aiming to capture more discriminative contents for effective spam image identification. In addition, a resampling based learning framework …


Endogenous Network Effects, Platform Pricing And Market Liquidity, Mei Lin, Ruhai Wu, Wen Zhou Oct 2015

Endogenous Network Effects, Platform Pricing And Market Liquidity, Mei Lin, Ruhai Wu, Wen Zhou

Research Collection School Of Computing and Information Systems

This paper examines a monopoly platform's two-sided pricing strategies in a setting with seller competition, which gives rise to not only positive cross-side network effects between buyers and sellers, but also a negative same-side network effect among sellers. We show that platform pricing depends crucially on the characteristics associated with market liquidity, which contrasts with the previous studies that point to the two sides' relative demand elasticities and/or network effects. A market is said to be more liquid when it has less friction, resulting in a larger total surplus for the platform economy and hence greater equilibrium entry on both …


Choosing Your Weapons: On Sentiment Analysis Tools For Software Engineering Research, Robbert Jongeling, Subhajit Datta, Alexander Serebrenik Oct 2015

Choosing Your Weapons: On Sentiment Analysis Tools For Software Engineering Research, Robbert Jongeling, Subhajit Datta, Alexander Serebrenik

Research Collection School Of Computing and Information Systems

Recent years have seen an increasing attention to social aspects of software engineering, including studies of emotions and sentiments experienced and expressed by the software developers. Most of these studies reuse existing sentiment analysis tools such as SentiStrength and NLTK. However, these tools have been trained on product reviews and movie reviews and, therefore, their results might not be applicable in the software engineering domain. In this paper we study whether the sentiment analysis tools agree with the sentiment recognized by human evaluators (as reported in an earlier study) as well as with each other. Furthermore, we evaluate the impact …


The Importance Of Being Isolated: An Empirical Study On Chromium Reviews, Subhajit Datta, Devarshi Bhatt, Manish Jain, Proshanta Sarkar, Santonu Sarkar Oct 2015

The Importance Of Being Isolated: An Empirical Study On Chromium Reviews, Subhajit Datta, Devarshi Bhatt, Manish Jain, Proshanta Sarkar, Santonu Sarkar

Research Collection School Of Computing and Information Systems

As large scale software development has become more collaborative, and software teams more globally distributed, several studies have explored how developer interaction influences software development outcomes. The emphasis so far has been largely on outcomes like defect count, the time to close modification requests etc. In the paper, we examine data from the Chromium project to understand how different aspects of developer discussion relate to the closure time of reviews. On the basis of analyzing reviews discussed by 2000+ developers, our results indicate that quicker closure of reviews owned by a developer relates to higher reception of information and insights …


Seeing Your Face Is Not Enough: An Inertial Sensor-Based Liveness Detection For Face Authentication, Yan Li, Yingjiu Li, Qiang Yan, Hancong Kong, Robert H. Deng Oct 2015

Seeing Your Face Is Not Enough: An Inertial Sensor-Based Liveness Detection For Face Authentication, Yan Li, Yingjiu Li, Qiang Yan, Hancong Kong, Robert H. Deng

Research Collection School Of Computing and Information Systems

Leveraging built-in cameras on smartphones and tablets, face authentication provides an attractive alternative of legacy passwords due to its memory-less authentication process. However, it has an intrinsic vulnerability against the media-based facial forgery (MFF) where adversaries use photos/videos containing victims' faces to circumvent face authentication systems. In this paper, we propose FaceLive, a practical and robust liveness detection mechanism to strengthen the face authentication on mobile devices in fighting the MFF-based attacks. FaceLive detects the MFF-based attacks by measuring the consistency between device movement data from the inertial sensors and the head pose changes from the facial video captured by …


Analyzing Educational Comments For Topics And Sentiments: A Text Analytics Approach, Gokran Ila Nitin, Swapna Gottipati, Venky Shankararaman Oct 2015

Analyzing Educational Comments For Topics And Sentiments: A Text Analytics Approach, Gokran Ila Nitin, Swapna Gottipati, Venky Shankararaman

Research Collection School Of Computing and Information Systems

Universities collect qualitative and quantitative feedback from students upon course completion in order to improve course quality and students’ learning experience. Combining program-wide and module-specific questions, universities collect feedback from students on three main aspects of a course namely, teaching style, content, and learning experience. The feedback is collected through both qualitative comments and quantitative scores. Current methods for analyzing the student course evaluations are manual and majorly focus on quantitative feedback and fall short of an in-depth exploration of qualitative feedback. In this paper, we develop student feedback mining system (SFMS) which applies text analytics and opinion mining approach …


