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  1. Article ; Online: Semi-Supervised Learning Using Hierarchical Mixture Models

    Michael W. Daniels / Daniel Dvorkin / Rani K. Powers / Katerina Kechris

    Mathematical and Computational Applications, Vol 26, Iss 40, p

    Gene Essentiality Case Study

    2021  Volume 40

    Abstract: Integrating gene-level data is useful for predicting the role of genes in biological processes. This problem has typically focused on supervised classification, which requires large training sets of positive and negative examples. However, training data ... ...

    Abstract Integrating gene-level data is useful for predicting the role of genes in biological processes. This problem has typically focused on supervised classification, which requires large training sets of positive and negative examples. However, training data sets that are too small for supervised approaches can still provide valuable information. We describe a hierarchical mixture model that uses limited positively labeled gene training data for semi-supervised learning. We focus on the problem of predicting essential genes, where a gene is required for the survival of an organism under particular conditions. We applied cross-validation and found that the inclusion of positively labeled samples in a semi-supervised learning framework with the hierarchical mixture model improves the detection of essential genes compared to unsupervised, supervised, and other semi-supervised approaches. There was also improved prediction performance when genes are incorrectly assumed to be non-essential. Our comparisons indicate that the incorporation of even small amounts of existing knowledge improves the accuracy of prediction and decreases variability in predictions. Although we focused on gene essentiality, the hierarchical mixture model and semi-supervised framework is standard for problems focused on prediction of genes or other features, with multiple data types characterizing the feature, and a small set of positive labels.
    Keywords semi-supervised ; hierarchical mixture models ; essential genes ; genomic ; integration ; Applied mathematics. Quantitative methods ; T57-57.97 ; Mathematics ; QA1-939 ; Electronic computers. Computer science ; QA75.5-76.95
    Subject code 006
    Language English
    Publishing date 2021-05-01T00:00:00Z
    Publisher MDPI AG
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  2. Article ; Online: Risk of occult spinal dysraphism based on lumbosacral cutaneous manifestations

    Lisa BE Shields / Ian S Mutchnick / Michael W Daniels / Dennis S Peppas / Eran Rosenberg

    SAGE Open Medicine, Vol

    2021  Volume 9

    Abstract: Objectives: Occult spinal dysraphism is a congenital failure of fusion of the posterior vertebral arches with intact skin overlying the defect. Lumbosacral cutaneous manifestations are associated with a variable risk of occult spinal dysraphism. Tethered ...

    Abstract Objectives: Occult spinal dysraphism is a congenital failure of fusion of the posterior vertebral arches with intact skin overlying the defect. Lumbosacral cutaneous manifestations are associated with a variable risk of occult spinal dysraphism. Tethered cord syndrome is a type of occult spinal dysraphism that puts abnormal traction on the spinal cord. This study analyzed neonates and infants who were referred to our pediatric urology practice and had evidence of lumbosacral cutaneous manifestation on physical examination. Methods: We reviewed the presence of lumbosacral cutaneous manifestations in neonates and infants evaluated in our pediatric urology clinic at our Institution over a 6-year period (1 March, 2015–28 February, 2021) with no prior diagnosis of lumbosacral cutaneous manifestation. All patients underwent a spinal ultrasound. Results: The most common lumbosacral cutaneous manifestations were bifurcated/duplicated gluteal folds (33%), gluteal asymmetry (19%), and sacral dimples (14%). A total of 34 (24%) patients had an abnormal spinal ultrasound; 15 (44%) of these infants underwent a lumbar magnetic resonance imaging. A coccygeal pit was statistically marginally higher in abnormal versus normal spinal ultrasound (p = 0.07). Patients with only one lumbosacral cutaneous manifestation (N = 121) were significantly more likely to have a normal spinal ultrasound compared to those with two or more lumbosacral cutaneous manifestation (N = 17) (79% vs 53%, p = 0.03). Conclusion: Due to the varying risk of certain lumbosacral cutaneous manifestations with occult spinal dysraphism, all patients with a lumbosacral cutaneous manifestation should undergo spinal ultrasound. This study also highlights the importance of urodynamic studies when there are abnormal cutaneous findings. Routine physical examinations of the lumbar region for cutaneous manifestations of occult spinal dysraphism are vital to ensure prompt management of tethered cord syndrome and avoid potentially devastating consequences.
    Keywords Medicine (General) ; R5-920
    Subject code 610
    Language English
    Publishing date 2021-08-01T00:00:00Z
    Publisher SAGE Publishing
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

    Full text online

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    Inter-library loan at ZB MED

    Your chosen title can be delivered directly to ZB MED Cologne location if you are registered as a user at ZB MED Cologne.

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