Computer Sciences Commons^™

Using Architecture Models To Design Adaptive Socio-Technical Systems, Holly A. H. Handley

Engineering Management & Systems Engineering Faculty Publications

An architecture framework is used to capture the overall design and structure of a complex system. The Human Viewpoint was developed to augment existing architectural frameworks with additional information relevant to the human component in the system. The Human View models collect and organize social parameters in order to understand the way that humans interact with other elements of the system; the Human View models define the socio-technological boundaries of the system. Analyses performed with the architectural data provide information regarding the congruence, or fit of the human and the system. For example, different key thread analyses identify problematic paths …

Interpreting Individual Classifications Of Hierarchical Networks, Will Landecker, Michael David Thomure, Luis M.A. Bettencourt, Melanie Mitchell, Garrett T. Kenyon, Steven P. Brumby

Computer Science Faculty Publications and Presentations

Hierarchical networks are known to achieve high classification accuracy on difficult machine-learning tasks. For many applications, a clear explanation of why the data was classified a certain way is just as important as the classification itself. However, the complexity of hierarchical networks makes them ill-suited for existing explanation methods. We propose a new method, contribution propagation, that gives per-instance explanations of a trained network's classifications. We give theoretical foundations for the proposed method, and evaluate its correctness empirically. Finally, we use the resulting explanations to reveal unexpected behavior of networks that achieve high accuracy on visual object-recognition tasks using well-known …

Modules And Dialects As Objects In Grace, Michael Homer, James Noble, Kim B. Bruce, Andrew P. Black

Computer Science Faculty Publications and Presentations

Grace is a gradually typed, object-oriented language for use in education; consonant with that use, we have tried to keep Grace as simple and straightforward as possible. Grace needs a module system for several reasons: to teach students about modular program design, to organise large programs, especially its self-hosted implementation, to provide access to resources defined in other languages, and to support different “dialects”—language subsets, or domain specific languages, for particular parts of the curriculum. Grace already has several organising constructs; this paper describes how Grace uses two of them, objects and lexical scope, to provide modules and dialects.

Taming The Metadata Mess, Veronika Margaret Megler

Computer Science Faculty Publications and Presentations

The rapid growth of scientific data shows no sign of abating. This growth has led to a new problem: with so much scientific data at hand, stored in thousands of datasets, how can scientists find the datasets most relevant to their research interests? We have addressed this problem by adapting Information Retrieval techniques, developed for searching text documents, into the world of (primarily numeric) scientific data. We propose an approach that uses a blend of automated and “semi-curated” methods to extract metadata from large archives of scientific data, then evaluates ranked searches over this metadata. We describe a challenge identified …

The Problem Of Semantics In The Metadata Mess, Veronika Margaret Megler, David Maier

Computer Science Faculty Publications and Presentations

This presentation addresses problems related to the volume of available scientific data, and its accessibility or inaccessibility to researchers who seek it. Topics addressed include metadata and reducing semantic diversity, especially as they refer to geospatial and other architectures

Interactive Ambient Visualizations For Soft Advice, Emerson Murphy-Hill, Titus Barik, Andrew P. Black

Computer Science Faculty Publications and Presentations

Some software packages offer the user soft advice: recommendations that are intended to help the user create high quality artifacts, but which may turn out to be bad advice. It is left to the user to determine whether the soft advice really will improve quality, and to decide whether or not to adopt it. Visualizations can help the user in making this decision, but we believe that conventional visualizations are less than ideal. In this paper, we describe an interactive ambient visualization to help users identify, understand and interpret soft advice.

Our visualization was developed to help programmers interpret code …

On The Role Of Shape Prototypes In Hierarchical Models Of Vision, Michael David Thomure, Melanie Mitchell, Garrett T. Kenyon

Computer Science Faculty Publications and Presentations

We investigate the role of learned shape-prototypes in an influential family of hierarchical neural-network models of vision. Central to these networks’ design is a dictionary of learned shapes, which are meant to respond to discriminative visual patterns in the input. While higher-level features based on such learned prototypes have been cited as key for viewpointinvariant object-recognition in these models [1], [2], we show that high performance on invariant object-recognition tasks can be obtained by using a simple set of unlearned, “shape-free” features. This behavior is robust to the size of the network. These results call into question the roles of …

Assessment Of An Enterprise Employee Portal Using Dashboard Monitoring System: A Case Study, Aditi Mishra

