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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- Genre: Doctoral Dissertation
Description
Genomic and proteomic sequences, which are in the form of deoxyribonucleic acid (DNA) and amino acids respectively, play a vital role in the structure, function and diversity of every living cell. As a result, various genomic and proteomic sequence processing methods have been proposed from diverse disciplines, including biology, chemistry, physics, computer science and electrical engineering. In particular, signal processing techniques were applied to the problems of sequence querying and alignment, that compare and classify regions of similarity in the sequences based on their composition. However, although current approaches obtain results that can be attributed to key biological properties, they require pre-processing and lack robustness to sequence repetitions. In addition, these approaches do not provide much support for efficiently querying sub-sequences, a process that is essential for tracking localized database matches. In this work, a query-based alignment method for biological sequences that maps sequences to time-domain waveforms before processing the waveforms for alignment in the time-frequency plane is first proposed. The mapping uses waveforms, such as time-domain Gaussian functions, with unique sequence representations in the time-frequency plane. The proposed alignment method employs a robust querying algorithm that utilizes a time-frequency signal expansion whose basis function is matched to the basic waveform in the mapped sequences. The resulting WAVEQuery approach is demonstrated for both DNA and protein sequences using the matching pursuit decomposition as the signal basis expansion. The alignment localization of WAVEQuery is specifically evaluated over repetitive database segments, and operable in real-time without pre-processing. It is demonstrated that WAVEQuery significantly outperforms the biological sequence alignment method BLAST for queries with repetitive segments for DNA sequences. A generalized version of the WAVEQuery approach with the metaplectic transform is also described for protein sequence structure prediction. For protein alignment, it is often necessary to not only compare the one-dimensional (1-D) primary sequence structure but also the secondary and tertiary three-dimensional (3-D) space structures. This is done after considering the conformations in the 3-D space due to the degrees of freedom of these structures. As a result, a novel directionality based 3-D waveform mapping for the 3-D protein structures is also proposed and it is used to compare protein structures using a matched filter approach. By incorporating a 3-D time axis, a highly-localized Gaussian-windowed chirp waveform is defined, and the amino acid information is mapped to the chirp parameters that are then directly used to obtain directionality in the 3-D space. This mapping is unique in that additional characteristic protein information such as hydrophobicity, that relates the sequence with the structure, can be added as another representation parameter. The additional parameter helps tracking similarities over local segments of the structure, this enabling classification of distantly related proteins which have partial structural similarities. This approach is successfully tested for pairwise alignments over full length structures, alignments over multiple structures to form a phylogenetic trees, and also alignments over local segments. Also, basic classification over protein structural classes using directional descriptors for the protein structure is performed.
ContributorsRavichandran, Lakshminarayan (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Spanias, Andreas S (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Lacroix, Zoé (Committee member) / Arizona State University (Publisher)
Created2011
Description
Structural integrity is an important characteristic of performance for critical components used in applications such as aeronautics, materials, construction and transportation. When appraising the structural integrity of these components, evaluation methods must be accurate. In addition to possessing capability to perform damage detection, the ability to monitor the level of damage over time can provide extremely useful information in assessing the operational worthiness of a structure and in determining whether the structure should be repaired or removed from service. In this work, a sequential Bayesian approach with active sensing is employed for monitoring crack growth within fatigue-loaded materials. The monitoring approach is based on predicting crack damage state dynamics and modeling crack length observations. Since fatigue loading of a structural component can change while in service, an interacting multiple model technique is employed to estimate probabilities of different loading modes and incorporate this information in the crack length estimation problem. For the observation model, features are obtained from regions of high signal energy in the time-frequency plane and modeled for each crack length damage condition. Although this observation model approach exhibits high classification accuracy, the resolution characteristics can change depending upon the extent of the damage. Therefore, several different transmission waveforms and receiver sensors are considered to create multiple modes for making observations of crack damage. Resolution characteristics of the different observation modes are assessed using a predicted mean squared error criterion and observations are obtained using the predicted, optimal observation modes based on these characteristics. Calculation of the predicted mean square error metric can be computationally intensive, especially if performed in real time, and an approximation method is proposed. With this approach, the real time computational burden is decreased significantly and the number of possible observation modes can be increased. Using sensor measurements from real experiments, the overall sequential Bayesian estimation approach, with the adaptive capability of varying the state dynamics and observation modes, is demonstrated for tracking crack damage.
