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- Creators: Arizona State University
Description
With the increase in computing power and availability of data, there has never been a greater need to understand data and make decisions from it. Traditional statistical techniques may not be adequate to handle the size of today's data or the complexities of the information hidden within the data. Thus knowledge discovery by machine learning techniques is necessary if we want to better understand information from data. In this dissertation, we explore the topics of asymmetric loss and asymmetric data in machine learning and propose new algorithms as solutions to some of the problems in these topics. We also studied variable selection of matched data sets and proposed a solution when there is non-linearity in the matched data. The research is divided into three parts. The first part addresses the problem of asymmetric loss. A proposed asymmetric support vector machine (aSVM) is used to predict specific classes with high accuracy. aSVM was shown to produce higher precision than a regular SVM. The second part addresses asymmetric data sets where variables are only predictive for a subset of the predictor classes. Asymmetric Random Forest (ARF) was proposed to detect these kinds of variables. The third part explores variable selection for matched data sets. Matched Random Forest (MRF) was proposed to find variables that are able to distinguish case and control without the restrictions that exists in linear models. MRF detects variables that are able to distinguish case and control even in the presence of interaction and qualitative variables.
ContributorsKoh, Derek (Author) / Runger, George C. (Thesis advisor) / Wu, Tong (Committee member) / Pan, Rong (Committee member) / Cesta, John (Committee member) / Arizona State University (Publisher)
Created2013
Description
Coronary heart disease (CHD) is the most prevalent cause of death worldwide. Atherosclerosis which is the condition of plaque buildup on the inside of the coronary artery wall is the main cause of CHD. Rupture of unstable atherosclerotic coronary plaque is known to be the cause of acute coronary syndrome. The composition of plaque is important for detection of plaque vulnerability. Due to prognostic importance of early stage identification, non-invasive assessment of plaque characterization is necessary. Computed tomography (CT) has emerged as a non-invasive alternative to coronary angiography. Recently, dual energy CT (DECT) coronary angiography has been performed clinically. DECT scanners use two different X-ray energies in order to determine the energy dependency of tissue attenuation values for each voxel. They generate virtual monochromatic energy images, as well as material basis pair images. The characterization of plaque components by DECT is still an active research topic since overlap between the CT attenuations measured in plaque components and contrast material shows that the single mean density might not be an appropriate measure for characterization. This dissertation proposes feature extraction, feature selection and learning strategies for supervised characterization of coronary atherosclerotic plaques. In my first study, I proposed an approach for calcium quantification in contrast-enhanced examinations of the coronary arteries, potentially eliminating the need for an extra non-contrast X-ray acquisition. The ambiguity of separation of calcium from contrast material was solved by using virtual non-contrast images. Additional attenuation data provided by DECT provides valuable information for separation of lipid from fibrous plaque since the change of their attenuation as the energy level changes is different. My second study proposed these as the input to supervised learners for a more precise classification of lipid and fibrous plaques. My last study aimed at automatic segmentation of coronary arteries characterizing plaque components and lumen on contrast enhanced monochromatic X-ray images. This required extraction of features from regions of interests. This study proposed feature extraction strategies and selection of important ones. The results show that supervised learning on the proposed features provides promising results for automatic characterization of coronary atherosclerotic plaques by DECT.
ContributorsYamak, Didem (Author) / Akay, Metin (Thesis advisor) / Muthuswamy, Jit (Committee member) / Akay, Yasemin (Committee member) / Pavlicek, William (Committee member) / Vernon, Brent (Committee member) / Arizona State University (Publisher)
Created2013
Description
Advances in data collection technologies have made it cost-effective to obtain heterogeneous data from multiple data sources. Very often, the data are of very high dimension and feature selection is preferred in order to reduce noise, save computational cost and learn interpretable models. Due to the multi-modality nature of heterogeneous data, it is interesting to design efficient machine learning models that are capable of performing variable selection and feature group (data source) selection simultaneously (a.k.a bi-level selection). In this thesis, I carry out research along this direction with a particular focus on designing efficient optimization algorithms. I start with a unified bi-level learning model that contains several existing feature selection models as special cases. Then the proposed model is further extended to tackle the block-wise missing data, one of the major challenges in the diagnosis of Alzheimer's Disease (AD). Moreover, I propose a novel interpretable sparse group feature selection model that greatly facilitates the procedure of parameter tuning and model selection. Last but not least, I show that by solving the sparse group hard thresholding problem directly, the sparse group feature selection model can be further improved in terms of both algorithmic complexity and efficiency. Promising results are demonstrated in the extensive evaluation on multiple real-world data sets.
