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- All Subjects: Computer Science
- Creators: Baral, Chitta
- Creators: Xue, Guoliang
Description
Sparse learning is a technique in machine learning for feature selection and dimensionality reduction, to find a sparse set of the most relevant features. In any machine learning problem, there is a considerable amount of irrelevant information, and separating relevant information from the irrelevant information has been a topic of focus. In supervised learning like regression, the data consists of many features and only a subset of the features may be responsible for the result. Also, the features might require special structural requirements, which introduces additional complexity for feature selection. The sparse learning package, provides a set of algorithms for learning a sparse set of the most relevant features for both regression and classification problems. Structural dependencies among features which introduce additional requirements are also provided as part of the package. The features may be grouped together, and there may exist hierarchies and over- lapping groups among these, and there may be requirements for selecting the most relevant groups among them. In spite of getting sparse solutions, the solutions are not guaranteed to be robust. For the selection to be robust, there are certain techniques which provide theoretical justification of why certain features are selected. The stability selection, is a method for feature selection which allows the use of existing sparse learning methods to select the stable set of features for a given training sample. This is done by assigning probabilities for the features: by sub-sampling the training data and using a specific sparse learning technique to learn the relevant features, and repeating this a large number of times, and counting the probability as the number of times a feature is selected. Cross-validation which is used to determine the best parameter value over a range of values, further allows to select the best parameter value. This is done by selecting the parameter value which gives the maximum accuracy score. With such a combination of algorithms, with good convergence guarantees, stable feature selection properties and the inclusion of various structural dependencies among features, the sparse learning package will be a powerful tool for machine learning research. Modular structure, C implementation, ATLAS integration for fast linear algebraic subroutines, make it one of the best tool for a large sparse setting. The varied collection of algorithms, support for group sparsity, batch algorithms, are a few of the notable functionality of the SLEP package, and these features can be used in a variety of fields to infer relevant elements. The Alzheimer Disease(AD) is a neurodegenerative disease, which gradually leads to dementia. The SLEP package is used for feature selection for getting the most relevant biomarkers from the available AD dataset, and the results show that, indeed, only a subset of the features are required to gain valuable insights.
ContributorsThulasiram, Ramesh (Author) / Ye, Jieping (Thesis advisor) / Xue, Guoliang (Committee member) / Sen, Arunabha (Committee member) / Arizona State University (Publisher)
Created2011
Description
Reverse engineering gene regulatory networks (GRNs) is an important problem in the domain of Systems Biology. Learning GRNs is challenging due to the inherent complexity of the real regulatory networks and the heterogeneity of samples in available biomedical data. Real world biological data are commonly collected from broad surveys (profiling studies) and aggregate highly heterogeneous biological samples. Popular methods to learn GRNs simplistically assume a single universal regulatory network corresponding to available data. They neglect regulatory network adaptation due to change in underlying conditions and cellular phenotype or both. This dissertation presents a novel computational framework to learn common regulatory interactions and networks underlying the different sets of relatively homogeneous samples from real world biological data. The characteristic set of samples/conditions and corresponding regulatory interactions defines the cellular context (context). Context, in this dissertation, represents the deterministic transcriptional activity within the specific cellular regulatory mechanism. The major contributions of this framework include - modeling and learning context specific GRNs; associating enriched samples with contexts to interpret contextual interactions using biological knowledge; pruning extraneous edges from the context-specific GRN to improve the precision of the final GRNs; integrating multisource data to learn inter and intra domain interactions and increase confidence in obtained GRNs; and finally, learning combinatorial conditioning factors from the data to identify regulatory cofactors. The framework, Expattern, was applied to both real world and synthetic data. Interesting insights were obtained into mechanism of action of drugs on analysis of NCI60 drug activity and gene expression data. Application to refractory cancer data and Glioblastoma multiforme yield GRNs that were readily annotated with context-specific phenotypic information. Refractory cancer GRNs also displayed associations between distinct cancers, not observed through only clustering. Performance comparisons on multi-context synthetic data show the framework Expattern performs better than other comparable methods.
