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Description
Despite significant advances in digital pathology and automation sciences, current diagnostic practice for cancer detection primarily relies on a qualitative manual inspection of tissue architecture and cell and nuclear morphology in stained biopsies using low-magnification, two-dimensional (2D) brightfield microscopy. The efficacy of this process is limited by inter-operator variations in sample preparation and imaging, and by inter-observer variability in assessment. Over the past few decades, the predictive value quantitative morphology measurements derived from computerized analysis of micrographs has been compromised by the inability of 2D microscopy to capture information in the third dimension, and by the anisotropic spatial resolution inherent to conventional microscopy techniques that generate volumetric images by stacking 2D optical sections to approximate 3D. To gain insight into the analytical 3D nature of cells, this dissertation explores the application of a new technology for single-cell optical computed tomography (optical cell CT) that is a promising 3D tomographic imaging technique which uses visible light absorption to image stained cells individually with sub-micron, isotropic spatial resolution. This dissertation provides a scalable analytical framework to perform fully-automated 3D morphological analysis from transmission-mode optical cell CT images of hematoxylin-stained cells. The developed framework performs rapid and accurate quantification of 3D cell and nuclear morphology, facilitates assessment of morphological heterogeneity, and generates shape- and texture-based biosignatures predictive of the cell state. Custom 3D image segmentation methods were developed to precisely delineate volumes of interest (VOIs) from reconstructed cell images. Comparison with user-defined ground truth assessments yielded an average agreement (DICE coefficient) of 94% for the cell and its nucleus. Seventy nine biologically relevant morphological descriptors (features) were computed from the segmented VOIs, and statistical classification methods were implemented to determine the subset of features that best predicted cell health. The efficacy of our proposed framework was demonstrated on an in vitro model of multistep carcinogenesis in human Barrett's esophagus (BE) and classifier performance using our 3D morphometric analysis was compared against computerized analysis of 2D image slices that reflected conventional cytological observation. Our results enable sensitive and specific nuclear grade classification for early cancer diagnosis and underline the value of the approach as an objective adjunctive tool to better understand morphological changes associated with malignant transformation.
ContributorsNandakumar, Vivek (Author) / Meldrum, Deirdre R (Thesis advisor) / Nelson, Alan C. (Committee member) / Karam, Lina J (Committee member) / Ye, Jieping (Committee member) / Johnson, Roger H (Committee member) / Bussey, Kimberly J (Committee member) / Arizona State University (Publisher)
Created2013
Description
We solve the problem of activity verification in the context of sustainability. Activity verification is the process of proving the user assertions pertaining to a certain activity performed by the user. Our motivation lies in incentivizing the user for engaging in sustainable activities like taking public transport or recycling. Such incentivization schemes require the system to verify the claim made by the user. The system verifies these claims by analyzing the supporting evidence captured by the user while performing the activity. The proliferation of portable smart-phones in the past few years has provided us with a ubiquitous and relatively cheap platform, having multiple sensors like accelerometer, gyroscope, microphone etc. to capture this evidence data in-situ. In this research, we investigate the supervised and semi-supervised learning techniques for activity verification. Both these techniques make use the data set constructed using the evidence submitted by the user. Supervised learning makes use of annotated evidence data to build a function to predict the class labels of the unlabeled data points. The evidence data captured can be either unimodal or multimodal in nature. We use the accelerometer data as evidence for transportation mode verification and image data as evidence for recycling verification. After training the system, we achieve maximum accuracy of 94% when classifying the transport mode and 81% when detecting recycle activity. In the case of recycle verification, we could improve the classification accuracy by asking the user for more evidence. We present some techniques to ask the user for the next best piece of evidence that maximizes the probability of classification. Using these techniques for detecting recycle activity, the accuracy increases to 93%. The major disadvantage of using supervised models is that it requires extensive annotated training data, which expensive to collect. Due to the limited training data, we look at the graph based inductive semi-supervised learning methods to propagate the labels among the unlabeled samples. In the semi-supervised approach, we represent each instance in the data set as a node in the graph. Since it is a complete graph, edges interconnect these nodes, with each edge having some weight representing the similarity between the points. We propagate the labels in this graph, based on the proximity of the data points to the labeled nodes. We estimate the performance of these algorithms by measuring how close the probability distribution of the data after label propagation is to the probability distribution of the ground truth data. Since labeling has a cost associated with it, in this thesis we propose two algorithms that help us in selecting minimum number of labeled points to propagate the labels accurately. Our proposed algorithm achieves a maximum of 73% increase in performance when compared to the baseline algorithm.
