Matching Items (229)
Description
Currently Java is making its way into the embedded systems and mobile devices like androids. The programs written in Java are compiled into machine independent binary class byte codes. A Java Virtual Machine (JVM) executes these classes. The Java platform additionally specifies the Java Native Interface (JNI). JNI allows Java code that runs within a JVM to interoperate with applications or libraries that are written in other languages and compiled to the host CPU ISA. JNI plays an important role in embedded system as it provides a mechanism to interact with libraries specific to the platform. This thesis addresses the overhead incurred in the JNI due to reflection and serialization when objects are accessed on android based mobile devices. It provides techniques to reduce this overhead. It also provides an API to access objects through its reference through pinning its memory location. The Android emulator was used to evaluate the performance of these techniques and we observed that there was 5 - 10 % performance gain in the new Java Native Interface.
ContributorsChandrian, Preetham (Author) / Lee, Yann-Hang (Thesis advisor) / Davulcu, Hasan (Committee member) / Li, Baoxin (Committee member) / Arizona State University (Publisher)
Created2011
Description
As pointed out in the keynote speech by H. V. Jagadish in SIGMOD'07, and also commonly agreed in the database community, the usability of structured data by casual users is as important as the data management systems' functionalities. A major hardness of using structured data is the problem of easily retrieving information from them given a user's information needs. Learning and using a structured query language (e.g., SQL and XQuery) is overwhelmingly burdensome for most users, as not only are these languages sophisticated, but the users need to know the data schema. Keyword search provides us with opportunities to conveniently access structured data and potentially significantly enhances the usability of structured data. However, processing keyword search on structured data is challenging due to various types of ambiguities such as structural ambiguity (keyword queries have no structure), keyword ambiguity (the keywords may not be accurate), user preference ambiguity (the user may have implicit preferences that are not indicated in the query), as well as the efficiency challenges due to large search space. This dissertation performs an expansive study on keyword search processing techniques as a gateway for users to access structured data and retrieve desired information. The key issues addressed include: (1) Resolving structural ambiguities in keyword queries by generating meaningful query results, which involves identifying relevant keyword matches, identifying return information, composing query results based on relevant matches and return information. (2) Resolving structural, keyword and user preference ambiguities through result analysis, including snippet generation, result differentiation, result clustering, result summarization/query expansion, etc. (3) Resolving the efficiency challenge in processing keyword search on structured data by utilizing and efficiently maintaining materialized views. These works deliver significant technical contributions towards building a full-fledged search engine for structured data.
ContributorsLiu, Ziyang (Author) / Chen, Yi (Thesis advisor) / Candan, Kasim S (Committee member) / Davulcu, Hasan (Committee member) / Jagadish, H V (Committee member) / Arizona State University (Publisher)
Created2011
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
The North American Monsoon System (NAMS) contributes ~55% of the annual rainfall in the Chihuahuan Desert during the summer months. Relatively frequent, intense storms during the NAMS increase soil moisture, reduce surface temperature and lead to runoff in ephemeral channels. Quantifying these processes, however, is difficult due to the sparse nature of coordinated observations. In this study, I present results from a field network of rain gauges (n = 5), soil probes (n = 48), channel flumes (n = 4), and meteorological equipment in a small desert shrubland watershed (~0.05 km2) in the Jornada Experimental. Using this high-resolution network, I characterize the temporal and spatial variability of rainfall, soil conditions and channel runoff within the watershed from June 2010 to September 2011, covering two NAMS periods. In addition, CO2, water and energy measurements at an eddy covariance tower quantify seasonal, monthly and event-scale changes in land-atmosphere states and fluxes. Results from this study indicate a strong seasonality in water and energy fluxes, with a reduction in Bowen ratio (B, the ratio of sensible to latent heat fluxes) from winter (B = 14) to summer (B = 3.3). This reduction is tied to shallow soil moisture availability during the summer (s = 0.040 m3/m3) as compared to the winter (s = 0.004 m3/m3). During the NAMS, I analyzed four consecutive rainfall-runoff events to quantify the soil moisture and channel flow responses and how water availability impacted the land-atmosphere fluxes. Spatial hydrologic variations during events occur over distances as short as ~15 m. The field network also allowed comparisons of several approaches to estimate evapotranspiration (ET). I found a more accurate ET estimate (a reduction of mean absolute error by 38%) when using distributed soil moisture data, as compared to a standard water balance approach based on the tower site. In addition, use of spatially-varied soil moisture data yielded a more reasonable relationship between ET and soil moisture, an important parameterization in many hydrologic models. The analyses illustrates the value of high-resolution sampling for quantifying seasonal fluxes in desert shrublands and their improvements in closing the water balance in small watersheds.