ContributorsSen, Ina (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Bittner, Michael (Committee member) / Konjevod, Goran (Committee member) / Arizona State University (Publisher)
Created2011
Description
Action language C+ is a formalism for describing properties of actions, which is based on nonmonotonic causal logic. The definite fragment of C+ is implemented in the Causal Calculator (CCalc), which is based on the reduction of nonmonotonic causal logic to propositional logic. This thesis describes the language of CCalc in terms of answer set programming (ASP), based on the translation of nonmonotonic causal logic to formulas under the stable model semantics. I designed a standard library which describes the constructs of the input language of CCalc in terms of ASP, allowing a simple modular method to represent CCalc input programs in the language of ASP. Using the combination of system F2LP and answer set solvers, this method achieves functionality close to that of CCalc while taking advantage of answer set solvers to yield efficient computation that is orders of magnitude faster than CCalc for many benchmark examples. In support of this, I created an automated translation system Cplus2ASP that implements the translation and encoding method and automatically invokes the necessary software to solve the translated input programs.
ContributorsCasolary, Michael (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Arizona State University (Publisher)
Created2011
Description
Multi-task learning (MTL) aims to improve the generalization performance (of the resulting classifiers) by learning multiple related tasks simultaneously. Specifically, MTL exploits the intrinsic task relatedness, based on which the informative domain knowledge from each task can be shared across multiple tasks and thus facilitate the individual task learning. It is particularly desirable to share the domain knowledge (among the tasks) when there are a number of related tasks but only limited training data is available for each task. Modeling the relationship of multiple tasks is critical to the generalization performance of the MTL algorithms. In this dissertation, I propose a series of MTL approaches which assume that multiple tasks are intrinsically related via a shared low-dimensional feature space. The proposed MTL approaches are developed to deal with different scenarios and settings; they are respectively formulated as mathematical optimization problems of minimizing the empirical loss regularized by different structures. For all proposed MTL formulations, I develop the associated optimization algorithms to find their globally optimal solution efficiently. I also conduct theoretical analysis for certain MTL approaches by deriving the globally optimal solution recovery condition and the performance bound. To demonstrate the practical performance, I apply the proposed MTL approaches on different real-world applications: (1) Automated annotation of the Drosophila gene expression pattern images; (2) Categorization of the Yahoo web pages. Our experimental results demonstrate the efficiency and effectiveness of the proposed algorithms.
ContributorsChen, Jianhui (Author) / Ye, Jieping (Thesis advisor) / Kumar, Sudhir (Committee member) / Liu, Huan (Committee member) / Xue, Guoliang (Committee member) / Arizona State University (Publisher)
Created2011
Description
In this dissertation I develop a deep theory of temporal planning well-suited to analyzing, understanding, and improving the state of the art implementations (as of 2012). At face-value the work is strictly theoretical; nonetheless its impact is entirely real and practical. The easiest portion of that impact to highlight concerns the notable improvements to the format of the temporal fragment of the International Planning Competitions (IPCs). Particularly: the theory I expound upon here is the primary cause of--and justification for--the altered (i) selection of benchmark problems, and (ii) notion of "winning temporal planner". For higher level motivation: robotics, web service composition, industrial manufacturing, business process management, cybersecurity, space exploration, deep ocean exploration, and logistics all benefit from applying domain-independent automated planning technique. Naturally, actually carrying out such case studies has much to offer. For example, we may extract the lesson that reasoning carefully about deadlines is rather crucial to planning in practice. More generally, effectively automating specifically temporal planning is well-motivated from applications. Entirely abstractly, the aim is to improve the theory of automated temporal planning by distilling from its practice. My thesis is that the key feature of computational interest is concurrency. To support, I demonstrate by way of compilation methods, worst-case counting arguments, and analysis of algorithmic properties such as completeness that the more immediately pressing computational obstacles (facing would-be temporal generalizations of classical planning systems) can be dealt with in theoretically efficient manner. So more accurately the technical contribution here is to demonstrate: The computationally significant obstacle to automated temporal planning that remains is just concurrency.
