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High accuracy sequence classification often requires the use of higher order Markov models (MMs). However, the number of MM parameters increases exponentially with the range of direct dependencies between sequence elements, thereby increasing the risk of over fitting when the data set is limited in size. We present abstraction augmented Markov models (AAMMs) that effectively reduce the number of numeric...
Identification of nodes relevant to a given node in a relational network is a basic problem in network analysis with great practical importance. Most existing network analysis algorithms utilize one single relation to define relevancy among nodes. However, in real world applications multiple relationships exist between nodes in a network. Therefore, network analysis algorithms that can make use of...
Real-world data mining applications call for effective strategies for learning predictive models from richly structured relational data. In this paper, we address the problem of learning classifiers from structured relational data that are annotated with relevant meta data. Specifically, we show how to learn classifiers at different levels of abstraction in a relational setting, where the structured...
We describe an approach to learning predictive models from large databases in settings where direct access to data is not available because of massive size of data, access restrictions, or bandwidth requirements. We outline some techniques for minimizing the number of statistical queries needed; and for efficiently coping with missing values in the data. We provide open source implementation of the...
Alternative splicing is a mechanism for generating different gene transcripts (called isoforms) from the same genomic sequence. Finding alternative splicing events experimentally is both expensive and time consuming. Computational methods, in general, and machine learning algorithms,in particular, can be used to complement experimental methods in the process of identifying alternative splicing events...
As organization-based multiagent systems are applied to more complex problems, configuring and tuning the systems can become nearly as complex as the original problem a system was designed to solve. A robust system should be able to adapt. It should be able to self-configure and self-tune. To this end, we propose a method for self-tuning using the concept of guidance policies, that is policies that...
Protein-protein interactions (PPI) refer to the associations between proteins and the study of these associations. Several approaches have been used to address the problem of predicting PPI. Some of them are based on biological features extracted from a protein sequence (such as, amino acid composition, GO terms, etc.); others use relational and structural features extracted from the PPI network,...
In order for ontologies to be broadly useful to the scientific community, they need to capture knowledge and expertise of multiple experts and research groups. Consequently, the construction of such ontologies necessarily requires collaboration among individual experts or research groups. Support for such collaboration is largely lacking in existing ontology development environments. We describe some...
We present the first prototype of INDUS (intelligent data understanding system), a federated, query-centric system for information integration and knowledge acquisition from distributed, semantically heterogeneous data sources that can be viewed (conceptually) as tables. INDUS employs ontologies and inter-ontology mappings, to enable a user to view a collection of such data sources (regardless of...
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