Physical Sciences and Mathematics Commons^™

Ensemble Protein Inference Evaluation, Kyle Lee Lucke

Graduate Student Theses, Dissertations, & Professional Papers

The Protein inference problem is becoming an increasingly important tool that aids in the characterization of complex proteomes and analysis of complex protein samples. In bottom-up shotgun proteomics experiments the metrics for evaluation (like AUC and calibration error) are based on an often imperfect target-decoy database. These metrics make the inherent assumption that all of the proteins in the target set are present in the sample being analyzed. In general, this is not the case, they are typically a mix of present and absent proteins. To objectively evaluate inference methods, protein standard datasets are used. These datasets are special in …

View Synthesis Of Dynamic Scenes Based On Deep 3d Mask Volume, Kai-En Lin, Guowei Yang, Lei Xiao, Feng Liu, Ravi Ramamoorthi

Computer Science Faculty Publications and Presentations

Image view synthesis has seen great success in reconstructing photorealistic visuals, thanks to deep learning and various novel representations. The next key step in immersive virtual experiences is view synthesis of dynamic scenes. However, several challenges exist due to the lack of high-quality training datasets, and the additional time dimension for videos of dynamic scenes. To address this issue, we introduce a multi-view video dataset, captured with a custom 10-camera rig in 120FPS. The dataset contains 96 high-quality scenes showing various visual effects and human interactions in outdoor scenes. We develop a new algorithm, Deep 3D Mask Volume, which enables …

A Coastal N₂ Fixation Hotspot At The Cape Hatteras Front: Elucidating Spatial Heterogeneity In Diazotroph Activity Via Supervised Machine Learning, Corday R. Selden, P. Dreux Chappell, Sophie Clayton, Alfonso Macías-Tapia, Peter W. Bernhardt, Margaret R. Mulholland

OES Faculty Publications

In the North Atlantic Ocean, dinitrogen (N₂) fixation on the western continental shelf represents a significant fraction of basin‐wide nitrogen (N) inputs. However, the factors regulating coastal N₂ fixation remain poorly understood, in part due to sharp physico‐chemical gradients and dynamic water mass interactions that are difficult to constrain via traditional oceanographic approaches. This study sought to characterize the spatial heterogeneity of N₂ fixation on the western North Atlantic shelf, at the confluence of Mid‐ and South Atlantic Bight shelf waters and the Gulf Stream, in August 2016. Rates were quantified using the ¹⁵N_{2 …}

A Novel Method For Soc Estimation Of Li-Ion Batteries Using A Hybrid Machinelearning Technique, Eymen İpek, Murat Yilmaz

Turkish Journal of Electrical Engineering and Computer Sciences

The battery system is one of the key components of electric vehicles (EV) which has brought groundbreaking technologies. Since modern EVs have mostly Li-ion batteries, they need to be monitored and controlled to achieve safe and high-performance operation. Particularly, the battery management system (BMS) uses complex processing systems that perform measurements, estimation of the battery states, and protection of the system. State of charge (SOC) estimation is a major part of these processes which defines remaining capacity in the battery until the next charging operation as a proportion to the total battery capacity. Since SOC is not a parameter that …

Swft: Subbands Wavelet For Local Features Transform Descriptor For Cornealdiseases Diagnosis, Samer Al-Salihi, Sezgi̇n Aydin, Nebras Hussein

Turkish Journal of Electrical Engineering and Computer Sciences

Human cornea is the front see-through shield of the eye. It refracts light onto the retina to induce vision.Therefore, any defect in the cornea may lead to vision disturbance. This deficiency is estimated by sets of topographicalimages measured, and assessed by an ophthalmologist. Consequently, an important priority is the early and accuratediagnosis of diseases that may affect corneal integrity through the use of machine learning algorithms. Images producedby a Pentacam device can be subjected to rotation or some distortion during acquisition; therefore, accurate diagnosisrequires the use of local features in the image. Accordingly, a new algorithm called subbands wavelet for …

An Improved Version Of Multi-View K-Nearest Neighbors (Mvknn) For Multipleview Learning, Eli̇fe Öztürk Kiyak, Derya Bi̇rant, Kökten Ulaş Bi̇rant