ContributorsCushing, William Albemarle (Author) / Kambhampati, Subbarao (Thesis advisor) / Weld, Daniel S. (Committee member) / Smith, David E. (Committee member) / Baral, Chitta (Committee member) / Davalcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2012
Description
Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups or graphs. In this thesis, I first propose to solve a sparse learning model with a general group structure, where the predefined groups may overlap with each other. Then, I present three real world applications which can benefit from the group structured sparse learning technique. In the first application, I study the Alzheimer's Disease diagnosis problem using multi-modality neuroimaging data. In this dataset, not every subject has all data sources available, exhibiting an unique and challenging block-wise missing pattern. In the second application, I study the automatic annotation and retrieval of fruit-fly gene expression pattern images. Combined with the spatial information, sparse learning techniques can be used to construct effective representation of the expression images. In the third application, I present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores help us to illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes.
ContributorsYuan, Lei (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Xue, Guoliang (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
Description
Linear Temporal Logic is gaining increasing popularity as a high level specification language for robot motion planning due to its expressive power and scalability of LTL control synthesis algorithms. This formalism, however, requires expert knowledge and makes it inaccessible to non-expert users. This thesis introduces a graphical specification environment to create high level motion plans to control robots in the field by converting a visual representation of the motion/task plan into a Linear Temporal Logic (LTL) specification. The visual interface is built on the Android tablet platform and provides functionality to create task plans through a set of well defined gestures and on screen controls. It uses the notion of waypoints to quickly and efficiently describe the motion plan and enables a variety of complex Linear Temporal Logic specifications to be described succinctly and intuitively by the user without the need for the knowledge and understanding of LTL specification. Thus, it opens avenues for its use by personnel in military, warehouse management, and search and rescue missions. This thesis describes the construction of LTL for various scenarios used for robot navigation using the visual interface developed and leverages the use of existing LTL based motion planners to carry out the task plan by a robot.
ContributorsSrinivas, Shashank (Author) / Fainekos, Georgios (Thesis advisor) / Baral, Chitta (Committee member) / Burleson, Winslow (Committee member) / Arizona State University (Publisher)
Created2013
Description
Answer Set Programming (ASP) is one of the most prominent and successful knowledge representation paradigms. The success of ASP is due to its expressive non-monotonic modeling language and its efficient computational methods originating from building propositional satisfiability solvers. The wide adoption of ASP has motivated several extensions to its modeling language in order to enhance expressivity, such as incorporating aggregates and interfaces with ontologies. Also, in order to overcome the grounding bottleneck of computation in ASP, there are increasing interests in integrating ASP with other computing paradigms, such as Constraint Programming (CP) and Satisfiability Modulo Theories (SMT). Due to the non-monotonic nature of the ASP semantics, such enhancements turned out to be non-trivial and the existing extensions are not fully satisfactory. We observe that one main reason for the difficulties rooted in the propositional semantics of ASP, which is limited in handling first-order constructs (such as aggregates and ontologies) and functions (such as constraint variables in CP and SMT) in natural ways. This dissertation presents a unifying view on these extensions by viewing them as instances of formulas with generalized quantifiers and intensional functions. We extend the first-order stable model semantics by by Ferraris, Lee, and Lifschitz to allow generalized quantifiers, which cover aggregate, DL-atoms, constraints and SMT theory atoms as special cases. Using this unifying framework, we study and relate different extensions of ASP. We also present a tight integration of ASP with SMT, based on which we enhance action language C+ to handle reasoning about continuous changes. Our framework yields a systematic approach to study and extend non-monotonic languages.
