Matching Items (18)

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A Non-Parametric Semi-Supervised f-Divergence

Description

Divergence functions are both highly useful and fundamental to many areas in information theory and machine learning, but require either parametric approaches or prior knowledge of labels on the full data set. This paper presents a method to estimate the

Divergence functions are both highly useful and fundamental to many areas in information theory and machine learning, but require either parametric approaches or prior knowledge of labels on the full data set. This paper presents a method to estimate the divergence between two data sets in the absence of fully labeled data. This semi-labeled case is common in many domains where labeling data by hand is expensive or time-consuming, or wherever large data sets are present. The theory derived in this paper is demonstrated on a simulated example, and then applied to a feature selection and classification problem from pathological speech analysis.

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2016-05

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System complexity reduction via feature selection

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

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.

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2011

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Comparison of feature selection methods for robust dexterous decoding of finger movements from the primary motor cortex of a non-human primate using support vector machine

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

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%)

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2015

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Simultaneous variable and feature group selection in heterogeneous learning: optimization and applications

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

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.

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2014

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Machine learning methods for biosignature discovery

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

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.

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2012

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Learning from asymmetric models and matched pairs

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

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.

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2013

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Query expansion for handling exploratory and ambiguous keyword queries

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

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.

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2011

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Public health surveillance in high-dimensions with supervised learning

Description

Public health surveillance is a special case of the general problem where counts (or rates) of events are monitored for changes. Modern data complements event counts with many additional measurements (such as geographic, demographic, and others) that comprise high-dimensional covariates.

Public health surveillance is a special case of the general problem where counts (or rates) of events are monitored for changes. Modern data complements event counts with many additional measurements (such as geographic, demographic, and others) that comprise high-dimensional covariates. This leads to an important challenge to detect a change that only occurs within a region, initially unspecified, defined by these covariates. Current methods are typically limited to spatial and/or temporal covariate information and often fail to use all the information available in modern data that can be paramount in unveiling these subtle changes. Additional complexities associated with modern health data that are often not accounted for by traditional methods include: covariates of mixed type, missing values, and high-order interactions among covariates. This work proposes a transform of public health surveillance to supervised learning, so that an appropriate learner can inherently address all the complexities described previously. At the same time, quantitative measures from the learner can be used to define signal criteria to detect changes in rates of events. A Feature Selection (FS) method is used to identify covariates that contribute to a model and to generate a signal. A measure of statistical significance is included to control false alarms. An alternative Percentile method identifies the specific cases that lead to changes using class probability estimates from tree-based ensembles. This second method is intended to be less computationally intensive and significantly simpler to implement. Finally, a third method labeled Rule-Based Feature Value Selection (RBFVS) is proposed for identifying the specific regions in high-dimensional space where the changes are occurring. Results on simulated examples are used to compare the FS method and the Percentile method. Note this work emphasizes the application of the proposed methods on public health surveillance. Nonetheless, these methods can easily be extended to a variety of applications where counts (or rates) of events are monitored for changes. Such problems commonly occur in domains such as manufacturing, economics, environmental systems, engineering, as well as in public health.

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2010

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Open-Source Feature Selection Tool for Medical Imaging Diagnosis

Description

Open source image analytics and data mining software are widely available but can be overly-complicated and non-intuitive for medical physicians and researchers to use. The ASU-Mayo Clinic Imaging Informatics Lab has developed an in-house pipeline to process medical images, extract

Open source image analytics and data mining software are widely available but can be overly-complicated and non-intuitive for medical physicians and researchers to use. The ASU-Mayo Clinic Imaging Informatics Lab has developed an in-house pipeline to process medical images, extract imaging features, and develop multi-parametric models to assist disease staging and diagnosis. The tools have been extensively used in a number of medical studies including brain tumor, breast cancer, liver cancer, Alzheimer's disease, and migraine. Recognizing the need from users in the medical field for a simplified interface and streamlined functionalities, this project aims to democratize this pipeline so that it is more readily available to health practitioners and third party developers.

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2016-12

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On feature selection stability: a data perspective

Description

The rapid growth in the high-throughput technologies last few decades makes the manual processing of the generated data to be impracticable. Even worse, the machine learning and data mining techniques seemed to be paralyzed against these massive datasets. High-dimensionality is

The rapid growth in the high-throughput technologies last few decades makes the manual processing of the generated data to be impracticable. Even worse, the machine learning and data mining techniques seemed to be paralyzed against these massive datasets. High-dimensionality is one of the most common challenges for machine learning and data mining tasks. Feature selection aims to reduce dimensionality by selecting a small subset of the features that perform at least as good as the full feature set. Generally, the learning performance, e.g. classification accuracy, and algorithm complexity are used to measure the quality of the algorithm. Recently, the stability of feature selection algorithms has gained an increasing attention as a new indicator due to the necessity to select similar subsets of features each time when the algorithm is run on the same dataset even in the presence of a small amount of perturbation. In order to cure the selection stability issue, we should understand the cause of instability first. In this dissertation, we will investigate the causes of instability in high-dimensional datasets using well-known feature selection algorithms. As a result, we found that the stability mostly data-dependent. According to these findings, we propose a framework to improve selection stability by solving these main causes. In particular, we found that data noise greatly impacts the stability and the learning performance as well. So, we proposed to reduce it in order to improve both selection stability and learning performance. However, current noise reduction approaches are not able to distinguish between data noise and variation in samples from different classes. For this reason, we overcome this limitation by using Supervised noise reduction via Low Rank Matrix Approximation, SLRMA for short. The proposed framework has proved to be successful on different types of datasets with high-dimensionality, such as microarrays and images datasets. However, this framework cannot handle unlabeled, hence, we propose Local SVD to overcome this limitation.

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Date Created
2013