Computer Sciences Commons^™

Mcm-Test: A Fuzzy-Set-Theory-Based Approach To Differential Analysis Of Gene Pathways, Lily R. Liang, Vinay Mandal, Yi Lu, Deepak Kumar

Wayne State University Associated BioMed Central Scholarship

Abstract

Background

Gene pathway can be defined as a group of genes that interact with each other to perform some biological processes. Along with the efforts to identify the individual genes that play vital roles in a particular disease, there is a growing interest in identifying the roles of gene pathways in such diseases.

Results

This paper proposes an innovative fuzzy-set-theory-based approach, Multi-dimensional Cluster Misclassification test (MCM-test), to measure the significance of gene pathways in a particular disease. Experiments have been conducted on both synthetic data and real world data. Results on published diabetes gene expression dataset and a list …

Data Assimilation And Visualization For Ensemble Wildland Fire Models, Soham Chakraborty

University of Kentucky Master's Theses

This thesis describes an observation function for a dynamic data driven application system designed to produce short range forecasts of the behavior of a wildland fire. The thesis presents an overview of the atmosphere-fire model, which models the complex interactions between the fire and the surrounding weather and the data assimilation module which is responsible for assimilating sensor information into the model. Observation plays an important role in data assimilation as it is used to estimate the model variables at the sensor locations. Also described is the implementation of a portable and user friendly visualization tool which displays the locations …

Collective Outsourcing To Market (Com): A Market-Based Framework For Information Supply Chain Outsourcing, Fang Fang, Zhiling Guo, Andrew B. Whinston

Research Collection School Of Computing and Information Systems

This paper discusses the importance of and a solution to separating the information flow from the physical product flow in a supply chain. Motivated by the inefficient demand forecast caused by information asymmetry and lack of an incentive among supply chain partners to share valuable information, we propose a radically new framework called collective outsourcing to market (COM) to address many information supply chain design challenges. To validate the COM framework, we consider a supply chain with one manufacturer and multiple downstream retailers. Retailers privately acquire demand forecast information that they do not have incentive to share horizontally with other …

Document Selection For Extracting Entity And Relationship Instances Of Terrorist Events, Zhen Sun, Ee Peng Lim, Kuiyu Chang, Maggy Anastasia Suryanto, Rohan Kumar Gunaratna

Research Collection School Of Computing and Information Systems

In this chapter, we study the problem of selecting documents so as to extract terrorist event information from a collection of documents. We represent an event by its entity and relation instances. Very often, these entity and relation instances have to be extracted from multiple documents. We therefore define an information extraction (IE) task as selecting documents and extracting from which entity and relation instances relevant to a user-specified event (aka domain specific event entity and relation extraction). We adopt domain specific IE patterns to extract potentially relevant entity and relation instances from documents, and develop a number of document …

Fast Evaluation Of The Square Root And Other Nonlinear Functions In Fpga, Stefan Lachowicz, Hans-Joerg Pfleiderer

Research outputs pre 2011

The paper presents a novel method of evaluating the square root function in FPGA. The method uses a linear approximation subsystem with a reduced size of a look-up table. The reduction in the size of the lookup table is twofold. Firstly, a simple linear approximation subsystem uses the lookup table only for the node points. Secondly, a concept of a variable step look-up table is introduced, where the node points are not uniformly spaced, but the spacing is determined by how close to the linear function the approximated function is. The proposed method of evaluating nonlinear function and specifically the …

The Use Of Neural Networks In The Prediction Of The Stock Exchange Of Thailand (Set) Index, Suchira Chaigusin, Chaiyaporn Chirathamjaree, Judith Clayden

Research outputs pre 2011

Prediction of stock prices is an issue of interest to financial markets. Many prediction techniques have been reported in stock forecasting. Neural networks are viewed as one of the more suitable techniques. In this study, an experiment on the forecasting of the Stock Exchange of Thailand (SET) was conducted by using feedforward backpropagation neural networks. In the experiment, many combinations of parameters were investigated to identify the right set of parameters for the neural network models in the forecasting of SET. Several global and local factors influencing the Thai stock market were used in developing the models, including the Dow …

Preventing Location-Based Identity Inference In Anonymous Spatial Queries, Panos Kalnis, Gabriel Ghinita, Kyriakos Mouratidis, Dimitris Papadias

