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- All Subjects: Data Mining
- All Subjects: Natural Language Processing
- Creators: Li, Baoxin
Description
The technology expansion seen in the last decade for genomics research has permitted the generation of large-scale data sources pertaining to molecular biological assays, genomics, proteomics, transcriptomics and other modern omics catalogs. New methods to analyze, integrate and visualize these data types are essential to unveil relevant disease mechanisms. Towards these objectives, this research focuses on data integration within two scenarios: (1) transcriptomic, proteomic and functional information and (2) real-time sensor-based measurements motivated by single-cell technology. To assess relationships between protein abundance, transcriptomic and functional data, a nonlinear model was explored at static and temporal levels. The successful integration of these heterogeneous data sources through the stochastic gradient boosted tree approach and its improved predictability are some highlights of this work. Through the development of an innovative validation subroutine based on a permutation approach and the use of external information (i.e., operons), lack of a priori knowledge for undetected proteins was overcome. The integrative methodologies allowed for the identification of undetected proteins for Desulfovibrio vulgaris and Shewanella oneidensis for further biological exploration in laboratories towards finding functional relationships. In an effort to better understand diseases such as cancer at different developmental stages, the Microscale Life Science Center headquartered at the Arizona State University is pursuing single-cell studies by developing novel technologies. This research arranged and applied a statistical framework that tackled the following challenges: random noise, heterogeneous dynamic systems with multiple states, and understanding cell behavior within and across different Barrett's esophageal epithelial cell lines using oxygen consumption curves. These curves were characterized with good empirical fit using nonlinear models with simple structures which allowed extraction of a large number of features. Application of a supervised classification model to these features and the integration of experimental factors allowed for identification of subtle patterns among different cell types visualized through multidimensional scaling. Motivated by the challenges of analyzing real-time measurements, we further explored a unique two-dimensional representation of multiple time series using a wavelet approach which showcased promising results towards less complex approximations. Also, the benefits of external information were explored to improve the image representation.
ContributorsTorres Garcia, Wandaliz (Author) / Meldrum, Deirdre R. (Thesis advisor) / Runger, George C. (Thesis advisor) / Gel, Esma S. (Committee member) / Li, Jing (Committee member) / Zhang, Weiwen (Committee member) / Arizona State University (Publisher)
Created2011
Description
A statement appearing in social media provides a very significant challenge for determining the provenance of the statement. Provenance describes the origin, custody, and ownership of something. Most statements appearing in social media are not published with corresponding provenance data. However, the same characteristics that make the social media environment challenging, including the massive amounts of data available, large numbers of users, and a highly dynamic environment, provide unique and untapped opportunities for solving the provenance problem for social media. Current approaches for tracking provenance data do not scale for online social media and consequently there is a gap in provenance methodologies and technologies providing exciting research opportunities. The guiding vision is the use of social media information itself to realize a useful amount of provenance data for information in social media. This departs from traditional approaches for data provenance which rely on a central store of provenance information. The contemporary online social media environment is an enormous and constantly updated "central store" that can be mined for provenance information that is not readily made available to the average social media user. This research introduces an approach and builds a foundation aimed at realizing a provenance data capability for social media users that is not accessible today.
ContributorsBarbier, Geoffrey P (Author) / Liu, Huan (Thesis advisor) / Bell, Herbert (Committee member) / Li, Baoxin (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2011
Description
Multi-label learning, which deals with data associated with multiple labels simultaneously, is ubiquitous in real-world applications. To overcome the curse of dimensionality in multi-label learning, in this thesis I study multi-label dimensionality reduction, which extracts a small number of features by removing the irrelevant, redundant, and noisy information while considering the correlation among different labels in multi-label learning. Specifically, I propose Hypergraph Spectral Learning (HSL) to perform dimensionality reduction for multi-label data by exploiting correlations among different labels using a hypergraph. The regularization effect on the classical dimensionality reduction algorithm known as Canonical Correlation Analysis (CCA) is elucidated in this thesis. The relationship between CCA and Orthonormalized Partial Least Squares (OPLS) is also investigated. To perform dimensionality reduction efficiently for large-scale problems, two efficient implementations are proposed for a class of dimensionality reduction algorithms, including canonical correlation analysis, orthonormalized partial least squares, linear discriminant analysis, and hypergraph spectral learning. The first approach is a direct least squares approach which allows the use of different regularization penalties, but is applicable under a certain assumption; the second one is a two-stage approach which can be applied in the regularization setting without any assumption. Furthermore, an online implementation for the same class of dimensionality reduction algorithms is proposed when the data comes sequentially. A Matlab toolbox for multi-label dimensionality reduction has been developed and released. The proposed algorithms have been applied successfully in the Drosophila gene expression pattern image annotation. The experimental results on some benchmark data sets in multi-label learning also demonstrate the effectiveness and efficiency of the proposed algorithms.