ContributorsDesai, Vaishnav (Author) / Sundaram, Hari (Thesis advisor) / Li, Baoxin (Thesis advisor) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2013
Description
"Romantic Cyber-Engagement" offers a new type of dissertation organized around three projects that combine the core values of the Digital Humanities with the hypertext tradition of scholarly pursuits in the field of Romanticism. The first of the three Digital Humanities contributions is to the profession. "A Resource for the Future: The ICR Template and Template Guide" articulates a template for the construction and operation of an advanced conference in Romantic studies. This part of the project includes the conference web site template and guide, which is publicly available to all interested organizations; the template guide includes instructions, tutorials, and advice to govern modification of the template for easier adaptation for future conferences. The second project, "Collaborative Literature Projects in the Digital Age: The Frankenstein Project" is a functional pedagogical example of one way to incorporate Digital Humanities praxis as an interactive part of a college course. This part of the dissertation explains the "Frankenstein Project," a web site that I created for an undergraduate critical theory course where the students contributed various critical approaches for sections of the novel Frankenstein; or, The Modern Prometheus. The final project, "'[W]hat they half-create, / And what perceive': The Creation of a Hypertext Scholarly Edition of 'Tintern Abbey;'" is a critical approaches section in which I created an interactive web site that focused on the primary work, "Lines Written a Few Miles above Tintern Abbey: On Revisiting the Banks of the Wye during a Tour, July 13, 1798." This advanced, multimodal site allows viewers to examine various critical approaches to each section of the primary work, and the viewer/reader can interactively engage the text in dialogue by contributing their own interpretation or critical approach. In addition to the three products and analysis generated from this dissertation, the project as a whole offers an initial Digital Humanities model for future dissertations in discipline of English Literature.
ContributorsMatsunaga, Bruce (Author) / Lussier, Mark S (Thesis advisor) / Broglio, Ronald (Committee member) / Wright, Johnson K (Committee member) / Arizona State University (Publisher)
Created2013
Description
Answer Set Programming (ASP) is one of the most prominent and successful knowledge representation paradigms. The success of ASP is due to its expressive non-monotonic modeling language and its efficient computational methods originating from building propositional satisfiability solvers. The wide adoption of ASP has motivated several extensions to its modeling language in order to enhance expressivity, such as incorporating aggregates and interfaces with ontologies. Also, in order to overcome the grounding bottleneck of computation in ASP, there are increasing interests in integrating ASP with other computing paradigms, such as Constraint Programming (CP) and Satisfiability Modulo Theories (SMT). Due to the non-monotonic nature of the ASP semantics, such enhancements turned out to be non-trivial and the existing extensions are not fully satisfactory. We observe that one main reason for the difficulties rooted in the propositional semantics of ASP, which is limited in handling first-order constructs (such as aggregates and ontologies) and functions (such as constraint variables in CP and SMT) in natural ways. This dissertation presents a unifying view on these extensions by viewing them as instances of formulas with generalized quantifiers and intensional functions. We extend the first-order stable model semantics by by Ferraris, Lee, and Lifschitz to allow generalized quantifiers, which cover aggregate, DL-atoms, constraints and SMT theory atoms as special cases. Using this unifying framework, we study and relate different extensions of ASP. We also present a tight integration of ASP with SMT, based on which we enhance action language C+ to handle reasoning about continuous changes. Our framework yields a systematic approach to study and extend non-monotonic languages.
