Physical Sciences and Mathematics Commons^™

Crazy Sequential Representations Of Numbers For Small Bases, Tim Wylie

Computer Science Faculty Publications

Throughout history, recreational mathematics has always played a prominent role in advancing research. Following in this tradition, in this paper we extend some recent work with crazy sequential representations of numbers− equations made of sequences of one through nine (or nine through one) that evaluate to a number. All previous work on this type of puzzle has focused only on base ten numbers and whether a solution existed. We generalize this concept and examine how this extends to arbitrary bases, the ranges of possible numbers, the combinatorial challenge of finding the numbers, efficient algorithms, and some interesting patterns across any …

Zero-Knowledge De Novo Algorithms For Analyzing Small Molecules Using Mass Spectrometry, Patrick Anthony Kreitzberg

Graduate Student Theses, Dissertations, & Professional Papers

In the analysis of mass spectra, if a superset of the molecules thought to be in a sample is known a priori, then there are well established techniques for the identification of the molecules such as database search and spectral libraries. Linear molecules are chains of subunits. For example, a peptide is a linear molecule with an “alphabet” of 20 possible amino acid subunits. A peptide of length six will have 20⁶ = 64, 000, 000 different possible outcomes. Small molecules, such as sugars and metabolites, are not constrained to linear structures and may branch. These molecules are …

Validation Study Of Image Recognition Algorithms, Jacob Miller, Jeremy Evert

Student Research

Developments in machine learning in recent years have created opportunities that previously never existed. One such field with an explosion of opportunity is image recognition, also known as computer vision; the process in which a machine analyzes a digital image.

In order for a machine to ‘see’ as a human does, it must break down the image in a process called image segmentation. The way the machine goes about doing this is important, and many algorithms exist to determine just how a machine will decide to group the pixels in an image.

This research is a validation study of related …

Phase Contrast Time-Lapse Microscopy Datasets With Automated And Manual Cell Tracking Annotations, Dai Fei Elmer Ker, Zhaozheng Yin, For Full List Of Authors, See Publisher's Website.

Computer Science Faculty Research & Creative Works

Phase contrast time-lapse microscopy is a non-destructive technique that generates large volumes of image-based information to quantify the behaviour of individual cells or cell populations. To guide the development of algorithms for computer-aided cell tracking and analysis, 48 time-lapse image sequences, each spanning approximately 3.5 days, were generated with accompanying ground truths for C2C12 myoblast cells cultured under 4 different media conditions, including with fibroblast growth factor 2 (FGF2), bone morphogenetic protein 2 (BMP2), FGF2 + BMP2, and control (no growth factor). The ground truths generated contain information for tracking at least 3 parent cells and their descendants within these …

Quantifying Climate Sensitivity And Climate-Driven Change In North American Amphibian Communities, David A. W. Miller, Evan H Campbell Grant, Erin Muths, Staci M. Amburgey, Michael J. Adams, Maxwell B. Joseph, J. Hardin Waddle, Pieter T. J. Johnson, Maureen E. Ryan, Benedikt R. Schmidt, Daniel L. Calhoun, Courtney L. Davis, Robert N. Fisher, David M. Green, Blake R. Hossack, Tracy A. G. Rittenhouse, Susan C. Walls, Larissa L. Bailey, Sam S. Cruickshank, Gary M. Fellers, Thomas A. Gorman, Carola A. Haas, Ward Hughson, David S. Pilliod, Steve J. Price, Andrew M. Ray, Walt Sadinski, Daniel Saenz, William J. Barichivich, Adrianne Brand

Forestry and Natural Resources Faculty Publications

Changing climate will impact species’ ranges only when environmental variability directly impacts the demography of local populations. However, measurement of demographic responses to climate change has largely been limited to single species and locations. Here we show that amphibian communities are responsive to climatic variability, using > 500,000 time-series observations for 81 species across 86 North American study areas. The effect of climate on local colonization and persistence probabilities varies among eco-regions and depends on local climate, species life-histories, and taxonomic classification. We found that local species richness is most sensitive to changes in water availability during breeding and changes in …

