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- All Subjects: artificial intelligence
- All Subjects: engineering
- Creators: Davulcu, Hasan
- Creators: Chakrabarti, Chaitali
- Member of: ASU Electronic Theses and Dissertations
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
The increasing popularity of Twitter renders improved trustworthiness and relevance assessment of tweets much more important for search. However, given the limitations on the size of tweets, it is hard to extract measures for ranking from the tweet's content alone. I propose a method of ranking tweets by generating a reputation score for each tweet that is based not just on content, but also additional information from the Twitter ecosystem that consists of users, tweets, and the web pages that tweets link to. This information is obtained by modeling the Twitter ecosystem as a three-layer graph. The reputation score is used to power two novel methods of ranking tweets by propagating the reputation over an agreement graph based on tweets' content similarity. Additionally, I show how the agreement graph helps counter tweet spam. An evaluation of my method on 16~million tweets from the TREC 2011 Microblog Dataset shows that it doubles the precision over baseline Twitter Search and achieves higher precision than current state of the art method. I present a detailed internal empirical evaluation of RAProp in comparison to several alternative approaches proposed by me, as well as external evaluation in comparison to the current state of the art method.
ContributorsRavikumar, Srijith (Author) / Kambhampati, Subbarao (Thesis advisor) / Davulcu, Hasan (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2013
Description
There has been a lot of research in the field of artificial intelligence about thinking machines. Alan Turing proposed a test to observe a machine's intelligent behaviour with respect to natural language conversation. The Winograd schema challenge is suggested as an alternative, to the Turing test. It needs inferencing capabilities, reasoning abilities and background knowledge to get the answer right. It involves a coreference resolution task in which a machine is given a sentence containing a situation which involves two entities, one pronoun and some more information about the situation and the machine has to come up with the right resolution of a pronoun to one of the entities. The complexity of the task is increased with the fact that the Winograd sentences are not constrained by one domain or specific sentence structure and it also contains a lot of human proper names. This modification makes the task of association of entities, to one particular word in the sentence, to derive the answer, difficult. I have developed a pronoun resolver system for the confined domain Winograd sentences. I have developed a classifier or filter which takes input sentences and decides to accept or reject them based on a particular criteria. Once the sentence is accepted. I run parsers on it to obtain the detailed analysis. Furthermore I have developed four answering modules which use world knowledge and inferencing mechanisms to try and resolve the pronoun. The four techniques I use are : ConceptNet knowledgebase, Search engine pattern counts,Narrative event chains and sentiment analysis. I have developed a particular aggregation mechanism for the answers from these modules to arrive at a final answer. I have used caching technique for the association relations that I obtain for different modules, so as to boost the performance. I run my system on the standard ‘nyu dataset’ of Winograd sentences and questions. This dataset is then restricted, by my classifier, to 90 sentences. I evaluate my system on this 90 sentence dataset. When I compare my results against the state of the art system on the same dataset, I get nearly 4.5 % improvement in the restricted domain.
ContributorsBudukh, Tejas Ulhas (Author) / Baral, Chitta (Thesis advisor) / VanLehn, Kurt (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013
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
With increasing transistor volume and reducing feature size, it has become a major design constraint to reduce power consumption also. This has given rise to aggressive architectural changes for on-chip power management and rapid development to energy efficient hardware accelerators. Accordingly, the objective of this research work is to facilitate software developers to leverage these hardware techniques and improve energy efficiency of the system. To achieve this, I propose two solutions for Linux kernel: Optimal use of these architectural enhancements to achieve greater energy efficiency requires accurate modeling of processor power consumption. Though there are many models available in literature to model processor power consumption, there is a lack of such models to capture power consumption at the task-level. Task-level energy models are a requirement for an operating system (OS) to perform real-time power management as OS time multiplexes tasks to enable sharing of hardware resources. I propose a detailed design methodology for constructing an architecture agnostic task-level power model and incorporating it into a modern operating system to build an online task-level power profiler. The profiler is implemented inside the latest Linux kernel and validated for Intel Sandy Bridge processor. It has a negligible overhead of less than 1\% hardware resource consumption. The profiler power prediction was demonstrated for various application benchmarks from SPEC to PARSEC with less than 4\% error. I also demonstrate the importance of the proposed profiler for emerging architectural techniques through use case scenarios, which include heterogeneous computing and fine grained per-core DVFS. Along with architectural enhancement in general purpose processors to improve energy efficiency, hardware accelerators like Coarse Grain reconfigurable architecture (CGRA) are gaining popularity. Unlike vector processors, which rely on data parallelism, CGRA can provide greater flexibility and compiler level control making it more suitable for present SoC environment. To provide streamline development environment for CGRA, I propose a flexible framework in Linux to do design space exploration for CGRA. With accurate and flexible hardware models, fine grained integration with accurate architectural simulator, and Linux memory management and DMA support, a user can carry out limitless experiments on CGRA in full system environment.
