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- All Subjects: Computer Science
- Creators: Ye, Jieping
- Creators: Turaga, Pavan
Description
Image understanding has been playing an increasingly crucial role in vision applications. Sparse models form an important component in image understanding, since the statistics of natural images reveal the presence of sparse structure. Sparse methods lead to parsimonious models, in addition to being efficient for large scale learning. In sparse modeling, data is represented as a sparse linear combination of atoms from a "dictionary" matrix. This dissertation focuses on understanding different aspects of sparse learning, thereby enhancing the use of sparse methods by incorporating tools from machine learning. With the growing need to adapt models for large scale data, it is important to design dictionaries that can model the entire data space and not just the samples considered. By exploiting the relation of dictionary learning to 1-D subspace clustering, a multilevel dictionary learning algorithm is developed, and it is shown to outperform conventional sparse models in compressed recovery, and image denoising. Theoretical aspects of learning such as algorithmic stability and generalization are considered, and ensemble learning is incorporated for effective large scale learning. In addition to building strategies for efficiently implementing 1-D subspace clustering, a discriminative clustering approach is designed to estimate the unknown mixing process in blind source separation. By exploiting the non-linear relation between the image descriptors, and allowing the use of multiple features, sparse methods can be made more effective in recognition problems. The idea of multiple kernel sparse representations is developed, and algorithms for learning dictionaries in the feature space are presented. Using object recognition experiments on standard datasets it is shown that the proposed approaches outperform other sparse coding-based recognition frameworks. Furthermore, a segmentation technique based on multiple kernel sparse representations is developed, and successfully applied for automated brain tumor identification. Using sparse codes to define the relation between data samples can lead to a more robust graph embedding for unsupervised clustering. By performing discriminative embedding using sparse coding-based graphs, an algorithm for measuring the glomerular number in kidney MRI images is developed. Finally, approaches to build dictionaries for local sparse coding of image descriptors are presented, and applied to object recognition and image retrieval.
ContributorsJayaraman Thiagarajan, Jayaraman (Author) / Spanias, Andreas (Thesis advisor) / Frakes, David (Committee member) / Tepedelenlioğlu, Cihan (Committee member) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Drosophila melanogaster, as an important model organism, is used to explore the mechanism which governs cell differentiation and embryonic development. Understanding the mechanism will help to reveal the effects of genes on other species or even human beings. Currently, digital camera techniques make high quality Drosophila gene expression imaging possible. On the other hand, due to the advances in biology, gene expression images which can reveal spatiotemporal patterns are generated in a high-throughput pace. Thus, an automated and efficient system that can analyze gene expression will become a necessary tool for investigating the gene functions, interactions and developmental processes. One investigation method is to compare the expression patterns of different developmental stages. Recently, however, the expression patterns are manually annotated with rough stage ranges. The work of annotation requires professional knowledge from experienced biologists. Hence, how to transfer the domain knowledge in biology into an automated system which can automatically annotate the patterns provides a challenging problem for computer scientists. In this thesis, the problem of stage annotation for Drosophila embryo is modeled in the machine learning framework. Three sparse learning algorithms and one ensemble algorithm are used to attack the problem. The sparse algorithms are Lasso, group Lasso and sparse group Lasso. The ensemble algorithm is based on a voting method. Besides that the proposed algorithms can annotate the patterns to stages instead of stage ranges with high accuracy; the decimal stage annotation algorithm presents a novel way to annotate the patterns to decimal stages. In addition, some analysis on the algorithm performance are made and corresponding explanations are given. Finally, with the proposed system, all the lateral view BDGP and FlyFish images are annotated and several interesting applications of decimal stage value are revealed.
ContributorsPan, Cheng (Author) / Ye, Jieping (Thesis advisor) / Li, Baoxin (Committee member) / Farin, Gerald (Committee member) / Arizona State University (Publisher)
Created2012
Description
In recent years, machine learning and data mining technologies have received growing attention in several areas such as recommendation systems, natural language processing, speech and handwriting recognition, image processing and biomedical domain. Many of these applications which deal with physiological and biomedical data require person specific or person adaptive systems. The greatest challenge in developing such systems is the subject-dependent data variations or subject-based variability in physiological and biomedical data, which leads to difference in data distributions making the task of modeling these data, using traditional machine learning algorithms, complex and challenging. As a result, despite the wide application of machine learning, efficient deployment of its principles to model real-world data is still a challenge. This dissertation addresses the problem of subject based variability in physiological and biomedical data and proposes person adaptive prediction models based on novel transfer and active learning algorithms, an emerging field in machine learning. One of the significant contributions of this dissertation is a person adaptive method, for early detection of muscle fatigue using Surface Electromyogram signals, based on a new multi-source transfer learning algorithm. This dissertation also proposes a subject-independent algorithm for grading the progression of muscle fatigue from 0 to 1 level in a test subject, during isometric or dynamic contractions, at real-time. Besides subject based variability, biomedical image data also varies due to variations in their imaging techniques, leading to distribution differences between the image databases. Hence a classifier learned on one database may perform poorly on the other database. Another significant contribution of this dissertation has been the design and development of an efficient biomedical image data annotation framework, based on a novel combination of transfer learning and a new batch-mode active learning method, capable of addressing the distribution differences across databases. The methodologies developed in this dissertation are relevant and applicable to a large set of computing problems where there is a high variation of data between subjects or sources, such as face detection, pose detection and speech recognition. From a broader perspective, these frameworks can be viewed as a first step towards design of automated adaptive systems for real world data.