ContributorsXiang, Shuo (Author) / Ye, Jieping (Thesis advisor) / Mittelmann, Hans D (Committee member) / Davulcu, Hasan (Committee member) / He, Jingrui (Committee member) / Arizona State University (Publisher)
Created2014
Description
Query Expansion is a functionality of search engines that suggest a set of related queries for a user issued keyword query. In case of exploratory or ambiguous keyword queries, the main goal of the user would be to identify and select a specific category of query results among different categorical options, in order to narrow down the search and reach the desired result. Typical corpus-driven keyword query expansion approaches return popular words in the results as expanded queries. These empirical methods fail to cover all semantics of categories present in the query results. More importantly these methods do not consider the semantic relationship between the keywords featured in an expanded query. Contrary to a normal keyword search setting, these factors are non-trivial in an exploratory and ambiguous query setting where the user's precise discernment of different categories present in the query results is more important for making subsequent search decisions. In this thesis, I propose a new framework for keyword query expansion: generating a set of queries that correspond to the categorization of original query results, which is referred as Categorizing query expansion. Two approaches of algorithms are proposed, one that performs clustering as pre-processing step and then generates categorizing expanded queries based on the clusters. The other category of algorithms handle the case of generating quality expanded queries in the presence of imperfect clusters.
ContributorsNatarajan, Sivaramakrishnan (Author) / Chen, Yi (Thesis advisor) / Candan, Selcuk (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2011
Description
This dissertation transforms a set of system complexity reduction problems to feature selection problems. Three systems are considered: classification based on association rules, network structure learning, and time series classification. Furthermore, two variable importance measures are proposed to reduce the feature selection bias in tree models. Associative classifiers can achieve high accuracy, but the combination of many rules is difficult to interpret. Rule condition subset selection (RCSS) methods for associative classification are considered. RCSS aims to prune the rule conditions into a subset via feature selection. The subset then can be summarized into rule-based classifiers. Experiments show that classifiers after RCSS can substantially improve the classification interpretability without loss of accuracy. An ensemble feature selection method is proposed to learn Markov blankets for either discrete or continuous networks (without linear, Gaussian assumptions). The method is compared to a Bayesian local structure learning algorithm and to alternative feature selection methods in the causal structure learning problem. Feature selection is also used to enhance the interpretability of time series classification. Existing time series classification algorithms (such as nearest-neighbor with dynamic time warping measures) are accurate but difficult to interpret. This research leverages the time-ordering of the data to extract features, and generates an effective and efficient classifier referred to as a time series forest (TSF). The computational complexity of TSF is only linear in the length of time series, and interpretable features can be extracted. These features can be further reduced, and summarized for even better interpretability. Lastly, two variable importance measures are proposed to reduce the feature selection bias in tree-based ensemble models. It is well known that bias can occur when predictor attributes have different numbers of values. Two methods are proposed to solve the bias problem. One uses an out-of-bag sampling method called OOBForest, and the other, based on the new concept of a partial permutation test, is called a pForest. Experimental results show the existing methods are not always reliable for multi-valued predictors, while the proposed methods have advantages.
