Computer Sciences Commons^™

Algorithms And Variations On The Positional Burrows-Wheeler Transform And Their Applications, Ahsan Sanaullah

Electronic Theses and Dissertations, 2020-2023

In this dissertation, we develop algorithms and variations on the Positional Burrows-Wheeler Transform (PBWT). The PBWT is a data structure that stores M binary strings of length N while allowing efficient search. We develop the dynamic-PBWT (d-PBWT). The d-PBWT is a variation of the PBWT that allows its relevant algorithms to run with unchanged time complexity, but also allows efficient insertion and deletion of haplotypes. We provide insertion and deletion algorithms on the PBWT with average case O(N) time complexity. We also improve upon the query algorithms for the PBWT. Durbin described a set maximal match query algorithm on the …

An Empirical Analysis Of Algorithms For Simple Stochastic Games, Cody William Klingler

Graduate Theses, Dissertations, and Problem Reports (ETD)

This thesis presents the findings of a computational study on algorithms for Simple Stochastic Games (SSG). Simple Stochastic Games are a restriction of the Shapley stochastic model motivated by their applications in AI planning, logic synthesis, and theoretical computer science. This thesis seeks to empirically assess the performance of these algorithms to compensate for their lack of strong complexity results. Where applicable, we include both variations of algorithms where stable strategies are computed by a linear-programming and naive approach. These algorithms are evaluated on random inputs, in addition to specific difficult cases that were identified experimentally. We are interested in …

I Know What You Are Searching For: Code Snippet Recommendation From Stack Overflow Posts, Zhipeng Gao, Xin Xia, David Lo, John C. Grundy, Xindong Zhang, Zhenchang Xing

Research Collection School Of Computing and Information Systems

Stack Overflow has been heavily used by software developers to seek programming-related information. More and more developers use Community Question and Answer forums, such as Stack Overflow, to search for code examples of how to accomplish a certain coding task. This is often considered to be more efficient than working from source documentation, tutorials, or full worked examples. However, due to the complexity of these online Question and Answer forums and the very large volume of information they contain, developers can be overwhelmed by the sheer volume of available information. This makes it hard to find and/or even be aware …

Face Anti-Spoofing And Deep Learning Based Unsupervised Image Recognition Systems, Enoch Solomon

Theses and Dissertations

One of the main problems of a supervised deep learning approach is that it requires large amounts of labeled training data, which are not always easily available. This PhD dissertation addresses the above-mentioned problem by using a novel unsupervised deep learning face verification system called UFace, that does not require labeled training data as it automatically, in an unsupervised way, generates training data from even a relatively small size of data. The method starts by selecting, in unsupervised way, k-most similar and k-most dissimilar images for a given face image. Moreover, this PhD dissertation proposes a new loss function to …

Fast Multiscale Functional Estimation In Optimal Emg Placement For Robotic Prosthesis Controllers, Jin Ren, Guohui Song, Lucia Tabacu, Yuesheng Xu

Mathematics & Statistics Faculty Publications

Electromyogram (EMG) signals play a significant role in decoding muscle contraction information for robotic hand prosthesis controllers. Widely applied decoders require a large amount of EMG signals sensors, resulting in complicated calculations and unsatisfactory predictions. By the biomechanical process of single degree-of-freedom human hand movements, only several EMG signals are essential for accurate predictions. Recently, a novel predictor of hand movements adopted a multistage sequential adaptive functional estimation (SAFE) method based on the historical functional linear model (FLM) to select important EMG signals and provide precise projections.

However, SAFE repeatedly performs matrix-vector multiplications with a dense representation matrix of the …

Assessing The Performance Of A Particle Swarm Optimization Mobility Algorithm In A Hybrid Wi-Fi/Lora Flying Ad Hoc Network, William David Paredes

UNF Graduate Theses and Dissertations

Research on Flying Ad-Hoc Networks (FANETs) has increased due to the availability of Unmanned Aerial Vehicles (UAVs) and the electronic components that control and connect them. Many applications, such as 3D mapping, construction inspection, or emergency response operations could benefit from an application and adaptation of swarm intelligence-based deployments of multiple UAVs. Such groups of cooperating UAVs, through the use of local rules, could be seen as network nodes establishing an ad-hoc network for communication purposes.

