Physical Sciences and Mathematics Commons^™

Improving Reusability Of Software Libraries Through Usage Pattern Mining, Mohamed Aymen Saied, Ali Ouni, Houari A. Sahraoui, Raula Gaikovina Kula, Katsuro Inoue, David Lo

Research Collection School Of Computing and Information Systems

Modern software systems are increasingly dependent on third-party libraries. It is widely recognized that using mature and well-tested third-party libraries can improve developers’ productivity, reduce time-to-market, and produce more reliable software. Today’s open-source repositories provide a wide range of libraries that can be freely downloaded and used. However, as software libraries are documented separately but intended to be used together, developers are unlikely to fully take advantage of these reuse opportunities. In this paper, we present a novel approach to automatically identify third-party library usage patterns, i.e., collections of libraries that are commonly used together by developers. Our approach employs …

Recommending Who To Follow In The Software Engineering Twitter Space, Abhabhisheksh Sharma, Yuan Tian, Agus Sulistya, Dinusha Wijedasa, David Lo

Research Collection School Of Computing and Information Systems

With the advent of social media, developers are increasingly using it in their software development activities. Twitter is one of the popular social mediums used by developers. A recent study by Singer et al. found that software developers use Twitter to “keep up with the fast-paced development landscape.” Unfortunately, due to the general-purpose nature of Twitter, it’s challenging for developers to use Twitter for their development activities. Our survey with 36 developers who use Twitter in their development activities highlights that developers are interested in following specialized software gurus who share relevant technical tweets.To help developers perform this task, in …

A Deep Eastern Equatorial Pacific Thermocline During The Last Glacial Maximum, H. L. Ford, C. L. Mcchesney, J. E. Hertzberg, J. F. Mcmanus

OES Faculty Publications

The mean state and variability of the tropical Pacificis influenced by the depth of the thermocline. During the Last Glacial Maximum (~21,000 years ago), the zonal sea surface temperature gradient across the equatorial Pacific was reduced and productivity was generally lower than modern. To understand the thermocline depth’s role in determining the Last Glacial Maximum tropical mean state, we reconstruct the upper ocean δ¹⁸O profile from multiple species of planktic foraminifera. We synthesize existing records of surface and subsurface dwelling foraminifera to reconstruct the vertical δ¹⁸O gradient throughout the eastern equatorial Pacific. We find the thermocline …

Efficient Blind Image Deblurring Using Nonparametric Regression And Local Pixel Clustering, Yicheng Kang, Partha Sarathi Mukherjee, Peihua Qiu

Mathematics Faculty Publications and Presentations

Blind image deblurring is a challenging ill-posed problem. It would have an infinite number of solutions even in cases when an observed image contains no noise. In reality, however, observed images almost always contain noise. The presence of noise would make the image deblurring problem even more challenging because the noise can cause numerical instability in many existing image deblurring procedures. In this paper, a novel blind image deblurring approach is proposed, which can remove both pointwise noise and spatial blur efficiently without imposing restrictive assumptions on either the point spread function (psf) or the true image. It even allows …

Galaxy And Mass Assembly (Gama): Accurate Number Densities And Environments Of Massive Ultra-Compact Galaxies At 0.02 < Z < 0.3, F. Buitrago, I. Ferreras, L. S. Kelvin, I. K. Baldry, L. Davies, J. Angthopo, S. Khochfar, A. M. Hopkins, S. P. Driver, S. Brough, J. Sabater, C. J. Conselice, J. Liske, Benne W. Holwerda, M. N. Bremer, S. Phillipps, A. R. López-Sánchez, A. W. Graham