ContributorsMeng, Yunsong (Author) / Lee, Joohyung (Thesis advisor) / Ahn, Gail-Joon (Committee member) / Baral, Chitta (Committee member) / Fainekos, Georgios (Committee member) / Lifschitz, Vladimir (Committee member) / Arizona State University (Publisher)
Created2013
Description
Automating aspects of biocuration through biomedical information extraction could significantly impact biomedical research by enabling greater biocuration throughput and improving the feasibility of a wider scope. An important step in biomedical information extraction systems is named entity recognition (NER), where mentions of entities such as proteins and diseases are located within natural-language text and their semantic type is determined. This step is critical for later tasks in an information extraction pipeline, including normalization and relationship extraction. BANNER is a benchmark biomedical NER system using linear-chain conditional random fields and the rich feature set approach. A case study with BANNER locating genes and proteins in biomedical literature is described. The first corpus for disease NER adequate for use as training data is introduced, and employed in a case study of disease NER. The first corpus locating adverse drug reactions (ADRs) in user posts to a health-related social website is also described, and a system to locate and identify ADRs in social media text is created and evaluated. The rich feature set approach to creating NER feature sets is argued to be subject to diminishing returns, implying that additional improvements may require more sophisticated methods for creating the feature set. This motivates the first application of multivariate feature selection with filters and false discovery rate analysis to biomedical NER, resulting in a feature set at least 3 orders of magnitude smaller than the set created by the rich feature set approach. Finally, two novel approaches to NER by modeling the semantics of token sequences are introduced. The first method focuses on the sequence content by using language models to determine whether a sequence resembles entries in a lexicon of entity names or text from an unlabeled corpus more closely. The second method models the distributional semantics of token sequences, determining the similarity between a potential mention and the token sequences from the training data by analyzing the contexts where each sequence appears in a large unlabeled corpus. The second method is shown to improve the performance of BANNER on multiple data sets.
ContributorsLeaman, James Robert (Author) / Gonzalez, Graciela (Thesis advisor) / Baral, Chitta (Thesis advisor) / Cohen, Kevin B (Committee member) / Liu, Huan (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
Description
There has been a lot of research in the field of artificial intelligence about thinking machines. Alan Turing proposed a test to observe a machine's intelligent behaviour with respect to natural language conversation. The Winograd schema challenge is suggested as an alternative, to the Turing test. It needs inferencing capabilities, reasoning abilities and background knowledge to get the answer right. It involves a coreference resolution task in which a machine is given a sentence containing a situation which involves two entities, one pronoun and some more information about the situation and the machine has to come up with the right resolution of a pronoun to one of the entities. The complexity of the task is increased with the fact that the Winograd sentences are not constrained by one domain or specific sentence structure and it also contains a lot of human proper names. This modification makes the task of association of entities, to one particular word in the sentence, to derive the answer, difficult. I have developed a pronoun resolver system for the confined domain Winograd sentences. I have developed a classifier or filter which takes input sentences and decides to accept or reject them based on a particular criteria. Once the sentence is accepted. I run parsers on it to obtain the detailed analysis. Furthermore I have developed four answering modules which use world knowledge and inferencing mechanisms to try and resolve the pronoun. The four techniques I use are : ConceptNet knowledgebase, Search engine pattern counts,Narrative event chains and sentiment analysis. I have developed a particular aggregation mechanism for the answers from these modules to arrive at a final answer. I have used caching technique for the association relations that I obtain for different modules, so as to boost the performance. I run my system on the standard ‘nyu dataset’ of Winograd sentences and questions. This dataset is then restricted, by my classifier, to 90 sentences. I evaluate my system on this 90 sentence dataset. When I compare my results against the state of the art system on the same dataset, I get nearly 4.5 % improvement in the restricted domain.
ContributorsBudukh, Tejas Ulhas (Author) / Baral, Chitta (Thesis advisor) / VanLehn, Kurt (Committee member) / Davulcu, Hasan (Committee member) / Arizona State University (Publisher)
Created2013