Structural Constraints For Multipartite Entity Resolution With Markov Logic Network, Tengyuan Ye, Hady W. Lauw Oct 2015

Structural Constraints For Multipartite Entity Resolution With Markov Logic Network, Tengyuan Ye, Hady W. Lauw

Research Collection School Of Computing and Information Systems

Multipartite entity resolution seeks to match entity mentions across several collections. An entity mention is presumed unique within a collection, and thus could match at most one entity mention in each of the other collections. In addition to domain-specific features considered in entity resolution, there are a number of domain-invariant structural contraints that apply in this scenario, including one-to-one assignment as well as cross-collection transitivity. We propose a principled solution to the multipartite entity resolution problem, building on the foundation of Markov Logic Network (MLN) that combines probabilistic graphical model and first-order logic. We describe how the domain-invariant structural constraints …


Targeted Blended Learning Through Competency Assessment In An Undergraduate Information Systems Program, Joelle Elmaleh, Shankararaman, Venky Oct 2015

Targeted Blended Learning Through Competency Assessment In An Undergraduate Information Systems Program, Joelle Elmaleh, Shankararaman, Venky

Research Collection School Of Computing and Information Systems

In this paper we report our study on the problem of competency acquisition when students progress from one course to another and more generally, from one term to the next. We observed that some students moved on to a second programming course without acquiring some of the competencies in the first programming course. This leads to problem in the second course, especially when these competencies are pre-requisites for this course. We applied blended learning, which allows a student to learn at least in part through delivery of content and instruction via online media, to overcome this problem. Our approach is …


Density Peaks Clustering Approach For Discovering Demand Hot Spots In City-Scale Taxi Fleet Dataset, Dongchang Liu, Shih-Fen Cheng, Yiping Yang Oct 2015

Density Peaks Clustering Approach For Discovering Demand Hot Spots In City-Scale Taxi Fleet Dataset, Dongchang Liu, Shih-Fen Cheng, Yiping Yang

Research Collection School Of Computing and Information Systems

In this paper, we introduce a variant of the density peaks clustering (DPC) approach for discovering demand hot spots from a low-frequency, low-quality taxi fleet operational dataset. From the literature, the DPC approach mainly uses density peaks as features to discover potential cluster centers, and this requires distances between all pairs of data points to be calculated. This implies that the DPC approach can only be applied to cases with relatively small numbers of data points. For the domain of urban taxi operations that we are interested in, we could have millions of demand points per day, and calculating all-pair …


What's Hot In Software Engineering Twitter Space?, Abhishek Sharma, Tian Yuan, David Lo Oct 2015

What's Hot In Software Engineering Twitter Space?, Abhishek Sharma, Tian Yuan, David Lo

Research Collection School Of Computing and Information Systems

Twitter is a popular means to disseminate information and currently more than 300 million people are using it actively. Software engineers are no exception; Singer et al. have shown that many developers use Twitter to stay current with recent technological trends. At various time points, many users are posting microblogs (i.e., tweets) about the same topic in Twitter. We refer to this reasonably large set of topically-coherent microblogs in the Twitter space made at a particular point in time as an event. In this work, we perform an exploratory study on software engineering related events in Twitter. We collect a …


Inferring Door Locations From A Teammate's Trajectory In Stealth Human-Robot Team Operations, Jean Oh, Arne Suppe, Arne Suppe, Anthony Stentz, Martial Hebert Oct 2015

Inferring Door Locations From A Teammate's Trajectory In Stealth Human-Robot Team Operations, Jean Oh, Arne Suppe, Arne Suppe, Anthony Stentz, Martial Hebert

Research Collection School Of Computing and Information Systems

Robot perception is generally viewed as the interpretation of data from various types of sensors such as cameras. In this paper, we study indirect perception where a robot can perceive new information by making inferences from non-visual observations of human teammates. As a proof-of-concept study, we specifically focus on a door detection problem in a stealth mission setting where a team operation must not be exposed to the visibility of the team's opponents. We use a special type of the Noisy-OR model known as BN2O model of Bayesian inference network to represent the inter-visibility and to infer the locations of …


Face Recognition On Large-Scale Video In The Wild With Hybrid Euclidean-And-Riemannian Metric Learning, Zhiwu Huang, R. Wang, S. Shan, X Chen Oct 2015

Face Recognition On Large-Scale Video In The Wild With Hybrid Euclidean-And-Riemannian Metric Learning, Zhiwu Huang, R. Wang, S. Shan, X Chen

