315 research outputs found
Graph kernels based on tree patterns for molecules
Motivated by chemical applications, we revisit and extend a family of
positive definite kernels for graphs based on the detection of common subtrees,
initially proposed by Ramon et al. (2003). We propose new kernels with a
parameter to control the complexity of the subtrees used as features to
represent the graphs. This parameter allows to smoothly interpolate between
classical graph kernels based on the count of common walks, on the one hand,
and kernels that emphasize the detection of large common subtrees, on the other
hand. We also propose two modular extensions to this formulation. The first
extension increases the number of subtrees that define the feature space, and
the second one removes noisy features from the graph representations. We
validate experimentally these new kernels on binary classification tasks
consisting in discriminating toxic and non-toxic molecules with support vector
machines
Inductive queries for a drug designing robot scientist
It is increasingly clear that machine learning algorithms need to be integrated in an iterative scientific discovery loop, in which data is queried repeatedly by means of inductive queries and where the computer provides guidance to the experiments that are being performed. In this chapter, we summarise several key challenges in achieving this integration of machine learning and data mining algorithms in methods for the discovery of Quantitative Structure Activity Relationships (QSARs). We introduce the concept of a robot scientist, in which all steps of the discovery process are automated; we discuss the representation of molecular data such that knowledge discovery tools can analyse it, and we discuss the adaptation of machine learning and data mining algorithms to guide QSAR experiments
Shift Aggregate Extract Networks
We introduce an architecture based on deep hierarchical decompositions to
learn effective representations of large graphs. Our framework extends classic
R-decompositions used in kernel methods, enabling nested "part-of-part"
relations. Unlike recursive neural networks, which unroll a template on input
graphs directly, we unroll a neural network template over the decomposition
hierarchy, allowing us to deal with the high degree variability that typically
characterize social network graphs. Deep hierarchical decompositions are also
amenable to domain compression, a technique that reduces both space and time
complexity by exploiting symmetries. We show empirically that our approach is
competitive with current state-of-the-art graph classification methods,
particularly when dealing with social network datasets
Graph Kernels
We present a unified framework to study graph kernels, special cases of which include the random
walk (Gärtner et al., 2003; Borgwardt et al., 2005) and marginalized (Kashima et al., 2003, 2004;
MahĂŠ 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 FrĂśhlich et al. (2006) yet provably positive semi-definite
A Survey on Graph Kernels
Graph kernels have become an established and widely-used technique for
solving classification tasks on graphs. This survey gives a comprehensive
overview of techniques for kernel-based graph classification developed in the
past 15 years. We describe and categorize graph kernels based on properties
inherent to their design, such as the nature of their extracted graph features,
their method of computation and their applicability to problems in practice. In
an extensive experimental evaluation, we study the classification accuracy of a
large suite of graph kernels on established benchmarks as well as new datasets.
We compare the performance of popular kernels with several baseline methods and
study the effect of applying a Gaussian RBF kernel to the metric induced by a
graph kernel. In doing so, we find that simple baselines become competitive
after this transformation on some datasets. Moreover, we study the extent to
which existing graph kernels agree in their predictions (and prediction errors)
and obtain a data-driven categorization of kernels as result. Finally, based on
our experimental results, we derive a practitioner's guide to kernel-based
graph classification
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