Computer Sciences Commons^™

Data For Cybersecurity Research: Process And ‘Wish List’, Jean Camp, Lorrie Cranor, Nick Feamster, Joan Feigenbaum, Stephanie Forrest, David Kotz, Wenke Lee, Patrick Lincoln, Vern Paxson, Mike Reiter, Ron Rivest, William Sanders, Stefan Savage, Sean Smith, Eugene Spafford, Sal Stolfo

Other Faculty Materials

This document identifies data needs of the security research community. This document is in response to a request for a “data wish list”. Because specific data needs will evolve in conjunction with evolving threats and research problems, we augment the wish list with commentary about some of the broader issues for data usage.

An Efficient And Effective Implementation Of The Trust System For Power Grid Compartmentalization, Juan M. Carlos Gonzalez

Theses and Dissertations

As utility companies develop and incorporate new technologies, such as moving to utility Internet technology based architecture and standard; it is crucial that we do so with history in mind. We know that traditional utility protection and control systems were not designed with security in their top priorities. This presents a danger in an environment where near real-time responses are required to ensure safe operations. As a consequence, system security becomes a burden to the system rather than necessary protection. Unfortunately, technology implementation is not the only concern. The number of utility privately-owned companies has multiplied as the market has …

Automatic Red Tide Detection Using Modis Satellite Images, Wijian Cheng

USF Tampa Graduate Theses and Dissertations

Red tides pose a significant economic and environmental threat in the Gulf of Mexico. Detecting red tide is important for understanding this phenomenon. In this thesis, machine learning approaches based on Random Forests, Support Vector Machines and K-Nearest Neighbors have been evaluated for red tide detection from MODIS satellite images. Detection results using machine learning algorithms were compared to ship collected ground truth red tide data. This work has three major contributions. First, machine learning approaches outperformed two of the latest thresholding red tide detection algorithms based on bio-optical characterization by more than 10% in terms of F measure and …

Automated Tracking Of Dividing Nuclei In Microscopy Videos Of Living Cells, Evan L. Tice

Dartmouth College Undergraduate Theses

Many cell biologists perform analysis of multinucleated cell data in order to better under- stand the mechanisms that regulate cell division. Sbalzarini, et al., have developed methods for automatically tracking nuclei in cell data in order to aid in this time-consuming analysis. In this paper, we present an implementation of the Sbalzarini tracking algorithm, introduce a new algorithm we developed which is able to identify mitosis events, and present other software tools we have developed to aid in the automated detection of nucleus data.

Developing An Improved, Web-Based Classroom Response System With Web Services, Oleg B. Seletsky

Dartmouth College Undergraduate Theses

Classroom Response Systems (CRS) are an in-class technology used to poll students and instantly display an aggregate representation of their responses. CRS have been around since the 1970s and have become increasingly more popular in higher education lecture halls. Even though technology, specifically computers and communications, has improved significantly since the 1970s, CRS have remained surprisingly unchanged. The purpose of this project was to develop an innovative web-based CRS using web services. The web-based aspect utilizes Dartmouth's wireless campus while the web services back-end makes the product more extensible. Lastly, we added a set of out-of-class learning tools for students …

The Effects Of Introspection On Computer Security Policies, Stephanie A. Trudeau

Dartmouth College Undergraduate Theses

What does it mean to be an expert? And what makes an expert more capable than a non-expert when it comes to evaluating and articulating their impressions about something as commonly practiced as food tasting? How do we explain those behaviors that humans perform very well, but don't quite know why? Studies have shown that there exists a class of activities that we as humans execute well intuitively, but that we perform much worse upon introspection. Evidence supports the claim that the act of introspection actually causes us to do more poorly at these tasks. My goal is to apply …

Understanding Terrorism Through The Use Of Gis - Crj 346: Terrorism And Society, Joseph F. Ryan, Ph.D., Daniel Farkas, Ph.D.

Cornerstone 3 Reports : Interdisciplinary Informatics

This is a study that concentrates on methodologies on collecting and analysis of intelligence information.

Routing In The Dark: Pitch Black, Nathan S. Evans

Electronic Theses and Dissertations

In many networks, such as mobile ad-hoc networks and friend-to-friend overlay networks, direct communication between nodes is limited to specific neighbors. Friendto-friend “darknet” networks have been shown to commonly have a small-world topology; while short paths exist between any pair of nodes in small-world networks, it is non-trivial to determine such paths with a distributed algorithm. Recently, Clarke and Sandberg proposed the first decentralized routing algorithm that achieves efficient routing in such small-world networks.

