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- All Subjects: artificial intelligence
- Creators: Arizona State University
Description
This thesis introduces the Model-Based Development of Multi-iRobot Toolbox (MBDMIRT), a Simulink-based toolbox designed to provide the means to acquire and practice the Model-Based Development (MBD) skills necessary to design real-time embedded system. The toolbox was developed in the Cyber-Physical System Laboratory at Arizona State University. The MBDMIRT toolbox runs under MATLAB/Simulink to simulate the movements of multiple iRobots and to control, after verification by simulation, multiple physical iRobots accordingly. It adopts the Simulink/Stateflow, which exemplifies an approach to MBD, to program the behaviors of the iRobots. The MBDMIRT toolbox reuses and augments the open-source MATLAB-Based Simulator for the iRobot Create from Cornell University to run the simulation. Regarding the mechanism of iRobot control, the MBDMIRT toolbox applies the MATLAB Toolbox for the iRobot Create (MTIC) from United States Naval Academy to command the physical iRobots. The MBDMIRT toolbox supports a timer in both the simulation and the control, which is based on the local clock of the PC running the toolbox. In addition to the build-in sensors of an iRobot, the toolbox can simulate four user-added sensors, which are overhead localization system (OLS), sonar sensors, a camera, and Light Detection And Ranging (LIDAR). While controlling a physical iRobot, the toolbox supports the StarGazer OLS manufactured by HAGISONIC, Inc.
ContributorsSu, Shih-Kai (Author) / Fainekos, Georgios E (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Artemiadis, Panagiotis K (Committee member) / Arizona State University (Publisher)
Created2012
Description
Biological organisms are made up of cells containing numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted, manifesting as disease symptoms. Thus, understanding these biochemical processes and their interrelationships is a primary task in biomedical research and a prerequisite for activities including diagnosing diseases and drug development. Scientists studying these interconnected processes have identified various pathways involved in drug metabolism, diseases, and signal transduction, etc. High-throughput technologies, new algorithms and speed improvements over the last decade have resulted in deeper knowledge about biological systems, leading to more refined pathways. Such pathways tend to be large and complex, making it difficult for an individual to remember all aspects. Thus, computer models are needed to represent and analyze them. The refinement activity itself requires reasoning with a pathway model by posing queries against it and comparing the results against the real biological system. Many existing models focus on structural and/or factoid questions, relying on surface-level information. These are generally not the kind of questions that a biologist may ask someone to test their understanding of biological processes. Examples of questions requiring understanding of biological processes are available in introductory college level biology text books. Such questions serve as a model for the question answering system developed in this thesis. Thus, the main goal of this thesis is to develop a system that allows the encoding of knowledge about biological pathways to answer questions demonstrating understanding of the pathways. To that end, a language is developed to specify a pathway and pose questions against it. Some existing tools are modified and used to accomplish this goal. The utility of the framework developed in this thesis is illustrated with applications in the biological domain. Finally, the question answering system is used in real world applications by extracting pathway knowledge from text and answering questions related to drug development.
ContributorsAnwar, Saadat (Author) / Baral, Chitta (Thesis advisor) / Inoue, Katsumi (Committee member) / Chen, Yi (Committee member) / Davulcu, Hasan (Committee member) / Lee, Joohyung (Committee member) / Arizona State University (Publisher)
Created2014
Description
Different logic-based knowledge representation formalisms have different limitations either with respect to expressivity or with respect to computational efficiency. First-order logic, which is the basis of Description Logics (DLs), is not suitable for defeasible reasoning due to its monotonic nature. The nonmonotonic formalisms that extend first-order logic, such as circumscription and default logic, are expressive but lack efficient implementations. The nonmonotonic formalisms that are based on the declarative logic programming approach, such as Answer Set Programming (ASP), have efficient implementations but are not expressive enough for representing and reasoning with open domains. This dissertation uses the first-order stable model semantics, which extends both first-order logic and ASP, to relate circumscription to ASP, and to integrate DLs and ASP, thereby partially overcoming the limitations of the formalisms. By exploiting the relationship between circumscription and ASP, well-known action formalisms, such as the situation calculus, the event calculus, and Temporal Action Logics, are reformulated in ASP. The advantages of these reformulations are shown with respect to the generality of the reasoning tasks that can be handled and with respect to the computational efficiency. The integration of DLs and ASP presented in this dissertation provides a framework for integrating rules and ontologies for the semantic web. This framework enables us to perform nonmonotonic reasoning with DL knowledge bases. Observing the need to integrate action theories and ontologies, the above results are used to reformulate the problem of integrating action theories and ontologies as a problem of integrating rules and ontologies, thus enabling us to use the computational tools developed in the context of the latter for the former.
