37,172 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
Fast Approximate -Means via Cluster Closures
-means, a simple and effective clustering algorithm, is one of the most
widely used algorithms in multimedia and computer vision community. Traditional
-means is an iterative algorithm---in each iteration new cluster centers are
computed and each data point is re-assigned to its nearest center. The cluster
re-assignment step becomes prohibitively expensive when the number of data
points and cluster centers are large.
In this paper, we propose a novel approximate -means algorithm to greatly
reduce the computational complexity in the assignment step. Our approach is
motivated by the observation that most active points changing their cluster
assignments at each iteration are located on or near cluster boundaries. The
idea is to efficiently identify those active points by pre-assembling the data
into groups of neighboring points using multiple random spatial partition
trees, and to use the neighborhood information to construct a closure for each
cluster, in such a way only a small number of cluster candidates need to be
considered when assigning a data point to its nearest cluster. Using complexity
analysis, image data clustering, and applications to image retrieval, we show
that our approach out-performs state-of-the-art approximate -means
algorithms in terms of clustering quality and efficiency
FRIOD: a deeply integrated feature-rich interactive system for effective and efficient outlier detection
In this paper, we propose an novel interactive outlier detection system called feature-rich interactive outlier detection (FRIOD), which features a deep integration of human interaction to improve detection performance and greatly streamline the detection process. A user-friendly interactive mechanism is developed to allow easy and intuitive user interaction in all the major stages of the underlying outlier detection algorithm which includes dense cell selection, location-aware distance thresholding, and final top outlier validation. By doing so, we can mitigate the major difficulty of the competitive outlier detection methods in specifying the key parameter values, such as the density and distance thresholds. An innovative optimization approach is also proposed to optimize the grid-based space partitioning, which is a critical step of FRIOD. Such optimization fully considers the high-quality outliers it detects with the aid of human interaction. The experimental evaluation demonstrates that FRIOD can improve the quality of the detected outliers and make the detection process more intuitive, effective, and efficient
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