112,325 research outputs found
Stable Feature Selection for Biomarker Discovery
Feature selection techniques have been used as the workhorse in biomarker
discovery applications for a long time. Surprisingly, the stability of feature
selection with respect to sampling variations has long been under-considered.
It is only until recently that this issue has received more and more attention.
In this article, we review existing stable feature selection methods for
biomarker discovery using a generic hierarchal framework. We have two
objectives: (1) providing an overview on this new yet fast growing topic for a
convenient reference; (2) categorizing existing methods under an expandable
framework for future research and development
Comparing clusterings and numbers of clusters by aggregation of calibrated clustering validity indexes
A key issue in cluster analysis is the choice of an appropriate clustering
method and the determination of the best number of clusters. Different
clusterings are optimal on the same data set according to different criteria,
and the choice of such criteria depends on the context and aim of clustering.
Therefore, researchers need to consider what data analytic characteristics the
clusters they are aiming at are supposed to have, among others within-cluster
homogeneity, between-clusters separation, and stability. Here, a set of
internal clustering validity indexes measuring different aspects of clustering
quality is proposed, including some indexes from the literature. Users can
choose the indexes that are relevant in the application at hand. In order to
measure the overall quality of a clustering (for comparing clusterings from
different methods and/or different numbers of clusters), the index values are
calibrated for aggregation. Calibration is relative to a set of random
clusterings on the same data. Two specific aggregated indexes are proposed and
compared with existing indexes on simulated and real data.Comment: 42 pages, 11 figure
How Many Topics? Stability Analysis for Topic Models
Topic modeling refers to the task of discovering the underlying thematic
structure in a text corpus, where the output is commonly presented as a report
of the top terms appearing in each topic. Despite the diversity of topic
modeling algorithms that have been proposed, a common challenge in successfully
applying these techniques is the selection of an appropriate number of topics
for a given corpus. Choosing too few topics will produce results that are
overly broad, while choosing too many will result in the "over-clustering" of a
corpus into many small, highly-similar topics. In this paper, we propose a
term-centric stability analysis strategy to address this issue, the idea being
that a model with an appropriate number of topics will be more robust to
perturbations in the data. Using a topic modeling approach based on matrix
factorization, evaluations performed on a range of corpora show that this
strategy can successfully guide the model selection process.Comment: Improve readability of plots. Add minor clarification
Robust Temporally Coherent Laplacian Protrusion Segmentation of 3D Articulated Bodies
In motion analysis and understanding it is important to be able to fit a
suitable model or structure to the temporal series of observed data, in order
to describe motion patterns in a compact way, and to discriminate between them.
In an unsupervised context, i.e., no prior model of the moving object(s) is
available, such a structure has to be learned from the data in a bottom-up
fashion. In recent times, volumetric approaches in which the motion is captured
from a number of cameras and a voxel-set representation of the body is built
from the camera views, have gained ground due to attractive features such as
inherent view-invariance and robustness to occlusions. Automatic, unsupervised
segmentation of moving bodies along entire sequences, in a temporally-coherent
and robust way, has the potential to provide a means of constructing a
bottom-up model of the moving body, and track motion cues that may be later
exploited for motion classification. Spectral methods such as locally linear
embedding (LLE) can be useful in this context, as they preserve "protrusions",
i.e., high-curvature regions of the 3D volume, of articulated shapes, while
improving their separation in a lower dimensional space, making them in this
way easier to cluster. In this paper we therefore propose a spectral approach
to unsupervised and temporally-coherent body-protrusion segmentation along time
sequences. Volumetric shapes are clustered in an embedding space, clusters are
propagated in time to ensure coherence, and merged or split to accommodate
changes in the body's topology. Experiments on both synthetic and real
sequences of dense voxel-set data are shown. This supports the ability of the
proposed method to cluster body-parts consistently over time in a totally
unsupervised fashion, its robustness to sampling density and shape quality, and
its potential for bottom-up model constructionComment: 31 pages, 26 figure
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A hybrid stabilization technique for simulating water wave - Structure interaction by incompressible Smoothed Particle Hydrodynamics (ISPH) method
The Smoothed Particle Hydrodynamics (SPH) method is emerging as a potential tool for studying water wave related problems, especially for violent free surface flow and large deformation problems. The incompressible SPH (ISPH) computations have been found not to be able to maintain the stability in certain situations and there exist some spurious oscillations in the pressure time history, which is similar to the weakly compressible SPH (WCSPH). One main cause of this problem is related to the non-uniform and clustered distribution of the moving particles. In order to improve the model performance, the paper proposed an efficient hybrid numerical technique aiming to correct the ill particle distributions. The correction approach is realized through the combination of particle shifting and pressure gradient improvement. The advantages of the proposed hybrid technique in improving ISPH calculations are demonstrated through several applications that include solitary wave impact on a slope or overtopping a seawall, and regular wave slamming on the subface of open-piled structure
Identifying Overlapping and Hierarchical Thematic Structures in Networks of Scholarly Papers: A Comparison of Three Approaches
We implemented three recently proposed approaches to the identification of
overlapping and hierarchical substructures in graphs and applied the
corresponding algorithms to a network of 492 information-science papers coupled
via their cited sources. The thematic substructures obtained and overlaps
produced by the three hierarchical cluster algorithms were compared to a
content-based categorisation, which we based on the interpretation of titles
and keywords. We defined sets of papers dealing with three topics located on
different levels of aggregation: h-index, webometrics, and bibliometrics. We
identified these topics with branches in the dendrograms produced by the three
cluster algorithms and compared the overlapping topics they detected with one
another and with the three pre-defined paper sets. We discuss the advantages
and drawbacks of applying the three approaches to paper networks in research
fields.Comment: 18 pages, 9 figure
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