ContributorsHuff, Daniel W (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Kovvali, Narayan (Committee member) / Chakrabarti, Chaitali (Committee member) / Chattopadhyay, Aditi (Committee member) / Arizona State University (Publisher)
Created2013
Description
Adaptive processing and classification of electrocardiogram (ECG) signals are important in eliminating the strenuous process of manually annotating ECG recordings for clinical use. Such algorithms require robust models whose parameters can adequately describe the ECG signals. Although different dynamic statistical models describing ECG signals currently exist, they depend considerably on a priori information and user-specified model parameters. Also, ECG beat morphologies, which vary greatly across patients and disease states, cannot be uniquely characterized by a single model. In this work, sequential Bayesian based methods are used to appropriately model and adaptively select the corresponding model parameters of ECG signals. An adaptive framework based on a sequential Bayesian tracking method is proposed to adaptively select the cardiac parameters that minimize the estimation error, thus precluding the need for pre-processing. Simulations using real ECG data from the online Physionet database demonstrate the improvement in performance of the proposed algorithm in accurately estimating critical heart disease parameters. In addition, two new approaches to ECG modeling are presented using the interacting multiple model and the sequential Markov chain Monte Carlo technique with adaptive model selection. Both these methods can adaptively choose between different models for various ECG beat morphologies without requiring prior ECG information, as demonstrated by using real ECG signals. A supervised Bayesian maximum-likelihood (ML) based classifier uses the estimated model parameters to classify different types of cardiac arrhythmias. However, the non-availability of sufficient amounts of representative training data and the large inter-patient variability pose a challenge to the existing supervised learning algorithms, resulting in a poor classification performance. In addition, recently developed unsupervised learning methods require a priori knowledge on the number of diseases to cluster the ECG data, which often evolves over time. In order to address these issues, an adaptive learning ECG classification method that uses Dirichlet process Gaussian mixture models is proposed. This approach does not place any restriction on the number of disease classes, nor does it require any training data. This algorithm is adapted to be patient-specific by labeling or identifying the generated mixtures using the Bayesian ML method, assuming the availability of labeled training data.
ContributorsEdla, Shwetha Reddy (Author) / Papandreou-Suppappola, Antonia (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Kovvali, Narayan (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Characterization of standard cells is one of the crucial steps in the IC design. Scaling of CMOS technology has lead to timing un-certainties such as that of cross coupling noise due to interconnect parasitic, skew variation due to voltage jitter and proximity effect of multiple inputs switching (MIS). Due to increased operating frequency and process variation, the probability of MIS occurrence and setup / hold failure within a clock cycle is high. The delay variation due to temporal proximity of MIS is significant for multiple input gates in the standard cell library. The shortest paths are affected by MIS due to the lack of averaging effect. Thus, sensitive designs such as that of SRAM row and column decoder circuits have high probability for MIS impact. The traditional static timing analysis (STA) assumes single input switching (SIS) scenario which is not adequate enough to capture gate delay accurately, as the delay variation due to temporal proximity of the MIS is ~15%-45%. Whereas, considering all possible scenarios of MIS for characterization is computationally intensive with huge data volume. Various modeling techniques are developed for the characterization of MIS effect. Some techniques require coefficient extraction through multiple spice simulation, and do not discuss speed up approach or apply models with complicated algorithms to account for MIS effect. The STA flow accounts for process variation through uncertainty parameter to improve product yield. Some of the MIS delay variability models account for MIS variation through table look up approach, resulting in huge data volume or do not consider propagation of RAT in the design flow. Thus, there is a need for a methodology to model MIS effect with less computational resource, and integration of such effect into design flow without trading off the accuracy. A finite-point based analytical model for MIS effect is proposed for multiple input logic gates and similar approach is extended for setup/hold characterization of sequential elements. Integration of MIS variation into design flow is explored. The proposed methodology is validated using benchmark circuits at 45nm technology node under process variation. Experimental results show significant reduction in runtime and data volume with ~10% error compared to that of SPICE simulation.
