Physical Sciences and Mathematics Commons^™

Extending The Convolution In Graph Neural Networks To Solve Materials Science And Node Classification Problems, Steph-Yves Mike Louis

Theses and Dissertations

The usage of graph to represent one's data in machine learning has grown in popularity in both academia and the industry due to its inherent benefits. With its flexible nature and immediate translation to real life observed objects, graph representation had a considerable contribution in advancing the state-of-the-art performance of machine learning in materials.

In this dissertation proposal, we discuss how machines can learn from graph encoded data and provide excellent results through graph neural networks (GNN). Notably, we focus our adaptation of graph neural networks on three tasks: predicting crystal materials properties, nullifying the negative impact of inferior graph …

Predicting Material Structures And Properties Using Deep Learning And Machine Learning Algorithms, Yuqi Song

Theses and Dissertations

Discovering new materials and understanding their crystal structures and chemical properties are critical tasks in the material sciences. Although computational methodologies such as Density Functional Theory (DFT), provide a convenient means for calculating certain properties of materials or predicting crystal structures when combined with search algorithms, DFT is computationally too demanding for structure prediction and property calculation for most material families, especially for those materials with a large number of atoms. This dissertation aims to address this limitation by developing novel deep learning and machine learning algorithms for effective prediction of material crystal structures and properties. Our data-driven machine learning …

Utilizing Deep Learning Methods In The Identification And Synthesis Of Gene Regulations, Jiandong Wang

Theses and Dissertations

Gene expression is the fundamental differentiation and development process of life. Although all cells in an organism have essentially the same DNA, cell types and activities vary due to changes in gene expression. Gene expression can be influenced by many gene regulations. RNA editing contributes to the variety of RNA and proteins by allowing single nucleotide substitution. Reverse transcription can alter the expression status of genes by inducing genetic diversity and polymorphism via novel insertions, deletions, and recombination events. Gene regulation is critical to normal development because it enables cells to respond rapidly to environmental changes. However, identifying gene regulations …

Templates To Transition: Making Solar-Generated Electricity Accessible For Lagos Residents, Adeola O. Adebajo

Senior Theses

According to the EPA, direct energy production results in at least 25% of the world’s emissions. This refers to emissions produced by burning coal, natural gas, and oil for electricity and heat. With the increasing effects of climate change, sustainable energy is becoming increasingly important as the world shifts away from fossil fuels. However, implementation of renewable energy sources is not as fast or as widespread as necessary. This paper aims to identify feasible solutions to the problem of renewable energy affordability in Nigeria especially in growing megacities like Lagos to ensure long lasting and climatefriendly energy sources. Two major …

Semantics-Based Data Security Models, Theppatorn Rhujittawiwat

Theses and Dissertations

In this dissertation, we studied how an adversary could attack databases and how the system could prevent or recover from such an attack. Our motivation to improve the current security capabilities of database management systems. We provided better recovery capabilities of database management systems by incorporating data provenance. We also expand our study to express security and privacy needs of data in the Internet of Things (IoT) environments such as a smart home environment. For this, we proposed a stream data security model to theoretically represent the data in the IoT network. We built a dynamic authorization model on our …

Cnn-Based Dendrite Core Detection From Microscopic Images Of Directionally Solidified Ni-Base Alloys, Xiaoguang Li

Theses and Dissertations

Dendrite core is the center point of the dendrite. The information of dendrite core is very helpful for material scientists to analyze the properties of materials. Therefore, detecting the dendrite core is a very important task in the material science field. Meanwhile, because of some special properties of the dendrites, this task is also very challenging. Different from the typical detection problems in the computer vision field, detecting the dendrite core aims to detect a single point location instead of the bounding-box. As a result, the existing regressing bounding-box based detection methods can not work well on this task because …

Empirical Studies On Automated Software Testing Practices, Alireza Salahirad

Theses and Dissertations

Software testing is notoriously difficult and expensive, and improper testing carries economic, legal, and even environmental or medical risks. Research in software testing is critical to enabling the development of the robust software that our society relies upon. This dissertation aims to lower the cost of software testing without decreasing the quality by focusing on the use of automation. The dissertation consists of three empirical studies on aspects of software testing. Specifically, these three projects focus on (1) mapping the connections between research topics and the evolution of research topics in the field of software testing, (2) an assessment of …

Learning Depth From Images, Zhenyao Wu

Theses and Dissertations

Estimating depth from images has become a very popular task in computer vision which aims to restore the 3D scene from 2D images and identify important geometric knowledge of the scene. Its performance has been significantly improved by convolutional neural networks in recent years, which surpass the traditional methods by a large margin. However, the natural scenes are usually complicated, and hard to build the correspondence between pixels across frames, such as the region containing moving objects, illumination changes, occlusions, and reflections. This research explores rich and comprehensive spatial correspondence across images and designs three new network architectures for depth …