Research Collection School Of Computing and Information Systems

The increasing trend of embedding positioning capabilities (for example, GPS) in mobile devices facilitates the widespread use of location-based services. For such applications to succeed, privacy and confidentiality are essential. Existing privacy-enhancing techniques rely on encryption to safeguard communication channels, and on pseudonyms to protect user identities. Nevertheless, the query contents may disclose the physical location of the user. In this paper, we present a framework for preventing location-based identity inference of users who issue spatial queries to location-based services. We propose transformations based on the well-established K-anonymity concept to compute exact answers for range and nearest neighbor search, without …

On Improving Wikipedia Search Using Article Quality, Meiqun Hu, Ee Peng Lim, Aixin Sun, Hady Wirawan Lauw, Ba-Quy Vuong

Research Collection School Of Computing and Information Systems

Wikipedia is presently the largest free-and-open online encyclopedia collaboratively edited and maintained by volunteers. While Wikipedia offers full-text search to its users, the accuracy of its relevance-based search can be compromised by poor quality articles edited by non-experts and inexperienced contributors. In this paper, we propose a framework that re-ranks Wikipedia search results considering article quality. We develop two quality measurement models, namely Basic and PeerReview, to derive article quality based on co-authoring data gathered from articles' edit history. Compared with Wikipedia's full-text search engine, Google and Wikiseek, our experimental results showed that (i) quality-only ranking produced by PeerReview gives …

Comment-Oriented Blog Summarization By Sentence Extraction, Meishan Hu, Ee Peng Lim, Aixin Sun

Research Collection School Of Computing and Information Systems

Much existing research on blogs focused on posts only, ignoring their comments. Our user study conducted on summarizing blog posts, however, showed that reading comments does change one's understanding about blog posts. In this research, we aim to extract representative sentences from a blog post that best represent the topics discussed among its comments. The proposed solution first derives representative words from comments and then selects sentences containing representative words. The representativeness of words is measured using ReQuT (i.e., Reader, Quotation, and Topic). Evaluated on human labeled sentences, ReQuT together with summation-based sentence selection showed promising results.

Sloque: Slot-Based Query Expansion For Complex Questions, Maggy Anastasia Suryanto, Ee Peng Lim, Aixin Sun, Roger Hsiang-Li Chiang

Research Collection School Of Computing and Information Systems

Searching answers to complex questions is a challenging IR task. In this paper, we examine the use of query templates with semantic slots to formulate slot-based queries. These queries have query terms assigned to entity and relationship slots. We develop several query expansion methods for slot-based queries so as to improve their retrieval effectiveness on a document collection. Each method consists of a combination of term scoring scheme, term scoring formula, and term assignment scheme. Our preliminary experiments evaluate these different slot-based query expansion methods on a collection of news documents,and conclude that:(1) slot-based queries yield better retrieval accuracy compared …

Measuring Article Quality In Wikipedia: Models And Evaluation, Meiqun Hu, Ee Peng Lim, Aixin Sun, Hady W. Lauw, Ba-Quy Vuong

Research Collection School Of Computing and Information Systems

Wikipedia has grown to be the world largest and busiest free encyclopedia, in which articles are collaboratively written and maintained by volunteers online. Despite its success as a means of knowledge sharing and collaboration, the public has never stopped criticizing the quality of Wikipedia articles edited by non-experts and inexperienced contributors. In this paper, we investigate the problem of assessing the quality of articles in collaborative authoring of Wikipedia. We propose three article quality measurement models that make use of the interaction data between articles and their contributors derived from the article edit history. Our Basic model is designed based …

Mining Web-Functional Dependencies For Flexible Information Access, Saverio Perugini, Naren Ramakrishnan

Computer Science Faculty Publications

We present an approach to enhancing information access through Web structure mining in contrast to traditional approaches involving usage mining. Specifically, we mine the hardwired hierarchical hyperlink structure of Web sites to identify patterns of term-term co-occurrences we call Web functional dependencies (FDs). Intuitively, a Web FD ‘x y’ declares that all paths through a site involving a hyperlink labeled x also contain a hyperlink labeled y. The complete set of FDs satisfied by a site help characterize (flexible and expressive) interaction paradigms supported by a site, where a paradigm is the set of explorable sequences therein. …