One FANET application is to provide communication coverage over an area where communication infrastructure is unavailable. A crucial part of a FANET implementation is …

Cooperative Deep Q -Learning Framework For Environments Providing Image Feedback, Krishnan Raghavan, Vignesh Narayanan, Sarangapani Jagannathan

Publications

In this article, we address two key challenges in deep reinforcement learning (DRL) setting, sample inefficiency, and slow learning, with a dual-neural network (NN)-driven learning approach. In the proposed approach, we use two deep NNs with independent initialization to robustly approximate the action-value function in the presence of image inputs. In particular, we develop a temporal difference (TD) error-driven learning (EDL) approach, where we introduce a set of linear transformations of the TD error to directly update the parameters of each layer in the deep NN. We demonstrate theoretically that the cost minimized by the EDL regime is an approximation …

The Effect Of The Width Of The Incident Pulse To The Dielectric Transition Layer In The Scattering Of An Electromagnetic Pulse — A Qubit Lattice Algorithm Simulation, George Vahala, Linda Vahala, Abhay K. Ram, Min Soe

Electrical & Computer Engineering Faculty Publications

The effect of the thickness of the dielectric boundary layer that connects a material of refractive index n₁ to another of index n₂is considered for the propagation of an electromagnetic pulse. A qubit lattice algorithm (QLA), which consists of a specially chosen non-commuting sequence of collision and streaming operators acting on a basis set of qubits, is theoretically determined that recovers the Maxwell equations to second-order in a small parameter ϵ. For very thin boundary layer the scattering properties of the pulse mimics that found from the Fresnel jump conditions for a plane wave - except that …

Adaptive Critic Network For Person Tracking Using 3d Skeleton Data, Joseph G. Zalameda, Alex Glandon, Khan M. Iftekharuddin, Mohammad S. Alam (Ed.), Vijayan K. Asari (Ed.)

Electrical & Computer Engineering Faculty Publications

Analysis of human gait using 3-dimensional co-occurrence skeleton joints extracted from Lidar sensor data has been shown a viable method for predicting person identity. The co-occurrence based networks rely on the spatial changes between frames of each joint in the skeleton data sequence. Normally, this data is obtained using a Lidar skeleton extraction method to estimate these co-occurrence features from raw Lidar frames, which can be prone to incorrect joint estimations when part of the body is occluded. These datasets can also be time consuming and expensive to collect and typically offer a small number of samples for training and …

Class Activation Mapping And Uncertainty Estimation In Multi-Organ Segmentation, Md. Shibly Sadique, Walia Farzana, Ahmed Temtam, Khan Iftekharuddin, Khan Iftekharuddin (Ed.), Weijie Chen (Ed.)

Electrical & Computer Engineering Faculty Publications

Deep learning (DL)-based medical imaging and image segmentation algorithms achieve impressive performance on many benchmarks. Yet the efficacy of deep learning methods for future clinical applications may become questionable due to the lack of ability to reason with uncertainty and interpret probable areas of failures in prediction decisions. Therefore, it is desired that such a deep learning model for segmentation classification is able to reliably predict its confidence measure and map back to the original imaging cases to interpret the prediction decisions. In this work, uncertainty estimation for multiorgan segmentation task is evaluated to interpret the predictive modeling in DL …

A Survey Of Using Machine Learning In Iot Security And The Challenges Faced By Researchers, Khawlah M. Harahsheh, Chung-Hao Chen

Electrical & Computer Engineering Faculty Publications

The Internet of Things (IoT) has become more popular in the last 15 years as it has significantly improved and gained control in multiple fields. We are nowadays surrounded by billions of IoT devices that directly integrate with our lives, some of them are at the center of our homes, and others control sensitive data such as military fields, healthcare, and datacenters, among others. This popularity makes factories and companies compete to produce and develop many types of those devices without caring about how secure they are. On the other hand, IoT is considered a good insecure environment for cyber …

An Explainable Artificial Intelligence Framework For The Predictive Analysis Of Hypo And Hyper Thyroidism Using Machine Learning Algorithms, Md. Bipul Hossain, Anika Shama, Apurba Adhikary, Avi Deb Raha, K. M. Aslam Uddin, Mohammad Amzad Hossain, Imtia Islam, Saydul Akbar Murad, Md. Shirajum Munir, Anupam Kumur Bairagi