Chain Ejection Model For Electrospray Ionization Of Unfolded Proteins: Evidence From Atomistic Simulations And Ion Mobility Spectrometry., Haidy Metwally, Quentin Duez, Lars Konermann

Chemistry Publications

The ion evaporation model (IEM) and the charged residue model (CRM) represent cornerstones of any discussion related to the mechanism of electrospray ionization (ESI). Molecular dynamics (MD) simulations have confirmed that small ions such as Na⁺ are ejected from the surface of aqueous ESI droplets (IEM), while folded proteins in native ESI are released by water evaporation to dryness (CRM). ESI of unfolded proteins yields [M + zH] ^z+ ions that are much more highly charged than their folded counterparts. A chain ejection model (CEM) has been proposed to account for the protein ESI behavior under such non-native conditions …

Improving Time And Space Efficiency Of Trie Data Structure, Nirmik Milind Kale

Computer Science and Engineering Theses - Archive

Trie or prefix tree is a data structure that has been used widely in some applications such as prefix-matching, auto-complete suggestions, and IP routing tables for a long time. What makes tries even more interesting is that its time complexity is dependent on the length of the keys inserted or searched in the trie, instead of on the total number of keys in the data structure. Tries are also strong contenders to consider against hash tables in various applications due to two reasons - their almost deterministic time complexity based on average key length, especially when using large number of …

Algorithms For Exploratory Queries Over Web Database, Md Farhadur Rahman

Computer Science and Engineering Dissertations - Archive

In recent years we have seen an increase in the popularity of many web applications. The functionality of these applications range from allowing users to interact using online social network, to assist users in their everyday activity such as selecting a hotel in an area, locating a nearby restaurant etc. Google Maps, WeChat, FourSquare, AirBnB, TripAdvisor, and Hotels.com are a few such examples. The backed database of these applications can be a rich source of information for the corresponding application domain. For example, using Google Maps a user can find the ratings, reviews, and price of a restaurant, using Zillow …

Offensive And Defensive Security For Everyday Computer Systems, Ian Markwood

USF Tampa Graduate Theses and Dissertations

This dissertation treats a variety of topics in the computer security domain which have direct impact on everyday life. The first extends false data injection attacks against state estimation in electric power grids and then provides a novel power flow model camouflage method to hamper these attacks. The second deals with automotive theft response, detailing a method for a car to intelligently identify when it has been stolen, based on collected behavioral traits of its driver. The third demonstrates a new attack against the content integrity of the PDF file format, caus- ing humans and computers to see different information …

Gaussian Processes With Context-Supported Priors For Active Object Localization, Bruno Jedynak

Portland Institute for Computational Science Publications

We devise an algorithm using a Bayesian optimization framework in conjunction with contextual visual data for the efficient localization of objects in still images. Recent research has demonstrated substantial progress in object localization and related tasks for computer vision. However, many current state-of-the-art object localization procedures still suffer from inaccuracy and inefficiency, in addition to failing to provide a principled and interpretable system amenable to high-level vision tasks. We address these issues with the current research.

Our method encompasses an active search procedure that uses contextual data to generate initial bounding-box proposals for a target object. We train a convolutional …

Cox Processes For Counting By Detection, Purnima Rajan, Yongming Ma, Bruno Jedynak

Portland Institute for Computational Science Publications

In this work, doubly stochastic Poisson (Cox) processes and convolutional neural net (CNN) classifiers are used to estimate the number of instances of an object in an image. Poisson processes are well suited to model events that occur randomly in space, such as the location of objects in an image or the enumeration of objects in a scene. The proposed algorithm selects a subset of bounding boxes in the image domain, then queries them for the presence of the object of interest by running a pre-trained CNN classifier. The resulting observations are then aggregated, and a posterior distribution over the …

Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu

School of Computing: Dissertations, Theses, and Student Research

Finding similar sequences to an input query sequence (DNA or proteins) from a sequence data set is an important problem in bioinformatics. It provides researchers an intuition of what could be related or how the search space can be reduced for further tasks. An exact brute-force nearest-neighbor algorithm used for this task has complexity O(m * n) where n is the database size and m is the query size. Such an algorithm faces time-complexity issues as the database and query sizes increase. Furthermore, the use of alignment-based similarity measures such as minimum edit distance adds an additional complexity to the …

