Numerical Analysis and Scientific Computing Commons^™

Comparison Of Multiple Imputation Algorithms And Verification Using Whole-Genome Sequencing In The Cmuh Genetic Biobank, Ting-Yuan Liu, Chih-Fan Lin, Hsing-Tsung Wu, Ya-Lun Wu, Yu-Chia Chen, Chi-Chou Liao, Yu-Pao Chou, Dysan Chao, Hsing-Fang Lu, Ya-Sian Chang, Jan-Gowth Chang, Kai-Cheng Hsu, Fuu‑Jen Tsai

BioMedicine

A genome-wide association study (GWAS) can be conducted to systematically analyze the contributions of genetic factors to a wide variety of complex diseases. Nevertheless, existing GWASs have provided highly ethnic specific data. Accordingly, to provide data specific to Taiwan, we established a large-scale genetic database in a single medical institution at the China Medical University Hospital. With current technological limitations, microarray analysis can detect only a limited number of single-nucleotide polymorphisms (SNPs) with a minor allele frequency of >1%. Nevertheless, imputation represents a useful alternative means of expanding data. In this study, we compared four imputation algorithms in terms of …

On A Multistage Discrete Stochastic Optimization Problem With Stochastic Constraints And Nested Sampling, Thuy Anh Ta, Tien Mai, Fabian Bastin, Pierre L'Ecuyer

Research Collection School Of Computing and Information Systems

We consider a multistage stochastic discrete program in which constraints on any stage might involve expectations that cannot be computed easily and are approximated by simulation. We study a sample average approximation (SAA) approach that uses nested sampling, in which at each stage, a number of scenarios are examined and a number of simulation replications are performed for each scenario to estimate the next-stage constraints. This approach provides an approximate solution to the multistage problem. To establish the consistency of the SAA approach, we first consider a two-stage problem and show that in the second-stage problem, given a scenario, the …

Adaptive Posterior Knowledge Selection For Improving Knowledge-Grounded Dialogue Generation, Weichao Wang, Wei Gao, Shi Feng, Ling Chen, Daling Wang

Research Collection School Of Computing and Information Systems

In open-domain dialogue systems, knowledge information such as unstructured persona profiles, text descriptions and structured knowledge graph can help incorporate abundant background facts for delivering more engaging and informative responses. Existing studies attempted to model a general posterior distribution over candidate knowledge by considering the entire response utterance as a whole at the beginning of decoding process for knowledge selection. However, a single smooth distribution could fail to model the variability of knowledge selection patterns over different decoding steps, and make the knowledge expression less consistent. To remedy this issue, we propose an adaptive posterior knowledge selection framework, which sequentially …

Ensemble Data Fitting For Bathymetric Models Informed By Nominal Data, Samantha Zambo

Dissertations

Due to the difficulty and expense of collecting bathymetric data, modeling is the primary tool to produce detailed maps of the ocean floor. Current modeling practices typically utilize only one interpolator; the industry standard is splines-in-tension.

In this dissertation we introduce a new nominal-informed ensemble interpolator designed to improve modeling accuracy in regions of sparse data. The method is guided by a priori domain knowledge provided by artificially intelligent classifiers. We recast such geomorphological classifications, such as ‘seamount’ or ‘ridge’, as nominal data which we utilize as foundational shapes in an expanded ordinary least squares regression-based algorithm. To our knowledge …

Solving Large-Scale Extensive-Form Network Security Games Via Neural Fictitious Self-Play, Wanqi Xue, Youzhi Zhang, Shuxin Li, Xinrun Wang, Bo An, Chai Kiat Yeo

Research Collection School Of Computing and Information Systems

Securing networked infrastructures is important in the real world. The problem of deploying security resources to protect against an attacker in networked domains can be modeled as Network Security Games (NSGs). Unfortunately, existing approaches, including the deep learning-based approaches, are inefficient to solve large-scale extensive-form NSGs. In this paper, we propose a novel learning paradigm, NSG-NFSP, to solve large-scale extensive-form NSGs based on Neural Fictitious Self-Play (NFSP). Our main contributions include: i) reforming the best response (BR) policy network in NFSP to be a mapping from action-state pair to action-value, to make the calculation of BR possible in NSGs; ii) …

Computational Studies Of Carbon Nanocluster Solidification, Chathuri C. Silva

Dissertations

A subset of micron-size meteoritic carbon particles formed in red giant atmospheres show a core-rim structure, likely condensed from a vapor phase into super-cooled carbon droplets that nucleated graphene sheets (~40Å) on randomly oriented 5-atom loops during solidification, followed by coating with a graphite rim. Similar particles form during slow cooling of carbon vapor in the lab.