Cnn-Based Semantic Segmentation With Shape Prior Knowledge, Yuhang Lu

Theses and Dissertations

Semantic segmentation that aims at grouping discrete pixels into connected regions is a fundamental step in many high-level computer vision tasks. In recent years, Convolutional Neural Networks (CNNs) have made breakthrough progresses in public semantic segmentation benchmarks. The ability of learning from large-scale labeled datasets empowers them to generalize to unseen images better than traditional nonlearning-based methods. Nevertheless, the heavy dependency on labeled data also limits their applications in tasks where high-quality ground truth segmentation masks are scarce or difficult to acquire. In this dissertation, we study the problem of alleviating the data dependency for CNN-based segmentation with a focus …

Knowledge-Infused Learning, Manas Gaur

Theses and Dissertations

In DARPA’s view of the three waves of AI, the first wave of AI, symbolic AI, focused on explicit knowledge. The second and current wave of AI is termed statistical AI. Deep learning techniques have been able to exploit large amounts of data and massive computational power to improve human levels of performance in narrowly defined tasks. Separately, knowledge graphs have emerged as a powerful tool to capture and exploit a variety of explicit knowledge to make algorithms better apprehend the content and enable the next generation of data processing, such as semantic search. After initial hesitancy about the scalability …

Image Restoration Under Adverse Illumination For Various Applications, Lan Fu

Theses and Dissertations

Many images are captured in sub-optimal environment, resulting in various kinds of degradations, such as noise, blur, and shadow. Adverse illumination is one of the most important factors resulting in image degradation with color and illumination distortion or even unidentified image content. Degradation caused by the adverse illumination makes the images suffer from worse visual quality, which might also lead to negative effects on high-level perception tasks, e.g., object detection.

Image restoration under adverse illumination is an effective way to remove such kind of degradations to obtain visual pleasing images. Existing state-of-the-art deep neural networks (DNNs) based image restoration …

Cross Domain Semantic Segmentation, Xinyi Wu

Theses and Dissertations

As a long-standing computer vision task, semantic segmentation is still extensively researched till now because of its importance to visual understanding and analysis. The goal of semantic segmentation is to classify each pixel of images based on the pre-defined classes. In the era of deep learning, convolutional neural networks largely improve the accuracy and efficiency of semantic segmentation. However, this success is achieved with two limitations: 1) a large-scale labeled dataset is required for training while the labeling process for this task is quite labor-intensive and tedious; 2) the trained deep networks can get promising results when testing on the …

Identifying And Discovering Curve Pattern Designs From Fragments Of Pottery, Jun Zhou

Theses and Dissertations

The surface of many cultural heritage objects, such as pottery sherds found in the Southeastern Woodlands, were embellished with curve patterns. The original full designs of these patterns reflect rich historical and cultural information. However, in practice, most objects are fragmentary, making the complete underlying designs unknowable at the scale of the sherd fragment. The challenge to reconstruct and study complete designs is stymied because 1) most pottery sherds contain only a small portion of the underlying full design, 2) curve patterns detected on a sherd are usually incomplete and noisy, and 3) in the case of a stamping application, …

Quadratic Neural Network Architecture As Evaluated Relative To Conventional Neural Network Architecture, Reid Taylor

Senior Theses

Current work in the field of deep learning and neural networks revolves around several variations of the same mathematical model for associative learning. These variations, while significant and exceptionally applicable in the real world, fail to push the limits of modern computational prowess. This research does just that: by leveraging high order tensors in place of 2nd order tensors, quadratic neural networks can be developed and can allow for substantially more complex machine learning models which allow for self-interactions of collected and analyzed data. This research shows the theorization and development of mathematical model necessary for such an idea to …

Concurrent Identification, Characterization, And Reconstruction Of Protein Structure And Mixed-Mode Dynamics From Rdc Data Using Redcraft, Hanin Rafiq Omar

Theses and Dissertations

A complete understanding of the structure-function relationship of proteins requires an analysis of their dynamic behaviors and the static structure. However, all current approaches to studying dynamics in proteins have their shortcomings. A conceptually attractive and alternative approach simultaneously characterizes a protein's structure and its intrinsic dynamics⁠. Ideally, such an approach could solely rely on RDC data-carrying both structural and dynamical information. The major bottleneck in utilizing RDC data in recent years has been attributed to a lack of RDC analysis tools capable of extracting the pertinent information embedded within this complex data source.