A Multitude Of Opinions: Mining Online Rating Data, Hady Wirawan Lauw, Ee Peng Lim

Research Collection School Of Computing and Information Systems

Online rating system is a popular feature of Web 2.0 applications. It typically involves a set of reviewers assigning rating scores (based on various evaluation criteria) to a set of objects. We identify two objectives for research on online rating data, namely achieving effective evaluation of objects and learning behaviors of reviewers/objects. These two objectives have conventionally been pursued separately. We argue that the future research direction should focus on the integration of these two objectives, as well as the integration between rating data and other types of data.

Efficient Discovery Of Frequent Approximate Sequential Patterns, Feida Zhu, Xifeng Yan, Jiawei Han, Philip S. Yu

Research Collection School Of Computing and Information Systems

We propose an efficient algorithm for mining frequent approximate sequential patterns under the Hamming distance model. Our algorithm gains its efficiency by adopting a "break-down-and-build-up" methodology. The "breakdown" is based on the observation that all occurrences of a frequent pattern can be classified into groups, which we call strands. We developed efficient algorithms to quickly mine out all strands by iterative growth. In the "build-up" stage, these strands are grouped up to form the support sets from which all approximate patterns would be identified. A salient feature of our algorithm is its ability to grow the frequent patterns by iteratively …

Gapprox: Mining Frequent Approximate Patterns From A Massive Network, Chen Chen, Xifeng Yan, Feida Zhu, Jiawei Han

Research Collection School Of Computing and Information Systems

Recently, there arise a large number of graphs with massive sizes and complex structures in many new applications, such as biological networks, social networks, and the Web, demanding powerful data mining methods. Due to inherent noise or data diversity, it is crucial to address the issue of approximation, if one wants to mine patterns that are potentially interesting with tolerable variations. In this paper, we investigate the problem of mining frequent approximate patterns from a massive network and propose a method called gApprox. gApprox not only finds approximate network patterns, which is the key for many knowledge discovery applications on …

Option-Based Risk Management: A Field Study Of Sequential Information Technology Investment Decisions, Michel Benaroch, Mark Jeffery, Robert John Kauffman, Sandeep Shah

Research Collection School Of Computing and Information Systems

This field study research evaluates the viability of applying an option-based risk management (OBRiM) framework, and its accompanying theoretical perspective and methodology, to real-world sequential information technology (IT) investment problems. These problems involve alternative investment structures that bear different risk profiles for the firm, and also may improve the payoffs of the associated projects and the organization's performance. We sought to surface the costs, benefits, and risks associated with a complex sequential investment setting that has the key features that OBRiM treats. We combine traditional, purchased real options that subsequently create strategic flexibility for the decision maker, with implicit or …

A Computational Chemistry Study Of Spin Traps., Jacob Fosso-Tande

Electronic Theses and Dissertations

Many defects in physiological processes are due to free radical damage: reactive oxygen species, nitric oxide, and hydroxyl radicals have been implicated in the parthenogenesis of cancer, diabetes mellitus, and rheumatoid arthritis. We herein characterize the phenyl-N-ter-butyl nitrone (PBN) type spin traps in conjunction with the most studied dimethyl-1-pyrroline-N-oxide (DMPO) type spin traps using the hydroxyl radical. In this study, theoretical calculations are carried out on the two main types of spin traps (DMPO and PBN) at the density functional theory level (DFT). The energies of the optimized structures, hyperfine calculations in gaseous and aqueous phases of the spin traps …

Theoretical And Practical Complexity Of Modeling Methods, John Erickson, Keng Siau

Research Collection School Of Computing and Information Systems

The estimation of theoretical and practical complexity of a system development method is discussed. Executable model capability allow developers to transform models developed during the Systems Analysis and Design portion of the systems development process into working applications. Systems are becoming more complex mostly because of influencing factors such as required and enhanced functionality, interoperability, and security. Other trends that impact the complexity of applications include systems such as enterprise resource planning, supply chain management, and customer relationship management. These types of systems are very large and complex and require close internal cooperation for the implementing organizations individually and also …