ContributorsSun, Liang (Author) / Ye, Jieping (Thesis advisor) / Li, Baoxin (Committee member) / Liu, Huan (Committee member) / Mittelmann, Hans D. (Committee member) / Arizona State University (Publisher)
Created2011
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
How to teach a machine to understand natural language? This question is a long-standing challenge in Artificial Intelligence. Several tasks are designed to measure the progress of this challenge. Question Answering is one such task that evaluates a machine's ability to understand natural language, where it reads a passage of text or an image and answers comprehension questions. In recent years, the development of transformer-based language models and large-scale human-annotated datasets has led to remarkable progress in the field of question answering. However, several disadvantages of fully supervised question answering systems have been observed. Such as generalizing to unseen out-of-distribution domains, linguistic style differences in questions, and adversarial samples. This thesis proposes implicitly supervised question answering systems trained using knowledge acquisition from external knowledge sources and new learning methods that provide inductive biases to learn question answering. In particular, the following research projects are discussed: (1) Knowledge Acquisition methods: these include semantic and abductive information retrieval for seeking missing knowledge, a method to represent unstructured text corpora as a knowledge graph, and constructing a knowledge base for implicit commonsense reasoning. (2) Learning methods: these include Knowledge Triplet Learning, a method over knowledge graphs; Test-Time Learning, a method to generalize to an unseen out-of-distribution context; WeaQA, a method to learn visual question answering using image captions without strong supervision; WeaSel, weakly supervised method for relative spatial reasoning; and a new paradigm for unsupervised natural language inference. These methods potentially provide a new research direction to overcome the pitfalls of direct supervision.
ContributorsBanerjee, Pratyay (Author) / Baral, Chitta (Thesis advisor) / Yang, Yezhou (Committee member) / Blanco, Eduardo (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2022
Description
Data mining, also known as big data analysis, has been identified as a critical and challenging process for a variety of applications in real-world problems. Numerous datasets are collected and generated every day to store the information. The rise in the number of data volumes and data modality has resulted in the increased demand for data mining methods and strategies of finding anomalies, patterns, and correlations within large data sets to predict outcomes. Effective machine learning methods are widely adapted to build the data mining pipeline for various purposes like business understanding, data understanding, data preparation, modeling, evaluation, and deployment. The major challenges for effectively and efficiently mining big data include (1) data heterogeneity and (2) missing data. Heterogeneity is the natural characteristic of big data, as the data is typically collected from different sources with diverse formats. The missing value is the most common issue faced by the heterogeneous data analysis, which resulted from variety of factors including the data collecting processing, user initiatives, erroneous data entries, and so on. In response to these challenges, in this thesis, three main research directions with application scenarios have been investigated: (1) Mining and Formulating Heterogeneous Data, (2) missing value imputation strategy in various application scenarios in both offline and online manner, and (3) missing value imputation for multi-modality data. Multiple strategies with theoretical analysis are presented, and the evaluation of the effectiveness of the proposed algorithms compared with state-of-the-art methods is discussed.
Contributorsliu, Xu (Author) / He, Jingrui (Thesis advisor) / Xue, Guoliang (Thesis advisor) / Li, Baoxin (Committee member) / Tong, Hanghang (Committee member) / Arizona State University (Publisher)
Created2021
Description
The rapid advancements of technology have greatly extended the ubiquitous nature of smartphones acting as a gateway to numerous social media applications. This brings an immense convenience to the users of these applications wishing to stay connected to other individuals through sharing their statuses, posting their opinions, experiences, suggestions, etc on online social networks (OSNs). Exploring and analyzing this data has a great potential to enable deep and fine-grained insights into the behavior, emotions, and language of individuals in a society. This proposed dissertation focuses on utilizing these online social footprints to research two main threads – 1) Analysis: to study the behavior of individuals online (content analysis) and 2) Synthesis: to build models that influence the behavior of individuals offline (incomplete action models for decision-making).
A large percentage of posts shared online are in an unrestricted natural language format that is meant for human consumption. One of the demanding problems in this context is to leverage and develop approaches to automatically extract important insights from this incessant massive data pool. Efforts in this direction emphasize mining or extracting the wealth of latent information in the data from multiple OSNs independently. The first thread of this dissertation focuses on analytics to investigate the differentiated content-sharing behavior of individuals. The second thread of this dissertation attempts to build decision-making systems using social media data.
The results of the proposed dissertation emphasize the importance of considering multiple data types while interpreting the content shared on OSNs. They highlight the unique ways in which the data and the extracted patterns from text-based platforms or visual-based platforms complement and contrast in terms of their content. The proposed research demonstrated that, in many ways, the results obtained by focusing on either only text or only visual elements of content shared online could lead to biased insights. On the other hand, it also shows the power of a sequential set of patterns that have some sort of precedence relationships and collaboration between humans and automated planners.
A large percentage of posts shared online are in an unrestricted natural language format that is meant for human consumption. One of the demanding problems in this context is to leverage and develop approaches to automatically extract important insights from this incessant massive data pool. Efforts in this direction emphasize mining or extracting the wealth of latent information in the data from multiple OSNs independently. The first thread of this dissertation focuses on analytics to investigate the differentiated content-sharing behavior of individuals. The second thread of this dissertation attempts to build decision-making systems using social media data.