Here we investigate the nucleation and growth of carbon rings and graphene sheets using density functional theory (DFT). Our objectives: (1). explore different computational techniques in DFT-VASP for various carbon structures and compare the results with literature, (2). investigate the nucleation and growth …

Design And Development Of Techniques To Ensure Integrity In Fog Computing Based Databases, Abdulwahab Fahad S. Alazeb

Graduate Theses and Dissertations

The advancement of information technology in coming years will bring significant changes to the way sensitive data is processed. But the volume of generated data is rapidly growing worldwide. Technologies such as cloud computing, fog computing, and the Internet of things (IoT) will offer business service providers and consumers opportunities to obtain effective and efficient services as well as enhance their experiences and services; increased availability and higher-quality services via real-time data processing augment the potential for technology to add value to everyday experiences. This improves human life quality and easiness. As promising as these technological innovations, they are prone …

Mmconv: An Environment For Multimodal Conversational Search Across Multiple Domains, Lizi Liao, Le Hong Long, Zheng Zhang, Minlie Huang, Tat-Seng Chua

Research Collection School Of Computing and Information Systems

Although conversational search has become a hot topic in both dialogue research and IR community, the real breakthrough has been limited by the scale and quality of datasets available. To address this fundamental obstacle, we introduce the Multimodal Multi-domain Conversational dataset (MMConv), a fully annotated collection of human-to-human role-playing dialogues spanning over multiple domains and tasks. The contribution is two-fold. First, beyond the task-oriented multimodal dialogues among user and agent pairs, dialogues are fully annotated with dialogue belief states and dialogue acts. More importantly, we create a relatively comprehensive environment for conducting multimodal conversational search with real user settings, structured …

A Comparison Of Word Embedding Techniques For Similarity Analysis, Tyler Gerth

Computer Science and Computer Engineering Undergraduate Honors Theses

There have been a multitude of word embedding techniques developed that allow a computer to process natural language and compare the relationships between different words programmatically. In this paper, similarity analysis, or the testing of words for synonymic relations, is used to compare several of these techniques to see which performs the best. The techniques being compared all utilize the method of creating word vectors, reducing words down into a single vector of numerical values that denote how the word relates to other words that appear around it. In order to get a holistic comparison, multiple analyses were made, with …

Improving Bayesian Graph Convolutional Networks Using Markov Chain Monte Carlo Graph Sampling, Aneesh Komanduri

Computer Science and Computer Engineering Undergraduate Honors Theses

In the modern age of social media and networks, graph representations of real-world phenomena have become incredibly crucial. Often, we are interested in understanding how entities in a graph are interconnected. Graph Neural Networks (GNNs) have proven to be a very useful tool in a variety of graph learning tasks including node classification, link prediction, and edge classification. However, in most of these tasks, the graph data we are working with may be noisy and may contain spurious edges. That is, there is a lot of uncertainty associated with the underlying graph structure. Recent approaches to modeling uncertainty have been …

Trunctrimmer: A First Step Towards Automating Standard Bioinformatic Analysis, Z. Gunner Lawless, Dana Dittoe, Dale R. Thompson, Steven C. Ricke

Computer Science and Computer Engineering Undergraduate Honors Theses

Bioinformatic analysis is a time-consuming process for labs performing research on various microbiomes. Researchers use tools like Qiime2 to help standardize the bioinformatic analysis methods, but even large, extensible platforms like Qiime2 have drawbacks due to the attention required by researchers. In this project, we propose to automate additional standard lab bioinformatic procedures by eliminating the existing manual process of determining the trim and truncate locations for paired end 2 sequences. We introduce a new Qiime2 plugin called TruncTrimmer to automate the process that usually requires the researcher to make a decision on where to trim and truncate manually after …

Urban Perception: Sensing Cities Via A Deep Interactive Multi-Task Learning Framework, Weili Guan, Zhaozheng Chen, Fuli Feng, Weifeng Liu, Liqiang Nie