ContributorsSubramaniam, Anupama R (Author) / Cao, Yu (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Roveda, Janet (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Multicore processors have proliferated in nearly all forms of computing, from servers, desktop, to smartphones. The primary reason for this large adoption of multicore processors is due to its ability to overcome the power-wall by providing higher performance at a lower power consumption rate. With multi-cores, there is increased need for dynamic energy management (DEM), much more than for single-core processors, as DEM for multi-cores is no more a mechanism just to ensure that a processor is kept under specified temperature limits, but also a set of techniques that manage various processor controls like dynamic voltage and frequency scaling (DVFS), task migration, fan speed, etc. to achieve a stated objective. The objectives span a wide range from maximizing throughput, minimizing power consumption, reducing peak temperature, maximizing energy efficiency, maximizing processor reliability, and so on, along with much more wider constraints of temperature, power, timing, and reliability constraints. Thus DEM can be very complex and challenging to achieve. Since often times many DEMs operate together on a single processor, there is a need to unify various DEM techniques. This dissertation address such a need. In this work, a framework for DEM is proposed that provides a unifying processor model that includes processor power, thermal, timing, and reliability models, supports various DEM control mechanisms, many different objective functions along with equally diverse constraint specifications. Using the framework, a range of novel solutions is derived for instances of DEM problems, that include maximizing processor performance, energy efficiency, or minimizing power consumption, peak temperature under constraints of maximum temperature, memory reliability and task deadlines. Finally, a robust closed-loop controller to implement the above solutions on a real processor platform with a very low operational overhead is proposed. Along with the controller design, a model identification methodology for obtaining the required power and thermal models for the controller is also discussed. The controller is architecture independent and hence easily portable across many platforms. The controller has been successfully deployed on Intel Sandy Bridge processor and the use of the controller has increased the energy efficiency of the processor by over 30%
ContributorsHanumaiah, Vinay (Author) / Vrudhula, Sarma (Thesis advisor) / Chatha, Karamvir (Committee member) / Chakrabarti, Chaitali (Committee member) / Rodriguez, Armando (Committee member) / Askin, Ronald (Committee member) / Arizona State University (Publisher)
Created2013
Description
We are expecting hundreds of cores per chip in the near future. However, scaling the memory architecture in manycore architectures becomes a major challenge. Cache coherence provides a single image of memory at any time in execution to all the cores, yet coherent cache architectures are believed will not scale to hundreds and thousands of cores. In addition, caches and coherence logic already take 20-50% of the total power consumption of the processor and 30-60% of die area. Therefore, a more scalable architecture is needed for manycore architectures. Software Managed Manycore (SMM) architectures emerge as a solution. They have scalable memory design in which each core has direct access to only its local scratchpad memory, and any data transfers to/from other memories must be done explicitly in the application using Direct Memory Access (DMA) commands. Lack of automatic memory management in the hardware makes such architectures extremely power-efficient, but they also become difficult to program. If the code/data of the task mapped onto a core cannot fit in the local scratchpad memory, then DMA calls must be added to bring in the code/data before it is required, and it may need to be evicted after its use. However, doing this adds a lot of complexity to the programmer's job. Now programmers must worry about data management, on top of worrying about the functional correctness of the program - which is already quite complex. This dissertation presents a comprehensive compiler and runtime integration to automatically manage the code and data of each task in the limited local memory of the core. We firstly developed a Complete Circular Stack Management. It manages stack frames between the local memory and the main memory, and addresses the stack pointer problem as well. Though it works, we found we could further optimize the management for most cases. Thus a Smart Stack Data Management (SSDM) is provided. In this work, we formulate the stack data management problem and propose a greedy algorithm for the same. Later on, we propose a general cost estimation algorithm, based on which CMSM heuristic for code mapping problem is developed. Finally, heap data is dynamic in nature and therefore it is hard to manage it. We provide two schemes to manage unlimited amount of heap data in constant sized region in the local memory. In addition to those separate schemes for different kinds of data, we also provide a memory partition methodology.
ContributorsBai, Ke (Author) / Shrivastava, Aviral (Thesis advisor) / Chatha, Karamvir (Committee member) / Xue, Guoliang (Committee member) / Chakrabarti, Chaitali (Committee member) / Arizona State University (Publisher)
Created2014
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
In recent years, we have observed the prevalence of stream applications in many embedded domains. Stream programs distinguish themselves from traditional sequential programming languages through well defined independent actors, explicit data communication, and stable code/data access patterns. In order to achieve high performance and low power, scratch pad memory (SPM) has been introduced in today's embedded multicore processors. Current design frameworks for developing stream applications on SPM enhanced embedded architectures typically do not include a compiler that can perform automatic partitioning, mapping and scheduling under limited on-chip SPM capacities and memory access delays. Consequently, many designs are implemented manually, which leads to lengthy tasks and inferior designs. In this work, optimization techniques that automatically compile stream programs onto embedded multi-core architectures are proposed. As an initial case study, we implemented an automatic target recognition (ATR) algorithm on the IBM Cell Broadband Engine (BE). Then integer linear programming (ILP) and heuristic approaches were proposed to schedule stream programs on a single core embedded processor that has an SPM with code overlay. Later, ILP and heuristic approaches for Compiling Stream programs on SPM enhanced Multicore Processors (CSMP) were studied. The proposed CSMP ILP and heuristic approaches do not optimize for cycles in stream applications. Further, the number of software pipeline stages in the implementation is dependent on actor to processing engine (PE) mapping and is uncontrollable. We next presented a Retiming technique for Throughput optimization on Embedded Multi-core processors (RTEM). RTEM approach inherently handles cycles and can accept an upper bound on the number of software pipeline stages to be generated. We further enhanced RTEM by incorporating unrolling (URSTEM) that preserves all the beneficial properties of RTEM heuristic and also scales with the number of PEs through unrolling.