ContributorsDeng, Houtao (Author) / Runger, George C. (Thesis advisor) / Lohr, Sharon L (Committee member) / Pan, Rong (Committee member) / Zhang, Muhong (Committee member) / Arizona State University (Publisher)
Created2011
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
Robust and stable decoding of neural signals is imperative for implementing a useful neuroprosthesis capable of carrying out dexterous tasks. A nonhuman primate (NHP) was trained to perform combined flexions of the thumb, index and middle fingers in addition to individual flexions and extensions of the same digits. An array of microelectrodes was implanted in the hand area of the motor cortex of the NHP and used to record action potentials during finger movements. A Support Vector Machine (SVM) was used to classify which finger movement the NHP was making based upon action potential firing rates. The effect of four feature selection techniques, Wilcoxon signed-rank test, Relative Importance, Principal Component Analysis, and Mutual Information Maximization was compared based on SVM classification performance. SVM classification was used to examine the functional parameters of (i) efficacy (ii) endurance to simulated failure and (iii) longevity of classification. The effect of using isolated-neuron and multi-unit firing rates was compared as the feature vector supplied to the SVM. The best classification performance was on post-implantation day 36, when using multi-unit firing rates the worst classification accuracy resulted from features selected with Wilcoxon signed-rank test (51.12 ± 0.65%) and the best classification accuracy resulted from Mutual Information Maximization (93.74 ± 0.32%). On this day when using single-unit firing rates, the classification accuracy from the Wilcoxon signed-rank test was 88.85 ± 0.61 % and Mutual Information Maximization was 95.60 ± 0.52% (degrees of freedom =10, level of chance =10%)
ContributorsPadmanaban, Subash (Author) / Greger, Bradley (Thesis advisor) / Santello, Marco (Thesis advisor) / Helms Tillery, Stephen (Committee member) / Arizona State University (Publisher)
Created2015
Description
Due to vast resources brought by social media services, social data mining has
received increasing attention in recent years. The availability of sheer amounts of
user-generated data presents data scientists both opportunities and challenges. Opportunities are presented with additional data sources. The abundant link information
in social networks could provide another rich source in deriving implicit information
for social data mining. However, the vast majority of existing studies overwhelmingly
focus on positive links between users while negative links are also prevailing in real-
world social networks such as distrust relations in Epinions and foe links in Slashdot.
Though recent studies show that negative links have some added value over positive
links, it is dicult to directly employ them because of its distinct characteristics from
positive interactions. Another challenge is that label information is rather limited
in social media as the labeling process requires human attention and may be very
expensive. Hence, alternative criteria are needed to guide the learning process for
many tasks such as feature selection and sentiment analysis.
To address above-mentioned issues, I study two novel problems for signed social
networks mining, (1) unsupervised feature selection in signed social networks; and
(2) unsupervised sentiment analysis with signed social networks. To tackle the first problem, I propose a novel unsupervised feature selection framework SignedFS. In
particular, I model positive and negative links simultaneously for user preference
learning, and then embed the user preference learning into feature selection. To study the second problem, I incorporate explicit sentiment signals in textual terms and
implicit sentiment signals from signed social networks into a coherent model Signed-
Senti. Empirical experiments on real-world datasets corroborate the effectiveness of
these two frameworks on the tasks of feature selection and sentiment analysis.
received increasing attention in recent years. The availability of sheer amounts of
user-generated data presents data scientists both opportunities and challenges. Opportunities are presented with additional data sources. The abundant link information
in social networks could provide another rich source in deriving implicit information
for social data mining. However, the vast majority of existing studies overwhelmingly
focus on positive links between users while negative links are also prevailing in real-
world social networks such as distrust relations in Epinions and foe links in Slashdot.
Though recent studies show that negative links have some added value over positive
links, it is dicult to directly employ them because of its distinct characteristics from
positive interactions. Another challenge is that label information is rather limited
in social media as the labeling process requires human attention and may be very
expensive. Hence, alternative criteria are needed to guide the learning process for
many tasks such as feature selection and sentiment analysis.
To address above-mentioned issues, I study two novel problems for signed social
networks mining, (1) unsupervised feature selection in signed social networks; and
(2) unsupervised sentiment analysis with signed social networks. To tackle the first problem, I propose a novel unsupervised feature selection framework SignedFS. In
particular, I model positive and negative links simultaneously for user preference
learning, and then embed the user preference learning into feature selection. To study the second problem, I incorporate explicit sentiment signals in textual terms and
implicit sentiment signals from signed social networks into a coherent model Signed-
Senti. Empirical experiments on real-world datasets corroborate the effectiveness of
these two frameworks on the tasks of feature selection and sentiment analysis.