Research Collection School Of Computing and Information Systems

Social scientists have shown evidence that visual perceptions of urban attributes, such as safe, wealthy, and beautiful perspectives of the given cities, are highly correlated to the residents' behaviors and quality of life. Despite their significance, measuring visual perceptions of urban attributes is challenging due to the following facts: (1) Visual perceptions are subjectively contradistinctive rather than absolute. (2) Perception comparisons between image pairs are usually conducted region by region, and highly related to the specific urban attributes. And (3) the urban attributes have both the shared and specific information. To address these problems, in this article, we present a …

Quantum Simulation Of Schrödinger's Equation, Mohamed Eltohfa

Capstone and Graduation Projects

Quantum computing is one of the promising active areas in physics research. This is because of the potential of quantum algorithms to outperform their classical counterparts. Grover’s search algorithm has a quadratic speed-up compared to the classical linear search. The quantum simulation of Schrödinger’s equation has an exponential memory save-up compared to the classical simulation. In this thesis, the ideas and tools of quantum computing are reviewed. Grover’s algorithm is studied and simulated as an example. Using the Qiskit quantum computing library, a code to simulate Schrödinger’s equation for a particle in one dimension is developed, simulated locally, and run …

Efficient Algorithms For Trajectory-Aware Mobile Crowdsourcing, Chung-Kyun Han

Dissertations and Theses Collection (Open Access)

Mobile crowdsourcing, a subclass of crowdsourcing dealing with location-specific tasks, is prevalent in our daily life. From sensing urban environment such as noise, air pollution to package delivery, various location-specific tasks are posted on mobile crowdsourcing platforms to tap on the pool of crowdsourced workers. Many digital platforms compete with each other to expand and retain their pool of crowdsourced workers. Comparing with the traditional workforce, crowdsourced workers do not dedicate their time to do tasks fully and have strong spatiotemporal preferences. The ignorance of crowdsourced workers’ mobility patterns and the lack of personalization would lead to crowdsourced workers’ exodus, …

An Update On The Computational Theory Of Hamiltonian Period Functions, Bradley Joseph Klee

Graduate Theses and Dissertations

Lately, state-of-the-art calculation in both physics and mathematics has expanded to include the field of symbolic computing. The technical content of this dissertation centers on a few Creative Telescoping algorithms of our own design (Mathematica implementations are given as a supplement). These algorithms automate analysis of integral period functions at a level of difficulty and detail far beyond what is possible using only pencil and paper (unless, perhaps, you happen to have savant-level mental acuity). We can then optimize analysis in classical physics by using the algorithms to calculate Hamiltonian period functions as solutions to ordinary differential equations. The simple …

Base-Package Recommendation Framework Based On Consumer Behaviours In Iptv Platform, Kuruparan Shanmugalingam, Ruwinda Ranganayanke, Chanka Gunawardhaha, Rajitha Navarathna

Research Collection School Of Computing and Information Systems

Internet Protocol TeleVision (IPTV) provides many services such as live television streaming, time-shifted media, and Video On Demand (VOD). However, many customers do not engage properly with their subscribed packages due to a lack of knowledge and poor guidance. Many customers fail to identify the proper IPTV service package based on their needs and to utilise their current package to the maximum. In this paper, we propose a base-package recommendation model with a novel customer scoring-meter based on customers behaviour. Initially, our paper describes an algorithm to measure customers engagement score, which illustrates a novel approach to track customer engagement …

Reducing Estimation Bias Via Triplet-Average Deep Deterministic Policy Gradient, Dongming Wu, Xingping Dong, Jianbing Shen, Steven C. H. Hoi

Research Collection School Of Computing and Information Systems

The overestimation caused by function approximation is a well-known property in Q-learning algorithms, especially in single-critic models, which leads to poor performance in practical tasks. However, the opposite property, underestimation, which often occurs in Q-learning methods with double critics, has been largely left untouched. In this article, we investigate the underestimation phenomenon in the recent twin delay deep deterministic actor-critic algorithm and theoretically demonstrate its existence. We also observe that this underestimation bias does indeed hurt performance in various experiments. Considering the opposite properties of single-critic and double-critic methods, we propose a novel triplet-average deep deterministic policy gradient algorithm that …

Espade: An Efficient And Semantically Secure Shortest Path Discovery For Outsourced Location-Based Services, Bharath K. Samanthula, Divyadharshini Karthikeyan, Boxiang Dong, K. Anitha Kumari