ContributorsPalla, Ravi (Author) / Lee, Joohyung (Thesis advisor) / Baral, Chitta (Committee member) / Kambhampati, Subbarao (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2012
Description
Electronic devices based on various stimuli responsive polymers are anticipated to have great potential for applications in innovative electronics due to their inherent intelligence and flexibility. However, the electronic properties of these soft materials are poor and the applications have been limited due to their weak compatibility with functional materials. Therefore, the integration of stimuli responsive polymers with other functional materials like Silicon is strongly demanded. Here, we present successful strategies to integrate environmentally sensitive hydrogels with Silicon, a typical high-performance electronic material, and demonstrate the intelligent and stretchable capability of this system. The goal of this project is to develop integrated smart devices comprising of soft stimuli responsive polymeric-substrates with conventional semiconductor materials such as Silicon, which can respond to various external stimuli like pH, temperature, light etc. Specifically, these devices combine the merits of high quality crystalline semiconductor materials and the mechanical flexibility/stretchability of polymers. Our innovative system consists of ultra-thin Silicon ribbons bonded to an intelligently stretchable substrate which is intended to interpret and exert environmental signals and provide the desired stress relief. As one of the specific examples, we chose as a substrate the standard thermo-sensitive poly(N-isopropylacrylamide) (PNIPAAm) hydrogel with fast response and large deformation. In order to make the surface of the hydrogel waterproof and smooth for high-quality Silicon transfer, we introduced an intermediate layer of poly(dimethylsiloxane) (PDMS) between the substrate and the Silicon ribbons. The optical microscope results have shown that the system enables stiff Silicon ribbons to become adaptive and drivable by the soft environmentally sensitive substrate. Furthermore, we pioneered the development of complex geometries with two different methods: one is using stereolithography to electronically control the patterns and build up their profiles layer by layer; the other is integrating different multifunctional polymers. In this report, we have designed a bilayer structure comprising of a PNIPAAm hydrogel and a hybrid hydrogel of N-isopropylacrylamide (NIPAAm) and acrylic acid (AA). Typical variable curvatures can be obtained by the hydrogels with different dimensional expansion. These structures hold interesting possibilities in the design of electronic devices with tunable curvature.
ContributorsPan, Yuping (Author) / Dai, Lenore (Thesis advisor) / Jiang, Hanqing (Thesis advisor) / Lind, Mary Laura (Committee member) / Arizona State University (Publisher)
Created2012
Description
Automated planning problems classically involve finding a sequence of actions that transform an initial state to some state satisfying a conjunctive set of goals with no temporal constraints. But in many real-world problems, the best plan may involve satisfying only a subset of goals or missing defined goal deadlines. For example, this may be required when goals are logically conflicting, or when there are time or cost constraints such that achieving all goals on time may be too expensive. In this case, goals and deadlines must be declared as soft. I call these partial satisfaction planning (PSP) problems. In this work, I focus on particular types of PSP problems, where goals are given a quantitative value based on whether (or when) they are achieved. The objective is to find a plan with the best quality. A first challenge is in finding adequate goal representations that capture common types of goal achievement rewards and costs. One popular representation is to give a single reward on each goal of a planning problem. I further expand on this approach by allowing users to directly introduce utility dependencies, providing for changes of goal achievement reward directly based on the goals a plan achieves. After, I introduce time-dependent goal costs, where a plan incurs penalty if it will achieve a goal past a specified deadline. To solve PSP problems with goal utility dependencies, I look at using state-of-the-art methodologies currently employed for classical planning problems involving heuristic search. In doing so, one faces the challenge of simultaneously determining the best set of goals and plan to achieve them. This is complicated by utility dependencies defined by a user and cost dependencies within the plan. To address this, I introduce a set of heuristics based on combinations using relaxed plans and integer programming formulations. Further, I explore an approach to improve search through learning techniques by using automatically generated state features to find new states from which to search. Finally, the investigation into handling time-dependent goal costs leads us to an improved search technique derived from observations based on solving discretized approximations of cost functions.
