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- Genre: Masters Thesis
- Member of: Theses and Dissertations
Description
In many classication problems data samples cannot be collected easily, example in drug trials, biological experiments and study on cancer patients. In many situations the data set size is small and there are many outliers. When classifying such data, example cancer vs normal patients the consequences of mis-classication are probably more important than any other data type, because the data point could be a cancer patient or the classication decision could help determine what gene might be over expressed and perhaps a cause of cancer. These mis-classications are typically higher in the presence of outlier data points. The aim of this thesis is to develop a maximum margin classier that is suited to address the lack of robustness of discriminant based classiers (like the Support Vector Machine (SVM)) to noise and outliers. The underlying notion is to adopt and develop a natural loss function that is more robust to outliers and more representative of the true loss function of the data. It is demonstrated experimentally that SVM's are indeed susceptible to outliers and that the new classier developed, here coined as Robust-SVM (RSVM), is superior to all studied classier on the synthetic datasets. It is superior to the SVM in both the synthetic and experimental data from biomedical studies and is competent to a classier derived on similar lines when real life data examples are considered.
ContributorsGupta, Sidharth (Author) / Kim, Seungchan (Thesis advisor) / Welfert, Bruno (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2011
Description
Real-world environments are characterized by non-stationary and continuously evolving data. Learning a classification model on this data would require a framework that is able to adapt itself to newer circumstances. Under such circumstances, transfer learning has come to be a dependable methodology for improving classification performance with reduced training costs and without the need for explicit relearning from scratch. In this thesis, a novel instance transfer technique that adapts a "Cost-sensitive" variation of AdaBoost is presented. The method capitalizes on the theoretical and functional properties of AdaBoost to selectively reuse outdated training instances obtained from a "source" domain to effectively classify unseen instances occurring in a different, but related "target" domain. The algorithm is evaluated on real-world classification problems namely accelerometer based 3D gesture recognition, smart home activity recognition and text categorization. The performance on these datasets is analyzed and evaluated against popular boosting-based instance transfer techniques. In addition, supporting empirical studies, that investigate some of the less explored bottlenecks of boosting based instance transfer methods, are presented, to understand the suitability and effectiveness of this form of knowledge transfer.
ContributorsVenkatesan, Ashok (Author) / Panchanathan, Sethuraman (Thesis advisor) / Li, Baoxin (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2011
Description
Sparse learning is a technique in machine learning for feature selection and dimensionality reduction, to find a sparse set of the most relevant features. In any machine learning problem, there is a considerable amount of irrelevant information, and separating relevant information from the irrelevant information has been a topic of focus. In supervised learning like regression, the data consists of many features and only a subset of the features may be responsible for the result. Also, the features might require special structural requirements, which introduces additional complexity for feature selection. The sparse learning package, provides a set of algorithms for learning a sparse set of the most relevant features for both regression and classification problems. Structural dependencies among features which introduce additional requirements are also provided as part of the package. The features may be grouped together, and there may exist hierarchies and over- lapping groups among these, and there may be requirements for selecting the most relevant groups among them. In spite of getting sparse solutions, the solutions are not guaranteed to be robust. For the selection to be robust, there are certain techniques which provide theoretical justification of why certain features are selected. The stability selection, is a method for feature selection which allows the use of existing sparse learning methods to select the stable set of features for a given training sample. This is done by assigning probabilities for the features: by sub-sampling the training data and using a specific sparse learning technique to learn the relevant features, and repeating this a large number of times, and counting the probability as the number of times a feature is selected. Cross-validation which is used to determine the best parameter value over a range of values, further allows to select the best parameter value. This is done by selecting the parameter value which gives the maximum accuracy score. With such a combination of algorithms, with good convergence guarantees, stable feature selection properties and the inclusion of various structural dependencies among features, the sparse learning package will be a powerful tool for machine learning research. Modular structure, C implementation, ATLAS integration for fast linear algebraic subroutines, make it one of the best tool for a large sparse setting. The varied collection of algorithms, support for group sparsity, batch algorithms, are a few of the notable functionality of the SLEP package, and these features can be used in a variety of fields to infer relevant elements. The Alzheimer Disease(AD) is a neurodegenerative disease, which gradually leads to dementia. The SLEP package is used for feature selection for getting the most relevant biomarkers from the available AD dataset, and the results show that, indeed, only a subset of the features are required to gain valuable insights.