Department of Computer Science Faculty Scholarship and Creative Works

With the rapid growth of smart devices and technological advancements in tracking geospatial data, the demand for Location-Based Services (LBS) is facing a constant rise in several domains, including military, healthcare and transportation. It is a natural step to migrate LBS to a cloud environment to achieve on-demand scalability and increased resiliency. Nonetheless, outsourcing sensitive location data to a third-party cloud provider raises a host of privacy concerns as the data owners have reduced visibility and control over the outsourced data. In this paper, we consider outsourced LBS where users want to retrieve map directions without disclosing their location information. …

Efficient Sampling Algorithms For Approximate Temporal Motif Counting, Jingjing Wang, Yanhao Wang, Wenjun Jiang, Yuchen Li, Kian-Lee Tan

Research Collection School Of Computing and Information Systems

A great variety of complex systems ranging from user interactions in communication networks to transactions in financial markets can be modeled as temporal graphs, which consist of a set of vertices and a series of timestamped and directed edges. Temporal motifs in temporal graphs are generalized from subgraph patterns in static graphs which take into account edge orderings and durations in addition to structures. Counting the number of occurrences of temporal motifs is a fundamental problem for temporal network analysis. However, existing methods either cannot support temporal motifs or suffer from performance issues. In this paper, we focus on approximate …

A Hybrid Framework Using A Qubo Solver For Permutation-Based Combinatorial Optimization, Siong Thye Goh, Sabrish Gopalakrishnan, Jianyuan Bo, Hoong Chuin Lau

Research Collection School Of Computing and Information Systems

In this paper, we propose a hybrid framework to solve large-scale permutation-based combinatorial problems effectively using a high-performance quadratic unconstrained binary optimization (QUBO) solver. To do so, transformations are required to change a constrained optimization model to an unconstrained model that involves parameter tuning. We propose techniques to overcome the challenges in using a QUBO solver that typically comes with limited numbers of bits. First, to smooth the energy landscape, we reduce the magnitudes of the input without compromising optimality. We propose a machine learning approach to tune the parameters for good performance effectively. To handle possible infeasibility, we introduce …

Find Me If You Can: Aligning Users In Different Social Networks, Priyanka Kasbekar, Katerina Potika, Chris Pollett

Faculty Publications, Computer Science

Online Social Networks allow users to share experiences with friends and relatives, make announcements, find news and jobs, and more. Several have user bases that number in the hundred of millions and even billions. Very often many users belong to multiple social networks at the same time under possibly different user names. Identifying a user from one social network on another social network gives information about a user's behavior on each platform, which in turn can help companies perform graph mining tasks, such as community detection and link prediction. The process of identifying or aligning users in multiple networks is …

Investigating Single Precision Floating General Matrix Multiply In Heterogeneous Hardware, Steven Harris

McKelvey School of Engineering Graduate Student Theses & Dissertations

The fundamental operation of matrix multiplication is ubiquitous across a myriad of disciplines. Yet, the identification of new optimizations for matrix multiplication remains relevant for emerging hardware architectures and heterogeneous systems. Frameworks such as OpenCL enable computation orchestration on existing systems, and its availability using the Intel High Level Synthesis compiler allows users to architect new designs for reconfigurable hardware using C/C++. Using the HARPv2 as a vehicle for exploration, we investigate the utility of several of the most notable matrix multiplication optimizations to better understand the performance portability of OpenCL and the implications for such optimizations on this and …

Graphical Representation Of Text Semantics, Karl Kevin Tiba Fossoh

Master of Science in Computer Science Theses

A text is a set of words conveying a particular semantic based on their order, representation and structure. Those elements can be associated through a different set of interpretations, based on frequency and proportionality. The problem with context is that numbers do not help understand the semantics and fall short to convey the message of the text. The graphical representation of text semantics focuses on the conversion of text to images. Contrarily to word clouds that simply produce frequency mapping of words within the text and topic models that essentially give context to word frequencies and proportionalities, images keep intact …

Shakespeare In The Eighteenth Century: Algorithm For Quotation Identification, Marion Pauline Chiariglione

