9,602 research outputs found

    Machine Learning and Integrative Analysis of Biomedical Big Data.

    Get PDF
    Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

    Manifold Elastic Net: A Unified Framework for Sparse Dimension Reduction

    Full text link
    It is difficult to find the optimal sparse solution of a manifold learning based dimensionality reduction algorithm. The lasso or the elastic net penalized manifold learning based dimensionality reduction is not directly a lasso penalized least square problem and thus the least angle regression (LARS) (Efron et al. \cite{LARS}), one of the most popular algorithms in sparse learning, cannot be applied. Therefore, most current approaches take indirect ways or have strict settings, which can be inconvenient for applications. In this paper, we proposed the manifold elastic net or MEN for short. MEN incorporates the merits of both the manifold learning based dimensionality reduction and the sparse learning based dimensionality reduction. By using a series of equivalent transformations, we show MEN is equivalent to the lasso penalized least square problem and thus LARS is adopted to obtain the optimal sparse solution of MEN. In particular, MEN has the following advantages for subsequent classification: 1) the local geometry of samples is well preserved for low dimensional data representation, 2) both the margin maximization and the classification error minimization are considered for sparse projection calculation, 3) the projection matrix of MEN improves the parsimony in computation, 4) the elastic net penalty reduces the over-fitting problem, and 5) the projection matrix of MEN can be interpreted psychologically and physiologically. Experimental evidence on face recognition over various popular datasets suggests that MEN is superior to top level dimensionality reduction algorithms.Comment: 33 pages, 12 figure

    GSplit LBI: Taming the Procedural Bias in Neuroimaging for Disease Prediction

    Full text link
    In voxel-based neuroimage analysis, lesion features have been the main focus in disease prediction due to their interpretability with respect to the related diseases. However, we observe that there exists another type of features introduced during the preprocessing steps and we call them "\textbf{Procedural Bias}". Besides, such bias can be leveraged to improve classification accuracy. Nevertheless, most existing models suffer from either under-fit without considering procedural bias or poor interpretability without differentiating such bias from lesion ones. In this paper, a novel dual-task algorithm namely \emph{GSplit LBI} is proposed to resolve this problem. By introducing an augmented variable enforced to be structural sparsity with a variable splitting term, the estimators for prediction and selecting lesion features can be optimized separately and mutually monitored by each other following an iterative scheme. Empirical experiments have been evaluated on the Alzheimer's Disease Neuroimaging Initiative\thinspace(ADNI) database. The advantage of proposed model is verified by improved stability of selected lesion features and better classification results.Comment: Conditional Accepted by Miccai,201

    Elastic-Net Regularization in Learning Theory

    Get PDF
    Within the framework of statistical learning theory we analyze in detail the so-called elastic-net regularization scheme proposed by Zou and Hastie for the selection of groups of correlated variables. To investigate on the statistical properties of this scheme and in particular on its consistency properties, we set up a suitable mathematical framework. Our setting is random-design regression where we allow the response variable to be vector-valued and we consider prediction functions which are linear combination of elements ({\em features}) in an infinite-dimensional dictionary. Under the assumption that the regression function admits a sparse representation on the dictionary, we prove that there exists a particular ``{\em elastic-net representation}'' of the regression function such that, if the number of data increases, the elastic-net estimator is consistent not only for prediction but also for variable/feature selection. Our results include finite-sample bounds and an adaptive scheme to select the regularization parameter. Moreover, using convex analysis tools, we derive an iterative thresholding algorithm for computing the elastic-net solution which is different from the optimization procedure originally proposed by Zou and HastieComment: 32 pages, 3 figure
    • …
    corecore