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- All Subjects: Bioinformatics
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Description
Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. Genes have widely different pertinences to the etiology and pathology of diseases. Thus, they can be ranked according to their disease-significance on a genomic scale, which is the subject of gene prioritization. Given a set of genes known to be related to a disease, it is reasonable to use them as a basis to determine the significance of other candidate genes, which will then be ranked based on the association they exhibit with respect to the given set of known genes. Experimental and computational data of various kinds have different reliability and relevance to a disease under study. This work presents a gene prioritization method based on integrated biological networks that incorporates and models the various levels of relevance and reliability of diverse sources. The method is shown to achieve significantly higher performance as compared to two well-known gene prioritization algorithms. Essentially, no bias in the performance was seen as it was applied to diseases of diverse ethnology, e.g., monogenic, polygenic and cancer. The method was highly stable and robust against significant levels of noise in the data. Biological networks are often sparse, which can impede the operation of associationbased gene prioritization algorithms such as the one presented here from a computational perspective. As a potential approach to overcome this limitation, we explore the value that transcription factor binding sites can have in elucidating suitable targets. Transcription factors are needed for the expression of most genes, especially in higher organisms and hence genes can be associated via their genetic regulatory properties. While each transcription factor recognizes specific DNA sequence patterns, such patterns are mostly unknown for many transcription factors. Even those that are known are inconsistently reported in the literature, implying a potentially high level of inaccuracy. We developed computational methods for prediction and improvement of transcription factor binding patterns. Tests performed on the improvement method by employing synthetic patterns under various conditions showed that the method is very robust and the patterns produced invariably converge to nearly identical series of patterns. Preliminary tests were conducted to incorporate knowledge from transcription factor binding sites into our networkbased model for prioritization, with encouraging results. To validate these approaches in a disease-specific context, we built a schizophreniaspecific network based on the inferred associations and performed a comprehensive prioritization of human genes with respect to the disease. These results are expected to be validated empirically, but computational validation using known targets are very positive.
ContributorsLee, Jang (Author) / Gonzalez, Graciela (Thesis advisor) / Ye, Jieping (Committee member) / Davulcu, Hasan (Committee member) / Gallitano-Mendel, Amelia (Committee member) / Arizona State University (Publisher)
Created2011
Description
Situations of sensory overload are steadily becoming more frequent as the ubiquity of technology approaches reality--particularly with the advent of socio-communicative smartphone applications, and pervasive, high speed wireless networks. Although the ease of accessing information has improved our communication effectiveness and efficiency, our visual and auditory modalities--those modalities that today's computerized devices and displays largely engage--have become overloaded, creating possibilities for distractions, delays and high cognitive load; which in turn can lead to a loss of situational awareness, increasing chances for life threatening situations such as texting while driving. Surprisingly, alternative modalities for information delivery have seen little exploration. Touch, in particular, is a promising candidate given that it is our largest sensory organ with impressive spatial and temporal acuity. Although some approaches have been proposed for touch-based information delivery, they are not without limitations including high learning curves, limited applicability and/or limited expression. This is largely due to the lack of a versatile, comprehensive design theory--specifically, a theory that addresses the design of touch-based building blocks for expandable, efficient, rich and robust touch languages that are easy to learn and use. Moreover, beyond design, there is a lack of implementation and evaluation theories for such languages. To overcome these limitations, a unified, theoretical framework, inspired by natural, spoken language, is proposed called Somatic ABC's for Articulating (designing), Building (developing) and Confirming (evaluating) touch-based languages. To evaluate the usefulness of Somatic ABC's, its design, implementation and evaluation theories were applied to create communication languages for two very unique application areas: audio described movies and motor learning. These applications were chosen as they presented opportunities for complementing communication by offloading information, typically conveyed visually and/or aurally, to the skin. For both studies, it was found that Somatic ABC's aided the design, development and evaluation of rich somatic languages with distinct and natural communication units.