ContributorsThulasiram, Ramesh (Author) / Ye, Jieping (Thesis advisor) / Xue, Guoliang (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2011
Description
Detecting anatomical structures, such as the carina, the pulmonary trunk and the aortic arch, is an important step in designing a CAD system of detection Pulmonary Embolism. The presented CAD system gets rid of the high-level prior defined knowledge to become a system which can easily extend to detect other anatomic structures. The system is based on a machine learning algorithm --- AdaBoost and a general feature --- Haar. This study emphasizes on off-line and on-line AdaBoost learning. And in on-line AdaBoost, the thesis further deals with extremely imbalanced condition. The thesis first reviews several knowledge-based detection methods, which are relied on human being's understanding of the relationship between anatomic structures. Then the thesis introduces a classic off-line AdaBoost learning. The thesis applies different cascading scheme, namely multi-exit cascading scheme. The comparison between the two methods will be provided and discussed. Both of the off-line AdaBoost methods have problems in memory usage and time consuming. Off-line AdaBoost methods need to store all the training samples and the dataset need to be set before training. The dataset cannot be enlarged dynamically. Different training dataset requires retraining the whole process. The retraining is very time consuming and even not realistic. To deal with the shortcomings of off-line learning, the study exploited on-line AdaBoost learning approach. The thesis proposed a novel pool based on-line method with Kalman filters and histogram to better represent the distribution of the samples' weight. Analysis of the performance, the stability and the computational complexity will be provided in the thesis. Furthermore, the original on-line AdaBoost performs badly in imbalanced conditions, which occur frequently in medical image processing. In image dataset, positive samples are limited and negative samples are countless. A novel Self-Adaptive Asymmetric On-line Boosting method is presented. The method utilized a new asymmetric loss criterion with self-adaptability according to the ratio of exposed positive and negative samples and it has an advanced rule to update sample's importance weight taking account of both classification result and sample's label. Compared to traditional on-line AdaBoost Learning method, the new method can achieve far more accuracy in imbalanced conditions.
ContributorsWu, Hong (Author) / Liang, Jianming (Thesis advisor) / Farin, Gerald (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2011
Description
Text classification, in the artificial intelligence domain, is an activity in which text documents are automatically classified into predefined categories using machine learning techniques. An example of this is classifying uncategorized news articles into different predefined categories such as "Business", "Politics", "Education", "Technology" , etc. In this thesis, supervised machine learning approach is followed, in which a module is first trained with pre-classified training data and then class of test data is predicted. Good feature extraction is an important step in the machine learning approach and hence the main component of this text classifier is semantic triplet based features in addition to traditional features like standard keyword based features and statistical features based on shallow-parsing (such as density of POS tags and named entities). Triplet {Subject, Verb, Object} in a sentence is defined as a relation between subject and object, the relation being the predicate (verb). Triplet extraction process, is a 5 step process which takes input corpus as a web text document(s), each consisting of one or many paragraphs, from RSS feeds to lists of extremist website. Input corpus feeds into the "Pronoun Resolution" step, which uses an heuristic approach to identify the noun phrases referenced by the pronouns. The next step "SRL Parser" is a shallow semantic parser and converts the incoming pronoun resolved paragraphs into annotated predicate argument format. The output of SRL parser is processed by "Triplet Extractor" algorithm which forms the triplet in the form {Subject, Verb, Object}. Generalization and reduction of triplet features is the next step. Reduced feature representation reduces computing time, yields better discriminatory behavior and handles curse of dimensionality phenomena. For training and testing, a ten- fold cross validation approach is followed. In each round SVM classifier is trained with 90% of labeled (training) data and in the testing phase, classes of remaining 10% unlabeled (testing) data are predicted. Concluding, this paper proposes a model with semantic triplet based features for story classification. The effectiveness of the model is demonstrated against other traditional features used in the literature for text classification tasks.