Electrical & Computer Engineering Faculty Publications

The thyroid gland is the crucial organ in the human body, secreting two hormones that help to regulate the human body's metabolism. Thyroid disease is a severe medical complaint that could be developed by high Thyroid Stimulating Hormone (TSH) levels or an infection in the thyroid tissues. Hypothyroidism and hyperthyroidism are two critical conditions caused by insufficient thyroid hormone production and excessive thyroid hormone production, respectively. Machine learning models can be used to precisely process the data generated from different medical sectors and to build a model to predict several diseases. In this paper, we use different machine-learning algorithms to …

Optimization Of Ported Cfd Kernels On Intel Data Center Gpu Max 1550 Using Oneapi Esimd, Mohammad Zubair, Aaron Walden, Gabriel Nastac, Eric Nielsen, Christoph Bauinger, Xiao Zhu

Computer Science Faculty Publications

We describe our experience porting FUN3D’s CUDA-optimized kernels to Intel oneAPI SYCL.We faced several challenges, including foremost the suboptimal performance of the oneAPI code on Intel’s new data center GPU. Suboptimal performance of the oneAPI code was due primarily to high register spills, memory latency, and poor vectorization. We addressed these issues by implementing the kernels using Intel oneAPI’s Explicit SIMD SYCL extension (ESIMD) API. The ESIMD API enables the writing of explicitly vectorized kernel code, gives more precise control over register usage and prefetching, and better handles thread divergence compared to SYCL. The ESIMD code outperforms the optimized SYCL …

A Structure-Aware Generative Adversarial Network For Bilingual Lexicon Induction, Bocheng Han, Qian Tao, Lusi Li, Zhihao Xiong

Computer Science Faculty Publications

Bilingual lexicon induction (BLI) is the task of inducing word translations with a learned mapping function that aligns monolingual word embedding spaces in two different languages. However, most previous methods treat word embeddings as isolated entities and fail to jointly consider both the intra-space and inter-space topological relations between words. This limitation makes it challenging to align words from embedding spaces with distinct topological structures, especially when the assumption of isomorphism may not hold. To this end, we propose a novel approach called the Structure-Aware Generative Adversarial Network (SA-GAN) model to explicitly capture multiple topological structure information to achieve accurate …

Unttangling Irregular Actin Cytoskeleton Architectures In Tomograms Of The Cell With Struwwel Tracer, Salim Sazzed, Peter Scheible, Jing He, Willy Wriggers

Computer Science Faculty Publications

In this work, we established, validated, and optimized a novel computational framework for tracing arbitrarily oriented actin filaments in cryo-electron tomography maps. Our approach was designed for highly complex intracellular architectures in which a long-range cytoskeleton network extends throughout the cell bodies and protrusions. The irregular organization of the actin network, as well as cryo-electron-tomography-specific noise, missing wedge artifacts, and map dimensions call for a specialized implementation that is both robust and efficient. Our proposed solution, Struwwel Tracer, accumulates densities along paths of a specific length in various directions, starting from locally determined seed points. The highest-density paths originating …

A Diversity-Enhanced Memetic Algorithm For Solving Electric Vehicle Routing Problems With Time Windows And Mixed Backhauls, Jianhua Xiao, Jingguo Du, Zhiguang Cao, Xingyi Zhang, Yunyun Niu

Research Collection School Of Computing and Information Systems

The electric vehicle routing problem (EVRP) has been studied increasingly because of environmental concerns. However, existing studies on the EVRP mainly focus on time windows and sole linehaul customers, which might not be practical as backhaul customers are also ubiquitous in reality. In this study, we investigate an EVRP with time windows and mixed backhauls (EVRPTWMB), where both linehaul and backhaul customers exist and can be served in any order. To address this challenging problem, we propose a diversity-enhanced memetic algorithm (DEMA) that integrates three types of novel operators, including genetic operators based on adaptive selection mechanism, a selection operator …

Intelligent Adaptive Gossip-Based Broadcast Protocol For Uav-Mec Using Multi-Agent Deep Reinforcement Learning, Zen Ren, Xinghua Li, Yinbin Miao, Zhuowen Li, Zihao Wang, Mengyao Zhu, Ximeng Liu, Deng, Robert H.