ContributorsChe, Weijia (Author) / Chatha, Karam Singh (Thesis advisor) / Vrudhula, Sarma (Committee member) / Chakrabarti, Chaitali (Committee member) / Shrivastava, Aviral (Committee member) / Arizona State University (Publisher)
Created2012
Description
Negative bias temperature instability (NBTI) is a leading aging mechanism in modern digital and analog circuits. Recent NBTI data exhibits an excessive amount of randomness and fast recovery, which are difficult to be handled by conventional power-law model (tn). Such discrepancies further pose the challenge on long-term reliability prediction under statistical variations and Dynamic Voltage Scaling (DVS) in real circuit operation. To overcome these barriers, the modeling effort in this work (1) practically explains the aging statistics due to randomness in number of traps with log(t) model, accurately predicting the mean and variance shift; (2) proposes cycle-to-cycle model (from the first-principle of trapping) to handle aging under multiple supply voltages, predicting the non-monotonic behavior under DVS (3) presents a long-term model to estimate a tight upper bound of dynamic aging over multiple cycles, and (4) comprehensively validates the new set of aging models with 65nm statistical silicon data. Compared to previous models, the new set of aging models capture the aging variability and the essential role of the recovery phase under DVS, reducing unnecessary guard-banding during the design stage. With CMOS technology scaling, design for reliability has become an important step in the design cycle, and increased the need for efficient and accurate aging simulation methods during the design stage. NBTI induced delay shifts in logic paths are asymmetric in nature, as opposed to averaging effect due to recovery assumed in traditional aging analysis. Timing violations due to aging, in particular, are very sensitive to the standby operation regime of a digital circuit. In this report, by identifying the critical moments in circuit operation and considering the asymmetric aging effects, timing violations under NBTI effect are correctly predicted. The unique contributions of the simulation flow include: (1) accurate modeling of aging induced delay shift due to threshold voltage (Vth) shift using only the delay dependence on supply voltage from cell library; (2) simulation flow for asymmetric aging analysis is proposed and conducted at critical points in circuit operation; (3) setup and hold timing violations due to NBTI aging in logic and clock buffer are investigated in sequential circuits and (4) proposed framework is tested in VLSI applications such DDR memory circuits. This methodology is comprehensively demonstrated with ISCAS89 benchmark circuits using a 45nm Nangate standard cell library characterized using predictive technology models. Our proposed design margin assessment provides design insights and enables resilient techniques for mitigating digital circuit aging.
ContributorsVelamala, Jyothi Bhaskarr (Author) / Cao, Yu (Thesis advisor) / Clark, Lawrence (Committee member) / Chakrabarti, Chaitali (Committee member) / Yu, Hongbin (Committee member) / Arizona State University (Publisher)
Created2012
Description
Thousands of high-resolution images are generated each day. Segmenting, classifying, and analyzing the contents of these images are the key steps in image understanding. This thesis focuses on image segmentation and classification and its applications in synthetic, texture, natural, biomedical, and industrial images. A robust level-set-based multi-region and texture image segmentation approach is proposed in this thesis to tackle most of the challenges in the existing multi-region segmentation methods, including computational complexity and sensitivity to initialization. Medical image analysis helps in understanding biological processes and disease pathologies. In this thesis, two cell evolution analysis schemes are proposed for cell cluster extraction in order to analyze cell migration, cell proliferation, and cell dispersion in different cancer cell images. The proposed schemes accurately segment both the cell cluster area and the individual cells inside and outside the cell cluster area. The method is currently used by different cell biology labs to study the behavior of cancer cells, which helps in drug discovery. Defects can cause failure to motherboards, processors, and semiconductor units. An automatic defect detection and classification methodology is very desirable in many industrial applications. This helps in producing consistent results, facilitating the processing, speeding up the processing time, and reducing the cost. In this thesis, three defect detection and classification schemes are proposed to automatically detect and classify different defects related to semiconductor unit images. The first proposed defect detection scheme is used to detect and classify the solder balls in the processor sockets as either defective (Non-Wet) or non-defective. The method produces a 96% classification rate and saves 89% of the time used by the operator. The second proposed defect detection scheme is used for detecting and measuring voids inside solder balls of different boards and products. The third proposed defect detection scheme is used to detect different defects in the die area of semiconductor unit images such as cracks, scratches, foreign materials, fingerprints, and stains. The three proposed defect detection schemes give high accuracy and are inexpensive to implement compared to the existing high cost state-of-the-art machines.
ContributorsSaid, Asaad F (Author) / Karam, Lina (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Patel, Nital (Committee member) / Arizona State University (Publisher)
Created2010