ContributorsChattopadhyay, Rita (Author) / Panchanathan, Sethuraman (Thesis advisor) / Ye, Jieping (Thesis advisor) / Li, Baoxin (Committee member) / Santello, Marco (Committee member) / Arizona State University (Publisher)
Created2013
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
Currently, to interact with computer based systems one needs to learn the specific interface language of that system. In most cases, interaction would be much easier if it could be done in natural language. For that, we will need a module which understands natural language and automatically translates it to the interface language of the system. NL2KR (Natural language to knowledge representation) v.1 system is a prototype of such a system. It is a learning based system that learns new meanings of words in terms of lambda-calculus formulas given an initial lexicon of some words and their meanings and a training corpus of sentences with their translations. As a part of this thesis, we take the prototype NL2KR v.1 system and enhance various components of it to make it usable for somewhat substantial and useful interface languages. We revamped the lexicon learning components, Inverse-lambda and Generalization modules, and redesigned the lexicon learning algorithm which uses these components to learn new meanings of words. Similarly, we re-developed an inbuilt parser of the system in Answer Set Programming (ASP) and also integrated external parser with the system. Apart from this, we added some new rich features like various system configurations and memory cache in the learning component of the NL2KR system. These enhancements helped in learning more meanings of the words, boosted performance of the system by reducing the computation time by a factor of 8 and improved the usability of the system. We evaluated the NL2KR system on iRODS domain. iRODS is a rule-oriented data system, which helps in managing large set of computer files using policies. This system provides a Rule-Oriented interface langauge whose syntactic structure is like any procedural programming language (eg. C). However, direct translation of natural language (NL) to this interface language is difficult. So, for automatic translation of NL to this language, we define a simple intermediate Policy Declarative Language (IPDL) to represent the knowledge in the policies, which then can be directly translated to iRODS rules. We develop a corpus of 100 policy statements and manually translate them to IPDL langauge. This corpus is then used for the evaluation of NL2KR system. We performed 10 fold cross validation on the system. Furthermore, using this corpus, we illustrate how different components of our NL2KR system work.
ContributorsKumbhare, Kanchan Ravishankar (Author) / Baral, Chitta (Thesis advisor) / Ye, Jieping (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2013
Description
Nowadays, wireless communications and networks have been widely used in our daily lives. One of the most important topics related to networking research is using optimization tools to improve the utilization of network resources. In this dissertation, we concentrate on optimization for resource-constrained wireless networks, and study two fundamental resource-allocation problems: 1) distributed routing optimization and 2) anypath routing optimization. The study on the distributed routing optimization problem is composed of two main thrusts, targeted at understanding distributed routing and resource optimization for multihop wireless networks. The first thrust is dedicated to understanding the impact of full-duplex transmission on wireless network resource optimization. We propose two provably good distributed algorithms to optimize the resources in a full-duplex wireless network. We prove their optimality and also provide network status analysis using dual space information. The second thrust is dedicated to understanding the influence of network entity load constraints on network resource allocation and routing computation. We propose a provably good distributed algorithm to allocate wireless resources. In addition, we propose a new subgradient optimization framework, which can provide findgrained convergence, optimality, and dual space information at each iteration. This framework can provide a useful theoretical foundation for many networking optimization problems. The study on the anypath routing optimization problem is composed of two main thrusts. The first thrust is dedicated to understanding the computational complexity of multi-constrained anypath routing and designing approximate solutions. We prove that this problem is NP-hard when the number of constraints is larger than one. We present two polynomial time K-approximation algorithms. One is a centralized algorithm while the other one is a distributed algorithm. For the second thrust, we study directional anypath routing and present a cross-layer design of MAC and routing. For the MAC layer, we present a directional anycast MAC. For the routing layer, we propose two polynomial time routing algorithms to compute directional anypaths based on two antenna models, and prove their ptimality based on the packet delivery ratio metric.