ContributorsMcDaniel, Troy Lee (Author) / Panchanathan, Sethuraman (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Santello, Marco (Committee member) / Arizona State University (Publisher)
Created2012
Description
Engineering an object means engineering the process that creates the object. Today, software can make the task of tracking these processes robust and straightforward. When engineering requirements are strict and strenuous, software custom-built for such processes can prove essential. The work for this project was developing ICDB, an inventory control and build management system created for spacecraft engineers at ASU to record each step of their engineering processes. In-house development means ICDB is more precisely designed around its users' functionality and cost requirements than most off-the-shelf commercial offerings. By placing a complex relational database behind an intuitive web application, ICDB enables organizations and their users to create and store parts libraries, assembly designs, purchasing and location records for inventory items, and more.
ContributorsNoss, Karl Friederich (Author) / Davulcu, Hasan (Thesis director) / Rios, Ken (Committee member) / Computer Science and Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Proliferation of social media websites and discussion forums in the last decade has resulted in social media mining emerging as an effective mechanism to extract consumer patterns. Most research on social media and pharmacovigilance have concentrated on
Adverse Drug Reaction (ADR) identification. Such methods employ a step of drug search followed by classification of the associated text as consisting an ADR or not. Although this method works efficiently for ADR classifications, if ADR evidence is present in users posts over time, drug mentions fail to capture such ADRs. It also fails to record additional user information which may provide an opportunity to perform an in-depth analysis for lifestyle habits and possible reasons for any medical problems.
Pre-market clinical trials for drugs generally do not include pregnant women, and so their effects on pregnancy outcomes are not discovered early. This thesis presents a thorough, alternative strategy for assessing the safety profiles of drugs during pregnancy by utilizing user timelines from social media. I explore the use of a variety of state-of-the-art social media mining techniques, including rule-based and machine learning techniques, to identify pregnant women, monitor their drug usage patterns, categorize their birth outcomes, and attempt to discover associations between drugs and bad birth outcomes.
The technique used models user timelines as longitudinal patient networks, which provide us with a variety of key information about pregnancy, drug usage, and post-
birth reactions. I evaluate the distinct parts of the pipeline separately, validating the usefulness of each step. The approach to use user timelines in this fashion has produced very encouraging results, and can be employed for a range of other important tasks where users/patients are required to be followed over time to derive population-based measures.
Adverse Drug Reaction (ADR) identification. Such methods employ a step of drug search followed by classification of the associated text as consisting an ADR or not. Although this method works efficiently for ADR classifications, if ADR evidence is present in users posts over time, drug mentions fail to capture such ADRs. It also fails to record additional user information which may provide an opportunity to perform an in-depth analysis for lifestyle habits and possible reasons for any medical problems.
Pre-market clinical trials for drugs generally do not include pregnant women, and so their effects on pregnancy outcomes are not discovered early. This thesis presents a thorough, alternative strategy for assessing the safety profiles of drugs during pregnancy by utilizing user timelines from social media. I explore the use of a variety of state-of-the-art social media mining techniques, including rule-based and machine learning techniques, to identify pregnant women, monitor their drug usage patterns, categorize their birth outcomes, and attempt to discover associations between drugs and bad birth outcomes.
The technique used models user timelines as longitudinal patient networks, which provide us with a variety of key information about pregnancy, drug usage, and post-
birth reactions. I evaluate the distinct parts of the pipeline separately, validating the usefulness of each step. The approach to use user timelines in this fashion has produced very encouraging results, and can be employed for a range of other important tasks where users/patients are required to be followed over time to derive population-based measures.
ContributorsChandrashekar, Pramod Bharadwaj (Author) / Davulcu, Hasan (Thesis advisor) / Gonzalez, Graciela (Thesis advisor) / Hsiao, Sharon (Committee member) / Arizona State University (Publisher)
Created2016
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
Continuous advancements in biomedical research have resulted in the production of vast amounts of scientific data and literature discussing them. The ultimate goal of computational biology is to translate these large amounts of data into actual knowledge of the complex biological processes and accurate life science models. The ability to rapidly and effectively survey the literature is necessary for the creation of large scale models of the relationships among biomedical entities as well as hypothesis generation to guide biomedical research. To reduce the effort and time spent in performing these activities, an intelligent search system is required. Even though many systems aid in navigating through this wide collection of documents, the vastness and depth of this information overload can be overwhelming. An automated extraction system coupled with a cognitive search and navigation service over these document collections would not only save time and effort, but also facilitate discovery of the unknown information implicitly conveyed in the texts. This thesis presents the different approaches used for large scale biomedical named entity recognition, and the challenges faced in each. It also proposes BioEve: an integrative framework to fuse a faceted search with information extraction to provide a search service that addresses the user's desire for "completeness" of the query results, not just the top-ranked ones. This information extraction system enables discovery of important semantic relationships between entities such as genes, diseases, drugs, and cell lines and events from biomedical text on MEDLINE, which is the largest publicly available database of the world's biomedical journal literature. It is an innovative search and discovery service that makes it easier to search
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
avigate and discover knowledge hidden in life sciences literature. To demonstrate the utility of this system, this thesis also details a prototype enterprise quality search and discovery service that helps researchers with a guided step-by-step query refinement, by suggesting concepts enriched in intermediate results, and thereby facilitating the "discover more as you search" paradigm.
