3,147 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
Laplacian Mixture Modeling for Network Analysis and Unsupervised Learning on Graphs
Laplacian mixture models identify overlapping regions of influence in
unlabeled graph and network data in a scalable and computationally efficient
way, yielding useful low-dimensional representations. By combining Laplacian
eigenspace and finite mixture modeling methods, they provide probabilistic or
fuzzy dimensionality reductions or domain decompositions for a variety of input
data types, including mixture distributions, feature vectors, and graphs or
networks. Provable optimal recovery using the algorithm is analytically shown
for a nontrivial class of cluster graphs. Heuristic approximations for scalable
high-performance implementations are described and empirically tested.
Connections to PageRank and community detection in network analysis demonstrate
the wide applicability of this approach. The origins of fuzzy spectral methods,
beginning with generalized heat or diffusion equations in physics, are reviewed
and summarized. Comparisons to other dimensionality reduction and clustering
methods for challenging unsupervised machine learning problems are also
discussed.Comment: 13 figures, 35 reference
Multiple Instance Learning: A Survey of Problem Characteristics and Applications
Multiple instance learning (MIL) is a form of weakly supervised learning
where training instances are arranged in sets, called bags, and a label is
provided for the entire bag. This formulation is gaining interest because it
naturally fits various problems and allows to leverage weakly labeled data.
Consequently, it has been used in diverse application fields such as computer
vision and document classification. However, learning from bags raises
important challenges that are unique to MIL. This paper provides a
comprehensive survey of the characteristics which define and differentiate the
types of MIL problems. Until now, these problem characteristics have not been
formally identified and described. As a result, the variations in performance
of MIL algorithms from one data set to another are difficult to explain. In
this paper, MIL problem characteristics are grouped into four broad categories:
the composition of the bags, the types of data distribution, the ambiguity of
instance labels, and the task to be performed. Methods specialized to address
each category are reviewed. Then, the extent to which these characteristics
manifest themselves in key MIL application areas are described. Finally,
experiments are conducted to compare the performance of 16 state-of-the-art MIL
methods on selected problem characteristics. This paper provides insight on how
the problem characteristics affect MIL algorithms, recommendations for future
benchmarking and promising avenues for research
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