Turkish Journal of Electrical Engineering and Computer Sciences

Multi-view learning (MVL) is a special type of machine learning that utilizes more than one views, where views include various descriptions of a given sample. Traditionally, classification algorithms such as k-nearest neighbors (KNN) are designed for learning from single-view data. However, many real-world applications involve datasets with multiple views and each view may contain different and partly independent information, which makes the traditional single-view classification approaches ineffective. Therefore, this article proposes an improved MVL algorithm, called multi-view k-nearest neighbors (MVKNN), based on the existing KNN algorithm. The experimental results conducted in this research show that a significant improvement is achieved …

Determining And Evaluating New Store Locations Using Remote Sensing Andmachine Learning, Berkan Höke, Zeynep Zerri̇n Turgay, Cem Ünsalan, Hande Küçükaydin

Turkish Journal of Electrical Engineering and Computer Sciences

Decision making for store locations is crucial for retail companies as the profit depends on the location. The key point for correct store location is profit approximation, which is highly dependent on population of the corresponding region, and hence, the volume of the residential area. Thus, estimating building volumes provides insight about the revenue if a new store is about to be opened there. Remote sensing through stereo/tri-stereo satellite images provides wide area coverage as well as adequate resolution for three dimensional reconstruction for volume estimation. We reconstruct 3D map of corresponding region with the help of semiglobal matching and …

A Case Study On Player Selection And Team Formation In Football With Machinelearning, Di̇dem Abi̇di̇n

Turkish Journal of Electrical Engineering and Computer Sciences

Machine learning has been widely used in different domains to extract information from raw data. Sports is one of the popular domains for researchers to work on recently. Although score prediction for matches is the most preferred application area for artificial intelligence, player selection, and team formation is also an application area worth working on. There are some studies in the literature about player selection and team formation which are examined in this study. The study has two important contributions: First one is to apply seven different machine learning algorithms on our dataset to find the best player combination for …

Deep Learning For Turkish Makam Music Composition, İsmai̇l Hakki Parlak, Yalçin Çebi̇, Ci̇han Işikhan, Derya Bi̇rant

Turkish Journal of Electrical Engineering and Computer Sciences

In this paper, we introduce a new deep-learning-based system that can compose structured Turkish makam music (TMM) in the symbolic domain. Presented artificial TMM composer (ATMMC) takes eight initial notes from a human user and completes the rest of the piece. The backbone of the composer system consists of multilayered long short-term memory (LSTM) networks. ATMMC can create pieces in Hicaz and Nihavent makams in Şarkı form, which can be viewed and played with Mus2, a notation software for microtonal music. Statistical analysis shows that pieces composed by ATMMC are approximately 84% similar to training data. ATMMC is an open-source …

Adaptive Physics-Based Non-Rigid Registration For Immersive Image-Guided Neuronavigation Systems, Fotis Drakopoulos, Christos Tsolakis, Angelos Angelopoulos, Yixun Liu, Chengjun Yao, Kyriaki Rafailia Kavazidi, Nikolaos Foroglou, Andrey Fedorov, Sarah Frisken, Ron Kikinis, Alexandra Golby, Nikos Chrisochoides

Computer Science Faculty Publications

Objective: In image-guided neurosurgery, co-registered preoperative anatomical, functional, and diffusion tensor imaging can be used to facilitate a safe resection of brain tumors in eloquent areas of the brain. However, the brain deforms during surgery, particularly in the presence of tumor resection. Non-Rigid Registration (NRR) of the preoperative image data can be used to create a registered image that captures the deformation in the intraoperative image while maintaining the quality of the preoperative image. Using clinical data, this paper reports the results of a comparison of the accuracy and performance among several non-rigid registration methods for handling brain deformation. A …

Applied Machine Learning In Extrusion-Based Bioprinting, Shuyu Tian

Theses and Dissertations

Optimization of extrusion-based bioprinting (EBB) parameters have been systematically conducted through experimentation. However, the process is time and resource-intensive and not easily translatable across different laboratories. A machine learning (ML) approach to EBB parameter optimization can accelerate this process for laboratories across the field through training using data collected from published literature. In this work, regression-based and classification-based ML models were investigated for their abilities to predict printing outcomes of cell viability and filament diameter for cell-containing alginate and gelatin composite hydrogels. Regression-based models were investigated for their ability to predict suitable extrusion pressure given desired cell viability when keeping …