ContributorsKarad, Ravi Chandravadan (Author) / Davulcu, Hasan (Thesis advisor) / Corman, Steven (Committee member) / Sen, Arunabha (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
Biological soil crusts (BSCs), topsoil microbial assemblages typical of arid land ecosystems, provide essential ecosystem services such as soil fertilization and stabilization against erosion. Cyanobacteria and lichens, sometimes mosses, drive BSC as primary producers, but metabolic activity is restricted to periods of hydration associated with precipitation. Climate models for the SW United States predict changes in precipitation frequency as a major outcome of global warming, even if models differ on the sign and magnitude of the change. BSC organisms are clearly well adapted to withstand desiccation and prolonged drought, but it is unknown if and how an alteration of the precipitation frequency may impact community composition, diversity, and ecosystem functions. To test this, we set up a BSC microcosm experiment with variable precipitation frequency treatments using a local, cyanobacteria-dominated, early-succession BSC maintained under controlled conditions in a greenhouse. Precipitation pulse size was kept constant but 11 different drought intervals were imposed, ranging between 416 to 3 days, during a period of 416 days. At the end of the experiments, bacterial community composition was analyzed by pyrosequencing of the 16s rRNA genes in the community, and a battery of functional assays were used to evaluate carbon and nitrogen cycling potentials. While changes in community composition were neither marked nor consistent at the Phylum level, there was a significant trend of decreased diversity with increasing precipitation frequency, and we detected particular bacterial phylotypes that responded to the frequency of precipitation in a consistent manner (either positively or negatively). A significant trend of increased respiration with increasingly long drought period was detected, but BSC could recover quickly from this effect. Gross photosynthesis, nitrification and denitrification remained essentially impervious to treatment. These results are consistent with the notion that BSC community structure adjustments sufficed to provide significant functional resilience, and allow us to predict that future alterations in precipitation frequency are unlikely to result in severe impacts to BSC biology or ecological relevance.
ContributorsMyers, Natalie Kristine (Author) / Garcia-Pichel, Ferran (Thesis advisor) / Hall, Sharon (Committee member) / Turner, Benjamin (Committee member) / Krajmalnik-Brown, Rosa (Committee member) / Arizona State University (Publisher)
Created2013
Description
Alzheimer's Disease (AD) is the most common form of dementia observed in elderly patients and has significant social-economic impact. There are many initiatives which aim to capture leading causes of AD. Several genetic, imaging, and biochemical markers are being explored to monitor progression of AD and explore treatment and detection options. The primary focus of this thesis is to identify key biomarkers to understand the pathogenesis and prognosis of Alzheimer's Disease. Feature selection is the process of finding a subset of relevant features to develop efficient and robust learning models. It is an active research topic in diverse areas such as computer vision, bioinformatics, information retrieval, chemical informatics, and computational finance. In this work, state of the art feature selection algorithms, such as Student's t-test, Relief-F, Information Gain, Gini Index, Chi-Square, Fisher Kernel Score, Kruskal-Wallis, Minimum Redundancy Maximum Relevance, and Sparse Logistic regression with Stability Selection have been extensively exploited to identify informative features for AD using data from Alzheimer's Disease Neuroimaging Initiative (ADNI). An integrative approach which uses blood plasma protein, Magnetic Resonance Imaging, and psychometric assessment scores biomarkers has been explored. This work also analyzes the techniques to handle unbalanced data and evaluate the efficacy of sampling techniques. Performance of feature selection algorithm is evaluated using the relevance of derived features and the predictive power of the algorithm using Random Forest and Support Vector Machine classifiers. Performance metrics such as Accuracy, Sensitivity and Specificity, and area under the Receiver Operating Characteristic curve (AUC) have been used for evaluation. The feature selection algorithms best suited to analyze AD proteomics data have been proposed. The key biomarkers distinguishing healthy and AD patients, Mild Cognitive Impairment (MCI) converters and non-converters, and healthy and MCI patients have been identified.
