4,339 research outputs found
Relational Data Mining Through Extraction of Representative Exemplars
With the growing interest on Network Analysis, Relational Data Mining is
becoming an emphasized domain of Data Mining. This paper addresses the problem
of extracting representative elements from a relational dataset. After defining
the notion of degree of representativeness, computed using the Borda
aggregation procedure, we present the extraction of exemplars which are the
representative elements of the dataset. We use these concepts to build a
network on the dataset. We expose the main properties of these notions and we
propose two typical applications of our framework. The first application
consists in resuming and structuring a set of binary images and the second in
mining co-authoring relation in a research team
Parametric t-Distributed Stochastic Exemplar-centered Embedding
Parametric embedding methods such as parametric t-SNE (pt-SNE) have been
widely adopted for data visualization and out-of-sample data embedding without
further computationally expensive optimization or approximation. However, the
performance of pt-SNE is highly sensitive to the hyper-parameter batch size due
to conflicting optimization goals, and often produces dramatically different
embeddings with different choices of user-defined perplexities. To effectively
solve these issues, we present parametric t-distributed stochastic
exemplar-centered embedding methods. Our strategy learns embedding parameters
by comparing given data only with precomputed exemplars, resulting in a cost
function with linear computational and memory complexity, which is further
reduced by noise contrastive samples. Moreover, we propose a shallow embedding
network with high-order feature interactions for data visualization, which is
much easier to tune but produces comparable performance in contrast to a deep
neural network employed by pt-SNE. We empirically demonstrate, using several
benchmark datasets, that our proposed methods significantly outperform pt-SNE
in terms of robustness, visual effects, and quantitative evaluations.Comment: fixed typo
Clustering by soft-constraint affinity propagation: Applications to gene-expression data
Motivation: Similarity-measure based clustering is a crucial problem
appearing throughout scientific data analysis. Recently, a powerful new
algorithm called Affinity Propagation (AP) based on message-passing techniques
was proposed by Frey and Dueck \cite{Frey07}. In AP, each cluster is identified
by a common exemplar all other data points of the same cluster refer to, and
exemplars have to refer to themselves. Albeit its proved power, AP in its
present form suffers from a number of drawbacks. The hard constraint of having
exactly one exemplar per cluster restricts AP to classes of regularly shaped
clusters, and leads to suboptimal performance, {\it e.g.}, in analyzing gene
expression data. Results: This limitation can be overcome by relaxing the AP
hard constraints. A new parameter controls the importance of the constraints
compared to the aim of maximizing the overall similarity, and allows to
interpolate between the simple case where each data point selects its closest
neighbor as an exemplar and the original AP. The resulting soft-constraint
affinity propagation (SCAP) becomes more informative, accurate and leads to
more stable clustering. Even though a new {\it a priori} free-parameter is
introduced, the overall dependence of the algorithm on external tuning is
reduced, as robustness is increased and an optimal strategy for parameter
selection emerges more naturally. SCAP is tested on biological benchmark data,
including in particular microarray data related to various cancer types. We
show that the algorithm efficiently unveils the hierarchical cluster structure
present in the data sets. Further on, it allows to extract sparse gene
expression signatures for each cluster.Comment: 11 pages, supplementary material:
http://isiosf.isi.it/~weigt/scap_supplement.pd
Parallel Hierarchical Affinity Propagation with MapReduce
The accelerated evolution and explosion of the Internet and social media is
generating voluminous quantities of data (on zettabyte scales). Paramount
amongst the desires to manipulate and extract actionable intelligence from vast
big data volumes is the need for scalable, performance-conscious analytics
algorithms. To directly address this need, we propose a novel MapReduce
implementation of the exemplar-based clustering algorithm known as Affinity
Propagation. Our parallelization strategy extends to the multilevel
Hierarchical Affinity Propagation algorithm and enables tiered aggregation of
unstructured data with minimal free parameters, in principle requiring only a
similarity measure between data points. We detail the linear run-time
complexity of our approach, overcoming the limiting quadratic complexity of the
original algorithm. Experimental validation of our clustering methodology on a
variety of synthetic and real data sets (e.g. images and point data)
demonstrates our competitiveness against other state-of-the-art MapReduce
clustering techniques
The impact of contact tracing in clustered populations
The tracing of potentially infectious contacts has become an important part of the control strategy for many infectious diseases, from early cases of novel infections to endemic sexually transmitted infections. Here, we make use of mathematical models to consider the case of partner notification for sexually transmitted infection, however these models are sufficiently simple to allow more general conclusions to be drawn. We show that, when contact network structure is considered in addition to contact tracing, standard “mass action” models are generally inadequate. To consider the impact of mutual contacts (specifically clustering) we develop an improvement to existing pairwise network models, which we use to demonstrate that ceteris paribus, clustering improves the efficacy of contact tracing for a large region of parameter space. This result is sometimes reversed, however, for the case of highly effective contact tracing. We also develop stochastic simulations for comparison, using simple re-wiring methods that allow the generation of appropriate comparator networks. In this way we contribute to the general theory of network-based interventions against infectious disease
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