ContributorsKanwar, Pradeep (Author) / Davulcu, Hasan (Thesis advisor) / Dinu, Valentin (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2010
Description
Access to real-time situational information including the relative position and motion of surrounding objects is critical for safe and independent travel. Object or obstacle (OO) detection at a distance is primarily a task of the visual system due to the high resolution information the eyes are able to receive from afar. As a sensory organ in particular, the eyes have an unparalleled ability to adjust to varying degrees of light, color, and distance. Therefore, in the case of a non-visual traveler, someone who is blind or low vision, access to visual information is unattainable if it is positioned beyond the reach of the preferred mobility device or outside the path of travel. Although, the area of assistive technology in terms of electronic travel aids (ETA’s) has received considerable attention over the last two decades; surprisingly, the field has seen little work in the area focused on augmenting rather than replacing current non-visual travel techniques, methods, and tools. Consequently, this work describes the design of an intuitive tactile language and series of wearable tactile interfaces (the Haptic Chair, HaptWrap, and HapBack) to deliver real-time spatiotemporal data. The overall intuitiveness of the haptic mappings conveyed through the tactile interfaces are evaluated using a combination of absolute identification accuracy of a series of patterns and subjective feedback through post-experiment surveys. Two types of spatiotemporal representations are considered: static patterns representing object location at a single time instance, and dynamic patterns, added in the HaptWrap, which represent object movement over a time interval. Results support the viability of multi-dimensional haptics applied to the body to yield an intuitive understanding of dynamic interactions occurring around the navigator during travel. Lastly, it is important to point out that the guiding principle of this work centered on providing the navigator with spatial knowledge otherwise unattainable through current mobility techniques, methods, and tools, thus, providing the \emph{navigator} with the information necessary to make informed navigation decisions independently, at a distance.
ContributorsDuarte, Bryan Joiner (Author) / McDaniel, Troy (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Venkateswara, Hemanth (Committee member) / Arizona State University (Publisher)
Created2020
Description
One of the most remarkable outcomes resulting from the evolution of the web into Web 2.0, has been the propelling of blogging into a widely adopted and globally accepted phenomenon. While the unprecedented growth of the Blogosphere has added diversity and enriched the media, it has also added complexity. To cope with the relentless expansion, many enthusiastic bloggers have embarked on voluntarily writing, tagging, labeling, and cataloguing their posts in hopes of reaching the widest possible audience. Unbeknown to them, this reaching-for-others process triggers the generation of a new kind of collective wisdom, a result of shared collaboration, and the exchange of ideas, purpose, and objectives, through the formation of associations, links, and relations. Mastering an understanding of the Blogosphere can greatly help facilitate the needs of the ever growing number of these users, as well as producers, service providers, and advertisers into facilitation of the categorization and navigation of this vast environment. This work explores a novel method to leverage the collective wisdom from the infused label space for blog search and discovery. The work demonstrates that the wisdom space can provide a most unique and desirable framework to which to discover the highly sought after background information that could aid in the building of classifiers. This work incorporates this insight into the construction of a better clustering of blogs which boosts the performance of classifiers for identifying more relevant labels for blogs, and offers a mechanism that can be incorporated into replacing spurious labels and mislabels in a multi-labeled space.
ContributorsGalan, Magdiel F (Author) / Liu, Huan (Thesis advisor) / Davulcu, Hasan (Committee member) / Ye, Jieping (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2015