ContributorsDubey, Rashmi (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Wu, Tong (Committee member) / Arizona State University (Publisher)
Created2012
Description
Learning from high dimensional biomedical data attracts lots of attention recently. High dimensional biomedical data often suffer from the curse of dimensionality and have imbalanced class distributions. Both of these features of biomedical data, high dimensionality and imbalanced class distributions, are challenging for traditional machine learning methods and may affect the model performance. In this thesis, I focus on developing learning methods for the high-dimensional imbalanced biomedical data. In the first part, a sparse canonical correlation analysis (CCA) method is presented. The penalty terms is used to control the sparsity of the projection matrices of CCA. The sparse CCA method is then applied to find patterns among biomedical data sets and labels, or to find patterns among different data sources. In the second part, I discuss several learning problems for imbalanced biomedical data. Note that traditional learning systems are often biased when the biomedical data are imbalanced. Therefore, traditional evaluations such as accuracy may be inappropriate for such cases. I then discuss several alternative evaluation criteria to evaluate the learning performance. For imbalanced binary classification problems, I use the undersampling based classifiers ensemble (UEM) strategy to obtain accurate models for both classes of samples. A small sphere and large margin (SSLM) approach is also presented to detect rare abnormal samples from a large number of subjects. In addition, I apply multiple feature selection and clustering methods to deal with high-dimensional data and data with highly correlated features. Experiments on high-dimensional imbalanced biomedical data are presented which illustrate the effectiveness and efficiency of my methods.
ContributorsYang, Tao (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Feature embeddings differ from raw features in the sense that the former obey certain properties like notion of similarity/dissimilarity in it's embedding space. word2vec is a preeminent example in this direction, where the similarity in the embedding space is measured in terms of the cosine similarity. Such language embedding models have seen numerous applications in both language and vision community as they capture the information in the modality (English language) efficiently. Inspired by these language models, this work focuses on learning embedding spaces for two visual computing tasks, 1. Image Hashing 2. Zero Shot Learning. The training set was used to learn embedding spaces over which similarity/dissimilarity is measured using several distance metrics like hamming / euclidean / cosine distances. While the above-mentioned language models learn generic word embeddings, in this work task specific embeddings were learnt which can be used for Image Retrieval and Classification separately.
Image Hashing is the task of mapping images to binary codes such that some notion of user-defined similarity is preserved. The first part of this work focuses on designing a new framework that uses the hash-tags associated with web images to learn the binary codes. Such codes can be used in several applications like Image Retrieval and Image Classification. Further, this framework requires no labelled data, leaving it very inexpensive. Results show that the proposed approach surpasses the state-of-art approaches by a significant margin.
Zero-shot classification is the task of classifying the test sample into a new class which was not seen during training. This is possible by establishing a relationship between the training and the testing classes using auxiliary information. In the second part of this thesis, a framework is designed that trains using the handcrafted attribute vectors and word vectors but doesn’t require the expensive attribute vectors during test time. More specifically, an intermediate space is learnt between the word vector space and the image feature space using the hand-crafted attribute vectors. Preliminary results on two zero-shot classification datasets show that this is a promising direction to explore.
Image Hashing is the task of mapping images to binary codes such that some notion of user-defined similarity is preserved. The first part of this work focuses on designing a new framework that uses the hash-tags associated with web images to learn the binary codes. Such codes can be used in several applications like Image Retrieval and Image Classification. Further, this framework requires no labelled data, leaving it very inexpensive. Results show that the proposed approach surpasses the state-of-art approaches by a significant margin.
Zero-shot classification is the task of classifying the test sample into a new class which was not seen during training. This is possible by establishing a relationship between the training and the testing classes using auxiliary information. In the second part of this thesis, a framework is designed that trains using the handcrafted attribute vectors and word vectors but doesn’t require the expensive attribute vectors during test time. More specifically, an intermediate space is learnt between the word vector space and the image feature space using the hand-crafted attribute vectors. Preliminary results on two zero-shot classification datasets show that this is a promising direction to explore.
ContributorsGattupalli, Jaya Vijetha (Author) / Li, Baoxin (Thesis advisor) / Yang, Yezhou (Committee member) / Venkateswara, Hemanth (Committee member) / Arizona State University (Publisher)
Created2019