7,604 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
Missing Value Imputation With Unsupervised Backpropagation
Many data mining and data analysis techniques operate on dense matrices or
complete tables of data. Real-world data sets, however, often contain unknown
values. Even many classification algorithms that are designed to operate with
missing values still exhibit deteriorated accuracy. One approach to handling
missing values is to fill in (impute) the missing values. In this paper, we
present a technique for unsupervised learning called Unsupervised
Backpropagation (UBP), which trains a multi-layer perceptron to fit to the
manifold sampled by a set of observed point-vectors. We evaluate UBP with the
task of imputing missing values in datasets, and show that UBP is able to
predict missing values with significantly lower sum-squared error than other
collaborative filtering and imputation techniques. We also demonstrate with 24
datasets and 9 supervised learning algorithms that classification accuracy is
usually higher when randomly-withheld values are imputed using UBP, rather than
with other methods
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
- …