ContributorsTempleton, Ryan (Author) / Vivoni, Enrique R (Thesis advisor) / Mays, Larry (Committee member) / Fox, Peter (Committee member) / Arizona State University (Publisher)
Created2011
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
Most existing approaches to complex event processing over streaming data rely on the assumption that the matches to the queries are rare and that the goal of the system is to identify these few matches within the incoming deluge of data. In many applications, such as stock market analysis and user credit card purchase pattern monitoring, however the matches to the user queries are in fact plentiful and the system has to efficiently sift through these many matches to locate only the few most preferable matches. In this work, we propose a complex pattern ranking (CPR) framework for specifying top-k pattern queries over streaming data, present new algorithms to support top-k pattern queries in data streaming environments, and verify the effectiveness and efficiency of the proposed algorithms. The developed algorithms identify top-k matching results satisfying both patterns as well as additional criteria. To support real-time processing of the data streams, instead of computing top-k results from scratch for each time window, we maintain top-k results dynamically as new events come and old ones expire. We also develop new top-k join execution strategies that are able to adapt to the changing situations (e.g., sorted and random access costs, join rates) without having to assume a priori presence of data statistics. Experiments show significant improvements over existing approaches.
ContributorsWang, Xinxin (Author) / Candan, K. Selcuk (Thesis advisor) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011
Description
K-Nearest-Neighbors (KNN) search is a fundamental problem in many application domains such as database and data mining, information retrieval, machine learning, pattern recognition and plagiarism detection. Locality sensitive hash (LSH) is so far the most practical approximate KNN search algorithm for high dimensional data. Algorithms such as Multi-Probe LSH and LSH-Forest improve upon the basic LSH algorithm by varying hash bucket size dynamically at query time, so these two algorithms can answer different KNN queries adaptively. However, these two algorithms need a data access post-processing step after candidates' collection in order to get the final answer to the KNN query. In this thesis, Multi-Probe LSH with data access post-processing (Multi-Probe LSH with DAPP) algorithm and LSH-Forest with data access post-processing (LSH-Forest with DAPP) algorithm are improved by replacing the costly data access post-processing (DAPP) step with a much faster histogram-based post-processing (HBPP). Two HBPP algorithms: LSH-Forest with HBPP and Multi- Probe LSH with HBPP are presented in this thesis, both of them achieve the three goals for KNN search in large scale high dimensional data set: high search quality, high time efficiency, high space efficiency. None of the previous KNN algorithms can achieve all three goals. More specifically, it is shown that HBPP algorithms can always achieve high search quality (as good as LSH-Forest with DAPP and Multi-Probe LSH with DAPP) with much less time cost (one to several orders of magnitude speedup) and same memory usage. It is also shown that with almost same time cost and memory usage, HBPP algorithms can always achieve better search quality than LSH-Forest with random pick (LSH-Forest with RP) and Multi-Probe LSH with random pick (Multi-Probe LSH with RP). Moreover, to achieve a very high search quality, Multi-Probe with HBPP is always a better choice than LSH-Forest with HBPP, regardless of the distribution, size and dimension number of the data set.
