106,714 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
Multiscale Discriminant Saliency for Visual Attention
The bottom-up saliency, an early stage of humans' visual attention, can be
considered as a binary classification problem between center and surround
classes. Discriminant power of features for the classification is measured as
mutual information between features and two classes distribution. The estimated
discrepancy of two feature classes very much depends on considered scale
levels; then, multi-scale structure and discriminant power are integrated by
employing discrete wavelet features and Hidden markov tree (HMT). With wavelet
coefficients and Hidden Markov Tree parameters, quad-tree like label structures
are constructed and utilized in maximum a posterior probability (MAP) of hidden
class variables at corresponding dyadic sub-squares. Then, saliency value for
each dyadic square at each scale level is computed with discriminant power
principle and the MAP. Finally, across multiple scales is integrated the final
saliency map by an information maximization rule. Both standard quantitative
tools such as NSS, LCC, AUC and qualitative assessments are used for evaluating
the proposed multiscale discriminant saliency method (MDIS) against the
well-know information-based saliency method AIM on its Bruce Database wity
eye-tracking data. Simulation results are presented and analyzed to verify the
validity of MDIS as well as point out its disadvantages for further research
direction.Comment: 16 pages, ICCSA 2013 - BIOCA sessio
Distributed Holistic Clustering on Linked Data
Link discovery is an active field of research to support data integration in
the Web of Data. Due to the huge size and number of available data sources,
efficient and effective link discovery is a very challenging task. Common
pairwise link discovery approaches do not scale to many sources with very large
entity sets. We here propose a distributed holistic approach to link many data
sources based on a clustering of entities that represent the same real-world
object. Our clustering approach provides a compact and fused representation of
entities, and can identify errors in existing links as well as many new links.
We support a distributed execution of the clustering approach to achieve faster
execution times and scalability for large real-world data sets. We provide a
novel gold standard for multi-source clustering, and evaluate our methods with
respect to effectiveness and efficiency for large data sets from the geographic
and music domains
Pairwise gene GO-based measures for biclustering of high-dimensional expression data
Background: Biclustering algorithms search for groups of genes that share the same
behavior under a subset of samples in gene expression data. Nowadays, the biological
knowledge available in public repositories can be used to drive these algorithms to
find biclusters composed of groups of genes functionally coherent. On the other hand,
a distance among genes can be defined according to their information stored in Gene
Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each
pair of genes which establishes their functional similarity. A scatter search-based
algorithm that optimizes a merit function that integrates GO information is studied in
this paper. This merit function uses a term that addresses the information through a GO
measure.
Results: The effect of two possible different gene pairwise GO measures on the
performance of the algorithm is analyzed. Firstly, three well known yeast datasets with
approximately one thousand of genes are studied. Secondly, a group of human
datasets related to clinical data of cancer is also explored by the algorithm. Most of
these data are high-dimensional datasets composed of a huge number of genes. The
resultant biclusters reveal groups of genes linked by a same functionality when the
search procedure is driven by one of the proposed GO measures. Furthermore, a
qualitative biological study of a group of biclusters show their relevance from a cancer
disease perspective.
Conclusions: It can be concluded that the integration of biological information
improves the performance of the biclustering process. The two different GO measures
studied show an improvement in the results obtained for the yeast dataset. However, if
datasets are composed of a huge number of genes, only one of them really improves
the algorithm performance. This second case constitutes a clear option to explore
interesting datasets from a clinical point of view.Ministerio de Economía y Competitividad TIN2014-55894-C2-
Visual Integration of Data and Model Space in Ensemble Learning
Ensembles of classifier models typically deliver superior performance and can
outperform single classifier models given a dataset and classification task at
hand. However, the gain in performance comes together with the lack in
comprehensibility, posing a challenge to understand how each model affects the
classification outputs and where the errors come from. We propose a tight
visual integration of the data and the model space for exploring and combining
classifier models. We introduce a workflow that builds upon the visual
integration and enables the effective exploration of classification outputs and
models. We then present a use case in which we start with an ensemble
automatically selected by a standard ensemble selection algorithm, and show how
we can manipulate models and alternative combinations.Comment: 8 pages, 7 picture
Multi-scale Discriminant Saliency with Wavelet-based Hidden Markov Tree Modelling
The bottom-up saliency, an early stage of humans' visual attention, can be
considered as a binary classification problem between centre and surround
classes. Discriminant power of features for the classification is measured as
mutual information between distributions of image features and corresponding
classes . As the estimated discrepancy very much depends on considered scale
level, multi-scale structure and discriminant power are integrated by employing
discrete wavelet features and Hidden Markov Tree (HMT). With wavelet
coefficients and Hidden Markov Tree parameters, quad-tree like label structures
are constructed and utilized in maximum a posterior probability (MAP) of hidden
class variables at corresponding dyadic sub-squares. Then, a saliency value for
each square block at each scale level is computed with discriminant power
principle. Finally, across multiple scales is integrated the final saliency map
by an information maximization rule. Both standard quantitative tools such as
NSS, LCC, AUC and qualitative assessments are used for evaluating the proposed
multi-scale discriminant saliency (MDIS) method against the well-know
information based approach AIM on its released image collection with
eye-tracking data. Simulation results are presented and analysed to verify the
validity of MDIS as well as point out its limitation for further research
direction.Comment: arXiv admin note: substantial text overlap with arXiv:1301.396
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