25,065 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
Machine Learning of User Profiles: Representational Issues
As more information becomes available electronically, tools for finding
information of interest to users becomes increasingly important. The goal of
the research described here is to build a system for generating comprehensible
user profiles that accurately capture user interest with minimum user
interaction. The research described here focuses on the importance of a
suitable generalization hierarchy and representation for learning profiles
which are predictively accurate and comprehensible. In our experiments we
evaluated both traditional features based on weighted term vectors as well as
subject features corresponding to categories which could be drawn from a
thesaurus. Our experiments, conducted in the context of a content-based
profiling system for on-line newspapers on the World Wide Web (the IDD News
Browser), demonstrate the importance of a generalization hierarchy and the
promise of combining natural language processing techniques with machine
learning (ML) to address an information retrieval (IR) problem.Comment: 6 page
ModHMM: A Modular Supra-Bayesian Genome Segmentation Method
Genome segmentation methods are powerful tools to obtain cell type or tissue-specific genome-wide annotations and are frequently used to discover regulatory elements. However, traditional segmentation methods show low predictive accuracy and their data-driven annotations have some undesirable properties. As an alternative, we developed ModHMM, a highly modular genome segmentation method. Inspired by the supra-Bayesian approach, it incorporates predictions from a set of classifiers. This allows to compute genome segmentations by utilizing state-of-the-art methodology. We demonstrate the method on ENCODE data and show that it outperforms traditional segmentation methods not only in terms of predictive performance, but also in qualitative aspects. Therefore, ModHMM is a valuable alternative to study the epigenetic and regulatory landscape across and within cell types or tissues
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