Searching Harder, Localizing Better, Classifying Faster: Optimizing Fast Radio Burst Detection And Analysis, Kshitij Aggarwal

Graduate Theses, Dissertations, and Problem Reports

Fast Radio Bursts (or FRBs) are millisecond-duration transients of extragalactic origin. They exhibit dispersion caused by propagation through an ionized medium, and quantified by Dispersion Measure (DM). Around 800 FRBs (24 repeaters) have been discovered; so far, 24 FRBs have been confidently associated with a host galaxy. In this thesis, we discuss multiple new FRB search and analysis techniques and the corresponding tools that enable us to search for FRBs harder, localize them better, and classify candidates faster.

We discuss five open-source software suites that can be used in FRB analysis. These suites are used to distinguish between FRBs and …

Identification And Classification Of Radio Pulsar Signals Using Machine Learning, Di Pang

Graduate Theses, Dissertations, and Problem Reports

Automated single-pulse search approaches are necessary as ever-increasing amount of observed data makes the manual inspection impractical. Detecting radio pulsars using single-pulse searches, however, is a challenging problem for machine learning because pul- sar signals often vary significantly in brightness, width, and shape and are only detected in a small fraction of observed data.

The research work presented in this dissertation is focused on development of ma- chine learning algorithms and approaches for single-pulse searches in the time domain. Specifically, (1) We developed a two-stage single-pulse search approach, named Single- Pulse Event Group IDentification (SPEGID), which automatically identifies and clas- …

Continuity Of Chen-Fliess Series For Applications In System Identification And Machine Learning, Rafael Dahmen, W. Steven Gray, Alexander Schmeding

Electrical & Computer Engineering Faculty Publications

Model continuity plays an important role in applications like system identification, adaptive control, and machine learning. This paper provides sufficient conditions under which input-output systems represented by locally convergent Chen-Fliess series are jointly continuous with respect to their generating series and as operators mapping a ball in an Lp-space to a ball in an Lq-space, where p and q are conjugate exponents. The starting point is to introduce a class of topological vector spaces known as Silva spaces to frame the problem and then to employ the concept of a direct limit to describe convergence. The proof of the main …

Using Text Mining And Machine Learning Classifiers To Analyze Stack Overflow, Taylor Morris

Dissertations, Master's Theses and Master's Reports

StackOverflow is an extensively used platform for programming questions. In this report, text mining and machine learning classifiers such as decision trees and Naive Bayes are used to evaluate whether a given question posted on StackOverflow will be closed or answered. While multiple models were used in the analysis, the performance for the models was no better than the majority classifier. Future work to develop better performing classifiers to understand why a question is closed or answered will require additional natural language processing or methods to address the imbalanced data.

Revisiting Absolute Pose Regression, Hunter Blanton

Theses and Dissertations--Computer Science

Images provide direct evidence for the position and orientation of the camera in space, known as camera pose. Traditionally, the problem of estimating the camera pose requires reference data for determining image correspondence and leveraging geometric relationships between features in the image. Recent advances in deep learning have led to a new class of methods that regress the pose directly from a single image.

This thesis proposes methods for absolute camera pose regression. Absolute pose regression estimates the pose of a camera from a single image as the output of a fixed computation pipeline. These methods have many practical benefits …

Countering Internet Packet Classifiers To Improve User Online Privacy, Sina Fathi-Kazerooni

Dissertations

Internet traffic classification or packet classification is the act of classifying packets using the extracted statistical data from the transmitted packets on a computer network. Internet traffic classification is an essential tool for Internet service providers to manage network traffic, provide users with the intended quality of service (QoS), and perform surveillance. QoS measures prioritize a network's traffic type over other traffic based on preset criteria; for instance, it gives higher priority or bandwidth to video traffic over website browsing traffic. Internet packet classification methods are also used for automated intrusion detection. They analyze incoming traffic patterns and identify malicious …

Sensitivity Analysis Of An Agent-Based Simulation Model Using Reconstructability Analysis, Andey M. Nunes, Martin Zwick, Wayne Wakeland

Systems Science Faculty Publications and Presentations

Reconstructability analysis, a methodology based on information theory and graph theory, was used to perform a sensitivity analysis of an agent-based model. The NetLogo BehaviorSpace tool was employed to do a full 2^k factorial parameter sweep on Uri Wilensky’s Wealth Distribution NetLogo model, to which a Gini-coefficient convergence condition was added. The analysis identified the most influential predictors (parameters and their interactions) of the Gini coefficient wealth inequality outcome. Implications of this type of analysis for building and testing agent-based simulation models are discussed.

