9,602 research outputs found
Machine Learning and Integrative Analysis of Biomedical Big Data.
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
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
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
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
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