Herein this thesis we discuss the first independent security analysis of Clarke and Sandberg’s routing algorithm. We show that a relatively weak participating adversary can render …

An Information Complexity Approach To The Inner Product Problem, William B. Henderson-Frost

Dartmouth College Undergraduate Theses

We prove a lower bound of the randomized communication complexity of the inner product function on the uniform distribution.

Hawk: 3d Gestured-Based Interactive Bird Flight Simulation, Thomas Yale Eastman

Dartmouth College Undergraduate Theses

Control interfaces provide the most tangible connection between human users and computer software. This link is especially important in interactive real-time applications, like games and simulations, because users desire efficient controls that allow them to maximize their interactivity and immersion with the software. Traditionally, interfaces have been largely limited to keyboards and mice. Recently, however, technological advances have made motion-sensitive devices not only available to mainstream consumers but have also lifted restrictions limiting devices to two-dimensional motion. This work presents a 3-dimensional motion-sensitive interface alongside a natural application. Players can control a soaring red-tailed hawk and perform various intuitive flight …

Trykipedia: Collaborative Bio-Ontology Development Using Wiki Environment, Pramod Anantharam, Satya S. Sahoo, Brent Weatherly, Flora Logan, Raghava Mutharaju, Amit P. Sheth, Rick L. Tarleton

Kno.e.sis Publications

Biomedical ontology development is an intensely collaborative process between biology experts and computer scientists. With the proliferation of ontology based approach to solve informatics problems in biological domain, there is a need for collaborative environment that is intuitive and widely accepted for modeling the ontology.

Operational Verification Of A Relativistic Program, Robert T. Bauer

Computer Science Faculty Publications and Presentations

Engineering eorts to achieve scalable multiprocessor perfor- mance for concurrent reader-writer programs have resulted in a family of algorithms that are non-blocking and that tolerate interprocessor in- terference. Because these algorithms accept a unique frame of reference for each processor's accesses to memory, they typify a concurrent pro- gramming technique for shared memory multicore architectures called relativistic programmming.

Rigorous verification of these algorithms is not possible with existing semantic based approaches because the semantics under approximates multiprocessor behavior and the algorithms rely on abstruse interactions with the operating system that aren't reconciled with language seman- tics.

The Read-Copy Update (RCU) …

Reconstruction Of The Upper Torso Using X-Ray Imagery, Thomas Wischgoll, Christopher Koehler

Computer Science and Engineering Faculty Publications

No abstract provided.

A Novel Fuzzy Artmap Architecture With Adaptive Featureweights Based On Onicescu’S Informational Energy, Răzvan Andonie, Angel Caţaron, Lucian Mircea Sasu

All Faculty Scholarship for the College of the Sciences

Fuzzy ARTMAP with Relevance factor (FAMR) is a Fuzzy ARTMAP (FAM) neural architecture with the following property: Each training pair has a relevance factor assigned to it, proportional to the importance of that pair during the learning phase. Using a relevance factor adds more flexibility to the training phase, allowing ranking of sample pairs according to the confidence we have in the information source or in the pattern itself.

We introduce a novel FAMR architecture: FAMR with Feature Weighting (FAMRFW). In the first stage, the training data features are weighted. In our experiments, we use a feature weighting method based …

Sample Size Estimation While Controlling False Discovery Rate For Microarray Experiments Using The Ssize.Fdr Package, Megan Orr, Peng Liu

The R Journal

Microarray experiments are becoming more and more popular and critical in many biological disciplines. As in any statistical experiment, appropriate experimental design is essential for reliable statistical inference, and sample size has a crucial role in experimental design. Because microarray experiments are rather costly, it is important to have an adequate sample size that will achieve a desired power with out wasting resources.

For a given microarray data set, thousands of hypotheses, one for each gene, are simultaneously tested. Storey and Tibshirani (2003) argue that con trolling false discovery rate (FDR) is more reasonable and more powerful than controlling family-wise …

Emd: A Package For Empirical Mode Decomposition And Hilbert Spectrum, Donghoh Kim, Hee-Seok Oh

The R Journal

The concept of empirical mode decomposition (EMD)and the Hilber tspectrum (HS) has been developed rapidly in many disciplines of science and engineering since Huang et al. (1998) invented EMD. The key feature of EMD is to decompose a signal into so-called intrinsic mode function (IMF). Further more, the Hilbert spectral analysis of intrinsic mode functions provides frequency information evolving with time and quantifies the amount of variation due to oscillation at different time scales and time locations. In this article,we introduce an R package called EMD (KimandOh, 2008) that performs one and two-dimensional EMD and HS.