ContributorsBenton, J (Author) / Kambhampati, Subbarao (Thesis advisor) / Baral, Chitta (Committee member) / Do, Minh B. (Committee member) / Smith, David E. (Committee member) / Langley, Pat (Committee member) / Arizona State University (Publisher)
Created2012
Description
As we migrate into an era of personalized medicine, understanding how bio-molecules interact with one another to form cellular systems is one of the key focus areas of systems biology. Several challenges such as the dynamic nature of cellular systems, uncertainty due to environmental influences, and the heterogeneity between individual patients render this a difficult task. In the last decade, several algorithms have been proposed to elucidate cellular systems from data, resulting in numerous data-driven hypotheses. However, due to the large number of variables involved in the process, many of which are unknown or not measurable, such computational approaches often lead to a high proportion of false positives. This renders interpretation of the data-driven hypotheses extremely difficult. Consequently, a dismal proportion of these hypotheses are subject to further experimental validation, eventually limiting their potential to augment existing biological knowledge. This dissertation develops a framework of computational methods for the analysis of such data-driven hypotheses leveraging existing biological knowledge. Specifically, I show how biological knowledge can be mapped onto these hypotheses and subsequently augmented through novel hypotheses. Biological hypotheses are learnt in three levels of abstraction -- individual interactions, functional modules and relationships between pathways, corresponding to three complementary aspects of biological systems. The computational methods developed in this dissertation are applied to high throughput cancer data, resulting in novel hypotheses with potentially significant biological impact.
ContributorsRamesh, Archana (Author) / Kim, Seungchan (Thesis advisor) / Langley, Patrick W (Committee member) / Baral, Chitta (Committee member) / Kiefer, Jeffrey (Committee member) / Arizona State University (Publisher)
Created2012
Description
Building computational models of human problem solving has been a longstanding goal in Artificial Intelligence research. The theories of cognitive architectures addressed this issue by embedding models of problem solving within them. This thesis presents an extended account of human problem solving and describes its implementation within one such theory of cognitive architecture--ICARUS. The document begins by reviewing the standard theory of problem solving, along with how previous versions of ICARUS have incorporated and expanded on it. Next it discusses some limitations of the existing mechanism and proposes four extensions that eliminate these limitations, elaborate the framework along interesting dimensions, and bring it into closer alignment with human problem-solving abilities. After this, it presents evaluations on four domains that establish the benefits of these extensions. The results demonstrate the system's ability to solve problems in various domains and its generality. In closing, it outlines related work and notes promising directions for additional research.
ContributorsTrivedi, Nishant (Author) / Langley, Patrick W (Thesis advisor) / VanLehn, Kurt (Committee member) / Kambhampati, Subbarao (Committee member) / Arizona State University (Publisher)
Created2011
Description
In the current millennium, extensive use of computers and the internet caused an exponential increase in information. Few research areas are as important as information extraction, which primarily involves extracting concepts and the relations between them from free text. Limitations in the size of training data, lack of lexicons and lack of relationship patterns are major factors for poor performance in information extraction. This is because the training data cannot possibly contain all concepts and their synonyms; and it contains only limited examples of relationship patterns between concepts. Creating training data, lexicons and relationship patterns is expensive, especially in the biomedical domain (including clinical notes) because of the depth of domain knowledge required of the curators. Dictionary-based approaches for concept extraction in this domain are not sufficient to effectively overcome the complexities that arise because of the descriptive nature of human languages. For example, there is a relatively higher amount of abbreviations (not all of them present in lexicons) compared to everyday English text. Sometimes abbreviations are modifiers of an adjective (e.g. CD4-negative) rather than nouns (and hence, not usually considered named entities). There are many chemical names with numbers, commas, hyphens and parentheses (e.g. t(3;3)(q21;q26)), which will be separated by most tokenizers. In addition, partial words are used in place of full words (e.g. up- and downregulate); and some of the words used are highly specialized for the domain. Clinical notes contain peculiar drug names, anatomical nomenclature, other specialized names and phrases that are not standard in everyday English or in published articles (e.g. "l shoulder inj"). State of the art concept extraction systems use machine learning algorithms to overcome some of these challenges. However, they need a large annotated corpus for every concept class that needs to be extracted. A novel natural language processing approach to minimize this limitation in concept extraction is proposed here using distributional semantics. Distributional semantics is an emerging field arising from the notion that the meaning or semantics of a piece of text (discourse) depends on the distribution of the elements of that discourse in relation to its surroundings. Distributional information from large unlabeled data is used to automatically create lexicons for the concepts to be tagged, clusters of contextually similar words, and thesauri of distributionally similar words. These automatically generated lexical resources are shown here to be more useful than manually created lexicons for extracting concepts from both literature and narratives. Further, machine learning features based on distributional semantics are shown to improve the accuracy of BANNER, and could be used in other machine learning systems such as cTakes to improve their performance. In addition, in order to simplify the sentence patterns and facilitate association extraction, a new algorithm using a "shotgun" approach is proposed. The goal of sentence simplification has traditionally been to reduce the grammatical complexity of sentences while retaining the relevant information content and meaning to enable better readability for humans and enhanced processing by parsers. Sentence simplification is shown here to improve the performance of association extraction systems for both biomedical literature and clinical notes. It helps improve the accuracy of protein-protein interaction extraction from the literature and also improves relationship extraction from clinical notes (such as between medical problems, tests and treatments). Overall, the two main contributions of this work include the application of sentence simplification to association extraction as described above, and the use of distributional semantics for concept extraction. The proposed work on concept extraction amalgamates for the first time two diverse research areas -distributional semantics and information extraction. This approach renders all the advantages offered in other semi-supervised machine learning systems, and, unlike other proposed semi-supervised approaches, it can be used on top of different basic frameworks and algorithms.