Research Collection School Of Computing and Information Systems

UAV-assisted mobile edge computing (UAV-MEC) has been proposed to offer computing resources for smart devices and user equipment. UAV cluster aided MEC rather than one UAV-aided MEC as edge pool is the newest edge computing architecture. Unfortunately, the data packet exchange during edge computing within the UAV cluster hasn't received enough attention. UAVs need to collaborate for the wide implementation of MEC, relying on the gossip-based broadcast protocol. However, gossip has the problem of long propagation delay, where the forwarding probability and neighbors are two factors that are difficult to balance. The existing works improve gossip from only one factor, …

An Empirical Analysis Of Approximation Algorithms For The Unweighted Tree Augmentation Problem, Jacob Thomas Restanio

Graduate Theses, Dissertations, and Problem Reports (ETD)

In this thesis, we perform an experimental study of approximation algorithms for the tree augmentation problem (TAP). TAP is a fundamental problem in network design. The goal of TAP is to add the minimum number of edges from a given edge set to a tree so that it becomes 2-edge connected. Formally, given a tree T = (V, E), where V denotes the set of vertices and E denotes the set of edges in the tree, and a set of edges (or links) L ⊆ V × V disjoint from E, the objective is to find a set of edges …

Properties Of (Claw, 4k₁, Bridge)-Free Graphs, Taite Lagrange

Theses and Dissertations (Comprehensive)

Given a set H of graphs, a graph G is H-free if it does not contain any graph in H as an induced subgraph. The complexity of the colouring problem is known when H is a set of graphs on four vertices, with three exceptions. One of those exceptions is the case of {claw, 4K₁}-free graphs, for which our classes of {claw, 4K₁, bridge}-free and {claw, 4K₁, bridge,C₄-twin}-free graphs are subclasses.

The original goal of this work was to prove that {claw, 4K₁, …

The History Of The Enigma Machine, Jenna Siobhan Parkinson

History Publications

The history of the Enigma machine begins with the invention of the rotor-based cipher machine in 1915. Various models for rotor-based cipher machines were developed somewhat simultaneously in different parts of the world. However, the first documented rotor machine was developed by Dutch naval officers in 1915. Nonetheless, the Enigma machine was officially invented following the end of World War I by Arthur Scherbius in 1918 (Faint, 2016).

Improving Adjacency List Storage Methods For Polypeptide Similarity Analysis, Arianna Swensen

Honors Theses

Protein design is a complex biomolecular and computational problem. Working on increasingly large protein folding problems requires an improvement in current analysis methods available. This work first discusses various methods of protein design, including de novo protein design, which is the primary focus of this thesis. Then, a new approach utilizing a B+ tree to effectively store and query a graph of keys and vertices is proposed in order to store the number of times two polypeptides are considered to be similar. This approach is found to have a reduction in time complexity from current mapping methods and thus provides …

Obstacles In Learning Algorithm Run-Time Complexity Analysis, Bailey Licht

Theses/Capstones/Creative Projects

Algorithm run-time complexity analysis is an important topic in data structures and algorithms courses, but it is also a topic that many students struggle with. Commonly cited difficulties include the necessary mathematical background knowledge, the abstract nature of the topic, and the presentation style of the material. Analyzing the subject of algorithm analysis using multiple learning theories shows that course materials often leave out key steps in the learning process and neglect certain learning styles. Students can be more successful at learning algorithm run-time complexity analysis if these missing stages and learning styles are addressed.

Multivariate Fairness For Paper Selection, Reem Alsaffar

Graduate Theses and Dissertations

Peer review is the process by which publishers select the best publications for inclusion in a journal or a conference. Bias in the peer review process can impact which papers are selected for inclusion in conferences and journals. Although often implicit, race, gender and other demographics can prevent members of underrepresented groups from presenting at major conferences. To try to avoid bias, many conferences use a double-blind review process to increase fairness during reviewing. However, recent studies argue that the bias has not been removed completely. Our research focuses on developing fair algorithms that correct for these biases and select …

Forks Over Knives: Predictive Inconsistency In Criminal Justice Algorithmic Risk Assessment Tools, Travis Greene, Galit Shmueli, Jan Fell, Ching-Fu Lin, Han-Wei Liu

Research Collection Yong Pung How School Of Law

Big data and algorithmic risk prediction tools promise to improve criminal justice systems by reducing human biases and inconsistencies in decision-making. Yet different, equally justifiable choices when developing, testing and deploying these socio-technical tools can lead to disparate predicted risk scores for the same individual. Synthesising diverse perspectives from machine learning, statistics, sociology, criminology, law, philosophy and economics, we conceptualise this phenomenon as predictive inconsistency. We describe sources of predictive inconsistency at different stages of algorithmic risk assessment tool development and deployment and consider how future technological developments may amplify predictive inconsistency. We argue, however, that in a diverse and …

