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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

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
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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

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
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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

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
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Description

The research presented in this Honors Thesis provides development in machine learning models which predict future states of a system with unknown dynamics, based on observations of the system. Two case studies are presented for (1) a non-conservative pendulum and (2) a differential game dictating a two-car uncontrolled intersection scenario.

The research presented in this Honors Thesis provides development in machine learning models which predict future states of a system with unknown dynamics, based on observations of the system. Two case studies are presented for (1) a non-conservative pendulum and (2) a differential game dictating a two-car uncontrolled intersection scenario. In the paper we investigate how learning architectures can be manipulated for problem specific geometry. The result of this research provides that these problem specific models are valuable for accurate learning and predicting the dynamics of physics systems.<br/><br/>In order to properly model the physics of a real pendulum, modifications were made to a prior architecture which was sufficient in modeling an ideal pendulum. The necessary modifications to the previous network [13] were problem specific and not transferrable to all other non-conservative physics scenarios. The modified architecture successfully models real pendulum dynamics. This case study provides a basis for future research in augmenting the symplectic gradient of a Hamiltonian energy function to provide a generalized, non-conservative physics model.<br/><br/>A problem specific architecture was also utilized to create an accurate model for the two-car intersection case. The Costate Network proved to be an improvement from the previously used Value Network [17]. Note that this comparison is applied lightly due to slight implementation differences. The development of the Costate Network provides a basis for using characteristics to decompose functions and create a simplified learning problem.<br/><br/>This paper is successful in creating new opportunities to develop physics models, in which the sample cases should be used as a guide for modeling other real and pseudo physics. Although the focused models in this paper are not generalizable, it is important to note that these cases provide direction for future research.

ContributorsMerry, Tanner (Author) / Ren, Yi (Thesis director) / Zhang, Wenlong (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

High-entropy alloys possessing mechanical, chemical, and electrical properties that far exceed those of conventional alloys have the potential to make a significant impact on many areas of engineering. Identifying element combinations and configurations to form these alloys, however, is a difficult, time-consuming, computationally intensive task. Machine learning has revolutionized many

High-entropy alloys possessing mechanical, chemical, and electrical properties that far exceed those of conventional alloys have the potential to make a significant impact on many areas of engineering. Identifying element combinations and configurations to form these alloys, however, is a difficult, time-consuming, computationally intensive task. Machine learning has revolutionized many different fields due to its ability to generalize well to different problems and produce computationally efficient, accurate predictions regarding the system of interest. In this thesis, we demonstrate the effectiveness of machine learning models applied to toy cases representative of simplified physics that are relevant to high-entropy alloy simulation. We show these models are effective at learning nonlinear dynamics for single and multi-particle cases and that more work is needed to accurately represent complex cases in which the system dynamics are chaotic. This thesis serves as a demonstration of the potential benefits of machine learning applied to high-entropy alloy simulations to generate fast, accurate predictions of nonlinear dynamics.

ContributorsDaly, John H (Author) / Ren, Yi (Thesis director) / Zhuang, Houlong (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
Description

Robots are often used in long-duration scenarios, such as on the surface of Mars,where they may need to adapt to environmental changes. Typically, robots have been built specifically for single tasks, such as moving boxes in a warehouse

Robots are often used in long-duration scenarios, such as on the surface of Mars,where they may need to adapt to environmental changes. Typically, robots have been built specifically for single tasks, such as moving boxes in a warehouse or surveying construction sites. However, there is a modern trend away from human hand-engineering and toward robot learning. To this end, the ideal robot is not engineered,but automatically designed for a specific task. This thesis focuses on robots which learn path-planning algorithms for specific environments. Learning is accomplished via genetic programming. Path-planners are represented as Python code, which is optimized via Pareto evolution. These planners are encouraged to explore curiously and efficiently. This research asks the questions: “How can robots exhibit life-long learning where they adapt to changing environments in a robust way?”, and “How can robots learn to be curious?”.

ContributorsSaldyt, Lucas P (Author) / Ben Amor, Heni (Thesis director) / Pavlic, Theodore (Committee member) / Computer Science and Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Colorimetric assays are an important tool in point-of-care testing that offers several advantages to traditional testing methods such as rapid response times and inexpensive costs. A factor that currently limits the portability and accessibility of these assays are methods that can objectively determine the results of these assays. Current solutions

Colorimetric assays are an important tool in point-of-care testing that offers several advantages to traditional testing methods such as rapid response times and inexpensive costs. A factor that currently limits the portability and accessibility of these assays are methods that can objectively determine the results of these assays. Current solutions consist of creating a test reader that standardizes the conditions the strip is under before being measured in some way. However, this increases the cost and decreases the portability of these assays. The focus of this study is to create a machine learning algorithm that can objectively determine results of colorimetric assays under varying conditions. To ensure the flexibility of a model to several types of colorimetric assays, three models were trained on the same convolutional neural network with different datasets. The images these models are trained on consist of positive and negative images of ETG, fentanyl, and HPV Antibodies test strips taken under different lighting and background conditions. A fourth model is trained on an image set composed of all three strip types. The results from these models show it is able to predict positive and negative results to a high level of accuracy.

ContributorsFisher, Rachel (Author) / Blain Christen, Jennifer (Thesis director) / Anderson, Karen (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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Description

Developed a business product with a team of CS students.

ContributorsPerri, Cole Thomas (Co-author) / Hernandez, Maximilliano (Co-author) / Schneider, Kaitlin (Co-author) / Call, Andy (Thesis director) / Hunt, Neil (Committee member) / School of Accountancy (Contributor) / Watts College of Public Service & Community Solut (Contributor) / WPC Graduate Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2021-05
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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

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
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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

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