A Genetic Algorithm For Cellular Manufacturing Design And Layout, Xiaodan Wu, Chao-Hsien Chu, Yunfeng Wang, Weili Yan

Research Collection School Of Computing and Information Systems

Cellular manufacturing (CM) is an approach that can be used to enhance both flexibility and efficiency in today’s small-to-medium lot production environment. The design of a CM system (CMS) often involves three major decisions: cell formation, group layout, and group schedule. Ideally, these decisions should be addressed simultaneously in order to obtain the best results. However, due to the complexity and NP-complete nature of each decision and the limitations of traditional approaches, most researchers have only addressed these decisions sequentially or independently. In this study, a hierarchical genetic algorithm is developed to simultaneously form manufacturing cells and determine the group …

On Searching Continuous Nearest Neighbors In Wireless Data Broadcast Systems, Baihua Zheng, Wang-Chien Lee, Dik Lun Lee

Research Collection School Of Computing and Information Systems

A continuous nearest neighbor (CNN) search, which retrieves the nearest neighbors corresponding to every point in a given query line segment, is important for location-based services such as vehicular navigation and tourist guides. It is infeasible to answer a CNN search by issuing a traditional nearest neighbor query at every point of the line segment due to the large number of queries generated and the overhead on bandwidth. Algorithms have been proposed recently to support CNN search in the traditional client-server systems but not in the environment of wireless data broadcast, where uplink communication channels from mobile devices to the …

Learning Causal Models For Noisy Biological Data Mining: An Application To Ovarian Cancer Detection, Ghim-Eng Yap, Ah-Hwee Tan, Hwee Hwa Pang

Research Collection School Of Computing and Information Systems

Undetected errors in the expression measurements from highthroughput DNA microarrays and protein spectroscopy could seriously affect the diagnostic reliability in disease detection. In addition to a high resilience against such errors, diagnostic models need to be more comprehensible so that a deeper understanding of the causal interactions among biological entities like genes and proteins may be possible. In this paper, we introduce a robust knowledge discovery approach that addresses these challenges. First, the causal interactions among the genes and proteins in the noisy expression data are discovered automatically through Bayesian network learning. Then, the diagnosis of a disease based on …

Continuous Medoid Queries Over Moving Objects, Stavros Papadopoulos, Dimitris Sacharidis, Kyriakos Mouratidis

Research Collection School Of Computing and Information Systems

In the k-medoid problem, given a dataset P, we are asked to choose kpoints in P as the medoids. The optimal medoid set minimizes the average Euclidean distance between the points in P and their closest medoid. Finding the optimal k medoids is NP hard, and existing algorithms aim at approximate answers, i.e., they compute medoids that achieve a small, yet not minimal, average distance. Similarly in this paper, we also aim at approximate solutions. We consider, however, the continuous version of the problem, where the points in P move and our task is to maintain the medoid set on-the-fly …

Discovering And Exploiting Causal Dependencies For Robust Mobile Context-Aware Recommenders, Ghim-Eng Yap, Ah-Hwee Tan, Hwee Hwa Pang

Research Collection School Of Computing and Information Systems

Acquisition of context poses unique challenges to mobile context-aware recommender systems. The limited resources in these systems make minimizing their context acquisition a practical need, and the uncertainty in the mobile environment makes missing and erroneous context inputs a major concern. In this paper, we propose an approach based on Bayesian networks (BNs) for building recommender systems that minimize context acquisition. Our learning approach iteratively trims the BN-based context model until it contains only the minimal set of context parameters that are important to a user. In addition, we show that a two-tiered context model can effectively capture the causal …

Analyzing Feature Trajectories For Event Detection, Qi He, Kuiyu Chang, Ee Peng Lim

Research Collection School Of Computing and Information Systems

We consider the problem of analyzing word trajectories in both time and frequency domains, with the specific goal of identifying important and less-reported, periodic and aperiodic words. A set of words with identical trends can be grouped together to reconstruct an event in a completely un-supervised manner. The document frequency of each word across time is treated like a time series, where each element is the document frequency - inverse document frequency (DFIDF) score at one time point. In this paper, we 1) first applied spectral analysis to categorize features for different event characteristics: important and less-reported, periodic and aperiodic; …