ContributorsDesai, Digant Pareshkumar (Author) / Vrudhula, Sarma (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Wu, Carole-Jean (Committee member) / Arizona State University (Publisher)
Created2013
Description
Biological organisms are made up of cells containing numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted, manifesting as disease symptoms. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for activities including diagnosing diseases and drug development. Scientists studying these interconnected processes have identified various pathways involved in drug metabolism, diseases, and signal transduction, etc. High-throughput technologies, new algorithms and speed improvements over the last decade have resulted in deeper knowledge about biological systems, leading to more refined pathways. Such pathways tend to be large and complex, making it difficult for an individual to remember all aspects. Thus, computer models are needed to represent and analyze them. The refinement activity itself requires reasoning with a pathway model by posing queries against it and comparing the results against the real biological system. Many existing models focus on structural and/or factoid questions, relying on surface-level information. These are generally not the kind of questions that a biologist may ask someone to test their understanding of biological processes. Examples of questions requiring understanding of biological processes are available in introductory college level biology text books. Such questions serve as a model for the question answering system developed in this thesis. Thus, the main goal of this thesis is to develop a system that allows the encoding of knowledge about biological pathways to answer questions demonstrating understanding of the pathways. To that end, a language is developed to specify a pathway and pose questions against it. Some existing tools are modified and used to accomplish this goal. The utility of the framework developed in this thesis is illustrated with applications in the biological domain. Finally, the question answering system is used in real world applications by extracting pathway knowledge from text and answering questions related to drug development.
ContributorsAnwar, Saadat (Author) / Baral, Chitta (Thesis advisor) / Inoue, Katsumi (Committee member) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2014
Description
Situations of sensory overload are steadily becoming more frequent as the ubiquity of technology approaches reality--particularly with the advent of socio-communicative smartphone applications, and pervasive, high speed wireless networks. Although the ease of accessing information has improved our communication effectiveness and efficiency, our visual and auditory modalities--those modalities that today's computerized devices and displays largely engage--have become overloaded, creating possibilities for distractions, delays and high cognitive load; which in turn can lead to a loss of situational awareness, increasing chances for life threatening situations such as texting while driving. Surprisingly, alternative modalities for information delivery have seen little exploration. Touch, in particular, is a promising candidate given that it is our largest sensory organ with impressive spatial and temporal acuity. Although some approaches have been proposed for touch-based information delivery, they are not without limitations including high learning curves, limited applicability and/or limited expression. This is largely due to the lack of a versatile, comprehensive design theory--specifically, a theory that addresses the design of touch-based building blocks for expandable, efficient, rich and robust touch languages that are easy to learn and use. Moreover, beyond design, there is a lack of implementation and evaluation theories for such languages. To overcome these limitations, a unified, theoretical framework, inspired by natural, spoken language, is proposed called Somatic ABC's for Articulating (designing), Building (developing) and Confirming (evaluating) touch-based languages. To evaluate the usefulness of Somatic ABC's, its design, implementation and evaluation theories were applied to create communication languages for two very unique application areas: audio described movies and motor learning. These applications were chosen as they presented opportunities for complementing communication by offloading information, typically conveyed visually and/or aurally, to the skin. For both studies, it was found that Somatic ABC's aided the design, development and evaluation of rich somatic languages with distinct and natural communication units.
