158,041 research outputs found

    Transcription Factor-DNA Binding Via Machine Learning Ensembles

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    We present ensemble methods in a machine learning (ML) framework combining predictions from five known motif/binding site exploration algorithms. For a given TF the ensemble starts with position weight matrices (PWM's) for the motif, collected from the component algorithms. Using dimension reduction, we identify significant PWM-based subspaces for analysis. Within each subspace a machine classifier is built for identifying the TF's gene (promoter) targets (Problem 1). These PWM-based subspaces form an ML-based sequence analysis tool. Problem 2 (finding binding motifs) is solved by agglomerating k-mer (string) feature PWM-based subspaces that stand out in identifying gene targets. We approach Problem 3 (binding sites) with a novel machine learning approach that uses promoter string features and ML importance scores in a classification algorithm locating binding sites across the genome. For target gene identification this method improves performance (measured by the F1 score) by about 10 percentage points over the (a) motif scanning method and (b) the coexpression-based association method. Top motif outperformed 5 component algorithms as well as two other common algorithms (BEST and DEME). For identifying individual binding sites on a benchmark cross species database (Tompa et al., 2005) we match the best performer without much human intervention. It also improved the performance on mammalian TFs. The ensemble can integrate orthogonal information from different weak learners (potentially using entirely different types of features) into a machine learner that can perform consistently better for more TFs. The TF gene target identification component (problem 1 above) is useful in constructing a transcriptional regulatory network from known TF-target associations. The ensemble is easily extendable to include more tools as well as future PWM-based information.Comment: 33 page

    Learning to detect video events from zero or very few video examples

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    In this work we deal with the problem of high-level event detection in video. Specifically, we study the challenging problems of i) learning to detect video events from solely a textual description of the event, without using any positive video examples, and ii) additionally exploiting very few positive training samples together with a small number of ``related'' videos. For learning only from an event's textual description, we first identify a general learning framework and then study the impact of different design choices for various stages of this framework. For additionally learning from example videos, when true positive training samples are scarce, we employ an extension of the Support Vector Machine that allows us to exploit ``related'' event videos by automatically introducing different weights for subsets of the videos in the overall training set. Experimental evaluations performed on the large-scale TRECVID MED 2014 video dataset provide insight on the effectiveness of the proposed methods.Comment: Image and Vision Computing Journal, Elsevier, 2015, accepted for publicatio

    Positioning for conceptual development using latent semantic analysis

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    With increasing opportunities to learn online, the problem of positioning learners in an educational network of content offers new possibilities for the utilisation of geometry-based natural language processing techniques. In this article, the adoption of latent semantic analysis (LSA) for guiding learners in their conceptual development is investigated. We propose five new algorithmic derivations of LSA and test their validity for positioning in an experiment in order to draw back conclusions on the suitability of machine learning from previously accredited evidence. Special attention is thereby directed towards the role of distractors and the calculation of thresholds when using similarities as a proxy for assessing conceptual closeness. Results indicate that learning improves positioning. Distractors are of low value and seem to be replaceable by generic noise to improve threshold calculation. Furthermore, new ways to flexibly calculate thresholds could be identified
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