12,152 research outputs found
Transforming Graph Representations for Statistical Relational Learning
Relational data representations have become an increasingly important topic
due to the recent proliferation of network datasets (e.g., social, biological,
information networks) and a corresponding increase in the application of
statistical relational learning (SRL) algorithms to these domains. In this
article, we examine a range of representation issues for graph-based relational
data. Since the choice of relational data representation for the nodes, links,
and features can dramatically affect the capabilities of SRL algorithms, we
survey approaches and opportunities for relational representation
transformation designed to improve the performance of these algorithms. This
leads us to introduce an intuitive taxonomy for data representation
transformations in relational domains that incorporates link transformation and
node transformation as symmetric representation tasks. In particular, the
transformation tasks for both nodes and links include (i) predicting their
existence, (ii) predicting their label or type, (iii) estimating their weight
or importance, and (iv) systematically constructing their relevant features. We
motivate our taxonomy through detailed examples and use it to survey and
compare competing approaches for each of these tasks. We also discuss general
conditions for transforming links, nodes, and features. Finally, we highlight
challenges that remain to be addressed
Methods for protein complex prediction and their contributions towards understanding the organization, function and dynamics of complexes
Complexes of physically interacting proteins constitute fundamental
functional units responsible for driving biological processes within cells. A
faithful reconstruction of the entire set of complexes is therefore essential
to understand the functional organization of cells. In this review, we discuss
the key contributions of computational methods developed till date
(approximately between 2003 and 2015) for identifying complexes from the
network of interacting proteins (PPI network). We evaluate in depth the
performance of these methods on PPI datasets from yeast, and highlight
challenges faced by these methods, in particular detection of sparse and small
or sub- complexes and discerning of overlapping complexes. We describe methods
for integrating diverse information including expression profiles and 3D
structures of proteins with PPI networks to understand the dynamics of complex
formation, for instance, of time-based assembly of complex subunits and
formation of fuzzy complexes from intrinsically disordered proteins. Finally,
we discuss methods for identifying dysfunctional complexes in human diseases,
an application that is proving invaluable to understand disease mechanisms and
to discover novel therapeutic targets. We hope this review aptly commemorates a
decade of research on computational prediction of complexes and constitutes a
valuable reference for further advancements in this exciting area.Comment: 1 Tabl
Adaptive Graph via Multiple Kernel Learning for Nonnegative Matrix Factorization
Nonnegative Matrix Factorization (NMF) has been continuously evolving in
several areas like pattern recognition and information retrieval methods. It
factorizes a matrix into a product of 2 low-rank non-negative matrices that
will define parts-based, and linear representation of nonnegative data.
Recently, Graph regularized NMF (GrNMF) is proposed to find a compact
representation,which uncovers the hidden semantics and simultaneously respects
the intrinsic geometric structure. In GNMF, an affinity graph is constructed
from the original data space to encode the geometrical information. In this
paper, we propose a novel idea which engages a Multiple Kernel Learning
approach into refining the graph structure that reflects the factorization of
the matrix and the new data space. The GrNMF is improved by utilizing the graph
refined by the kernel learning, and then a novel kernel learning method is
introduced under the GrNMF framework. Our approach shows encouraging results of
the proposed algorithm in comparison to the state-of-the-art clustering
algorithms like NMF, GrNMF, SVD etc.Comment: This paper has been withdrawn by the author due to the terrible
writin
Classifying pairs with trees for supervised biological network inference
Networks are ubiquitous in biology and computational approaches have been
largely investigated for their inference. In particular, supervised machine
learning methods can be used to complete a partially known network by
integrating various measurements. Two main supervised frameworks have been
proposed: the local approach, which trains a separate model for each network
node, and the global approach, which trains a single model over pairs of nodes.
Here, we systematically investigate, theoretically and empirically, the
exploitation of tree-based ensemble methods in the context of these two
approaches for biological network inference. We first formalize the problem of
network inference as classification of pairs, unifying in the process
homogeneous and bipartite graphs and discussing two main sampling schemes. We
then present the global and the local approaches, extending the later for the
prediction of interactions between two unseen network nodes, and discuss their
specializations to tree-based ensemble methods, highlighting their
interpretability and drawing links with clustering techniques. Extensive
computational experiments are carried out with these methods on various
biological networks that clearly highlight that these methods are competitive
with existing methods.Comment: 22 page
Prior knowledge based mining functional modules from Yeast PPI networks with gene ontology
<p>Abstract</p> <p>Background</p> <p>In the literature, there are fruitful algorithmic approaches for identification functional modules in protein-protein interactions (PPI) networks. Because of accumulation of large-scale interaction data on multiple organisms and non-recording interaction data in the existing PPI database, it is still emergent to design novel computational techniques that can be able to correctly and scalably analyze interaction data sets. Indeed there are a number of large scale biological data sets providing indirect evidence for protein-protein interaction relationships.</p> <p>Results</p> <p>The main aim of this paper is to present a prior knowledge based mining strategy to identify functional modules from PPI networks with the aid of Gene Ontology. Higher similarity value in Gene Ontology means that two gene products are more functionally related to each other, so it is better to group such gene products into one functional module. We study (i) to encode the functional pairs into the existing PPI networks; and (ii) to use these functional pairs as pairwise constraints to supervise the existing functional module identification algorithms. Topology-based modularity metric and complex annotation in MIPs will be used to evaluate the identified functional modules by these two approaches.</p> <p>Conclusions</p> <p>The experimental results on Yeast PPI networks and GO have shown that the prior knowledge based learning methods perform better than the existing algorithms.</p
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