ContributorsYu, Renwei (Author) / Candan, Kasim S (Thesis advisor) / Sapino, Maria L (Committee member) / Chen, Yi (Committee member) / Sundaram, Hari (Committee member) / Arizona State University (Publisher)
Created2011
Description
Data-driven applications are becoming increasingly complex with support for processing events and data streams in a loosely-coupled distributed environment, providing integrated access to heterogeneous data sources such as relational databases and XML documents. This dissertation explores the use of materialized views over structured heterogeneous data sources to support multiple query optimization in a distributed event stream processing framework that supports such applications involving various query expressions for detecting events, monitoring conditions, handling data streams, and querying data. Materialized views store the results of the computed view so that subsequent access to the view retrieves the materialized results, avoiding the cost of recomputing the entire view from base data sources. Using a service-based metadata repository that provides metadata level access to the various language components in the system, a heuristics-based algorithm detects the common subexpressions from the queries represented in a mixed multigraph model over relational and structured XML data sources. These common subexpressions can be relational, XML or a hybrid join over the heterogeneous data sources. This research examines the challenges in the definition and materialization of views when the heterogeneous data sources are retained in their native format, instead of converting the data to a common model. LINQ serves as the materialized view definition language for creating the view definitions. An algorithm is introduced that uses LINQ to create a data structure for the persistence of these hybrid views. Any changes to base data sources used to materialize views are captured and mapped to a delta structure. The deltas are then streamed within the framework for use in the incremental update of the materialized view. Algorithms are presented that use the magic sets query optimization approach to both efficiently materialize the views and to propagate the relevant changes to the views for incremental maintenance. Using representative scenarios over structured heterogeneous data sources, an evaluation of the framework demonstrates an improvement in performance. Thus, defining the LINQ-based materialized views over heterogeneous structured data sources using the detected common subexpressions and incrementally maintaining the views by using magic sets enhances the efficiency of the distributed event stream processing environment.
ContributorsChaudhari, Mahesh Balkrishna (Author) / Dietrich, Suzanne W (Thesis advisor) / Urban, Susan D (Committee member) / Davulcu, Hasan (Committee member) / Chen, Yi (Committee member) / Arizona State University (Publisher)
Created2011
Description
Local municipalities in the Phoenix Metropolitan Area have voiced an interest in purchasing alternate source water with lower DBP precursors. Along the primary source is a hydroelectric dam in which water will be diverted from. This project is an assessment of optimizing the potential blends of source water to a water treatment plant in an effort to enable them to more readily meet DBP regulations. To perform this analysis existing water treatment models were used in conjunction with historic water quality sampling data to predict chemical usage necessary to meet DBP regulations. A retrospective analysis was performed for the summer months of 2007 regarding potential for the WTP to reduce cost through optimizing the source water by an average of 30% over the four-month period, accumulating to overall treatment savings of $154 per MG ($82 per AF).
ContributorsRice, Jacelyn (Author) / Westerhoff, Paul (Thesis advisor) / Fox, Peter (Committee member) / Hristovski, Kiril (Committee member) / Arizona State University (Publisher)
Created2011
Description
This thesis addresses the problem of online schema updates where the goal is to be able to update relational database schemas without reducing the database system's availability. Unlike some other work in this area, this thesis presents an approach which is completely client-driven and does not require specialized database management systems (DBMS). Also, unlike other client-driven work, this approach provides support for a richer set of schema updates including vertical split (normalization), horizontal split, vertical and horizontal merge (union), difference and intersection. The update process automatically generates a runtime update client from a mapping between the old the new schemas. The solution has been validated by testing it on a relatively small database of around 300,000 records per table and less than 1 Gb, but with limited memory buffer size of 24 Mb. This thesis presents the study of the overhead of the update process as a function of the transaction rates and the batch size used to copy data from the old to the new schema. It shows that the overhead introduced is minimal for medium size applications and that the update can be achieved with no more than one minute of downtime.
ContributorsTyagi, Preetika (Author) / Bazzi, Rida (Thesis advisor) / Candan, Kasim S (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2011