The results of the proposed dissertation emphasize the importance of considering multiple data types while interpreting the content shared on OSNs. They highlight the unique ways in which the data and the extracted patterns from text-based platforms or visual-based platforms complement and contrast in terms of their content. The proposed research demonstrated that, in many ways, the results obtained by focusing on either only text or only visual elements of content shared online could lead to biased insights. On the other hand, it also shows the power of a sequential set of patterns that have some sort of precedence relationships and collaboration between humans and automated planners.
ContributorsManikonda, Lydia (Author) / Kambhampati, Subbarao (Thesis advisor) / Liu, Huan (Committee member) / Li, Baoxin (Committee member) / De Choudhury, Munmun (Committee member) / Kamar, Ece (Committee member) / Arizona State University (Publisher)
Created2019
Description
Online health forums provide a convenient channel for patients, caregivers, and medical professionals to share their experience, support and encourage each other, and form health communities. The fast growing content in health forums provides a large repository for people to seek valuable information. A forum user can issue a keyword query to search health forums regarding to some specific questions, e.g., what treatments are effective for a disease symptom? A medical researcher can discover medical knowledge in a timely and large-scale fashion by automatically aggregating the latest evidences emerging in health forums.
This dissertation studies how to effectively discover information in health forums. Several challenges have been identified. First, the existing work relies on the syntactic information unit, such as a sentence, a post, or a thread, to bind different pieces of information in a forum. However, most of information discovery tasks should be based on the semantic information unit, a patient. For instance, given a keyword query that involves the relationship between a treatment and side effects, it is expected that the matched keywords refer to the same patient. In this work, patient-centered mining is proposed to mine patient semantic information units. In a patient information unit, the health information, such as diseases, symptoms, treatments, effects, and etc., is connected by the corresponding patient.
Second, the information published in health forums has varying degree of quality. Some information includes patient-reported personal health experience, while others can be hearsay. In this work, a context-aware experience extraction framework is proposed to mine patient-reported personal health experience, which can be used for evidence-based knowledge discovery or finding patients with similar experience.
At last, the proposed patient-centered and experience-aware mining framework is used to build a patient health information database for effectively discovering adverse drug reactions (ADRs) from health forums. ADRs have become a serious health problem and even a leading cause of death in the United States. Health forums provide valuable evidences in a large scale and in a timely fashion through the active participation of patients, caregivers, and doctors. Empirical evaluation shows the effectiveness of the proposed approach.
This dissertation studies how to effectively discover information in health forums. Several challenges have been identified. First, the existing work relies on the syntactic information unit, such as a sentence, a post, or a thread, to bind different pieces of information in a forum. However, most of information discovery tasks should be based on the semantic information unit, a patient. For instance, given a keyword query that involves the relationship between a treatment and side effects, it is expected that the matched keywords refer to the same patient. In this work, patient-centered mining is proposed to mine patient semantic information units. In a patient information unit, the health information, such as diseases, symptoms, treatments, effects, and etc., is connected by the corresponding patient.
Second, the information published in health forums has varying degree of quality. Some information includes patient-reported personal health experience, while others can be hearsay. In this work, a context-aware experience extraction framework is proposed to mine patient-reported personal health experience, which can be used for evidence-based knowledge discovery or finding patients with similar experience.
At last, the proposed patient-centered and experience-aware mining framework is used to build a patient health information database for effectively discovering adverse drug reactions (ADRs) from health forums. ADRs have become a serious health problem and even a leading cause of death in the United States. Health forums provide valuable evidences in a large scale and in a timely fashion through the active participation of patients, caregivers, and doctors. Empirical evaluation shows the effectiveness of the proposed approach.
ContributorsLiu, Yunzhong (Author) / Chen, Yi (Thesis advisor) / Liu, Huan (Thesis advisor) / Li, Baoxin (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2016
Description
With the advent of Internet, the data being added online is increasing at enormous rate. Though search engines are using IR techniques to facilitate the search requests from users, the results are not effective towards the search query of the user. The search engine user has to go through certain webpages before getting at the webpage he/she wanted. This problem of Information Overload can be solved using Automatic Text Summarization. Summarization is a process of obtaining at abridged version of documents so that user can have a quick view to understand what exactly the document is about. Email threads from W3C are used in this system. Apart from common IR features like Term Frequency, Inverse Document Frequency, Term Rank, a variation of page rank based on graph model, which can cluster the words with respective to word ambiguity, is implemented. Term Rank also considers the possibility of co-occurrence of words with the corpus and evaluates the rank of the word accordingly. Sentences of email threads are ranked as per features and summaries are generated. System implemented the concept of pyramid evaluation in content selection. The system can be considered as a framework for Unsupervised Learning in text summarization.
ContributorsNadella, Sravan (Author) / Davulcu, Hasan (Thesis advisor) / Li, Baoxin (Committee member) / Sen, Arunabha (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