Continuous Monitoring Of Top-K Queries Over Sliding Windows, Kyriakos Mouratidis, Spiridon Bakiras, Dimitris Papadias

Research Collection School Of Computing and Information Systems

Given a dataset P and a preference function f, a top-k query retrieves the k tuples in P with the highest scores according to f. Even though the problem is well-studied in conventional databases, the existing methods are inapplicable to highly dynamic environments involving numerous long-running queries. This paper studies continuous monitoring of top-k queries over a fixed-size window W of the most recent data. The window size can be expressed either in terms of the number of active tuples or time units. We propose a general methodology for top-k monitoring that restricts processing to the sub-domains of the workspace …

Usage-Based Versus Flat Pricing For E-Business Services With Differentiated Qos, Zhen Liu, Laura Wynter, Cathy Xia

Research Collection School Of Computing and Information Systems

Design of e-commerce services that are competitive, in such a quickly responding market, requires the analyses of prices and price structures. We present a general model of an e-commerce market that allows us to analyze optimal price structures, both flat and usage-based. Based on the price structure of a major web hosting provider, we consider both single-tier and two-tier (burst-rate) pricing, and our result suggests that the more complex two-tier structure may not be worth the marketing effort, as the firm?s equilibrium profits will not increase through the use of this structure. An essential feature of our approach is that …

Instance Weighting For Domain Adaptation In Nlp, Jing Jiang, Chengxiang Zhai

Research Collection School Of Computing and Information Systems

Domain adaptation is an important problem in natural language processing (NLP) due to the lack of labeled data in novel domains. In this paper, we study the domain adaptation problem from the instance weighting per- spective. We formally analyze and charac- terize the domain adaptation problem from a distributional view, and show that there are two distinct needs for adaptation, cor- responding to the different distributions of instances and classification functions in the source and the target domains. We then propose a general instance weighting frame- work for domain adaptation. Our empir- ical results on three NLP tasks show that …

Mobile G-Portal Supporting Collaborative Sharing And Learning In Geography Fieldwork: An Empirical Study, Yin-Leng Theng, Kuah-Li Tan, Ee Peng Lim, Jun Zhang, Dion Hoe-Lian Goh, Kalyani Chatterjea, Chew-Hung Chang, Aixin Sun, Han Yu, Nam Hai Dang, Yuanyuan Li, Minh Chanh Vo

Research Collection School Of Computing and Information Systems

Integrated with G-Portal, a Web-based geospatial digital library of geography resources, this paper describes the implementation of Mobile G-Portal, a group of mobile devices as learning assistant tools supporting collaborative sharing and learning for geography fieldwork. Based on a modified Technology Acceptance Model and a Task-Technology Fit model, an initial study with Mobile G-Portal was conducted involving 39 students in a local secondary school. The findings suggested positive indication of acceptance of Mobile G-Portal for geography fieldwork. The paper concludes with a discussion on technological challenges, recommendations for refinement of Mobile G-Portal, and design implications in general for digital libraries …

Continuous Nearest Neighbor Queries Over Sliding Windows, Kyriakos Mouratidis, Dimitris Papadias

Research Collection School Of Computing and Information Systems

Recent research has focused on continuous monitoring of nearest neighbors (NN) in highly dynamic scenarios, where the queries and the data objects move frequently and arbitrarily. All existing methods, however, assume the Euclidean distance metric. In this paper we study k-NN monitoring in road networks, where the distance between a query and a data object is determined by the length of the shortest path connecting them. We propose two methods that can handle arbitrary object and query moving patterns, as well as fluctuations of edge weights. The first one maintains the query results by processing only updates that may invalidate …

Gprune: A Constraint Pushing Framework For Graph Pattern Mining, Feida Zhu, Xifeng Yan, Jiawei Han, Philip S. Yu

Research Collection School Of Computing and Information Systems

In graph mining applications, there has been an increasingly strong urge for imposing user-specified constraints on the mining results. However, unlike most traditional itemset constraints, structural constraints, such as density and diameter of a graph, are very hard to be pushed deep into the mining process. In this paper, we give the first comprehensive study on the pruning properties of both traditional and structural constraints aiming to reduce not only the pattern search space but the data search space as well. A new general framework, called gPrune, is proposed to incorporate all the constraints in such a way that they …