29,221 research outputs found
Context-aware visual exploration of molecular databases
Facilitating the visual exploration of scientific data has
received increasing attention in the past decade or so. Especially
in life science related application areas the amount
of available data has grown at a breath taking pace. In this
paper we describe an approach that allows for visual inspection
of large collections of molecular compounds. In
contrast to classical visualizations of such spaces we incorporate
a specific focus of analysis, for example the outcome
of a biological experiment such as high throughout
screening results. The presented method uses this experimental
data to select molecular fragments of the underlying
molecules that have interesting properties and uses the
resulting space to generate a two dimensional map based
on a singular value decomposition algorithm and a self organizing
map. Experiments on real datasets show that
the resulting visual landscape groups molecules of similar
chemical properties in densely connected regions
Approximated and User Steerable tSNE for Progressive Visual Analytics
Progressive Visual Analytics aims at improving the interactivity in existing
analytics techniques by means of visualization as well as interaction with
intermediate results. One key method for data analysis is dimensionality
reduction, for example, to produce 2D embeddings that can be visualized and
analyzed efficiently. t-Distributed Stochastic Neighbor Embedding (tSNE) is a
well-suited technique for the visualization of several high-dimensional data.
tSNE can create meaningful intermediate results but suffers from a slow
initialization that constrains its application in Progressive Visual Analytics.
We introduce a controllable tSNE approximation (A-tSNE), which trades off speed
and accuracy, to enable interactive data exploration. We offer real-time
visualization techniques, including a density-based solution and a Magic Lens
to inspect the degree of approximation. With this feedback, the user can decide
on local refinements and steer the approximation level during the analysis. We
demonstrate our technique with several datasets, in a real-world research
scenario and for the real-time analysis of high-dimensional streams to
illustrate its effectiveness for interactive data analysis
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ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks.
BACKGROUND:The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links. RESULTS:We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2Ă—10-16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime. CONCLUSIONS:ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster
Hypothesis exploration with visualization of variance.
BackgroundThe Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes-to explore whether they are linked to syndromes including ADHD, Bipolar disorder, and Schizophrenia. An aim of the consortium was in moving from traditional categorical approaches for psychiatric syndromes towards more quantitative approaches based on large-scale analysis of the space of human variation. It represented an application of phenomics-wide-scale, systematic study of phenotypes-to neuropsychiatry research.ResultsThis paper reports on a system for exploration of hypotheses in data obtained from the LA2K, LA3C, and LA5C studies in CNP. ViVA is a system for exploratory data analysis using novel mathematical models and methods for visualization of variance. An example of these methods is called VISOVA, a combination of visualization and analysis of variance, with the flavor of exploration associated with ANOVA in biomedical hypothesis generation. It permits visual identification of phenotype profiles-patterns of values across phenotypes-that characterize groups. Visualization enables screening and refinement of hypotheses about variance structure of sets of phenotypes.ConclusionsThe ViVA system was designed for exploration of neuropsychiatric hypotheses by interdisciplinary teams. Automated visualization in ViVA supports 'natural selection' on a pool of hypotheses, and permits deeper understanding of the statistical architecture of the data. Large-scale perspective of this kind could lead to better neuropsychiatric diagnostics
Image mining: issues, frameworks and techniques
[Abstract]: Advances in image acquisition and storage technology have led to tremendous growth in significantly large and detailed image databases. These images, if analyzed, can reveal useful information to the human users. Image mining deals with the extraction of implicit knowledge, image data relationship, or other patterns not explicitly stored in the images. Image mining is more than just an extension of data mining to image domain. It is an
interdisciplinary endeavor that draws upon expertise in
computer vision, image processing, image retrieval, data
mining, machine learning, database, and artificial
intelligence. Despite the development of many
applications and algorithms in the individual research
fields cited above, research in image mining is still in its infancy. In this paper, we will examine the research issues in image mining, current developments in image mining, particularly, image mining frameworks, state-of-the-art techniques and systems. We will also identify some future research directions for image mining at the end of this paper
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