Research Collection School Of Computing and Information Systems

Face recognition on large-scale video in the wild is becoming increasingly important due to the ubiquity of video data captured by surveillance cameras, handheld devices, Internet uploads, and other sources. By treating each video as one image set, set-based methods recently have made great success in the field of video-based face recognition. In the wild world, videos often contain extremely complex data variations and thus pose a big challenge of set modeling for set-based methods. In this paper, we propose a novel Hybrid Euclidean-and-Riemannian Metric Learning (HERML) method to fuse multiple statistics of image set. Specifically, we represent each image …


Assessing Developer Contribution With Repository Mining-Based Metrics, Jalerson Lima, Christoph Treude, Fernando Figueira Filho, Uirá Kulesza Oct 2015

Assessing Developer Contribution With Repository Mining-Based Metrics, Jalerson Lima, Christoph Treude, Fernando Figueira Filho, Uirá Kulesza

Research Collection School Of Computing and Information Systems

Productivity as a result of individual developers' contributions is an important aspect for software companies to maintain their competitiveness in the market. However, there is no consensus in the literature on how to measure productivity or developer contribution. While some repository mining-based metrics have been proposed, they lack validation in terms of their applicability and usefulness from the individuals who will use them to assess developer contribution: team and project leaders. In this paper, we propose the design of a suite of metrics for the assessment of developer contribution, based on empirical evidence obtained from project and team leaders. In …


Privacy In Crowdsourced Platforms, Thivya Kandappu, Arik Friedman, Vijay Sivaraman, Roksana Boreli Oct 2015

Privacy In Crowdsourced Platforms, Thivya Kandappu, Arik Friedman, Vijay Sivaraman, Roksana Boreli

Research Collection School Of Computing and Information Systems

Emerging platforms, such as Amazon Mechanical Turk and Google Consumer Surveys, are increasingly being used by researchers and market analysts to crowdsource large-scale survey data from online populations at extremely low cost. However, by participating in successive surveys, workers risk being profiled and targeted, both by surveyors and by the platform itself. In this chapter we provide an overview of privacy in crowdsourcing platforms. We consider the state-of-the-art crowdsourcing platforms and the risks to worker privacy in such platforms, we survey the existing solutions, and later describe and evaluate the design of a privacy conscious crowdsourcing platform prototype, called Loki. …


Smartphones And Ble Services: Empirical Insights, Meera Radhakrishnan, Archan Misra, Rajesh Krishna Balan, Youngki Lee Oct 2015

Smartphones And Ble Services: Empirical Insights, Meera Radhakrishnan, Archan Misra, Rajesh Krishna Balan, Youngki Lee

Research Collection School Of Computing and Information Systems

Driven by the rapid market growth of sensors and beacons that offer Bluetooth Low Energy (BLE) based connectivity, this paper empirically investigates the performance characteristics of the BLE interface on multiple Android smartphones, and the consequent impact on a proposed BLE-based service: continuous indoor location. We first use extensive measurement studies with multiple Android devices to establish that the BLE interface on current smartphones is not as "low-energy" as nominally expected, and establish that continuous use of such a BLE interface is not feasible unless we choose a moderately large scan interval and a low duty cycle. We then explore …


Using Eye And Head Movements As A Control Mechanism For Tele-Operating A Ground-Based Robot And Its Payload, Kathryn C. Hicks Oct 2015

Using Eye And Head Movements As A Control Mechanism For Tele-Operating A Ground-Based Robot And Its Payload, Kathryn C. Hicks

Computational Modeling & Simulation Engineering Theses & Dissertations

To date, eye and head tracking has been used to indicate users' attention patterns while performing a task or as an aid for disabled persons, to allow hands-free interaction with a computer. The increasing accuracy and the reduced cost of eye- and head-tracking equipment make utilizing this technology feasible for explicit control tasks, especially in cases where there is confluence between the visual task and control.

The goal of this research was to investigate the use of eye-tracking as a more natural interface for the control of a camera-equipped, remotely operated robot in tasks that require the operator to simultaneously …


Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas Oct 2015

Efficient Algorithms For Prokaryotic Whole Genome Assembly And Finishing, Abhishek Biswas

Computer Science Theses & Dissertations

De-novo genome assembly from DNA fragments is primarily based on sequence overlap information. In addition, mate-pair reads or paired-end reads provide linking information for joining gaps and bridging repeat regions. Genome assemblers in general assemble long contiguous sequences (contigs) using both overlapping reads and linked reads until the assembly runs into an ambiguous repeat region. These contigs are further bridged into scaffolds using linked read information. However, errors can be made in both phases of assembly due to high error threshold of overlap acceptance and linking based on too few mate reads. Identical as well as similar repeat regions can …