ContributorsJonnalagadda, Siddhartha Reddy (Author) / Gonzalez, Graciela H (Thesis advisor) / Cohen, Trevor A (Committee member) / Greenes, Robert A (Committee member) / Fridsma, Douglas B (Committee member) / Arizona State University (Publisher)
Created2011
Description
Natural Language Processing is a subject that combines computer science and linguistics, aiming to provide computers with the ability to understand natural language and to develop a more intuitive human-computer interaction. The research community has developed ways to translate natural language to mathematical formalisms. It has not yet been shown, however, how to automatically translate different kinds of knowledge in English to distinct formal languages. Most of the recent work presents the problem that the translation method aims to a specific formal language or is hard to generalize. In this research, I take a first step to overcome this difficulty and present two algorithms which take as input two lambda-calculus expressions G and H and compute a lambda-calculus expression F. The expression F returned by the first algorithm satisfies F@G=H and, in the case of the second algorithm, we obtain G@F=H. The lambda expressions represent the meanings of words and sentences. For each formal language that one desires to use with the algorithms, the language must be defined in terms of lambda calculus. Also, some additional concepts must be included. After doing this, given a sentence, its representation and knowing the representation of several words in the sentence, the algorithms can be used to obtain the representation of the other words in that sentence. In this work, I define two languages and show examples of their use with the algorithms. The algorithms are illustrated along with soundness and completeness proofs, the latter with respect to typed lambda-calculus formulas up to the second order. These algorithms are a core part of a natural language semantics system that translates sentences from English to formulas in different formal languages.
ContributorsAlvarez Gonzalez, Marcos (Author) / Baral, Chitta (Thesis advisor) / Lee, Joohyung (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2010
Description
The fields of pattern recognition and machine learning are on a fundamental quest to design systems that can learn the way humans do. One important aspect of human intelligence that has so far not been given sufficient attention is the capability of humans to express when they are certain about a decision, or when they are not. Machine learning techniques today are not yet fully equipped to be trusted with this critical task. This work seeks to address this fundamental knowledge gap. Existing approaches that provide a measure of confidence on a prediction such as learning algorithms based on the Bayesian theory or the Probably Approximately Correct theory require strong assumptions or often produce results that are not practical or reliable. The recently developed Conformal Predictions (CP) framework - which is based on the principles of hypothesis testing, transductive inference and algorithmic randomness - provides a game-theoretic approach to the estimation of confidence with several desirable properties such as online calibration and generalizability to all classification and regression methods. This dissertation builds on the CP theory to compute reliable confidence measures that aid decision-making in real-world problems through: (i) Development of a methodology for learning a kernel function (or distance metric) for optimal and accurate conformal predictors; (ii) Validation of the calibration properties of the CP framework when applied to multi-classifier (or multi-regressor) fusion; and (iii) Development of a methodology to extend the CP framework to continuous learning, by using the framework for online active learning. These contributions are validated on four real-world problems from the domains of healthcare and assistive technologies: two classification-based applications (risk prediction in cardiac decision support and multimodal person recognition), and two regression-based applications (head pose estimation and saliency prediction in images). The results obtained show that: (i) multiple kernel learning can effectively increase efficiency in the CP framework; (ii) quantile p-value combination methods provide a viable solution for fusion in the CP framework; and (iii) eigendecomposition of p-value difference matrices can serve as effective measures for online active learning; demonstrating promise and potential in using these contributions in multimedia pattern recognition problems in real-world settings.
ContributorsNallure Balasubramanian, Vineeth (Author) / Panchanathan, Sethuraman (Thesis advisor) / Ye, Jieping (Committee member) / Li, Baoxin (Committee member) / Vovk, Vladimir (Committee member) / Arizona State University (Publisher)
Created2010