Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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- Creators: Malin, Anna
- Creators: Turaga, Pavan
Description
Immunosignaturing is a medical test for assessing the health status of a patient by applying microarrays of random sequence peptides to determine the patient's immune fingerprint by associating antibodies from a biological sample to immune responses. The immunosignature measurements can potentially provide pre-symptomatic diagnosis for infectious diseases or detection of biological threats. Currently, traditional bioinformatics tools, such as data mining classification algorithms, are used to process the large amount of peptide microarray data. However, these methods generally require training data and do not adapt to changing immune conditions or additional patient information. This work proposes advanced processing techniques to improve the classification and identification of single and multiple underlying immune response states embedded in immunosignatures, making it possible to detect both known and previously unknown diseases or biothreat agents. Novel adaptive learning methodologies for un- supervised and semi-supervised clustering integrated with immunosignature feature extraction approaches are proposed. The techniques are based on extracting novel stochastic features from microarray binding intensities and use Dirichlet process Gaussian mixture models to adaptively cluster the immunosignatures in the feature space. This learning-while-clustering approach allows continuous discovery of antibody activity by adaptively detecting new disease states, with limited a priori disease or patient information. A beta process factor analysis model to determine underlying patient immune responses is also proposed to further improve the adaptive clustering performance by formatting new relationships between patients and antibody activity. In order to extend the clustering methods for diagnosing multiple states in a patient, the adaptive hierarchical Dirichlet process is integrated with modified beta process factor analysis latent feature modeling to identify relationships between patients and infectious agents. The use of Bayesian nonparametric adaptive learning techniques allows for further clustering if additional patient data is received. Significant improvements in feature identification and immune response clustering are demonstrated using samples from patients with different diseases.
ContributorsMalin, Anna (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel (Committee member) / Chakrabarti, Chaitali (Committee member) / Kovvali, Narayan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2013
Description
This work examines two main areas in model-based time-varying signal processing with emphasis in speech processing applications. The first area concentrates on improving speech intelligibility and on increasing the proposed methodologies application for clinical practice in speech-language pathology. The second area concentrates on signal expansions matched to physical-based models but without requiring independent basis functions; the significance of this work is demonstrated with speech vowels.
A fully automated Vowel Space Area (VSA) computation method is proposed that can be applied to any type of speech. It is shown that the VSA provides an efficient and reliable measure and is correlated to speech intelligibility. A clinical tool that incorporates the automated VSA was proposed for evaluation and treatment to be used by speech language pathologists. Two exploratory studies are performed using two databases by analyzing mean formant trajectories in healthy speech for a wide range of speakers, dialects, and coarticulation contexts. It is shown that phonemes crowded in formant space can often have distinct trajectories, possibly due to accurate perception.
A theory for analyzing time-varying signals models with amplitude modulation and frequency modulation is developed. Examples are provided that demonstrate other possible signal model decompositions with independent basis functions and corresponding physical interpretations. The Hilbert transform (HT) and the use of the analytic form of a signal are motivated, and a proof is provided to show that a signal can still preserve desirable mathematical properties without the use of the HT. A visualization of the Hilbert spectrum is proposed to aid in the interpretation. A signal demodulation is proposed and used to develop a modified Empirical Mode Decomposition (EMD) algorithm.
A fully automated Vowel Space Area (VSA) computation method is proposed that can be applied to any type of speech. It is shown that the VSA provides an efficient and reliable measure and is correlated to speech intelligibility. A clinical tool that incorporates the automated VSA was proposed for evaluation and treatment to be used by speech language pathologists. Two exploratory studies are performed using two databases by analyzing mean formant trajectories in healthy speech for a wide range of speakers, dialects, and coarticulation contexts. It is shown that phonemes crowded in formant space can often have distinct trajectories, possibly due to accurate perception.
A theory for analyzing time-varying signals models with amplitude modulation and frequency modulation is developed. Examples are provided that demonstrate other possible signal model decompositions with independent basis functions and corresponding physical interpretations. The Hilbert transform (HT) and the use of the analytic form of a signal are motivated, and a proof is provided to show that a signal can still preserve desirable mathematical properties without the use of the HT. A visualization of the Hilbert spectrum is proposed to aid in the interpretation. A signal demodulation is proposed and used to develop a modified Empirical Mode Decomposition (EMD) algorithm.
ContributorsSandoval, Steven, 1984- (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Liss, Julie M (Committee member) / Turaga, Pavan (Committee member) / Kovvali, Narayan (Committee member) / Arizona State University (Publisher)
Created2016