Faculty and Staff Scholarship

Context. Massive ultra-compact galaxies (MUGs) are common at z = 2-3, but very rare in the nearby Universe. Simulations predict that the few surviving MUGs should reside in galaxy clusters, whose large relative velocities prevent them from merging, thus maintaining their original properties (namely stellar populations, masses, sizes and dynamical state). Aims. Our goal is to obtain a complete census of the MUG population at 0.02 < z < 0.3, determining the number density, population properties and environment. Methods. We have taken advantage of the high-completeness, large-area spectroscopic GAMA survey, complementing it with deeper imaging from the KiDS and VIKING surveys. We find a set of 22 bona-fide MUGs, defined as having high stellar mass (> 8 × 1010 M™) and compact size (Re < 2 kpc). An additional set of seven lower-mass objects (6 × 1010 < Ma/M™ < 8 × 1010) are also potential candidates according to typical mass uncertainties. Results. The comoving number density of MUGs at low redshift (z < 0.3) is constrained at (1.0 ± 0.4)×10-6 Mpc-3, consistent with galaxy evolution models. However, we find a mixed distribution of old and young galaxies, with a quarter of the sample representing (old) relics. MUGs have a predominantly early or swollen disk morphology (Sérsic index 1 < n < 2.5) with high stellar surface densities (â Σea ∼1010 M™ Kpc-2). Interestingly, a large fraction feature close companions- A t least in projection-suggesting that many (but not all) reside in the central regions of groups. Halo masses show these galaxies inhabit average-mass groups. Conclusions. As MUGs are found to be almost equally distributed among environments of different masses, their relative fraction is higher in more massive overdensities, matching the expectations that some of these galaxies fell in these regions at early times. However, there must be another channel leading some of these galaxies to an abnormally low merger history because our sample shows a number of objects that do not inhabit particularly dense environments.

Netlight: Cloud Baked Indirect Illumination, Nathan Andrew Zabriskie

Theses and Dissertations

Indirect lighting drastically increases the realism of rendered scenes but it has traditionally been very expensive to calculate. This has long precluded its use in real-time rendering applications such as video games which have mere milliseconds to respond to user input and produce a final image. As hardware power continues to increase, however, some recently developed algorithms have started to bring real-time indirect lighting closer to reality. Of specific interest to this paper, cloud-based rendering systems add indirect lighting to real-time scenes by splitting the rendering pipeline between a server and one or more connected clients. However, thus far they …

Postseismic Restoration Of The Ecological Environment In The Wenchuan Region Using Satellite Data, Zhibin Huang, Min Xu, Wei Chen, Xiaojuan Lin, Chunxiang Cao, Ramesh Singh

Mathematics, Physics, and Computer Science Faculty Articles and Research

Using Landsat remote-sensing data combined with geological information extracted from ALOS and Sentinel-1A radar data, the ecological environment was evaluated in the years 2007, 2008, 2013, and 2017 through gray correlation analysis on the basis of the construction of the pressure-state-response model. The main objective of this research was to assess the ecological environment changes in Wenchuan County before and after the earthquake, and to provide reference for future social development and policy implementation. The grading map of the ecological environment was obtained for every year, and the ecological restoration status of Wenchuan County after the earthquake was evaluated. The …

On The Origin Of Crystallinity: A Lower Bound For The Regularity Radius Of Delone Sets, Igor A. Baburin, Mikhail M. Bouniaev, Nikolay Dolbilin, Nikolay Yu. Erokhovets, Alexey Garber, Sergey V. Krivovichev, Egon Schulte

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

The mathematical conditions for the origin of long-range order or crystallinity in ideal crystals are one of the very fundamental problems of modern crystallography. It is widely believed that the (global) regularity of crystals is a consequence of `local order', in particular the repetition of local fragments, but the exact mathematical theory of this phenomenon is poorly known. In particular, most mathematical models for quasicrystals, for example Penrose tiling, have repetitive local fragments, but are not (globally) regular. The universal abstract models of any atomic arrangements are Delone sets, which are uniformly distributed discrete point sets in Euclidean d space. …

On The Qualitative Theory Of The Nonlinear Parabolic P-Laplacian Type Reaction-Diffusion Equations, Roqia Abdullah Jeli