ContributorsMeng, Yunsong (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Fainekos, Georgios (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2013
Description
In Everything I See Your Hand is a collection of short stories that takes place in the "Little Armenia" neighborhood of East Hollywood, California--an ethnic enclave made up of immigrants from the former Soviet state who came to Los Angeles following the collapse of the USSR in the early '90s. These fictions are rooted in my own personal experience and are about dispossession, domesticity, and the tangled ties between generations, focusing particularly around the tensions that arose from assimilation and disillusionment, from changing attitudes towards sex and homosexuality, violence and masculinity. Many of the stories grapple with the idea of self-exile, or ruminate on the difference between leaving the motherland, and leaving the mother, or other familial bodies, in order to pursue grander desires: a better life in America, superior education in distant universities, love in marriages with foreigners, etc. The body, therefore, becomes a central motif in the collection, principally the hands and forehead, which are traditionally areas in which the destinies are written for the Armenian people. The Armenian-American protagonists of In Everything I See Your Hand struggle with the belief that their lives are already written, their futures already decided, futures that they can only escape through death or departure--if they can escape them at all.
ContributorsKuzmich, Naira (Author) / McNally, Thomas (Thesis advisor) / Ison, Tara (Committee member) / Pritchard, Melissa (Committee member) / Arizona State University (Publisher)
Created2013
Description
Jazz continues, into its second century, as one of the most important musics taught in public middle and high schools. Even so, research related to how students learn, especially in their earliest interactions with jazz culture, is limited. Weaving together interviews and observations of junior and senior high school jazz players and teachers, private studio instructors, current university students majoring in jazz, and university and college jazz faculty, I developed a composite sketch of a secondary school student learning to play jazz. Using arts-based educational research methods, including the use of narrative inquiry and literary non-fiction, the status of current jazz education and the experiences by novice jazz learners is explored. What emerges is a complex story of students and teachers negotiating the landscape of jazz in and out of early twenty-first century public schools. Suggestions for enhancing jazz experiences for all stakeholders follow, focusing on access and the preparation of future jazz teachers.
ContributorsKelly, Keith B (Author) / Stauffer, Sandra (Thesis advisor) / Tobias, Evan (Committee member) / Kocour, Michael (Committee member) / Sullivan, Jill (Committee member) / Schmidt, Margaret (Committee member) / Arizona State University (Publisher)
Created2013
Description
Over 2 billion people are using online social network services, such as Facebook, Twitter, Google+, LinkedIn, and Pinterest. Users update their status, post their photos, share their information, and chat with others in these social network sites every day; however, not everyone shares the same amount of information. This thesis explores methods of linking publicly available data sources as a means of extrapolating missing information of Facebook. An application named "Visual Friends Income Map" has been created on Facebook to collect social network data and explore geodemographic properties to link publicly available data, such as the US census data. Multiple predictors are implemented to link data sets and extrapolate missing information from Facebook with accurate predictions. The location based predictor matches Facebook users' locations with census data at the city level for income and demographic predictions. Age and relationship based predictors are created to improve the accuracy of the proposed location based predictor utilizing social network link information. In the case where a user does not share any location information on their Facebook profile, a kernel density estimation location predictor is created. This predictor utilizes publicly available telephone record information of all people with the same surname of this user in the US to create a likelihood distribution of the user's location. This is combined with the user's IP level information in order to narrow the probability estimation down to a local regional constraint.