Geometric Algorithms For Intervals And Related Problems, Shimin Li

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In this dissertation, we study several problems related to intervals and develop efficient algorithms for them. Interval problems have many applications in reality because many objects, values, and ranges are intervals in nature, such as time intervals, distances, line segments, probabilities, etc. Problems on intervals are gaining attention also because intervals are among the most basic geometric objects, and for the same reason, computational geometry techniques find useful for attacking these problems. Specifically, the problems we study in this dissertation includes the following: balanced splitting on weighted intervals, minimizing the movements of spreading points, dispersing points on intervals, multiple barrier …

A Legal Perspective On The Trials And Tribulations Of Ai: How Artificial Intelligence, The Internet Of Things, Smart Contracts, And Other Technologies Will Affect The Law, Iria Giuffrida, Fredric Lederer, Nicolas Vermeys

Faculty Publications

No abstract provided.

Pulse Height Spectra Analysis Of A Neutron Energy Tuning Assembly, Jason R. Stickney

Theses and Dissertations

An energy tuning assembly (ETA) was previously designed and built for the purpose of irradiating samples with a combination of a thermonuclear and a prompt fission neutron spectrum. Initial research was performed to characterize the performance of the ETA at the Lawrence Berkeley National Laboratory 88-Inch Cyclotron using 33 MeV deuteron breakup on tantalum as the neutron source. This research analyzes detector responses collected from three EJ-309 detectors used to characterize the ETA generated neutron field. A signal processing chain was developed to reduce the full waveform data into a pulse height spectrum. The primary goal was to develop a …

Policy-Preferred Paths In As-Level Internet Topology Graphs, Mehmet Engin Tozal

Theory & Applications of Graphs

Using Autonomous System (AS) level Internet topology maps to determine accurate AS-level paths is essential for network diagnostics, performance optimization, security enforcement, business policy management and topology-aware application development. One significant drawback that we have observed in many studies is simplifying the AS-level topology map of the Internet to an undirected graph, and then using the hop distance as a means to find the shortest paths between the ASes. A less significant drawback is restricting the shortest paths to only valley-free paths. Both approaches usually inflate the number of paths between ASes; introduce erroneous paths that do not conform to …

Forecasting Lightning Initiation Utilizing Dual-Polarization Radar Parameters Over Washington, D.C., Sarah A. Olsen

Theses and Dissertations

Accurate forecasts of thunderstorms are vital to space launch, aviation, and public safety. Prior studies by Woodard (2011), Thurmond (2014), and Travis (2015) show that dual-polarization radar can be utilized to identify the presence of hydrometeors necessary for cloud charging. These studies emphasized that a combination of radar reflectivity (Z) and differential reflectivity (Z_DR) predictors have the potential to improve forecast skill of lightning initiation over methods that rely on Z alone (Roeder and Pinder, 1998; Yang and King, 2010). Travis (2015) discovered two parameters, when used together, produced the best results: Z ≥ 36.5 dBZ and ZDR …

Opportunity Identification For New Product Planning: Ontological Semantic Patent Classification, Farshad Madani

Dissertations and Theses

Intelligence tools have been developed and applied widely in many different areas in engineering, business and management. Many commercialized tools for business intelligence are available in the market. However, no practically useful tools for technology intelligence are available at this time, and very little academic research in technology intelligence methods has been conducted to date.

Patent databases are the most important data source for technology intelligence tools, but patents inherently contain unstructured data. Consequently, extracting text data from patent databases, converting that data to meaningful information and generating useful knowledge from this information become complex tasks. These tasks are currently …

Auditing Snomed Ct Hierarchical Relations Based On Lexical Features Of Concepts In Non-Lattice Subgraphs, Licong Cui, Olivier Bodenreider, Jay Shi, Guo-Qiang Zhang

Computer Science Faculty Publications

Objective—We introduce a structural-lexical approach for auditing SNOMED CT using a combination of non-lattice subgraphs of the underlying hierarchical relations and enriched lexical attributes of fully specified concept names. Our goal is to develop a scalable and effective approach that automatically identifies missing hierarchical IS-A relations.