Theses and Dissertations

This dissertation presents full classification of the evolution of the interfaces and asymptotics of the local solution near the interfaces and at infinity for the nonlinear second order parabolic p-Laplacian type reaction-diffusion equation of non-Newtonian elastic filtration ut − ( |ux| p−2 ux ) x +buβ = 0, p > 1, β > 0. (1) Nonlinear partial differential equation (1) is a key model example expressing competition between nonlinear diffusion with gradient dependent diffusivity in either slow (p > 2) or fast (1 < p < 2) regime and nonlinear state dependent reaction (b > 0) or absorption (b < 0) forces. If interface is finite, it may expand, shrink, or remain stationary as a result of the competition of the diffusion and reaction terms near the interface, expressed in terms of the parameters p, β,sign b, and asymptotics of the initial function near its support. In the fast diffusion regime strong domination of the diffusion causes infinite speed of propagation and interfaces are absent. In all cases with finite interfaces we prove the explicit formula for the interface and the local solution with accuracy up to constant coefficients. We prove explicit asymptotics of the local solution at infinity in all cases with infinite speed of propagation. The methods of the proof are generaliii ization of the methods developed in U.G. Abdulla & J. King, SIAM J. Math. Anal., 32, 2(2000), 235-260; U.G. Abdulla, Nonlinear Analysis, 50, 4(2002), 541-560 and based on rescaling laws for the nonlinear PDE and blow-up techniques for the identification of the asymptotics of the solution near the interfaces, construction of barriers using special comparison theorems in irregular domains with characteristic boundary curves.

Clean Indices Of Common Rings, Benjamin L. Schoonmaker

Theses and Dissertations

Lee and Zhou introduced the clean index of rings in 2004. Motivated by this work, Basnet and Bhattacharyya introduced both the weak clean index of rings and the nil clean index of rings and Cimpean and Danchev introduced the weakly nil clean index of rings. In this work, we calculate each of these indices for the rings ℤ/nℤ and matrix rings with entries in ℤ/nℤ. A generalized index is also introduced.

Centroid-Amenities: An Interactive Visual Analytical Tool For Exploring And Analyzing Amenities In Singapore, Xue Qian Jazreel Siew, Sean Jia Ming Koh

Research Collection School Of Computing and Information Systems

Planning for civic amenities in a fast-changing urban setting such as Singapore is never an easy task. And as urban planners look toward more data-driven approaches toward urban planning, so grows the demand for more flexible geospatial analytics tools to facilitate a more iterative and granular approach toward urban planning. Such specific tools however, are not always readily available as plugins for traditional desktop GIS software, as numerous customizations must be made to model specific temporal planning scenarios for quick analysis, which could prove both costly and time-consuming. Hence, to address this need, open-source tools such as R Shiny could …

Double Learning Or Double Blinding: An Investigation Of Vendor Private Information Acquisition And Consumer Learning Via Online Reviews, Nan Hu, Kevin E. Dow, Alain Yee Loong Chong, Ling Liu

Research Collection School Of Computing and Information Systems

In this paper, building upon information acquisition theory and using portfolio methods and system equations, we made an empirical investigation into how online vendors and consumers are learning from each other, and how online reviews, prices, and sales interact among each other. First, this study shows that vendors acquire information from both private and public channels to learn the quality of their products to make price adjustment. Second, for the more popular products and newly released products, vendors are more motivated to acquire private information that is more precise than the average precision to adjust their price. Third, we document …

Cross-Modal Recipe Retrieval With Stacked Attention Model, Jing-Jing Chen, Lei Pang, Chong-Wah Ngo

Research Collection School Of Computing and Information Systems

Taking a picture of delicious food and sharing it in social media has been a popular trend. The ability to recommend recipes along will benefit users who want to cook a particular dish, and the feature is yet to be available. The challenge of recipe retrieval, nevertheless, comes from two aspects. First, the current technology in food recognition can only scale up to few hundreds of categories, which are yet to be practical for recognizing tens of thousands of food categories. Second, even one food category can have variants of recipes that differ in ingredient composition. Finding the best-match recipe …

