7 research outputs found
A Fast Quartet Tree Heuristic for Hierarchical Clustering
The Minimum Quartet Tree Cost problem is to construct an optimal weight tree
from the weighted quartet topologies on objects, where
optimality means that the summed weight of the embedded quartet topologies is
optimal (so it can be the case that the optimal tree embeds all quartets as
nonoptimal topologies). We present a Monte Carlo heuristic, based on randomized
hill climbing, for approximating the optimal weight tree, given the quartet
topology weights. The method repeatedly transforms a dendrogram, with all
objects involved as leaves, achieving a monotonic approximation to the exact
single globally optimal tree. The problem and the solution heuristic has been
extensively used for general hierarchical clustering of nontree-like
(non-phylogeny) data in various domains and across domains with heterogeneous
data. We also present a greatly improved heuristic, reducing the running time
by a factor of order a thousand to ten thousand. All this is implemented and
available, as part of the CompLearn package. We compare performance and running
time of the original and improved versions with those of UPGMA, BioNJ, and NJ,
as implemented in the SplitsTree package on genomic data for which the latter
are optimized.
Keywords: Data and knowledge visualization, Pattern
matching--Clustering--Algorithms/Similarity measures, Hierarchical clustering,
Global optimization, Quartet tree, Randomized hill-climbing,Comment: LaTeX, 40 pages, 11 figures; this paper has substantial overlap with
arXiv:cs/0606048 in cs.D
Normalized Web Distance and Word Similarity
There is a great deal of work in cognitive psychology, linguistics, and
computer science, about using word (or phrase) frequencies in context in text
corpora to develop measures for word similarity or word association, going back
to at least the 1960s. The goal of this chapter is to introduce the
normalizedis a general way to tap the amorphous low-grade knowledge available
for free on the Internet, typed in by local users aiming at personal
gratification of diverse objectives, and yet globally achieving what is
effectively the largest semantic electronic database in the world. Moreover,
this database is available for all by using any search engine that can return
aggregate page-count estimates for a large range of search-queries. In the
paper introducing the NWD it was called `normalized Google distance (NGD),' but
since Google doesn't allow computer searches anymore, we opt for the more
neutral and descriptive NWD. web distance (NWD) method to determine similarity
between words and phrases. ItComment: Latex, 20 pages, 7 figures, to appear in: Handbook of Natural
Language Processing, Second Edition, Nitin Indurkhya and Fred J. Damerau
Eds., CRC Press, Taylor and Francis Group, Boca Raton, FL, 2010, ISBN
978-142008592
Normalized Information Distance
The normalized information distance is a universal distance measure for
objects of all kinds. It is based on Kolmogorov complexity and thus
uncomputable, but there are ways to utilize it. First, compression algorithms
can be used to approximate the Kolmogorov complexity if the objects have a
string representation. Second, for names and abstract concepts, page count
statistics from the World Wide Web can be used. These practical realizations of
the normalized information distance can then be applied to machine learning
tasks, expecially clustering, to perform feature-free and parameter-free data
mining. This chapter discusses the theoretical foundations of the normalized
information distance and both practical realizations. It presents numerous
examples of successful real-world applications based on these distance
measures, ranging from bioinformatics to music clustering to machine
translation.Comment: 33 pages, 12 figures, pdf, in: Normalized information distance, in:
Information Theory and Statistical Learning, Eds. M. Dehmer, F.
Emmert-Streib, Springer-Verlag, New-York, To appea
Personalized Web Image Organization
Due to the problem of semantic gap, i.e. the visual content of an image may not represent its semantics well, existing efforts on web image organization usually transform this task to clustering the surrounding text. However, because the surrounding text is usually short and the words therein usually appear only once, existing text clustering algorithms can hardly use the statistical information for image representation and may achieve downgraded performance with higher computational cost caused by learning from noisy tags. This chapter presents using the Probabilistic ART with user preference architecture, as introduced in Sects. 3.5 and 3.4, for personalized web image organization. This fused algorithm is named Probabilistic Fusion ART (PF-ART), which groups images of similar semantics together and simultaneously mines the key tags/topics of individual clusters. Moreover, it performs semi-supervised learning using the user-provided taggings for images to give users direct control of the generated clusters. An agglomerative merging strategy is further used to organize the clusters into a hierarchy, which is of a multi-branch tree structure rather than a binary tree generated by traditional hierarchical clustering algorithms. The entire two-step algorithm is called Personalized Hierarchical Theme-based Clustering (PHTC), for tag-based web image organization. Two large-scale real-world web image collections, namely the NUS-WIDE and the Flickr datasets, are used to evaluate PHTC and compare it with existing algorithms in terms of clustering performance and time cost