Masters Theses

"A portal is a browser-based application that provides a web platform for users to improve inter-department collaboration and customer service. Portals are classified either as internal facing portals or external public facing portals. This study addresses the problems facing an internal portal related to its contents, functions and usability and provides a list of essential contents and functions that it should include through integrating theories and industry best practices. The theory framework is based on literature review and the industry best practices are based on the analysis of a number of internal portals of companies used as case studies. These …

Practical End-To-End Performance Evaluation Of Backend Software Applications, Tuli Nivas

Computer Science and Engineering Dissertations - Archive

This dissertation makes contributions to four areas of performance testing - the test process itself, monitoring, automation and end-to-end performance evaluation of backend applications. The first contribution deals with the testing process. Performance testing is a key element of industrial software development, but we still encountered the following two problems. (1) While testing textbooks prescribe writing tests against performance goals, we find that it is impractical to gather from business analysts performance goals that are detailed enough for finding subtle performance bugs. (2) Once performance tests are conducted, we were asked questions such as - how do you make sure …

New Matrix Completion Models For Social Information Retrieval Application, Jin Huang

Computer Science and Engineering Dissertations - Archive

Many popular social web sites have emerged during the past decade and completely changed many users' everyday live. Recently, social information retrieval models, where conventional information retrieval meets the social context of search and recommendation, have become the central topic in machine learning, data mining, information retrieval and many other areas.A particular application of social information retrieval is the recommendation. Such recommendation ranges from classic recommendation movie rating recommendation in user-item matrices, trust and reputation modeling between members in any social network. If we model such recommendation in the form of matrices, then such recommendation can be formulated as recovering …

Quantitative Analysis Of Surface Enhanced Raman Spectra, Shuo Li

Computer Science and Engineering Dissertations - Archive

Quantitative analysis of Raman spectra using surface-enhanced Raman scattering (SERS) nanoparticles has shown the potential and promising trend of development in vivo molecular imaging. One of the key job is from the intensities of Raman signals to predict the quantities of analytes. Direct classical least squares (DCLS) and multivariate calibration (MC) are commonly used methods. DCLS relies on source Raman signals as the references. But the inherent Instability of Raman signals make the DCLS model not robust enough. MC model relies on a batch of training mixture Raman signals together with the ground truth mixing concentrations to build the multivariate …

Spectral Characterization Of The Nigerian Shoreline Using Landsat Imagery, Olumide Fadahunsi, Shachak Pe'eri, Christopher Parrish, Andy Armstrong, Lee Alexander

Center for Coastal and Ocean Mapping

The challenges of shoreline mapping include the high costs of acquiring up-to-date survey data over the coastal area. As a result, in many developing countries, the shoreline has not been consistently mapped. The variety of methods used for this mapping and the large time differences between the surveys (on the order of decades) could result in inaccuracies in shoreline data. This study presents the development of a shoreline characterization procedure for the Nigerian coastline using satellite remote sensing technology. The study goal is to produce a complete, consistent and continuous shoreline map using publicly available data processed in a GIS …

Image Annotation And Feature Engineering Via Structural Sparsity And Low Rank Approximation, Deguang Kong

Computer Science and Engineering Dissertations - Archive

Nowadays, in order to sense environment and understand human behaviors, data analysis plays a more and more important role to handle heterogeneous data ranging from different domains, e.g., image categorization/annotation, customer segmentation, traffic prediction, ad optimization, recommendation systems, privacy analysis, etc. The large amount of multivariate data raises the fundamental problem of data mining: how to discover meaningful compact patterns hidden in the high-dimensional noisy observations? One approach is to do dimension reduction, which finds the low-dimensional subspace and thus encodes data in a low-dimensional structure. The other approach is to do feature selection or feature engineering, which manipulates the …

Sparse And Large-Scale Learning Models And Algorithms For Mining Heterogeneous Big Data, Xiao Cai

Computer Science and Engineering Dissertations - Archive

With the development of PC, internet as well as mobile devices, we are facing a data exploding era. On one hand, more and more features can be collected to describe the data, making the size of the data descriptor larger and larger. On the other hand, the number of data itself explodes and can be collected from multiple resources. When the data becomes large scale, the traditional data analysis method may fail, suffering the curse of dimensionality and etc. In order to explore and analyze the large-scale data more accurately and more efficiently, based on the characteristic of the data, …

An Interpolation Based Approach For Pattern Recognition And Generation, Vishnukumar Galigekere Nagabhushana