Here we present a comprehensive strategy …

On Providing Efficient Real-Time Solutions To Motion Planning Problems Of High Complexity, Marios Xanthidis

Theses and Dissertations

The holy grail of robotics is producing robotic systems capable of efficiently executing all the tasks that are hard, or even impossible, for humans. Humans, undoubtedly, from both a hardware and software perspective, are extremely complex systems capable of executing many complicated tasks. Thus, the complexity of many state-of-the-art robotic systems is also expected to progressively increase, with the goal to match or even surpass human abilities. Recent developments have emphasized mostly hardware, providing highly complex robots with exceptional capabilities. On the other hand, they have illustrated that one important bottleneck of realizing such systems as a common reality is …

Deep Learning Based Generative Materials Design, Yong Zhao

Theses and Dissertations

Discovery of novel functional materials is playing an increasingly important role in many key industries such as lithium batteries for electric vehicles and cell phones. However experimental tinkering of existing materials or Density Functional Theory (DFT) based screening of known crystal structures, two of the major current materials design approaches, are both severely constrained by the limited scale (around 250,000 in ICSD database) and diversity of existing materials and the lack of a sufficient number of materials with annotated properties. How to generate a large number of physically feasible, stable, and synthesizable crystal materials and build accurate property prediction models …

Robot Area Coverage Path Planning In Aquatic Environments, Nare Karapetyan

Theses and Dissertations

This thesis is motivated by real world problems faced in aquatic environments. It addresses the problem of area coverage path planning with robots - the problem of moving an end-effector of a robot over all available space while avoiding existing obstacles. The problem is considered first in a 2D space with a single robot for specific environmental monitoring operations, and then with multi-robot systems — a known NP-complete problem. Next we tackle the coverage problem in 3D space - a step towards underwater mapping of shipwrecks or monitoring of coral reefs.

The first part of this thesis leverages human expertise …

Multi-Robot Coordination With Environmental Disturbances, Adem Coskun

Theses and Dissertations

Multi-robot systems are increasingly deployed in environments where they interact with humans. From the perspective of a robot, such interaction could be considered a disturbance that causes a well-planned trajectory to fail. This dissertation addresses the problem of multi-robot coordination in scenarios where the robots may experience unexpected delays in their movements.

Prior work by Čáp, Gregoire, and Frazzoli introduced a control law, called RMTRACK, which enables robots in such scenarios to execute pre-planned paths in spite of disturbances that affect the execution speed of each robot while guaranteeing that each robot can reach its goal without collisions and without …

Deep Learning Based Sound Event Detection And Classification, Alireza Nasiri

Theses and Dissertations

Hearing sense has an important role in our daily lives. During the recent years, there has been many studies to transfer this capability to the computers. In this dissertation, we design and implement deep learning based algorithms to improve the ability of the computers in recognizing the different sound events.

In the first topic, we investigate sound event detection, which identifies the time boundaries of the sound events in addition to the type of the events. For sound event detection, we propose a new method, AudioMask, to benefit from the object-detection techniques in computer vision. In this method, we convert …

Algorithmic Robot Design: Label Maps, Procrustean Graphs, And The Boundary Of Non-Destructiveness, Shervin Ghasemlou

Theses and Dissertations

This dissertation is focused on the problem of algorithmic robot design. The process of designing a robot or a team of robots that can reliably accomplish a task in an environment requires several key elements. How the problem is formulated can play a big role in the design process. The ability of the model to correctly reflect the environment, the events, and different pieces of the problem is crucial. Another key element is the ability of the model to show the relationship between different designs of a single system. These two elements can enable design algorithms to navigate through the …

An Overlay Architecture For Pattern Matching, Rasha Elham Karakchi

Theses and Dissertations

Deterministic and Non-deterministic Finite Automata (DFA and NFA) comprise the fundamental unit of work for many emerging big data applications, motivating recent efforts to develop Domain-Specific Architectures (DSAs) to exploit fine-grain parallelism available in automata workloads.

This dissertation presents NAPOLY (Non-Deterministic Automata Processor Over- LaY), an overlay architecture and associated software that attempt to maximally exploit on-chip memory parallelism for NFA evaluation. In order to avoid an upper bound in NFA size that commonly affects prior efforts, NAPOLY is optimized for runtime reconfiguration, allowing for full reconfiguration in 10s of microseconds. NAPOLY is also parameterizable, allowing for offline generation of …

A Machine Learning Based Approach To Accelerate Catalyst Discovery, Asif Jamil Chowdhury

Theses and Dissertations

Computational catalysis, in contrast to experimental catalysis, uses approximations such as density functional theory (DFT) to compute properties of reaction intermediates. But DFT calculations for a large number of surface species on variety of active site models are resource intensive. In this work, we are building a machine learning based predictive framework for adsorption energies of intermediate species, which can reduce the computational overhead significantly. Our work includes the study and development of appropriate machine learning models and effective fingerprints or descriptors to predict energies accurately for different scenarios. Furthermore, Bayesian inverse problem, that integrates experimental catalysis with its computational …