ContributorsMcDaniel, Troy Lee (Author) / Panchanathan, Sethuraman (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Santello, Marco (Committee member) / Arizona State University (Publisher)
Created2012
Description
Fraud is defined as the utilization of deception for illegal gain by hiding the true nature of the activity. While organizations lose around $3.7 trillion in revenue due to financial crimes and fraud worldwide, they can affect all levels of society significantly. In this dissertation, I focus on credit card fraud in online transactions. Every online transaction comes with a fraud risk and it is the merchant's liability to detect and stop fraudulent transactions. Merchants utilize various mechanisms to prevent and manage fraud such as automated fraud detection systems and manual transaction reviews by expert fraud analysts. Many proposed solutions mostly focus on fraud detection accuracy and ignore financial considerations. Also, the highly effective manual review process is overlooked. First, I propose Profit Optimizing Neural Risk Manager (PONRM), a selective classifier that (a) constitutes optimal collaboration between machine learning models and human expertise under industrial constraints, (b) is cost and profit sensitive. I suggest directions on how to characterize fraudulent behavior and assess the risk of a transaction. I show that my framework outperforms cost-sensitive and cost-insensitive baselines on three real-world merchant datasets. While PONRM is able to work with many supervised learners and obtain convincing results, utilizing probability outputs directly from the trained model itself can pose problems, especially in deep learning as softmax output is not a true uncertainty measure. This phenomenon, and the wide and rapid adoption of deep learning by practitioners brought unintended consequences in many situations such as in the infamous case of Google Photos' racist image recognition algorithm; thus, necessitated the utilization of the quantified uncertainty for each prediction. There have been recent efforts towards quantifying uncertainty in conventional deep learning methods (e.g., dropout as Bayesian approximation); however, their optimal use in decision making is often overlooked and understudied. Thus, I present a mixed-integer programming framework for selective classification called MIPSC, that investigates and combines model uncertainty and predictive mean to identify optimal classification and rejection regions. I also extend this framework to cost-sensitive settings (MIPCSC) and focus on the critical real-world problem, online fraud management and show that my approach outperforms industry standard methods significantly for online fraud management in real-world settings.
ContributorsYildirim, Mehmet Yigit (Author) / Davulcu, Hasan (Thesis advisor) / Bakkaloglu, Bertan (Committee member) / Huang, Dijiang (Committee member) / Hsiao, Ihan (Committee member) / Arizona State University (Publisher)
Created2019
Description
Object tracking refers to the problem of estimating a moving object's time-varying parameters that are indirectly observed in measurements at each time step. Increased noise and clutter in the measurements reduce estimation accuracy as they increase the uncertainty of tracking in the field of view. Whereas tracking is performed using a Bayesian filter, a Bayesian smoother can be utilized to refine parameter state estimations that occurred before the current time. In practice, smoothing can be widely used to improve state estimation or correct data association errors, and it can lead to significantly better estimation performance as it reduces the impact of noise and clutter. In this work, a single object tracking method is proposed based on integrating Kalman filtering and smoothing with thresholding to remove unreliable measurements. As the new method is effective when the noise and clutter in the measurements are high, the main goal is to find these measurements using a moving average filter and a thresholding method to improve estimation. Thus, the proposed method is designed to reduce estimation errors that result from measurements corrupted with high noise and clutter. Simulations are provided to demonstrate the improved performance of the new method when compared to smoothing without thresholding. The root-mean-square error in estimating the object state parameters is shown to be especially reduced under high noise conditions.
ContributorsSeo, Yongho (Author) / Papandreaou-Suppappola, Antonia (Thesis advisor) / Bliss, Daniel W (Committee member) / Chakrabarti, Chaitali (Committee member) / Moraffah, Bahman (Committee member) / Arizona State University (Publisher)
Created2022
Description
Adversarial threats of deep learning are increasingly becoming a concern due to the ubiquitous deployment of deep neural networks(DNNs) in many security-sensitive domains. Among the existing threats, adversarial weight perturbation is an emerging class of threats that attempts to perturb the weight parameters of DNNs to breach security and privacy.In this thesis, the first weight perturbation attack introduced is called Bit-Flip Attack (BFA), which can maliciously flip a small number of bits within a computer’s main memory system storing the DNN weight parameter to achieve malicious objectives. Our developed algorithm can achieve three specific attack objectives: I) Un-targeted accuracy degradation attack, ii) Targeted attack, & iii) Trojan attack. Moreover, BFA utilizes the rowhammer technique to demonstrate the bit-flip attack in an actual computer prototype. While the bit-flip attack is conducted in a white-box setting, the subsequent contribution of this thesis is to develop another novel weight perturbation attack in a black-box setting. Consequently, this thesis discusses a new study of DNN model vulnerabilities in a multi-tenant Field Programmable Gate Array (FPGA) cloud under a strict black-box framework. This newly developed attack framework injects faults in the malicious tenant by duplicating specific DNN weight packages during data transmission between off-chip memory and on-chip buffer of a victim FPGA. The proposed attack is also experimentally validated in a multi-tenant cloud FPGA prototype. In the final part, the focus shifts toward deep learning model privacy, popularly known as model extraction, that can steal partial DNN weight parameters remotely with the aid of a memory side-channel attack. In addition, a novel training algorithm is designed to utilize the partially leaked DNN weight bit information, making the model extraction attack more effective. The algorithm effectively leverages the partial leaked bit information and generates a substitute prototype of the victim model with almost identical performance to the victim.
ContributorsRakin, Adnan Siraj (Author) / Fan, Deliang (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Seo, Jae-Sun (Committee member) / Cao, Yu (Committee member) / Arizona State University (Publisher)
Created2022