Graduate Theses and Dissertations

Quoting a borrowed excerpt of text within another literary work was infrequently done prior to the beginning of the eighteenth century. However, quoting other texts, particularly Shakespeare, became quite common after that. Our work develops automatic approaches to identify that trend. Initial work focuses on identifying exact and modified sections of texts taken from works of Shakespeare in novels spanning the eighteenth century. We then introduce a novel approach to identifying modified quotes by adapting the Edit Distance metric, which is character based, to a word based approach. This paper offers an introduction to previous uses of this metric within …

Nonlinear Least Squares 3-D Geolocation Solutions Using Time Differences Of Arrival, Michael V. Bredemann

Mathematics & Statistics ETDs

This thesis uses a geometric approach to derive and solve nonlinear least squares minimization problems to geolocate a signal source in three dimensions using time differences of arrival at multiple sensor locations. There is no restriction on the maximum number of sensors used. Residual errors reach the numerical limits of machine precision. Symmetric sensor orientations are found that prevent closed form solutions of source locations lying within the null space. Maximum uncertainties in relative sensor positions and time difference of arrivals, required to locate a source within a maximum specified error, are found from these results. Examples illustrate potential requirements …

Storage Management Strategy In Mobile Phones For Photo Crowdsensing, En Wang, Zhengdao Qu, Xinyao Liang, Xiangyu Meng, Yongjian Yang, Dawei Li, Weibin Meng

Department of Computer Science Faculty Scholarship and Creative Works

In mobile crowdsensing, some users jointly finish a sensing task through the sensors equipped in their intelligent terminals. In particular, the photo crowdsensing based on Mobile Edge Computing (MEC) collects pictures for some specific targets or events and uploads them to nearby edge servers, which leads to richer data content and more efficient data storage compared with the common mobile crowdsensing; hence, it has attracted an important amount of attention recently. However, the mobile users prefer uploading the photos through Wifi APs (PoIs) rather than cellular networks. Therefore, photos stored in mobile phones are exchanged among users, in order to …

The Evolving Fuzzy Clustering Approach For Discriminating Neutron And Gamma-Ray Pulses, Shirkhorshidi Ali Seyed

Student Works (2020-2029)

Having a significant amount of data is not useful unless the data can be processed for extracting knowledge and information. One of the elementary steps in crunching data is to break it down into groups. When the data is small and collected in a controlled manner, and when the training data is appropriately labelled, the trivial approach is to use supervised learning to perform the grouping. Supervised methods need training data and information about groups beforehand; however, in the current reality, with an avalanche of data, this information is not available. Nevertheless, the need for grouping data remains. Clustering, as …

Developing A Computational Framework For A Construction Scheduling Decision Support Web Based Expert System, Feroz Ahmed

Dissertations

Decision-making is one of the basic cognitive processes of human behaviors by which a preferred option or a course of action is chosen from among a set of alternatives based on certain criteria. Decision-making is the thought process of selecting a logical choice from the available options. When trying to make a good decision, all the positives and negatives of each option should be evaluated. This decision-making process is particularly challenging during the preparation of a construction schedule, where it is difficult for a human to analyze all possible outcomes of each and every situation because, construction of a project …

Contrasting Geometric Variations Of Mathematical Models Of Self-Assembling Systems, Michael Sharp

Graduate Theses and Dissertations

Self-assembly is the process by which complex systems are formed and behave due to the interactions of relatively simple units. In this thesis, we explore multiple augmentations of well known models of self-assembly to gain a better understanding of the roles that geometry and space play in their dynamics. We begin in the abstract Tile Assembly Model (aTAM) with some examples and a brief survey of previous results to provide a foundation. We then introduce the Geometric Thermodynamic Binding Network model, a model that focuses on the thermodynamic stability of its systems while utilizing geometrically rigid components (dissimilar to other …

A Machine Learning Model For Clustering Securities, Vanessa Torres, Travis Deason, Michael Landrum, Nibhrat Lohria

SMU Data Science Review

In this paper, we evaluate the self-declared industry classifications and industry relationships between companies listed on either the Nasdaq or the New York Stock Exchange (NYSE) markets. Large corporations typically operate in multiple industries simultaneously; however, for investment purposes they are classified as belonging to a single industry. This simple classification obscures the actual industries within which a company operates, and, therefore, the investment risks of that company.
By using Natural Language Processing (NLP) techniques on Security and Exchange Commission (SEC) filings, we obtained self-defined industry classifications per company. Using clustering techniques such as Hierarchical Agglomerative and k-means clustering we …