3,429 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
Load curve data cleansing and imputation via sparsity and low rank
The smart grid vision is to build an intelligent power network with an
unprecedented level of situational awareness and controllability over its
services and infrastructure. This paper advocates statistical inference methods
to robustify power monitoring tasks against the outlier effects owing to faulty
readings and malicious attacks, as well as against missing data due to privacy
concerns and communication errors. In this context, a novel load cleansing and
imputation scheme is developed leveraging the low intrinsic-dimensionality of
spatiotemporal load profiles and the sparse nature of "bad data.'' A robust
estimator based on principal components pursuit (PCP) is adopted, which effects
a twofold sparsity-promoting regularization through an -norm of the
outliers, and the nuclear norm of the nominal load profiles. Upon recasting the
non-separable nuclear norm into a form amenable to decentralized optimization,
a distributed (D-) PCP algorithm is developed to carry out the imputation and
cleansing tasks using networked devices comprising the so-termed advanced
metering infrastructure. If D-PCP converges and a qualification inequality is
satisfied, the novel distributed estimator provably attains the performance of
its centralized PCP counterpart, which has access to all networkwide data.
Computer simulations and tests with real load curve data corroborate the
convergence and effectiveness of the novel D-PCP algorithm.Comment: 8 figures, submitted to IEEE Transactions on Smart Grid - Special
issue on "Optimization methods and algorithms applied to smart grid
Classification of Occluded Objects using Fast Recurrent Processing
Recurrent neural networks are powerful tools for handling incomplete data
problems in computer vision, thanks to their significant generative
capabilities. However, the computational demand for these algorithms is too
high to work in real time, without specialized hardware or software solutions.
In this paper, we propose a framework for augmenting recurrent processing
capabilities into a feedforward network without sacrificing much from
computational efficiency. We assume a mixture model and generate samples of the
last hidden layer according to the class decisions of the output layer, modify
the hidden layer activity using the samples, and propagate to lower layers. For
visual occlusion problem, the iterative procedure emulates feedforward-feedback
loop, filling-in the missing hidden layer activity with meaningful
representations. The proposed algorithm is tested on a widely used dataset, and
shown to achieve 2 improvement in classification accuracy for occluded
objects. When compared to Restricted Boltzmann Machines, our algorithm shows
superior performance for occluded object classification.Comment: arXiv admin note: text overlap with arXiv:1409.8576 by other author
Multiple imputation for continuous variables using a Bayesian principal component analysis
We propose a multiple imputation method based on principal component analysis
(PCA) to deal with incomplete continuous data. To reflect the uncertainty of
the parameters from one imputation to the next, we use a Bayesian treatment of
the PCA model. Using a simulation study and real data sets, the method is
compared to two classical approaches: multiple imputation based on joint
modelling and on fully conditional modelling. Contrary to the others, the
proposed method can be easily used on data sets where the number of individuals
is less than the number of variables and when the variables are highly
correlated. In addition, it provides unbiased point estimates of quantities of
interest, such as an expectation, a regression coefficient or a correlation
coefficient, with a smaller mean squared error. Furthermore, the widths of the
confidence intervals built for the quantities of interest are often smaller
whilst ensuring a valid coverage.Comment: 16 page
Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values
This work is motivated by the needs of predictive analytics on healthcare
data as represented by Electronic Medical Records. Such data is invariably
problematic: noisy, with missing entries, with imbalance in classes of
interests, leading to serious bias in predictive modeling. Since standard data
mining methods often produce poor performance measures, we argue for
development of specialized techniques of data-preprocessing and classification.
In this paper, we propose a new method to simultaneously classify large
datasets and reduce the effects of missing values. It is based on a multilevel
framework of the cost-sensitive SVM and the expected maximization imputation
method for missing values, which relies on iterated regression analyses. We
compare classification results of multilevel SVM-based algorithms on public
benchmark datasets with imbalanced classes and missing values as well as real
data in health applications, and show that our multilevel SVM-based method
produces fast, and more accurate and robust classification results.Comment: arXiv admin note: substantial text overlap with arXiv:1503.0625
Robust training of recurrent neural networks to handle missing data for disease progression modeling
Disease progression modeling (DPM) using longitudinal data is a challenging
task in machine learning for healthcare that can provide clinicians with better
tools for diagnosis and monitoring of disease. Existing DPM algorithms neglect
temporal dependencies among measurements and make parametric assumptions about
biomarker trajectories. In addition, they do not model multiple biomarkers
jointly and need to align subjects' trajectories. In this paper, recurrent
neural networks (RNNs) are utilized to address these issues. However, in many
cases, longitudinal cohorts contain incomplete data, which hinders the
application of standard RNNs and requires a pre-processing step such as
imputation of the missing values. We, therefore, propose a generalized training
rule for the most widely used RNN architecture, long short-term memory (LSTM)
networks, that can handle missing values in both target and predictor
variables. This algorithm is applied for modeling the progression of
Alzheimer's disease (AD) using magnetic resonance imaging (MRI) biomarkers. The
results show that the proposed LSTM algorithm achieves a lower mean absolute
error for prediction of measurements across all considered MRI biomarkers
compared to using standard LSTM networks with data imputation or using a
regression-based DPM method. Moreover, applying linear discriminant analysis to
the biomarkers' values predicted by the proposed algorithm results in a larger
area under the receiver operating characteristic curve (AUC) for clinical
diagnosis of AD compared to the same alternatives, and the AUC is comparable to
state-of-the-art AUCs from a recent cross-sectional medical image
classification challenge. This paper shows that built-in handling of missing
values in LSTM network training paves the way for application of RNNs in
disease progression modeling.Comment: 9 pages, 1 figure, MIDL conferenc
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