Methods—Our approach involves 3 stages. In stage 1, all non-lattice subgraphs of SNOMED CT’s IS-A hierarchical relations are extracted. In stage 2, lexical attributes of fully-specified concept names in such non-lattice subgraphs are extracted. For each concept in a non-lattice subgraph, we enrich its set of attributes with attributes from its ancestor …

The Accuracy, Fairness, And Limits Of Predicting Recidivism, Julie Dressel, Hany Farid

Dartmouth Scholarship

Algorithms for predicting recidivism are commonly used to assess a criminal defendant’s likelihood of committing a crime. These predictions are used in pretrial, parole, and sentencing decisions. Proponents of these systems argue that big data and advanced machine learning make these analyses more accurate and less biased than humans. We show, however, that the widely used commercial risk assessment software COMPAS is no more accurate or fair than predictions made by people with little or no criminal justice expertise. We further show that a simple linear predictor provided with only two features is nearly equivalent to COMPAS with its 137 …

Why I Believe People Need Painting By Numbers, Jason Makansi

Numeracy

Jason Makansi.2016. Painting By Numbers: How to Sharpen Your BS Detector and Smoke Out the Experts (Tucson AZ: Layla Dog Press). 196 pp. ISBN 978-0998425900.

This piece briefly introduces my Painting By Numbers, which aims to take the core messages of the QL/QR community from academic and professional circles to the rest of the citizenry. I describe the book in the context of the critical need for the most basic numeracy tools to help consumers of news, information, and analysis—delivered through traditional and contemporary social media outlets—determine where a reported numerical result lies on the scale from utter nonsense …

Algorithmic Issues In Some Disjoint Clustering Problems In Combinatorial Circuits, Zola Nailah Donovan

Graduate Theses, Dissertations, and Problem Reports (ETD)

As the modern integrated circuit continues to grow in complexity, the design of very large-scale integrated (VLSI) circuits involves massive teams employing state-of-the-art computer-aided design (CAD) tools. An old, yet significant CAD problem for VLSI circuits is physical design automation. In this problem, one needs to compute the best physical layout of millions to billions of circuit components on a tiny silicon surface. The process of mapping an electronic design to a chip involves several physical design stages, one of which is clustering. Even for combinatorial circuits, there exist several models for the clustering problem. In particular, we consider the …

Equity Trading Evaluation Strategies In Switzerland After The European Mifid Ii, Linn Kristina Karstadt

Walden Dissertations and Doctoral Studies

Swiss bank traders are affected by technological and regulatory challenges, which may affect their broker voting process and may result in a change of trading and evaluation behavior in 2018. Compounded challenges exist when broker evaluation strategies are not effective or Markets in Financial Instruments Directive (MiFID) II compliant. This qualitative, single case study, built on efficient capital market hypothesis and innovative disruption theory, was focused on effective broker evaluation strategies after MiFID II in Switzerland. The sample consisted of 4 buy-side traders, who shared their unique perspectives. Methodological triangulation was achieved through semistructured interviews, a review of the institution's …

A Selective-Discrete Particle Swarm Optimization Algorithm For Solving A Class Of Orienteering Problems, Aldy Gunawan, Vincent F. Yu, Perwira Redi, Parida Jewpanya, Hoong Chuin Lau

Research Collection School Of Computing and Information Systems

This study addresses a class of NP-hard problem called the Orienteering Problem (OP), which belongs to a well-known class of vehicle routing problems. In the OP, a set of nodes that associated with a location and a score is given. The time required to travel between each pair of nodes is known in advance. The total travel time is limited by a predetermined time budget. The objective is to select a subset of nodes to be visited that maximizes the total collected score within a path. The Team OP (TOP) is an extension of OP that incorporates multiple paths. Another …