Computer Science and Engineering Dissertations - Archive

A large number of problems in computer vision and computer graphics can essentially be reduced to a pattern recognition problem. In this thesis, we explore a novel interpolation based framework to address some of the various recognition problems in these areas. Our interpolation based framework is a supervised learning algorithm that allows for both generation (synthesis) of new patterns as well as perception (analysis) of existing patterns. The method is simple to implement and yet, expects a very straightforward and intuitive set of parameters to model the complex nature of such recognition problems.Specifically, given a set of training data along …

Blackops: Increasing Confidence In Variant Detection Through Mappability Filtering, Christopher R. Cabanski, Matthew D. Wilkerson, Matthew Soloway, Joel S. Parker, Jinze Liu, Jan F. Prins, J. S. Marron, Charles M. Perou, D. Neil Hayes

Computer Science Faculty Publications

Identifying variants using high-throughput sequencing data is currently a challenge because true biological variants can be indistinguishable from technical artifacts. One source of technical artifact results from incorrectly aligning experimentally observed sequences to their true genomic origin (‘mismapping’) and inferring differences in mismapped sequences to be true variants. We developed BlackOPs, an open-source tool that simulates experimental RNA-seq and DNA whole exome sequences derived from the reference genome, aligns these sequences by custom parameters, detects variants and outputs a blacklist of positions and alleles caused by mismapping. Blacklists contain thousands of artifact variants that are indistinguishable from true variants and, …

Diffsplice: The Genome-Wide Detection Of Differential Splicing Events With Rna-Seq, Yin Hu, Yan Huang, Ying Du, Christian F. Orellana, Darshan Singh, Amy R. Johnson, Anaïs Monroy, Pei-Fen Kuan, Scott M. Hammond, Liza M. Hammond, Scott H. Randell, Derek Y. Chiang, D. Neil Hayes, Corbin Jones, Yufeng Liu, Jan F. Prins, Jinze Liu

Computer Science Faculty Publications

The RNA transcriptome varies in response to cellular differentiation as well as environmental factors, and can be characterized by the diversity and abundance of transcript isoforms. Differential transcription analysis, the detection of differences between the transcriptomes of different cells, may improve understanding of cell differentiation and development and enable the identification of biomarkers that classify disease types. The availability of high-throughput short-read RNA sequencing technologies provides in-depth sampling of the transcriptome, making it possible to accurately detect the differences between transcriptomes. In this article, we present a new method for the detection and visualization of differential transcription. Our approach does …

College Student Home Computer Security Adoption, Chet L. Claar, Robert C. Shields, David Rawlinson, Robert Lupton

All Faculty Scholarship for the College of the Sciences

The home Internet user faces a hostile environment abundant in potential attacks on their computers. These attacks have been increasing at an alarming rate and cause damage to individuals and organizations regularly, and have the potential to cripple the critical infrastructures of entire countries. Recent research has determined that some individuals are not utilizing additional software protections available to mitigate these potential security risks. This paper seeks to clarify the reasons by proposing a conceptual framework that utilizes the Health Belief Model as a possible way to explain why some people do not perceive a threat sufficient to prompt the …

Centerline Extraction For Image Segmentation Using Gradient And Direction Vector Flow Active Contours, Shuqun Zhang, Jianyang Zhou

Publications and Research

In this paper, we propose a fast centerline extraction method to be used for gradient and direction vector flow of active contours. The gradient and direction vector flow is a recently reported active contour model capable of significantly improving the image segmentation performance especially for complex object shape, by seamlessly integrating gradient vector flow and prior directional information. Since the prior directional information is provided by manual line drawing, it can be inconvenient for inexperienced users who might have difficulty in finding the best place to draw the directional lines to achieve the best segmentation performance. This paper describes a …

Computational Methods For Comparative Non-Coding Rna Analysis: From Structural Motif Identification To Genome-Wide Functional Classification, Cuncong Zhong

Electronic Theses and Dissertations

Recent advances in biological research point out that many ribonucleic acids (RNAs) are transcribed from the genome to perform a variety of cellular functions, rather than merely acting as information carriers for protein synthesis. These RNAs are usually referred to as the non-coding RNAs (ncRNAs). The versatile regulation mechanisms and functionalities of the ncRNAs contribute to the amazing complexity of the biological system. The ncRNAs perform their biological functions by folding into specific structures. In this case, the comparative study of the ncRNA structures is key to the inference of their molecular and cellular functions. We are especially interested in …

Personal Reflections From Eportfolio: Ahrc New York City, Juliette Nieves

Community Action Forum: Seidenberg School

No abstract provided.

Personal Reflections From Eportfolio: Ahrc New York City, Erika Wong Zhang

Community Action Forum: Seidenberg School

No abstract provided.