Lablineup: An Intuitive Web Application For Queueing Help Requests In Academic Labs, Graham Mcdonald

Senior Theses

LabLineup is a start-up project designed to address the needs of large, lab-based classes, where teaching assistants (TAs) struggle to assist students in the order in which they request help. LabLineup is a lightweight web application that allows TAs and professors to accept requests for help in order. LabLineup allows professors to view the requests for a lab and see frequently asked questions that can be addressed en masse rather than individually. LabLineup also allows students to provide TA feedback. LabLineup addresses issues arising from requesting help in large, lab-based classes in the most efficient manner possible.

Properties, Learning Algorithms, And Applications Of Chain Graphs And Bayesian Hypergraphs, Mohammad Ali Javidian

Theses and Dissertations

Probabilistic graphical models (PGMs) use graphs, either undirected, directed, or mixed, to represent possible dependencies among the variables of a multivariate probability distri- bution. PGMs, such as Bayesian networks and Markov networks, are now widely accepted as a powerful and mature framework for reasoning and decision making under uncertainty in knowledge-based systems. With the increase of their popularity, the range of graphical models being investigated and used has also expanded. Several types of graphs with dif- ferent conditional independence interpretations - also known as Markov properties - have been proposed and used in graphical models.

The graphical structure of a …

Person Identification With Convolutional Neural Networks, Kang Zheng

Theses and Dissertations

Person identification aims at matching persons across images or videos captured by different cameras, without requiring the presence of persons’ faces. It is an important problem in computer vision community and has many important real-world applica- tions, such as person search, security surveillance, and no-checkout stores. However, this problem is very challenging due to various factors, such as illumination varia- tion, view changes, human pose deformation, and occlusion. Traditional approaches generally focus on hand-crafting features and/or learning distance metrics for match- ing to tackle these challenges. With Convolutional Neural Networks (CNNs), feature extraction and metric learning can be combined in …

Stacked Modelling Framework, Kareem Abdelfatah

Theses and Dissertations

The thesis develops a predictive modeling framework based on stacked Gaussian processes and applies it to two main applications in environmental and chemical en- gineering. First, a network of independently trained Gaussian processes (StackedGP) is introduced to obtain analytical predictions of quantities of interest (model out- puts) with quantified uncertainties. StackedGP framework supports component- based modeling in different fields such as environmental and chemical science, en- hances predictions of quantities of interest through a cascade of intermediate predic- tions usually addressed by cokriging, and propagates uncertainties through emulated dynamical systems driven by uncertain forcing variables. By using analytical first and …

Cybersecurity Issues In The Context Of Cryptographic Shuffling Algorithms And Concept Drift: Challenges And Solutions, Hatim Alsuwat

Theses and Dissertations

In this dissertation, we investigate and address two kinds of data integrity threats. We first study the limitations of secure cryptographic shuffling algorithms regarding preservation of data dependencies. We then study the limitations of machine learning models regarding concept drift detection. We propose solutions to address these threats.

Shuffling Algorithms have been used to protect the confidentiality of sensitive data. However, these algorithms may not preserve data dependencies, such as functional de- pendencies and data-driven associations. We present two solutions for addressing these shortcomings: (1) Functional dependencies preserving shuffle, and (2) Data-driven asso- ciations preserving shuffle. For preserving functional dependencies, …

Challenges In Large-Scale Machine Learning Systems: Security And Correctness, Emad Alsuwat

Theses and Dissertations

In this research, we address the impact of data integrity on machine learning algorithms. We study how an adversary could corrupt Bayesian network structure learning algorithms by inserting contaminated data items. We investigate the resilience of two commonly used Bayesian network structure learning algorithms, namely the PC and LCD algorithms, against data poisoning attacks that aim to corrupt the learned Bayesian network model.

Data poisoning attacks are one of the most important emerging security threats against machine learning systems. These attacks aim to corrupt machine learning models by con- taminating datasets in the training phase. The lack of resilience of …

Authenticating Users With 3d Passwords Captured By Motion Sensors, Jing Tian

Theses and Dissertations

Authentication plays a key role in securing various resources including corporate facilities or electronic assets. As the most used authentication scheme, knowledgebased authentication is easy to use but its security is bounded by how much a user can remember. Biometrics-based authentication requires no memorization but ‘resetting’ a biometric password may not always be possible. Thus, we propose study several behavioral biometrics (i.e., mid-air gestures) for authentication which does not have the same privacy or availability concerns as of physiological biometrics.

In this dissertation, we first propose a user-friendly authentication system Kin- Write that allows users to choose arbitrary, short and …