ContributorsMao, Jingxian (Author) / Maciejewski, Ross (Thesis advisor) / Farin, Gerald (Committee member) / Wang, Yalin (Committee member) / Arizona State University (Publisher)
Created2012
Description
With the rapid development of mobile sensing technologies like GPS, RFID, sensors in smartphones, etc., capturing position data in the form of trajectories has become easy. Moving object trajectory analysis is a growing area of interest these days owing to its applications in various domains such as marketing, security, traffic monitoring and management, etc. To better understand movement behaviors from the raw mobility data, this doctoral work provides analytic models for analyzing trajectory data. As a first contribution, a model is developed to detect changes in trajectories with time. If the taxis moving in a city are viewed as sensors that provide real time information of the traffic in the city, a change in these trajectories with time can reveal that the road network has changed. To detect changes, trajectories are modeled with a Hidden Markov Model (HMM). A modified training algorithm, for parameter estimation in HMM, called m-BaumWelch, is used to develop likelihood estimates under assumed changes and used to detect changes in trajectory data with time. Data from vehicles are used to test the method for change detection. Secondly, sequential pattern mining is used to develop a model to detect changes in frequent patterns occurring in trajectory data. The aim is to answer two questions: Are the frequent patterns still frequent in the new data? If they are frequent, has the time interval distribution in the pattern changed? Two different approaches are considered for change detection, frequency-based approach and distribution-based approach. The methods are illustrated with vehicle trajectory data. Finally, a model is developed for clustering and outlier detection in semantic trajectories. A challenge with clustering semantic trajectories is that both numeric and categorical attributes are present. Another problem to be addressed while clustering is that trajectories can be of different lengths and also have missing values. A tree-based ensemble is used to address these problems. The approach is extended to outlier detection in semantic trajectories.
ContributorsKondaveeti, Anirudh (Author) / Runger, George C. (Thesis advisor) / Mirchandani, Pitu (Committee member) / Pan, Rong (Committee member) / Maciejewski, Ross (Committee member) / Arizona State University (Publisher)
Created2012
Description
This dissertation makes the case to reclaim the typically negative term, coterie, as a poetic method and offers the epithalamium as a valuable object for the study of coterie conditions and values. This examination of the historical poetics of the epithalamium shows how the form was reappropriated by gay postwar poets and those in related social circumstances. This study applies and builds on theories developed by Arthur Marotti (John Donne: Coterie Poet), and Lytle Shaw (Frank O'Hara: The Poetics of Coterie) and subsequent critics to develop a coterie poetics, the markers and terms for which I have arranged here to demonstrate conscious "sociable" poetics. It is thus to our advantage to study coterie conditions and methods to open readers to insights into twentieth-century poets that have deliberately exploited reception among those in private and public spheres, just as their Early-Modern precursors did--often as a matter of survival, but also as formative practice. The key figures in this study wrote significant epithalamia or made major theoretical claims for coterie poetics: John Donne (1572-1631), W. H. Auden (1907-1973), Paul Goodman (1910-1972), and Frank O'Hara (1926-1966). O'Hara's poetry is approached as the apex of coterie poetics; his personal immediacy and obscure personal references should alienate and exclude--yet, they invite.
ContributorsEisenberg, Jeremy (Author) / Horan, Elizabeth (Thesis advisor) / Hogue, Cynthia (Committee member) / Sturges, Robert (Committee member) / Arizona State University (Publisher)
Created2012
Description
The focus of this document is the examination of a new robot simulator developed to aid students in learning robotics programming and provide the ability to test their programs in a simulated world. The simulator, accessed via a website, provides a simulated environment, programming interface, and the ability to control a simulated robot. The simulated environment consists of a user-customizable maze and a robot, which can be controlled manually, via Web service, or by utilizing the Web programming interface. The Web programming interface provides dropdown boxes from which the users may select various options to program their implementations. It is designed to aid new students in the learning of basic skills and thought processes used to program robots. Data was collected and analyzed to determine how effective this system is in helping students learn. This included how quickly students were able to program the algorithms assigned to them and how many lines of code were used to implement them. Students' performance was also monitored to determine how well they were able to use the program and if there were any significant problems. The students also completed surveys to communicate how well the website helped them learn and understand various concepts. The data collected shows that the website was a helpful learning tool for the students and that they were able to use the programming interface quickly and effectively.
ContributorsDrown, Garrett (Author) / Tsai, Wei-Tek (Thesis advisor) / Chen, Yinong (Thesis advisor) / Claveau, David (Committee member) / Arizona State University (Publisher)
Created2012