Leveraging The Inductive Bias Of Large Language Models For Abstract Textual Reasoning, Christopher Michael Rytting

Theses and Dissertations

Large natural language models (such as GPT-2 or T5) demonstrate impressive abilities across a range of general NLP tasks. Here, we show that the knowledge embedded in such models provides a useful inductive bias, not just on traditional NLP tasks, but also in the nontraditional task of training a symbolic reasoning engine. We observe that these engines learn quickly and generalize in a natural way that reflects human intuition. For example, training such a system to model block-stacking might naturally generalize to stacking other types of objects because of structure in the real world that has been partially captured by …

Improving A Wireless Localization System Via Machine Learning Techniques And Security Protocols, Zachary Yorio

Masters Theses, 2020-current

The recent advancements made in Internet of Things (IoT) devices have brought forth new opportunities for technologies and systems to be integrated into our everyday life. In this work, we investigate how edge nodes can effectively utilize 802.11 wireless beacon frames being broadcast from pre-existing access points in a building to achieve room-level localization. We explain the needed hardware and software for this system and demonstrate a proof of concept with experimental data analysis. Improvements to localization accuracy are shown via machine learning by implementing the random forest algorithm. Using this algorithm, historical data can train the model and make …

An Assessment Of The Hydrological Trends Using Synergistic Approaches Of Remote Sensing And Model Evaluations Over Global Arid And Semi-Arid Regions, Wenzhao Li, Hesham El-Askary, Rejoice Thomas, Surya Prakash Tiwari, Karuppasamy Manikandan, Thomas Piechota, Daniele Struppa

Mathematics, Physics, and Computer Science Faculty Articles and Research

Drylands cover about 40% of the world’s land area and support two billion people, most of them living in developing countries that are at risk due to land degradation. Over the last few decades, there has been warming, with an escalation of drought and rapid population growth. This will further intensify the risk of desertification, which will seriously affect the local ecological environment, food security and people’s lives. The goal of this research is to analyze the hydrological and land cover characteristics and variability over global arid and semi-arid regions over the last decade (2010–2019) using an integrative approach of …

Unifying Chemistry And Machine Learning For The Study Of Noncovalent Interactions, Jacob A. Townsend

Doctoral Dissertations

Gas separations are in great demand for carbon emission reduction, natural gas purification, oxygen isolation, and much more. Many of these separations rely on cost-prohibitive methods such as cryogenic distillation or strong-binding solvents. As a result, novel materials are being developed to subvert the energetic expense of gas separation processes. These studies focus on improving the performance of alternative materials, including (but not limited to) metal-organic frameworks, covalent organic frameworks, dense polymeric membranes, porous polymers, and ionic liquids.

In this work, the atomistic effects of functional units are explored for gas separations processes using electronic structure theory and machine learning. …

Detecting Hacker Threats: Performance Of Word And Sentence Embedding Models In Identifying Hacker Communications, Susan Mckeever, Brian Keegan, Andrei Quieroz

Conference papers

Abstract—Cyber security is striving to find new forms of protection against hacker attacks. An emerging approach nowadays is the investigation of security-related messages exchanged on deep/dark web and even surface web channels. This approach can be supported by the use of supervised machine learning models and text mining techniques. In our work, we compare a variety of machine learning algorithms, text representations and dimension reduction approaches for the detection accuracies of software-vulnerability-related communications. Given the imbalanced nature of the three public datasets used, we investigate appropriate sampling approaches to boost detection accuracies of our models. In addition, we examine how …

Language-Driven Region Pointer Advancement For Controllable Image Captioning, Annika Lindh, Robert J. Ross, John D. Kelleher