ContributorsCheng, Kewei (Author) / Liu, Huan (Thesis advisor) / Tong, Hanghang (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2017
Description
In the last 15 years, there has been a significant increase in the number of motor neural prostheses used for restoring limb function lost due to neurological disorders or accidents. The aim of this technology is to enable patients to control a motor prosthesis using their residual neural pathways (central or peripheral). Recent studies in non-human primates and humans have shown the possibility of controlling a prosthesis for accomplishing varied tasks such as self-feeding, typing, reaching, grasping, and performing fine dexterous movements. A neural decoding system comprises mainly of three components: (i) sensors to record neural signals, (ii) an algorithm to map neural recordings to upper limb kinematics and (iii) a prosthetic arm actuated by control signals generated by the algorithm. Machine learning algorithms that map input neural activity to the output kinematics (like finger trajectory) form the core of the neural decoding system. The choice of the algorithm is thus, mainly imposed by the neural signal of interest and the output parameter being decoded. The various parts of a neural decoding system are neural data, feature extraction, feature selection, and machine learning algorithm. There have been significant advances in the field of neural prosthetic applications. But there are challenges for translating a neural prosthesis from a laboratory setting to a clinical environment. To achieve a fully functional prosthetic device with maximum user compliance and acceptance, these factors need to be addressed and taken into consideration. Three challenges in developing robust neural decoding systems were addressed by exploring neural variability in the peripheral nervous system for dexterous finger movements, feature selection methods based on clinically relevant metrics and a novel method for decoding dexterous finger movements based on ensemble methods.
ContributorsPadmanaban, Subash (Author) / Greger, Bradley (Thesis advisor) / Santello, Marco (Committee member) / Helms Tillery, Stephen (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Crook, Sharon (Committee member) / Arizona State University (Publisher)
Created2017
Description
Random forest (RF) is a popular and powerful technique nowadays. It can be used for classification, regression and unsupervised clustering. In its original form introduced by Leo Breiman, RF is used as a predictive model to generate predictions for new observations. Recent researches have proposed several methods based on RF for feature selection and for generating prediction intervals. However, they are limited in their applicability and accuracy. In this dissertation, RF is applied to build a predictive model for a complex dataset, and used as the basis for two novel methods for biomarker discovery and generating prediction interval.
Firstly, a biodosimetry is developed using RF to determine absorbed radiation dose from gene expression measured from blood samples of potentially exposed individuals. To improve the prediction accuracy of the biodosimetry, day-specific models were built to deal with day interaction effect and a technique of nested modeling was proposed. The nested models can fit this complex data of large variability and non-linear relationships.
Secondly, a panel of biomarkers was selected using a data-driven feature selection method as well as handpick, considering prior knowledge and other constraints. To incorporate domain knowledge, a method called Know-GRRF was developed based on guided regularized RF. This method can incorporate domain knowledge as a penalized term to regulate selection of candidate features in RF. It adds more flexibility to data-driven feature selection and can improve the interpretability of models. Know-GRRF showed significant improvement in cross-species prediction when cross-species correlation was used to guide selection of biomarkers. The method can also compete with existing methods using intrinsic data characteristics as alternative of domain knowledge in simulated datasets.
Lastly, a novel non-parametric method, RFerr, was developed to generate prediction interval using RF regression. This method is widely applicable to any predictive models and was shown to have better coverage and precision than existing methods on the real-world radiation dataset, as well as benchmark and simulated datasets.
Firstly, a biodosimetry is developed using RF to determine absorbed radiation dose from gene expression measured from blood samples of potentially exposed individuals. To improve the prediction accuracy of the biodosimetry, day-specific models were built to deal with day interaction effect and a technique of nested modeling was proposed. The nested models can fit this complex data of large variability and non-linear relationships.
Secondly, a panel of biomarkers was selected using a data-driven feature selection method as well as handpick, considering prior knowledge and other constraints. To incorporate domain knowledge, a method called Know-GRRF was developed based on guided regularized RF. This method can incorporate domain knowledge as a penalized term to regulate selection of candidate features in RF. It adds more flexibility to data-driven feature selection and can improve the interpretability of models. Know-GRRF showed significant improvement in cross-species prediction when cross-species correlation was used to guide selection of biomarkers. The method can also compete with existing methods using intrinsic data characteristics as alternative of domain knowledge in simulated datasets.
Lastly, a novel non-parametric method, RFerr, was developed to generate prediction interval using RF regression. This method is widely applicable to any predictive models and was shown to have better coverage and precision than existing methods on the real-world radiation dataset, as well as benchmark and simulated datasets.
ContributorsGuan, Xin (Author) / Liu, Li (Thesis advisor) / Runger, George C. (Thesis advisor) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2017