1,988 research outputs found
Rank discriminants for predicting phenotypes from RNA expression
Statistical methods for analyzing large-scale biomolecular data are
commonplace in computational biology. A notable example is phenotype prediction
from gene expression data, for instance, detecting human cancers,
differentiating subtypes and predicting clinical outcomes. Still, clinical
applications remain scarce. One reason is that the complexity of the decision
rules that emerge from standard statistical learning impedes biological
understanding, in particular, any mechanistic interpretation. Here we explore
decision rules for binary classification utilizing only the ordering of
expression among several genes; the basic building blocks are then two-gene
expression comparisons. The simplest example, just one comparison, is the TSP
classifier, which has appeared in a variety of cancer-related discovery
studies. Decision rules based on multiple comparisons can better accommodate
class heterogeneity, and thereby increase accuracy, and might provide a link
with biological mechanism. We consider a general framework ("rank-in-context")
for designing discriminant functions, including a data-driven selection of the
number and identity of the genes in the support ("context"). We then specialize
to two examples: voting among several pairs and comparing the median expression
in two groups of genes. Comprehensive experiments assess accuracy relative to
other, more complex, methods, and reinforce earlier observations that simple
classifiers are competitive.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS738 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
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
Feature Selection for Big Visual Data: Overview and Challenges
International Conference Image Analysis and Recognition (ICIAR 2018, Póvoa de Varzim, Portugal
A Taxonomy of Big Data for Optimal Predictive Machine Learning and Data Mining
Big data comes in various ways, types, shapes, forms and sizes. Indeed,
almost all areas of science, technology, medicine, public health, economics,
business, linguistics and social science are bombarded by ever increasing flows
of data begging to analyzed efficiently and effectively. In this paper, we
propose a rough idea of a possible taxonomy of big data, along with some of the
most commonly used tools for handling each particular category of bigness. The
dimensionality p of the input space and the sample size n are usually the main
ingredients in the characterization of data bigness. The specific statistical
machine learning technique used to handle a particular big data set will depend
on which category it falls in within the bigness taxonomy. Large p small n data
sets for instance require a different set of tools from the large n small p
variety. Among other tools, we discuss Preprocessing, Standardization,
Imputation, Projection, Regularization, Penalization, Compression, Reduction,
Selection, Kernelization, Hybridization, Parallelization, Aggregation,
Randomization, Replication, Sequentialization. Indeed, it is important to
emphasize right away that the so-called no free lunch theorem applies here, in
the sense that there is no universally superior method that outperforms all
other methods on all categories of bigness. It is also important to stress the
fact that simplicity in the sense of Ockham's razor non plurality principle of
parsimony tends to reign supreme when it comes to massive data. We conclude
with a comparison of the predictive performance of some of the most commonly
used methods on a few data sets.Comment: 18 pages, 2 figures 3 table
A Regularized Method for Selecting Nested Groups of Relevant Genes from Microarray Data
Gene expression analysis aims at identifying the genes able to accurately
predict biological parameters like, for example, disease subtyping or
progression. While accurate prediction can be achieved by means of many
different techniques, gene identification, due to gene correlation and the
limited number of available samples, is a much more elusive problem. Small
changes in the expression values often produce different gene lists, and
solutions which are both sparse and stable are difficult to obtain. We propose
a two-stage regularization method able to learn linear models characterized by
a high prediction performance. By varying a suitable parameter these linear
models allow to trade sparsity for the inclusion of correlated genes and to
produce gene lists which are almost perfectly nested. Experimental results on
synthetic and microarray data confirm the interesting properties of the
proposed method and its potential as a starting point for further biological
investigationsComment: 17 pages, 8 Post-script figure
Challenges of Big Data Analysis
Big Data bring new opportunities to modern society and challenges to data
scientists. On one hand, Big Data hold great promises for discovering subtle
population patterns and heterogeneities that are not possible with small-scale
data. On the other hand, the massive sample size and high dimensionality of Big
Data introduce unique computational and statistical challenges, including
scalability and storage bottleneck, noise accumulation, spurious correlation,
incidental endogeneity, and measurement errors. These challenges are
distinguished and require new computational and statistical paradigm. This
article give overviews on the salient features of Big Data and how these
features impact on paradigm change on statistical and computational methods as
well as computing architectures. We also provide various new perspectives on
the Big Data analysis and computation. In particular, we emphasis on the
viability of the sparsest solution in high-confidence set and point out that
exogeneous assumptions in most statistical methods for Big Data can not be
validated due to incidental endogeneity. They can lead to wrong statistical
inferences and consequently wrong scientific conclusions
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