Latent Dirichlet Allocation For Textual Student Feedback Analysis, Swapna Gottipati, Venky Shankararaman, Jeff Lin

Research Collection School Of Computing and Information Systems

Education institutions collect feedback from students upon course completion and analyse it to improve curriculum design, delivery methodology and students' learning experience. A large part of feedback comes in the form textual comments, which pose a challenge in quantifying and deriving insights. In this paper, we present a novel approach of the Latent Dirichlet Allocation (LDA) model to address this difficulty in handling textual student feedback. The analysis of quantitative part of student feedback provides generalratings and helps to identify aspects of the teaching that are successful and those that can improve. The reasons for the failure or success, however, …

Class Discussion Management And Analysis Application, Venky Shankararaman, Swapna Gottipati, Seshan Ramaswami, Chirag Chhablan

Research Collection School Of Computing and Information Systems

Discussion-based teaching is popular in several courses because it creates opportunities for students to practice important skills useful for the working environment. In order to make this pedagogy impactful and effective, instructors employ technologies such as online discussion forums and student response systems to conduct and manage classroom discussions. More recently mobile devices have become prevalent and researchers have been exploring how this device can help support education. In this paper we report the innovative use of mobile technology and supporting backend tools to manage classroom discussions. We have implemented a class discussion and management application, LiveClass. This application records …

Linky: Visualizing User Identity Linkage Results For Multiple Online Social Networks (Demo), Roy Ka-Wei Lee, Ming Shan Hee, Philips Kokoh Prasetyo, Ee-Peng Lim

Research Collection School Of Computing and Information Systems

User identity linkage across online social networks is an emerging research topic that has attracted attention in recent years. Many user identity linkage methods have been proposed so far and most of them utilize user profile, content and network information to determine if two social media accounts belong to the same person. In most cases, user identity linkage methods are evaluated by performing some prediction tasks with the results presented using some overall accuracy measures. However, the methods are rarely compared at the individual user level where a predicted matched (or linked) pair of user identities from different online social …

Improving Multi-Label Emotion Classification Via Sentiment Classification With Dual Attention Transfer Network, Jianfei Yu, Luis Marujo, Jing Jiang, Pradeep Karuturi, William Brendel

Research Collection School Of Computing and Information Systems

In this paper, we target at improving the performance of multi-label emotion classification with the help of sentiment classification. Specifically, we propose a new transfer learning architecture to divide the sentence representation into two different feature spaces, which are expected to respectively capture the general sentiment words and the other important emotion-specific words via a dual attention mechanism. Extensive experimental results demonstrate that our transfer learning approach can outperform several strong baselines and achieve the state-of-the-art performance on two benchmark datasets.

Infar: Insight Extraction From App Reviews, Cuiyun Gao, Jichuan Zeng, David Lo, Chin-Yew Lin, Michael R. Lyu, Irwin King

Research Collection School Of Computing and Information Systems

App reviews play an essential role for users to convey their feedback about using the app. The critical information contained in app reviews can assist app developers for maintaining and updating mobile apps. However, the noisy nature and large-quantity of daily generated app reviews make it difficult to understand essential information carried in app reviews. Several prior studies have proposed methods that can automatically classify or cluster user reviews into a few app topics (e.g., security). These methods usually act on a static collection of user reviews. However, due to the dynamic nature of user feedback (i.e., reviews keep coming …

On The Sequential Massart Algorithm For Statistical Model Checking, Cyrille Jegourel, Jun Sun, Jin Song Dong

Research Collection School Of Computing and Information Systems

Several schemes have been provided in Statistical Model Checking (SMC) for the estimation of property occurrence based on predefined confidence and absolute or relative error. Simulations might be however costly if many samples are required and the usual algorithms implemented in statistical model checkers tend to be conservative. Bayesian and rare event techniques can be used to reduce the sample size but they can not be applied without prerequisite or knowledge about the system under scrutiny. Recently, sequential algorithms based on Monte Carlo estimations and Massart bounds have been proposed to reduce the sample size while providing guarantees on error …

