119,038 research outputs found
On selecting interacting features from high-dimensional data
For high-dimensional data, most feature-selection methods, such as SIS and the lasso, involve ranking and selecting features individually. These methods do not require many computational resources, but they ignore feature interactions. A simple recursive approach, which, without requiring many more computational resources, also allows identification of interactions, is investigated. This approach can lead to substantial improvements in the performance of classifiers, and can provide insight into the way in which features work together in a given population. It also enjoys attractive statistical properties
The Naming Game in Social Networks: Community Formation and Consensus Engineering
We study the dynamics of the Naming Game [Baronchelli et al., (2006) J. Stat.
Mech.: Theory Exp. P06014] in empirical social networks. This stylized
agent-based model captures essential features of agreement dynamics in a
network of autonomous agents, corresponding to the development of shared
classification schemes in a network of artificial agents or opinion spreading
and social dynamics in social networks. Our study focuses on the impact that
communities in the underlying social graphs have on the outcome of the
agreement process. We find that networks with strong community structure hinder
the system from reaching global agreement; the evolution of the Naming Game in
these networks maintains clusters of coexisting opinions indefinitely. Further,
we investigate agent-based network strategies to facilitate convergence to
global consensus.Comment: The original publication is available at
http://www.springerlink.com/content/70370l311m1u0ng3
Cancer3D: understanding cancer mutations through protein structures.
The new era of cancer genomics is providing us with extensive knowledge of mutations and other alterations in cancer. The Cancer3D database at http://www.cancer3d.org gives an open and user-friendly way to analyze cancer missense mutations in the context of structures of proteins in which they are found. The database also helps users analyze the distribution patterns of the mutations as well as their relationship to changes in drug activity through two algorithms: e-Driver and e-Drug. These algorithms use knowledge of modular structure of genes and proteins to separately study each region. This approach allows users to find novel candidate driver regions or drug biomarkers that cannot be found when similar analyses are done on the whole-gene level. The Cancer3D database provides access to the results of such analyses based on data from The Cancer Genome Atlas (TCGA) and the Cancer Cell Line Encyclopedia (CCLE). In addition, it displays mutations from over 14,700 proteins mapped to more than 24,300 structures from PDB. This helps users visualize the distribution of mutations and identify novel three-dimensional patterns in their distribution
An Adaptive Interacting Wang-Landau Algorithm for Automatic Density Exploration
While statisticians are well-accustomed to performing exploratory analysis in
the modeling stage of an analysis, the notion of conducting preliminary
general-purpose exploratory analysis in the Monte Carlo stage (or more
generally, the model-fitting stage) of an analysis is an area which we feel
deserves much further attention. Towards this aim, this paper proposes a
general-purpose algorithm for automatic density exploration. The proposed
exploration algorithm combines and expands upon components from various
adaptive Markov chain Monte Carlo methods, with the Wang-Landau algorithm at
its heart. Additionally, the algorithm is run on interacting parallel chains --
a feature which both decreases computational cost as well as stabilizes the
algorithm, improving its ability to explore the density. Performance is studied
in several applications. Through a Bayesian variable selection example, the
authors demonstrate the convergence gains obtained with interacting chains. The
ability of the algorithm's adaptive proposal to induce mode-jumping is
illustrated through a trimodal density and a Bayesian mixture modeling
application. Lastly, through a 2D Ising model, the authors demonstrate the
ability of the algorithm to overcome the high correlations encountered in
spatial models.Comment: 33 pages, 20 figures (the supplementary materials are included as
appendices
Persistent Homology Guided Force-Directed Graph Layouts
Graphs are commonly used to encode relationships among entities, yet their
abstractness makes them difficult to analyze. Node-link diagrams are popular
for drawing graphs, and force-directed layouts provide a flexible method for
node arrangements that use local relationships in an attempt to reveal the
global shape of the graph. However, clutter and overlap of unrelated structures
can lead to confusing graph visualizations. This paper leverages the persistent
homology features of an undirected graph as derived information for interactive
manipulation of force-directed layouts. We first discuss how to efficiently
extract 0-dimensional persistent homology features from both weighted and
unweighted undirected graphs. We then introduce the interactive persistence
barcode used to manipulate the force-directed graph layout. In particular, the
user adds and removes contracting and repulsing forces generated by the
persistent homology features, eventually selecting the set of persistent
homology features that most improve the layout. Finally, we demonstrate the
utility of our approach across a variety of synthetic and real datasets
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