ContributorsFang, Xi (Author) / Xue, Guoliang (Thesis advisor) / Yau, Sik-Sang (Committee member) / Ye, Jieping (Committee member) / Zhang, Junshan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Motion capture using cost-effective sensing technology is challenging and the huge success of Microsoft Kinect has been attracting researchers to uncover the potential of using this technology into computer vision applications. In this thesis, an upper-body motion analysis in a home-based system for stroke rehabilitation using novel RGB-D camera - Kinect is presented. We address this problem by first conducting a systematic analysis of the usability of Kinect for motion analysis in stroke rehabilitation. Then a hybrid upper body tracking approach is proposed which combines off-the-shelf skeleton tracking with a novel depth-fused mean shift tracking method. We proposed several kinematic features reliably extracted from the proposed inexpensive and portable motion capture system and classifiers that correlate torso movement to clinical measures of unimpaired and impaired. Experiment results show that the proposed sensing and analysis works reliably on measuring torso movement quality and is promising for end-point tracking. The system is currently being deployed for large-scale evaluations.
ContributorsDu, Tingfang (Author) / Turaga, Pavan (Thesis advisor) / Spanias, Andreas (Committee member) / Rikakis, Thanassis (Committee member) / Arizona State University (Publisher)
Created2012
Description
Our research focuses on finding answers through decentralized search, for complex, imprecise queries (such as "Which is the best hair salon nearby?") in situations where there is a spatiotemporal constraint (say answer needs to be found within 15 minutes) associated with the query. In general, human networks are good in answering imprecise queries. We try to use the social network of a person to answer his query. Our research aims at designing a framework that exploits the user's social network in order to maximize the answers for a given query. Exploiting an user's social network has several challenges. The major challenge is that the user's immediate social circle may not possess the answer for the given query, and hence the framework designed needs to carry out the query diffusion process across the network. The next challenge involves in finding the right set of seeds to pass the query to in the user's social circle. One other challenge is to incentivize people in the social network to respond to the query and thereby maximize the quality and quantity of replies. Our proposed framework is a mobile application where an individual can either respond to the query or forward it to his friends. We simulated the query diffusion process in three types of graphs: Small World, Random and Preferential Attachment. Given a type of network and a particular query, we carried out the query diffusion by selecting seeds based on attributes of the seed. The main attributes are Topic relevance, Replying or Forwarding probability and Time to Respond. We found that there is a considerable increase in the number of replies attained, even without saturating the user's network, if we adopt an optimal seed selection process. We found the output of the optimal algorithm to be satisfactory as the number of replies received at the interrogator's end was close to three times the number of neighbors an interrogator has. We addressed the challenge of incentivizing people to respond by associating a particular amount of points for each query asked, and awarding the same to people involved in answering the query. Thus, we aim to design a mobile application based on our proposed framework so that it helps in maximizing the replies for the interrogator's query by diffusing the query across his/her social network.
ContributorsSwaminathan, Neelakantan (Author) / Sundaram, Hari (Thesis advisor) / Davulcu, Hasan (Thesis advisor) / Turaga, Pavan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Video denoising has been an important task in many multimedia and computer vision applications. Recent developments in the matrix completion theory and emergence of new numerical methods which can efficiently solve the matrix completion problem have paved the way for exploration of new techniques for some classical image processing tasks. Recent literature shows that many computer vision and image processing problems can be solved by using the matrix completion theory. This thesis explores the application of matrix completion in video denoising. A state-of-the-art video denoising algorithm in which the denoising task is modeled as a matrix completion problem is chosen for detailed study. The contribution of this thesis lies in both providing extensive analysis to bridge the gap in existing literature on matrix completion frame work for video denoising and also in proposing some novel techniques to improve the performance of the chosen denoising algorithm. The chosen algorithm is implemented for thorough analysis. Experiments and discussions are presented to enable better understanding of the problem. Instability shown by the algorithm at some parameter values in a particular case of low levels of pure Gaussian noise is identified. Artifacts introduced in such cases are analyzed. A novel way of grouping structurally-relevant patches is proposed to improve the algorithm. Experiments show that this technique is useful, especially in videos containing high amounts of motion. Based on the observation that matrix completion is not suitable for denoising patches containing relatively low amount of image details, a framework is designed to separate patches corresponding to low structured regions from a noisy image. Experiments are conducted by not subjecting such patches to matrix completion, instead denoising such patches in a different way. The resulting improvement in performance suggests that denoising low structured patches does not require a complex method like matrix completion and in fact it is counter-productive to subject such patches to matrix completion. These results also indicate the inherent limitation of matrix completion to deal with cases in which noise dominates the structural properties of an image. A novel method for introducing priorities to the ranked patches in matrix completion is also presented. Results showed that this method yields improved performance in general. It is observed that the artifacts in presence of low levels of pure Gaussian noise appear differently after introducing priorities to the patches and the artifacts occur at a wider range of parameter values. Results and discussion suggesting future ways to explore this problem are also presented.
ContributorsMaguluri, Hima Bindu (Author) / Li, Baoxin (Thesis advisor) / Turaga, Pavan (Committee member) / Claveau, Claude (Committee member) / Arizona State University (Publisher)
Created2013