Matching Items (8)
Filtering by
- All Subjects: Transfer Learning
- All Subjects: Gene Expression
- Creators: Ye, Jieping
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 The method capitalizes on the theoretical and functional properties of AdaBoost to selectively reuse outdated training instances obtained from a "source" domain to effectively classify unseen instances occurring in a different, but related "target" domain.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
Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups or graphs. In this thesis, I first propose to solve a sparse learning model with a general group structure, where the predefined groups may overlap with each other. Then, I present three real world applications which can benefit from the group structured sparse learning technique. In the first application, I study the Alzheimer's Disease diagnosis problem using multi-modality neuroimaging data. In this dataset, not every subject has all data sources available, exhibiting an unique and challenging block-wise missing pattern. In the second application, I study the automatic annotation and retrieval of fruit-fly gene expression pattern images. Combined with the spatial information, sparse learning techniques can be used to construct effective representation of the expression images. In the third application, I present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores help us to illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes.
ContributorsYuan, Lei (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Xue, Guoliang (Committee member) / Kumar, Sudhir (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
Discriminative learning when training and test data belong to different distributions is a challenging and complex task. Often times we have very few or no labeled data from the test or target distribution, but we may have plenty of labeled data from one or multiple related sources with different distributions. Due to its capability of migrating knowledge from related domains, transfer learning has shown to be effective for cross-domain learning problems. In this dissertation, I carry out research along this direction with a particular focus on designing efficient and effective algorithms for BioImaging and Bilingual applications. Specifically, I propose deep transfer learning algorithms which combine transfer learning and deep learning to improve image annotation performance. Firstly, I propose to generate the deep features for the Drosophila embryo images via pretrained deep models and build linear classifiers on top of the deep features. Secondly, I propose to fine-tune the pretrained model with a small amount of labeled images. The time complexity and performance of deep transfer learning methodologies are investigated. Promising results have demonstrated the knowledge transfer ability of proposed deep transfer algorithms. Moreover, I propose a novel Robust Principal Component Analysis (RPCA) approach to process the noisy images in advance. In addition, I also present a two-stage re-weighting framework for general domain adaptation problems. The distribution of source domain is mapped towards the target domain in the first stage, and an adaptive learning model is proposed in the second stage to incorporate label information from the target domain if it is available. Then the proposed model is applied to tackle cross lingual spam detection problem at LinkedIn’s website. Our experimental results on real data demonstrate the efficiency and effectiveness of the proposed algorithms.
ContributorsSun, Qian (Author) / Ye, Jieping (Committee member) / Xue, Guoliang (Committee member) / Liu, Huan (Committee member) / Li, Jing (Committee member) / Arizona State University (Publisher)
Created2015
Description
Understanding the complexity of temporal and spatial characteristics of gene expression over brain development is one of the crucial research topics in neuroscience. An accurate description of the locations and expression status of relative genes requires extensive experiment resources. The Allen Developing Mouse Brain Atlas provides a large number of in situ hybridization (ISH) images of gene expression over seven different mouse brain developmental stages. Studying mouse brain models helps us understand the gene expressions in human brains. This atlas collects about thousands of genes and now they are manually annotated by biologists. Due to the high labor cost of manual annotation, investigating an efficient approach to perform automated gene expression annotation on mouse brain images becomes necessary. In this thesis, a novel efficient approach based on machine learning framework is proposed. Features are extracted from raw brain images, and both binary classification and multi-class classification models are built with some supervised learning methods. To generate features, one of the most adopted methods in current research effort is to apply the bag-of-words (BoW) algorithm. However, both the efficiency and the accuracy of BoW are not outstanding when dealing with large-scale data. Thus, an augmented sparse coding method, which is called Stochastic Coordinate Coding, is adopted to generate high-level features in this thesis. In addition, a new multi-label classification model is proposed in this thesis. Label hierarchy is built based on the given brain ontology structure. Experiments have been conducted on the atlas and the results show that this approach is efficient and classifies the images with a relatively higher accuracy.