Autospearman: Automatically Mitigating Correlated Software Metrics For Interpreting Defect Models, Jirayus Jiarpakdee, Chakkrit Tantithamthavorn, Christoph Treude

Research Collection School Of Computing and Information Systems

The interpretation of defect models heavily relies on software metrics that are used to construct them. However, such software metrics are often correlated in defect models. Prior work often uses feature selection techniques to remove correlated metrics in order to improve the performance of defect models. Yet, the interpretation of defect models may be misleading if feature selection techniques produce subsets of inconsistent and correlated metrics. In this paper, we investigate the consistency and correlation of the subsets of metrics that are produced by nine commonly-used feature selection techniques. Through a case study of 13 publicly-available defect datasets, we find …

Using Carbon Isotope Fractionation To Constrain The Extent Of Methane Dissolution Into The Water Column Surrounding A Natural Hydrocarbon Gas Seep In The Northern Gulf Of Mexico, M. Leonte, B. Wang, Scott A. Socolofsky, John A. Breier, John D. Kessler

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

A gas bubble seep located in the northern Gulf of Mexico was investigated over several days to determine whether changes in the stable carbon isotopic ratio of methane can be used as a tracer for methane dissolution through the water column. Gas bubble and water samples were collected at the seafloor and throughout the water column for isotopic ratio analysis of methane. Our results show that changes in methane isotopic ratios are consistent with laboratory experiments that measured the isotopic fractionation from methane dissolution. A Rayleigh isotope model was applied to the isotope data to determine the fraction of methane …

Mesobot : An Autonomous Underwater Vehicle For Tracking And Sampling Midwater Targets, Dana R. Yoerger, Molly Curran, Justin Fujii, Christopher R. German, Daniel Gomez-Ibanez, Annette F. Govindarajan, Jonathan C. Howland, Joel K. Llopiz, Peter H. Wiebe, Brett W. Hobson, Kakani Katija, Michael Risi, Bruce H. Robison, Cailean J. Wilkinson, Stephen M. Rock, John A. Breier

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

Mesobot, a new class of autonomous underwater vehicle, will address specific unmet needs for observing slow-moving targets in the midwater ocean. Mesobot will track targets such as zooplankton, fish, and descending particle aggregates using a control system based on stereo cameras and a combination of thrusters and a variable buoyancy system. The vehicle will also be able to collect biogeochemical and environmental DNA (eDNA) samples using a pumped filter sampler.

Hot Water Treatment As A Kill-Step To Inactivate Escherichia Coli O157:H7, Salmonella Enterica, Listeria Monocytogenes And Enterococcus Faecium On In-Shell Pecans, Karuna Kharel, Veerachandra K. Yemmireddy, Charles J. Graham, Witoon Prinyawiwatkul, Achyut Adhikari

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

In-shell pecans are susceptible to microbial contamination. This study was performed to investigate feasibility of using hot water treatment as a kill-step for food-borne pathogens during pecan shelling. In-shell pecans were subjected to hot water at 70, 80 or 90 °C for 1, 2, 3, 4 or 5 min. The time-temperature treatments to achieve a 5-log reduction of Salmonella enterica, Escherichia coli O157:H7, Listeria monocytogenes, and non-pathogenic Enterococcus faecium were determined. Thermal death values were determined for each tested condition. L. monocytogenes was most susceptible to heat treatment and were reduced by 4.6 ± 0.35 log CFU/g at 70 …

Clio: An Autonomous Vertical Sampling Vehicle For Global Ocean Biogeochemical Mapping, Michael V. Jakuba, John A. Breier, Daniel Gomez-Ibanez, Kaitlyn Tradd, Mak A. Saito

School of Earth, Environmental, and Marine Sciences Faculty Publications and Presentations

We report the design, sea trials, and scientific operation of a fast vertical profiling autonomous underwater vehicle, called Clio, designed to cost-effectively improve the understanding of marine microorganism ecosystem dynamics on a global scale by collecting high-volume filter samples autonomously, in contrast to conventional techniques that require a ship’s wire.