Conference papers

Controllable Image Captioning is a recent sub-field in the multi-modal task of Image Captioning wherein constraints are placed on which regions in an image should be described in the generated natural language caption. This puts a stronger focus on producing more detailed descriptions, and opens the door for more end-user control over results. A vital component of the Controllable Image Captioning architecture is the mechanism that decides the timing of attending to each region through the advancement of a region pointer. In this paper, we propose a novel method for predicting the timing of region pointer advancement by treating the …

Acquisition, Processing, And Analysis Of Video, Audio And Meteorological Data In Multi-Sensor Electronic Beehive Monitoring, Sarbajit Mukherjee

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In recent years, a widespread decline has been seen in honey bee population and this is widely attributed to colony collapse disorder. Hence, it is of utmost importance that a system is designed to gather relevant information. This will allow for a deeper understanding of the possible reasons behind the above phenomenon to aid in the design of suitable countermeasures.

Electronic Beehive Monitoring is one such way of gathering critical information regarding a colony’s health and behavior without invasive beehive inspections. In this dissertation, we have presented an electronic beehive monitoring system called BeePi that can be placed on top …

Semi-Automatic Hand Pose Estimation Using A Single Depth Camera, Giffy Jerald Chris

Computer Science and Engineering Theses

This paper addresses the problem of 3D hand pose annotations using a single depth camera. Although hand pose estimation methods rely critically on accurate 3D training data, creating such reliable training data is challenging and labor intensive. We propose a semi-automatic method for efficiently and accurately labeling the 3D hand key-points in a hand depth video. The process starts by selecting a subset of frames that are representative of all the frames in the dataset and the annotator only provides an estimate of the 2D hand key-points in these selected frames. We use this information to infer the 3D location …

Generating Adversarial Examples For Recruitment Ranking Algorithms, Anahita Samadi

Computer Science and Engineering Theses

There is no doubt that recruitment process plays an important role for both employers and applicants. Based on huge number of job candidates and open vacancies, recruitment process is expensive, time consuming and stressful for both applicants and companies. In today’s world so many recruitment processes are based on machine learning techniques. Therefore, it is very important to ensure security of these algorithms. Adversarial examples are proposed to examine vulnerability of machine leaning algorithms. Many research studies have been done on evaluating the resistance of artificial intelligence-based systems, in computer vision and text classification, against adversarial examples. However, to the …

Modified-Half-Normal Distribution And Different Methods To Estimate Average Treatment Effect., Jingchao Sun

Electronic Theses and Dissertations

This dissertation consists of three projects related to Modified-Half-Normal distribution and causal inference. In my first project, a new distribution called Modified-Half-Normal distribution was introduced. I explored a few of its distributional properties, the procedures for generating random samples based on Bayesian approaches, and the parameter estimation based on the method of moments. The second project deals with the problem of selection bias of average treatment effect (ATE) if we use the observational data. I combined the propensity score based inverse probability of treatment weighting (IPTW) method and the directed acyclic graph (DAG) to solve this problem. The third project …

Deep Q Learning Applied To Stock Trading, Agnibh Dasgupta

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Developing a strategy for stock trading is a vital task for investors. However, it is challenging to obtain an optimal strategy, given the complex and dynamic nature of the stock market. This thesis aims to explore the applications of Reinforcement Learning with the goal of maximizing returns from market investment, keeping in mind the human aspect of trading by utilizing stock prices represented as candlestick graphs. Furthermore, the algorithm studies public interest patterns in form of graphs extracted from Google Trends to make predictions. Deep Q learning has been used to train an agent based on fused images of stock …

A Targeted Adversarial Attack On Support Vector Machine Using The Boundary Line, Yessenia Rodriguez

Theses and Dissertations

In this thesis, a targeted adversarial attack is explored on a Support Vector Machine (SVM). SVM is defined by creating a separating boundary between two classes. Using a target class, any input can be modified to cross the “boundary line,” making the model predict the target class. To limit the modification, a percentage of an image of the target class is used to get several random sections. Using these sections, the input will be moved in small steps closer to the boundary point. The section that took the least number of steps to cause the model to predict the target …