6,084 research outputs found
Space-efficient Feature Maps for String Alignment Kernels
String kernels are attractive data analysis tools for analyzing string data.
Among them, alignment kernels are known for their high prediction accuracies in
string classifications when tested in combination with SVM in various
applications. However, alignment kernels have a crucial drawback in that they
scale poorly due to their quadratic computation complexity in the number of
input strings, which limits large-scale applications in practice. We address
this need by presenting the first approximation for string alignment kernels,
which we call space-efficient feature maps for edit distance with moves
(SFMEDM), by leveraging a metric embedding named edit sensitive parsing (ESP)
and feature maps (FMs) of random Fourier features (RFFs) for large-scale string
analyses. The original FMs for RFFs consume a huge amount of memory
proportional to the dimension d of input vectors and the dimension D of output
vectors, which prohibits its large-scale applications. We present novel
space-efficient feature maps (SFMs) of RFFs for a space reduction from O(dD) of
the original FMs to O(d) of SFMs with a theoretical guarantee with respect to
concentration bounds. We experimentally test SFMEDM on its ability to learn SVM
for large-scale string classifications with various massive string data, and we
demonstrate the superior performance of SFMEDM with respect to prediction
accuracy, scalability and computation efficiency.Comment: Full version for ICDM'19 pape
Kernel methods in machine learning
We review machine learning methods employing positive definite kernels. These
methods formulate learning and estimation problems in a reproducing kernel
Hilbert space (RKHS) of functions defined on the data domain, expanded in terms
of a kernel. Working in linear spaces of function has the benefit of
facilitating the construction and analysis of learning algorithms while at the
same time allowing large classes of functions. The latter include nonlinear
functions as well as functions defined on nonvectorial data. We cover a wide
range of methods, ranging from binary classifiers to sophisticated methods for
estimation with structured data.Comment: Published in at http://dx.doi.org/10.1214/009053607000000677 the
Annals of Statistics (http://www.imstat.org/aos/) by the Institute of
Mathematical Statistics (http://www.imstat.org
Positive Definite Kernels in Machine Learning
This survey is an introduction to positive definite kernels and the set of
methods they have inspired in the machine learning literature, namely kernel
methods. We first discuss some properties of positive definite kernels as well
as reproducing kernel Hibert spaces, the natural extension of the set of
functions associated with a kernel defined
on a space . We discuss at length the construction of kernel
functions that take advantage of well-known statistical models. We provide an
overview of numerous data-analysis methods which take advantage of reproducing
kernel Hilbert spaces and discuss the idea of combining several kernels to
improve the performance on certain tasks. We also provide a short cookbook of
different kernels which are particularly useful for certain data-types such as
images, graphs or speech segments.Comment: draft. corrected a typo in figure
Graph Kernels
We present a unified framework to study graph kernels, special cases of which include the random
walk (GƤrtner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004;
MahƩ et al., 2004) graph kernels. Through reduction to a Sylvester equation we improve the time
complexity of kernel computation between unlabeled graphs with n vertices from O(n^6) to O(n^3).
We find a spectral decomposition approach even more efficient when computing entire kernel matrices.
For labeled graphs we develop conjugate gradient and fixed-point methods that take O(dn^3)
time per iteration, where d is the size of the label set. By extending the necessary linear algebra to
Reproducing Kernel Hilbert Spaces (RKHS) we obtain the same result for d-dimensional edge kernels,
and O(n^4) in the infinite-dimensional case; on sparse graphs these algorithms only take O(n^2)
time per iteration in all cases. Experiments on graphs from bioinformatics and other application
domains show that these techniques can speed up computation of the kernel by an order of magnitude
or more. We also show that certain rational kernels (Cortes et al., 2002, 2003, 2004) when
specialized to graphs reduce to our random walk graph kernel. Finally, we relate our framework to
R-convolution kernels (Haussler, 1999) and provide a kernel that is close to the optimal assignment
kernel of Frƶhlich et al. (2006) yet provably positive semi-definite
A tree-based kernel for graphs with continuous attributes
The availability of graph data with node attributes that can be either
discrete or real-valued is constantly increasing. While existing kernel methods
are effective techniques for dealing with graphs having discrete node labels,
their adaptation to non-discrete or continuous node attributes has been
limited, mainly for computational issues. Recently, a few kernels especially
tailored for this domain, and that trade predictive performance for
computational efficiency, have been proposed. In this paper, we propose a graph
kernel for complex and continuous nodes' attributes, whose features are tree
structures extracted from specific graph visits. The kernel manages to keep the
same complexity of state-of-the-art kernels while implicitly using a larger
feature space. We further present an approximated variant of the kernel which
reduces its complexity significantly. Experimental results obtained on six
real-world datasets show that the kernel is the best performing one on most of
them. Moreover, in most cases the approximated version reaches comparable
performances to current state-of-the-art kernels in terms of classification
accuracy while greatly shortening the running times.Comment: This work has been submitted to the IEEE Transactions on Neural
Networks and Learning Systems for possible publication. Copyright may be
transferred without notice, after which this version may no longer be
accessibl
Efficient LZ78 factorization of grammar compressed text
We present an efficient algorithm for computing the LZ78 factorization of a
text, where the text is represented as a straight line program (SLP), which is
a context free grammar in the Chomsky normal form that generates a single
string. Given an SLP of size representing a text of length , our
algorithm computes the LZ78 factorization of in time
and space, where is the number of resulting LZ78 factors.
We also show how to improve the algorithm so that the term in the
time and space complexities becomes either , where is the length of the
longest LZ78 factor, or where is a quantity
which depends on the amount of redundancy that the SLP captures with respect to
substrings of of a certain length. Since where
is the alphabet size, the latter is asymptotically at least as fast as
a linear time algorithm which runs on the uncompressed string when is
constant, and can be more efficient when the text is compressible, i.e. when
and are small.Comment: SPIRE 201
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