Inorganic Elemental Concentrations In Birch Bolete Mushroom (Leccinum Scabrum) And Top Soil: Contamination Profiles, Bioconcentation And Annual Variations, Malgorzata Medyk, Bommanna G. Loganathan, Leszek Bielawski, Jerzy Falandysz

Bommanna Loganathan

Intro To Command Line Coding (Fastqe & Fastp), Ray A. Enke

Ray Enke Ph.D.

‘Cassette’-Ises (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds For Hydrolytic Kinetic Resolution Across A Range Of Epoxides, Sangeeta Dey, Douglas R. Powell, Chunhua Hu, David B. Berkowitz

Chemistry Department: Faculty Publications

‘Cassette’-ISES (In Situ Enzymatic Screening) Identifies Complementary Chiral Scaffolds for Hydrolytic Kinetic Resolution Across a Range of Epoxides

A new ‘Cassette’-In Situ Enzymatic Screen (ISES) for combinatorial catalysis is introduced. This allows the experimentalist to obtain an information-rich readout, in real time, providing an estimate of the sense and magnitude of enantioselectivity across more than one substrate. In its first iteration, the screen identified Co^III-salen catalysts with β-pinene- and α-naphthylalanine-derived chiral scaffolds with broad, yet complementary, substrate specificities.

Model For Coordination Of Microtubule And Actin Dynamics In Growth Cone Turning, Erin M. Craig

All Faculty Scholarship for the College of the Sciences

In the developing nervous system, axons are guided to their synaptic targets by motile structures at the axon tip called growth cones, which reorganize their cytoskeleton in order to steer in response to chemotactic cues. Growth cone motility is mediated by an actin-adhesion “clutch” mechanism, in which mechanical attachment to a substrate, coupled with polarized actin growth, produces leading-edge protrusion. Several studies suggest that dynamic microtubules (MTs) in the growth cone periphery play an essential role in growth cone steering. It is not yet well-understood how the MT cytoskeleton and the dynamic actin-adhesion clutch system are coordinated to promote growth …

Comparing Powers Of Edge Ideals, Mike Janssen, Thomas Kamp, Jason Vander Woude

Faculty Work Comprehensive List

Given a nontrivial homogeneous ideal I ⊆ k[x1, x2, . . . ,xd], a problem of great recent interest has been the comparison of the rth ordinary power of I and the mth symbolic power I(m). This comparison has been undertaken directly via an exploration of which exponents m and r guarantee the subset containment I(m) ⊆ Ir and asymptotically via a computation of the resurgence ρ(I), a number for which any m/r > ρ(I) guarantees I(m) ⊆ Ir. Recently, a third quantity, the symbolic defect, was introduced; as It ⊆ I(t), the symbolic defect is the minimal number of generators …

Synthesis, Characterization And Application Of Structurally Diverse Poly(Chalcogenylene Vinylene)S, Zhen Zhang

Chemistry and Chemical Biology ETDs

Conjugated polymers have found widespread applications in flexible and printable electronic devices, among which poly(thienylene vinylene) (PTV) displays outstanding optoelectronic properties and promising applications. However, further studies of its structure-property-function relationship have been greatly impeded mainly due to the synthetic difficulty of generating new structures beyond its rudimentary form.

To further investigate this class of material, I have developed a facile methodology for the preparation of structurally diverse poly(chalcogenylene vinylene)s (PCVs) through a combination of acyclic diene metathesis (ADMET) polymerization and post-polymerization modification techniques. Specifically, a series of halogenated and cross-conjugated PCVs have been designed and synthesized, followed by complete …