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Transfer learning (TL) algorithms aim to improve the prediction performance in a target task (e.g. the prediction of cisplatin sensitivity in triple-negative breast cancer patients) via transferring knowledge from auxiliary data of a related task (e.g. the prediction of docetaxel sensitivity in breast cancer patients), where the distribution and even the feature space of the data pertaining to the tasks can be different. In real-world applications, we sometimes have a limited training set in a target task while we have auxiliary data from a related task. To obtain a better prediction performance in the target task, supervised learning requires a sufficiently large training set in the target task to perform well in predicting future test examples of the target task. In this paper, we propose a TL approach for cancer drug sensitivity prediction, where our approach combines three techniques. First, we shift the representation of a subset of examples from auxiliary data of a related task to a representation closer to a target training set of a target task. Second, we align the shifted representation of the selected examples of the auxiliary data to the target training set to obtain examples with representation aligned to the target training set. Third, we train machine learning algorithms using both the target training set and the aligned examples. We evaluate the performance of our approach against baseline approaches using the Area Under the receiver operating characteristic (ROC) Curve (AUC) on real clinical trial datasets pertaining to multiple myeloma, nonsmall cell lung cancer, triple-negative breast cancer, and breast cancer. Experimental results show that our approach is better than the baseline approaches in terms of performance and statistical significance. [ABSTRACT FROM AUTHOR]

Developing effective artificial intelligence tools to find motifs in DNA, RNA and proteins poses a challenging yet important problem in life science research. In this paper, we present a computational approach for finding RNA tertiary motifs in genomic sequences. Specifically, we predict genomic coordinate locations for coaxial helical stackings in 3-way RNA junctions. These predictions are provided by our tertiary motif search package, named CSminer, which utilizes two versatile methodologies: random forests and covariance models. A coaxial helical stacking tertiary motif occurs in a 3-way RNA junction where two separate helical elements form a pseudocontiguous helix and provide thermodynamic stability to the RNA molecule as a whole. Our CSminer tool first uses a genome-wide search method based on covariance models to find a genomic region that may potentially contain a coaxial helical stacking tertiary motif. CSminer then uses a random forests classifier to predict whether the genomic region indeed contains the tertiary motif. Experimental results demonstrate the effectiveness of our approach. [ABSTRACT FROM AUTHOR]

We propose an ab initio method, named DiscoverR, for finding common patterns from two RNA secondary structures. The method works by representing RNA secondary structures as ordered labeled trees and performs tree pattern discovery using an efficient dynamic programming algorithm. DiscoverR is able to identify and extract the largest common substructures from two RNA molecules having different sizes without prior knowledge of the locations and topologies of these substructures. We also extend DiscoverR to find repeated regions in an RNA secondary structure, and apply this extended method to detect structural repeats in the 3′-untranslated region of a protein kinase gene. We describe the biological significance of a repeated hairpin found by our method, demonstrating the usefulness of the method. DiscoverR is implemented in Java; a jar file including the source code of the program is available for download at http://bioinformatics.njit.edu/DiscoverR. [ABSTRACT FROM AUTHOR]

We present a method, called BlockMatch, for aligning two blocks, where a block is an RNA multiple sequence alignment with the consensus secondary structure of the alignment in Stockholm format. The method employs a quadratic-time dynamic programming algorithm for aligning columns and column pairs of the multiple alignments in the blocks. Unlike many other tools that can perform pairwise alignment of either single sequences or structures only, BlockMatch takes into account the characteristics of all the sequences in the blocks along with their consensus structures during the alignment process, thus being able to achieve a high-quality alignment result. We apply BlockMatch to phylogeny reconstruction on a set of 5S rRNA sequences taken from fifteen bacteria species. Experimental results showed that the phylogenetic tree generated by our method is more accurate than the tree constructed based on the widely used ClustalW tool. The BlockMatch algorithm is implemented into a web server, accessible at . A jar file of the program is also available for download from the web server. [ABSTRACT FROM AUTHOR]

XML is increasingly important in data exchange and information management. A great deal of efforts have been spent in developing efficient techniques for storing, querying, indexing and accessing XML documents. In this paper we propose a new approach to clustering XML data. In contrast to previous work, which focused on documents defined by different DTDs, the proposed method works for documents with the same DTD. Our approach is to extract features from documents, modeled by ordered labeled trees, and transform the documents to vectors in a high-dimensional Euclidean space based on the occurrences of the features in the documents. We then reduce the dimensionality of the vectors by principal component analysis (PCA) and cluster the vectors in the reduced dimensional space. The PCA enables one to identify vectors with co-occurrent features, thereby enhancing the accuracy of the clustering. We also discuss an extension of our techniques to XML retrieval. Experimental results based on documents obtained from Wisconsin's XML data bank show the effectiveness and good performance of the proposed techniques. [ABSTRACT FROM AUTHOR]

XML's tree structure provides a rich background for complicated structural searches. In this paper we present a new system, called XML Query by Example (XML QBE) that allows the user to query XML documents exploiting their inherent tree structure. We present some interesting queries and describe the underlying query processing algorithms. We also describe the system's architecture and report its implementation status. Finally we conclude the paper by pointing out some future work. [ABSTRACT FROM AUTHOR]

Biological data mining is the activity of finding significant information in biomolecular data. The significant information may refer to motifs, clusters, genes, and protein signatures. This paper presents an example of biological data mining: the recognition of promoters in DNA. We propose a two-level ensemble of classifiers to recognize E. Coli promoter sequences. The first-level classifiers include three Bayesian neural networks that learn from three different feature sets. The outputs of the first-level classifiers are combined in the second-level to give the final result. Empirical study shows that a precision rate of 92.2% is achieved, indicating an excellent performance of the proposed approach. [ABSTRACT FROM AUTHOR]