An Efficient Annealing-Assisted Differential Evolution For Multi-Parameter Adaptive Latent Factor Analysis, Qing Li, Guansong Pang, Mingsheng Shang

Research Collection School Of Computing and Information Systems

A high-dimensional and incomplete (HDI) matrix is a typical representation of big data. However, advanced HDI data analysis models tend to have many extra parameters. Manual tuning of these parameters, generally adopting the empirical knowledge, unavoidably leads to additional overhead. Although variable adaptive mechanisms have been proposed, they cannot balance the exploration and exploitation with early convergence. Moreover, learning such multi-parameters brings high computational time, thereby suffering gross accuracy especially when solving a bilinear problem like conducting the commonly used latent factor analysis (LFA) on an HDI matrix. Herein, an efficient annealing-assisted differential evolution for multi-parameter adaptive latent factor analysis …

Distilled Siamese Networks For Visual Tracking, Jianbing Shen, Yuanpei Liu, Xingping Dong, Xiankai Lu, Fahad Shahbaz Khan, Steven Hoi

Research Collection School Of Computing and Information Systems

In recent years, Siamese network based trackers have significantly advanced the state-of-the-art in real-time tracking. Despite their success, Siamese trackers tend to suffer from high memory costs, which restrict their applicability to mobile devices with tight memory budgets. To address this issue, we propose a distilled Siamese tracking framework to learn small, fast and accurate trackers (students), which capture critical knowledge from large Siamese trackers (teachers) by a teacher-students knowledge distillation model. This model is intuitively inspired by the one teacher versus multiple students learning method typically employed in schools. In particular, our model contains a single teacher-student distillation module …

A Quality Metric For K-Means Clustering Based On Centroid Locations, Manoj Thulasidas

Research Collection School Of Computing and Information Systems

K-Means clustering algorithm does not offer a clear methodology to determine the appropriate number of clusters; it does not have a built-in mechanism for K selection. In this paper, we present a new metric for clustering quality and describe its use for K selection. The proposed metric, based on the locations of the centroids, as well as the desired properties of the clusters, is developed in two stages. In the initial stage, we take into account the full covariance matrix of the clustering variables, thereby making it mathematically similar to a reduced chi2. We then extend it to account for …

Meta-Complementing The Semantics Of Short Texts In Neural Topic Models, Ce Zhang, Hady Wirawan Lauw

Research Collection School Of Computing and Information Systems

Topic models infer latent topic distributions based on observed word co-occurrences in a text corpus. While typically a corpus contains documents of variable lengths, most previous topic models treat documents of different lengths uniformly, assuming that each document is sufficiently informative. However, shorter documents may have only a few word co-occurrences, resulting in inferior topic quality. Some other previous works assume that all documents are short, and leverage external auxiliary data, e.g., pretrained word embeddings and document connectivity. Orthogonal to existing works, we remedy this problem within the corpus itself by proposing a Meta-Complement Topic Model, which improves topic quality …

Inception Transformer, Chenyang Si, Weihao Yu, Pan Zhou, Yichen Zhou, Xinchao Wang, Shuicheng Yan

Research Collection School Of Computing and Information Systems

Recent studies show that Transformer has strong capability of building long-range dependencies, yet is incompetent in capturing high frequencies that predominantly convey local information. To tackle this issue, we present a novel and general-purpose Inception Transformer, or iFormer for short, that effectively learns comprehensive features with both high- and low-frequency information in visual data. Specifically, we design an Inception mixer to explicitly graft the advantages of convolution and max-pooling for capturing the high-frequency information to Transformers. Different from recent hybrid frameworks, the Inception mixer brings greater efficiency through a channel splitting mechanism to adopt parallel convolution/max-pooling path and self-attention path …

An Algorithm For Indoor Sars-Cov-2 Transmission, Daniel Maxin, Spencer Gannon

Journal of Mind and Medical Sciences

We propose a computer modeling approach for SARS-CoV-2 transmission that can be preferable to a purely mathematical framework. It is illustrated its functionality in a specific case of indoor transmission. Based on literature, we assume that infection is due to aerosols with viral particles that persist and accumulate for hours in the air even after the persons who produced them left the space. We incorporate also restricted opening hours as a mitigation measure and one possible behavioral change in response to this measure. It is shown via several examples how this algorithmic modeling approach can be used to run various …