ContributorsZhao, Xinlin (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2016
Description
Imaging genetics is an emerging and promising technique that investigates how genetic variations affect brain development, structure, and function. By exploiting disorder-related neuroimaging phenotypes, this class of studies provides a novel direction to reveal and understand the complex genetic mechanisms. Oftentimes, imaging genetics studies are challenging due to the relatively small number of subjects but extremely high-dimensionality of both imaging data and genomic data. In this dissertation, I carry on my research on imaging genetics with particular focuses on two tasks---building predictive models between neuroimaging data and genomic data, and identifying disorder-related genetic risk factors through image-based biomarkers. To this end, I consider a suite of structured sparse methods---that can produce interpretable models and are robust to overfitting---for imaging genetics. With carefully-designed sparse-inducing regularizers, different biological priors are incorporated into learning models. More specifically, in the Allen brain image--gene expression study, I adopt an advanced sparse coding approach for image feature extraction and employ a multi-task learning approach for multi-class annotation. Moreover, I propose a label structured-based two-stage learning framework, which utilizes the hierarchical structure among labels, for multi-label annotation. In the Alzheimer's disease neuroimaging initiative (ADNI) imaging genetics study, I employ Lasso together with EDPP (enhanced dual polytope projections) screening rules to fast identify Alzheimer's disease risk SNPs. I also adopt the tree-structured group Lasso with MLFre (multi-layer feature reduction) screening rules to incorporate linkage disequilibrium information into modeling. Moreover, I propose a novel absolute fused Lasso model for ADNI imaging genetics. This method utilizes SNP spatial structure and is robust to the choice of reference alleles of genotype coding. In addition, I propose a two-level structured sparse model that incorporates gene-level networks through a graph penalty into SNP-level model construction. Lastly, I explore a convolutional neural network approach for accurate predicting Alzheimer's disease related imaging phenotypes. Experimental results on real-world imaging genetics applications demonstrate the efficiency and effectiveness of the proposed structured sparse methods.
ContributorsYang, Tao (Author) / Ye, Jieping (Thesis advisor) / Xue, Guoliang (Thesis advisor) / He, Jingrui (Committee member) / Li, Baoxin (Committee member) / Li, Jing (Committee member) / Arizona State University (Publisher)
Created2017
Description
The widespread adoption of computer vision models is often constrained by the issue of domain mismatch. Models that are trained with data belonging to one distribution, perform poorly when tested with data from a different distribution. Variations in vision based data can be attributed to the following reasons, viz., differences in image quality (resolution, brightness, occlusion and color), changes in camera perspective, dissimilar backgrounds and an inherent diversity of the samples themselves. Machine learning techniques like transfer learning are employed to adapt computational models across distributions. Domain adaptation is a special case of transfer learning, where knowledge from a source domain is transferred to a target domain in the form of learned models and efficient feature representations.
The dissertation outlines novel domain adaptation approaches across different feature spaces; (i) a linear Support Vector Machine model for domain alignment; (ii) a nonlinear kernel based approach that embeds domain-aligned data for enhanced classification; (iii) a hierarchical model implemented using deep learning, that estimates domain-aligned hash values for the source and target data, and (iv) a proposal for a feature selection technique to reduce cross-domain disparity. These adaptation procedures are tested and validated across a range of computer vision applications like object classification, facial expression recognition, digit recognition, and activity recognition. The dissertation also provides a unique perspective of domain adaptation literature from the point-of-view of linear, nonlinear and hierarchical feature spaces. The dissertation concludes with a discussion on the future directions for research that highlight the role of domain adaptation in an era of rapid advancements in artificial intelligence.
The dissertation outlines novel domain adaptation approaches across different feature spaces; (i) a linear Support Vector Machine model for domain alignment; (ii) a nonlinear kernel based approach that embeds domain-aligned data for enhanced classification; (iii) a hierarchical model implemented using deep learning, that estimates domain-aligned hash values for the source and target data, and (iv) a proposal for a feature selection technique to reduce cross-domain disparity. These adaptation procedures are tested and validated across a range of computer vision applications like object classification, facial expression recognition, digit recognition, and activity recognition. The dissertation also provides a unique perspective of domain adaptation literature from the point-of-view of linear, nonlinear and hierarchical feature spaces. The dissertation concludes with a discussion on the future directions for research that highlight the role of domain adaptation in an era of rapid advancements in artificial intelligence.
ContributorsDemakethepalli Venkateswara, Hemanth (Author) / Panchanathan, Sethuraman (Thesis advisor) / Li, Baoxin (Committee member) / Davulcu, Hasan (Committee member) / Ye, Jieping (Committee member) / Chakraborty, Shayok (Committee member) / Arizona State University (Publisher)
Created2017