Modeling Without Data Using Expert Opinion, Vincent Goulet, Michel Jacques, Mathieu Pigeon

The R Journal

The expert package provides tools to create and manipulate empirical statistical models using expert opinion (or judgment). Here, the latter expression refers to a specific body of techniques to elicit the distribution of a random variable when data is scarce or unavailable. Opinions on the quantiles of the distribution are sought from experts in the field and aggregated into a final estimate. The package supports aggregation by means of the Cooke, Mendel–Sheridan and predefined weights models.

We do not mean to give a complete introduction to the theory and practice of expert opinion elicitation in this paper. However, for the …

Admit, David Ardia, Lennart F. Hoogerheide, Herman K. Van Dijk

The R Journal

This note presents the package AdMit (Ardia et al., 2008, 2009), an R implementation of the adaptive mixture of Student-t distributions (AdMit) procedure developed by Hoogerheide (2006); see also Hoogerheide et al. (2007); Hoogerheide and van Dijk (2008). The AdMit strategy consists of the construction of a mixture of Student-t distributions which approximates a target distribution of interest. The fitting procedure relies only on a kernel of the tar get density, so that the normalizing constant is not required. In a second step, this approximation is used as an importance function in importance sampling or as a candidate density in …

The Hwriter Package: Composing Html Documents With R Objects, Gregoire Pau, Wolfgang Huber

The R Journal

HTML documents are structured documents made of diverse elements such as paragraphs, sections, columns, figures and tables organized in a hierarchical layout. Combination of HTML documents and hyperlinking is useful to report analysis results; for example, in the package array Quality Metrics (Kauffmannetal., 2009), estimating the quality of mi croarray data sets and cellHTS2(Boutrosetal.,2006), performing the analysis of cell-based screens.

There are several tools for exporting data from R into HTML documents. The package R2HTML is able to render a large diversity of R objects in HTML but does not easily support combining them in a structured layout and …

Collaborative Software Development Using R-Forge, Stefan Theußl, Achim Zeileis

The R Journal

Open source software (OSS) is typically created in a decentralized self-organizing process by a community of developers having the same or similar interests (see the famous essay by Raymond, 1999). A key factor for the success of OSS over the last two decades is the Internet: Developers who rarely meet face-to-face can employ new means of communication, both for rapidly writing and deploying software (in the spirit of Linus Torvald’s “release early, release often paradigm”). Therefore, many tools emerged that assist a collaborative software development process, including in particular tools for source code management (SCM) and version control.

In the …

Facets Of R, John M. Chambers

The R Journal

We are seeing today a widespread, and welcome, tendency for non-computer-specialists among statisticians and others to write collections of R functions that organize and communicate their work. Along with the flood of software sometimes comes an attitude that one need-only-learn, or teach, a sort of basic how-to-write-the-function level of R programming, beyond which most of the detail is unimportant or can be absorbed without much discussion. As delusions go, this one is not very objectionable if it encourages participation. Nevertheless, a delusion it is. In fact, functions are only one of a variety of important facets that R has acquired …

Easier Parallel Computing In R With Snowfall And Sfcluster, Jochen Knaus, Christine Porzelius, Harald Binder, Guido Schwarzer

The R Journal

Many statistical analysis tasks in areas such as bioinformatics are computationally very intensive, while lots of them rely on embarrassingly parallel computations (Grama et al., 2003). Multiple computers or even multiple processor cores on standard desktop computers, which are widespread nowadays, can easily contribute to faster analyses.

R itself does not allow parallel execution. There are some existing solutions for R to distribute calculations over many computers — a cluster — for ex ample Rmpi, rpvm, snow, nws or papply. However these solutions require the user to setup and manage the cluster on his own and …

The R Journal (June 2009) 1(1): Complete Issue, The R Foundation

The R Journal

Contributed Research Articles

Facets of R, John M. Chambers

Collaborative Software Development Using R-Forge, Stefan Theußl and Achim Zeileis

Drawing Diagrams with R, Paul Murrell

The hwriter package: Composing HTML Documents with R Objects, Gregoire Pau and Wolfgang Huber

AdMit, David Ardia, Lennart F. Hoogerheide, and Herman K. van Dijk

expert: Modeling Without Data Using Expert Opinion, Vincent Goulet, Michel Jacques, and Mathieu Pigeon

New Numerical Algorithm for Multivariate Normal Probabilities in Package mvtnorm, Xuefei Mi, Tetsuhisa Miwa, and Torsten Hothorn

EMD: A Package for Empirical Mode Decomposition and Hilbert Spectrum, Donghoh Kim, and Hee-Seok Oh

