15,133 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

    Multi-View Face Recognition From Single RGBD Models of the Faces

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    This work takes important steps towards solving the following problem of current interest: Assuming that each individual in a population can be modeled by a single frontal RGBD face image, is it possible to carry out face recognition for such a population using multiple 2D images captured from arbitrary viewpoints? Although the general problem as stated above is extremely challenging, it encompasses subproblems that can be addressed today. The subproblems addressed in this work relate to: (1) Generating a large set of viewpoint dependent face images from a single RGBD frontal image for each individual; (2) using hierarchical approaches based on view-partitioned subspaces to represent the training data; and (3) based on these hierarchical approaches, using a weighted voting algorithm to integrate the evidence collected from multiple images of the same face as recorded from different viewpoints. We evaluate our methods on three datasets: a dataset of 10 people that we created and two publicly available datasets which include a total of 48 people. In addition to providing important insights into the nature of this problem, our results show that we are able to successfully recognize faces with accuracies of 95% or higher, outperforming existing state-of-the-art face recognition approaches based on deep convolutional neural networks
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