Temporal Understanding Of Human Mobility: A Multi-Time Scale Analysis, Tongtong Liu, Zheng Yang, Yi Zhao, Chenshu Wu, Zimu Zhou, Yunhao Liu

Research Collection School Of Computing and Information Systems

The recent availability of digital traces generated by cellphone calls has significantly increased the scientific understanding of human mobility. Until now, however, based on low time resolution measurements, previous works have ignored to study human mobility under various time scales due to sparse and irregular calls, particularly in the era of mobile Internet. In this paper, we introduced Mobile Flow Records, flow-level data access records of online activity of smartphone users, to explore human mobility. Mobile Flow Records collect high-resolution information of large populations. By exploiting this kind of data, we show the models and statistics of human mobility at …

Registration And Grouping Algorithms In Protein Nmr Derived Peak Lists And Their Application In Protein Nmr Reference Correction, Andrey Smelter, Xi Chen, Eric C. Rouchka, Hunter N. B. Moseley

Commonwealth Computational Summit

Nuclear magnetic resonance spectroscopy of proteins (protein NMR) is a powerful analytical technique for studying structure and dynamics of proteins. Almost all aspects of protein NMR have been accelerated by the development of software tools that enable the analysis of NMR spectral data and its utilization in studying protein structure and dynamics. This includes software for raw NMR processing, spectral visualization, protein resonance assignment, and structure determination. However, full automation of protein NMR data analysis is still a work in progress and data analysis still requires an expert NMR spectroscopist utilizing an array of software tools.

While manual resonance assignment …

Detecting And Accounting For Multiple Sources Of Positional Variance In Peak List Registration Analysis And Spin System Grouping, Andrey Smelter, Eric C. Rouchka, Hunter N. B. Moseley

Molecular and Cellular Biochemistry Faculty Publications

Peak lists derived from nuclear magnetic resonance (NMR) spectra are commonly used as input data for a variety of computer assisted and automated analyses. These include automated protein resonance assignment and protein structure calculation software tools. Prior to these analyses, peak lists must be aligned to each other and sets of related peaks must be grouped based on common chemical shift dimensions. Even when programs can perform peak grouping, they require the user to provide uniform match tolerances or use default values. However, peak grouping is further complicated by multiple sources of variance in peak position limiting the effectiveness of …

Accelerating Dynamic Graph Analytics On Gpus, Mo Shan, Yuchen Li, Bingsheng He, Kian-Lee Tan

Research Collection School Of Computing and Information Systems

As graph analytics often involves compute-intensive operations,GPUs have been extensively used to accelerate the processing. However, in many applications such as social networks, cyber security, and fraud detection, their representative graphs evolve frequently and one has to perform are build of the graph structure on GPUs to incorporate the updates. Hence, rebuilding the graphs becomes the bottleneck of processing high-speed graph streams. In this paper,we propose a GPU-based dynamic graph storage scheme to support existing graph algorithms easily. Furthermore,we propose parallel update algorithms to support efficient stream updates so that the maintained graph is immediately available for high-speed analytic processing …

Geometric Facility Location Problems On Uncertain Data, Jingru Zhang

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

In this dissertation, we study several facility location problems on uncertain data. We mainly consider the k-center problem and many of its variations. These are classical problems in computer science and operations research. These problems on deterministic data have been studied extensively in the literature. We consider them on uncertain data because data in the real world is often associated with uncertainty due to measurement inaccuracy, sampling discrepancy, outdated data sources, resource limitation, etc. Although we focus on the theoretical study, the algorithms developed in this dissertation may find applications in other areas such as data clustering, wireless sensor …

Mechanism Design In Sequencing Problems., Parikshit De Dr.

Doctoral Theses

Collective decision making is an important social issue, since it depends on individual preferences that are not publicly observable. Therefore, the question is, whether it is possible to elicit the private information available to individuals and then how to extract the private information in various strategic environment; Mechanism design deals with these questions. The difference between game theory and mechanism design is that, the former tries to predict the outcome of a strategic environment in some “equilibrium” but the latter tries to design or restrict the environment in such a way that the desired objective is attained, that is, the …