Sample Size Estimation while …

Drawing Diagrams With R, Paul Murrell

The R Journal

R provides a number of well-known high-level facilities for producing sophisticated statistical plots, including the “traditional” plots in the graphics pack age (R Development Core Team, 2008), the Trellis style plots provided by lattice (Sarkar, 2008), and the grammar-of-graphics-inspired approach of ggplot2 (Wickham, 2009). However, R also provides a powerful set of low level graphics facilities for drawing basic shapes and, more importantly, for arranging those shapes relative to each other, which can be used to draw a wide variety of graphical images. This article highlights some of R’s low-level graphics facilities by demonstrating their use in the production of …

Pmml: An Open Standard For Sharing Models, Alex Guazzelli, Michael Zeller, Wen-Ching Lin, Graham Williams

The R Journal

The PMML package exports a variety of predictive and descriptive models from R to the Predictive Model Markup Language (Data Mining Group, 2008). PMML is an XML-based language and has become the de-facto standard to represent not only predictive and descriptive models, but also data pre- and post-processing. In so doing, it allows for the interchange of models among different tools and environments, mostly avoiding proprietary issues and incompatibilities.

The PMML package itself (Williams et al., 2009) was conceived at first as part of Togaware’s data mining toolkit Rattle, the R Analytical Tool To Learn Easily (Williams, 2009). Although it …

Cyber Attacks: Cross-Country Interdependence And Enforcement, Qiu-Hong Wang, Seung Hyun Kim

Research Collection School Of Computing and Information Systems

This study empirically characterizes the interdependence in cyber attacks and examines theimpact from the first international treaty against cybercrimes (Convention on Cybercrimes:Europe Treaty Series No. 185). With the data covering 62 countries over the period from year2003 to 2007, we find that, international cooperation in enforcement as measured by theindicator of joining the Convention on Cybercrimes, deterred cyber attacks originating from anyparticular country by 15.81% ~ 24.77% (in 95% confidence interval). Second, joining theConvention also affected the interdependence in cyber attacks from two angels. First, for anypair of country, closer status in joining or not joining the Convention was associated …

Boundless Fluids Using The Lattice-Boltzmann Method, Kyle J. Haughey

Master's Theses

Computer-generated imagery is ubiquitous in today's society, appearing in advertisements, video games, and computer-animated movies among other places. Much of this imagery needs to be as realistic as possible, and animators have turned to techniques such as fluid simulation to create scenes involving substances like smoke, fire, and water. The Lattice-Boltzmann Method (LBM) is one fluid simulation technique that has gained recent popularity due to its relatively simple basic algorithm and the ease with which it can be distributed across multiple processors. Unfortunately, current LBM simulations also suffer from high memory usage and restrict free surface fluids to domains of …

Applying Domain Knowledge From Structured Citation Formats To Text And Data Mining: Examples Using The Cite Architecture, D Neel Smith, Gabriel A. Weaver

Computer Science Technical Reports

Domain knowledge expressed in structured citation formats can be exploited in data mining. We propose four structural properties of canonically cited texts, then look at to two classic problems in the study of the scholia, or ancient scholarly commentary, found in the manuscripts of the Iliad. We cluster citations of scholia to analyze their distribution in different manuscripts; this leads to a revised view of how the manuscripts' scribes drew on their source material. Correlated frequencies of named entities suggest that one group of manuscripts had access to material more closely based on the work of the greatest Hellenistic editor …

A Computational Framework For Certificate Policy Operations, Gabriel A. Weaver, Scott Rea, Sean W. Smith

Computer Science Technical Reports

The trustworthiness of any Public Key Infrastructure (PKI) rests upon the expectations for trust, and the degree to which those ex- pectations are met. Policies, whether implicit as in PGP and SDSI/SPKI or explicitly required as in X.509, document expectations for trust in a PKI. The widespread use of X.509 in the context of global e-Science infrastructures, financial institutions, and the U.S. Federal government demands efficient, transparent, and reproducible policy decisions. Since current manual processes fall short of these goals, we designed, built, and tested computational tools to process the citation schemes of X.509 certificate policies defined in RFC 2527 …

Residual-Based Estimation Of Peer And Link Lifetimes In P2p Networks, Xiaoming Wang, Zhongmei Yao, Dmitri Loguinov

Computer Science Faculty Publications

Existing methods of measuring lifetimes in P2P systems usually rely on the so-called Create-BasedMethod (CBM), which divides a given observation window into two halves and samples users ldquocreatedrdquo in the first half every Delta time units until they die or the observation period ends. Despite its frequent use, this approach has no rigorous accuracy or overhead analysis in the literature. To shed more light on its performance, we first derive a model for CBM and show that small window size or large Delta may lead to highly inaccurate lifetime distributions. We then show that create-based sampling exhibits an inherent …