Using Mapreduce Streaming For Distributed Life Simulation On The Cloud, Atanas Radenski

Mathematics, Physics, and Computer Science Faculty Books and Book Chapters

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable …

The Informavore Shopper: Analysis Of Information Foraging, System Design, And Purchasing Behavior In Online Retail Stores, Jeff Min Teck Hong

Dissertations and Theses Collection (Open Access)

Global online retail sales are on the rise and are predicted to experience a double digit growth annually over the next three years. Given little marginal cost involved in adding new products and brands to their catalogues, online retailers tend to increase product and brand offerings to increase sales by selling products that could not have been sold due to space constraints in physical stores. Frank Urbanowski, Director of MIT Press, attributed the 12% increase in sales of backlist titles directly to increased accessibility to these titles through the Internet. For consumers, the ability to buy products that they would …

Fair Cost Sharing Auction Mechanisms In Last Mile Ridesharing, Duc Thien Nguyen

Dissertations and Theses Collection (Open Access)

With rapid growth of transportation demands in urban cities, one major challenge is to provide efficient and effective door-to-door service to passengers using the public transportation system. This is commonly known as the Last Mile problem. In this thesis, we consider a dynamic and demand responsive mechanism for Ridesharing on a non-dedicated commercial fleet (such as taxis). This problem is addressed as two sub-problems, the first of which is a special type of vehicle routing problems (VRP). The second sub-problem, which is more challenging, is to allocate the cost (i.e. total fare) fairly among passengers. We propose auction mechanisms where …

Table Of Contents

Journal of Digital Forensics, Security and Law

No abstract provided.

A Simple Experiment With Microsoft Office 2010 And Windows 7 Utilizing Digital Forensic Methodology, Gregory H. Carlton

Journal of Digital Forensics, Security and Law

Digital forensic examiners are tasked with retrieving data from digital storage devices, and frequently these examiners are expected to explain the circumstances that led to the data being in its current state. Through written reports or verbal, expert testimony delivered in court, digital forensic examiners are expected to describe whether data have been altered, and if so, then to what extent have data been altered. Addressing these expectations results from opinions digital forensic examiners reach concerning their understanding of electronic storage and retrieval methods. The credibility of these opinions evolves from the scientific basis from which they are drawn using …

The Advanced Data Acquisition Model (Adam): A Process Model For Digital Forensic Practice, Richard Adams, Val Hobbs, Graham Mann

Journal of Digital Forensics, Security and Law

As with other types of evidence, the courts make no presumption that digital evidence is reliable without some evidence of empirical testing in relation to the theories and techniques associated with its production. The issue of reliability means that courts pay close attention to the manner in which electronic evidence has been obtained and in particular the process in which the data is captured and stored. Previous process models have tended to focus on one particular area of digital forensic practice, such as law enforcement, and have not incorporated a formal description. We contend that this approach has prevented the …

Exploring The Baccalaureate Origin Of Domestic Ph.D. Students In Computing Fields, Susanne Hambrusch, Ran Libeskind-Hadas, Fen Zhao, David Rabson, Amy Csizmar Dalal, Ed Fox, Charles Isbell, Valerie Taylor

All HMC Faculty Publications and Research

Increasing the number of US students entering graduate school and receiving a Ph.D. in computer science is a goal as well as a challenge for many US Ph.D. granting institutions. Although the total computer science Ph.D. production in the U.S. has doubled between 2000 and 2010 (Figure 1), the fraction of domestic students receiving a Ph.D. from U.S. graduate programs has been below 50% since 2003 (Figure 2).

The goal of the Pipeline Project of CRA-E (PiPE) is to better understand the pipeline of US citizens and Permanent Residents (henceforth termed domestic students ) who apply, matriculate, and graduate from …

Virtual Machine Workloads: The Case For New Nas Benchmarks, Vasily Tarasov, Dean Hildebrand, Geoffrey H. Kuenning, Erez Zadok

All HMC Faculty Publications and Research

Network Attached Storage (NAS) and Virtual Machines (VMs) are widely used in data centers thanks to their manageability, scalability, and ability to consolidate resources. But the shift from physical to virtual clients drastically changes the I/O workloads to seen on NAS servers, due to guest file system encapsulation in virtual disk images and the multiplexing of request streams from different VMs. Unfortunately, current NAS workload generators and benchmarks produce workloads typical to physical machines.

This paper makes two contributions. First, we studied the extent to which virtualization is changing existing NAS workloads. We observed significant changes, including the disappearance of …