2,154 research outputs found
Global Network Alignment Using Multiscale Spectral Signatures
Motivation: Protein interaction networks provide an important system-level view of biological processes. One of the fundamental problems in biological network analysis is the global alignment of a pair of networks, which puts the proteins of one network into correspondence with the proteins of another network in a manner that conserves their interactions while respecting other evidence of their homology. By providing a mapping between the networks of different species, alignments can be used to inform hypotheses about the functions of unannotated proteins, the existence of unobserved interactions, the evolutionary divergence between the two species and the evolution of complexes and pathways.
Results: We introduce GHOST, a global pairwise network aligner that uses a novel spectral signature to measure topological similarity across disparate networks. It exhibits state-of-the-art performance on several network alignment tasks. We show that the spectral signature used by GHOST is highly discriminative, while the alignments it produces are also robust to experimental noise. When compared with other recent approaches, we find that GHOST is able to recover larger and biologically-significant, shared subnetworks between species.
Availability: An efficient and parallelized implementation of GHOST, released under the Apache 2.0 license, is available at http:// cbcb.umd.edu/kingsford-group/ghostFunding: This work was supported by the National Science Foundation [CCF-1053918, EF-0849899, and IIS-0812111]; the National Institutes of Health [1R21AI085376]; and a University of Maryland Institute for Advanced Studies New Frontiers Award
Fair Evaluation of Global Network Aligners
Biological network alignment identifies topologically and functionally
conserved regions between networks of different species. It encompasses two
algorithmic steps: node cost function (NCF), which measures similarities
between nodes in different networks, and alignment strategy (AS), which uses
these similarities to rapidly identify high-scoring alignments. Different
methods use both different NCFs and different ASs. Thus, it is unclear whether
the superiority of a method comes from its NCF, its AS, or both. We already
showed on MI-GRAAL and IsoRankN that combining NCF of one method and AS of
another method can lead to a new superior method. Here, we evaluate MI-GRAAL
against newer GHOST to potentially further improve alignment quality. Also, we
approach several important questions that have not been asked systematically
thus far. First, we ask how much of the node similarity information in NCF
should come from sequence data compared to topology data. Existing methods
determine this more-less arbitrarily, which could affect the resulting
alignment(s). Second, when topology is used in NCF, we ask how large the size
of the neighborhoods of the compared nodes should be. Existing methods assume
that larger neighborhood sizes are better.
We find that MI-GRAAL's NCF is superior to GHOST's NCF, while the performance
of the methods' ASs is data-dependent. Thus, the combination of MI-GRAAL's NCF
and GHOST's AS could be a new superior method for certain data. Also, which
amount of sequence information is used within NCF does not affect alignment
quality, while the inclusion of topological information is crucial. Finally,
larger neighborhood sizes are preferred, but often, it is the second largest
size that is superior, and using this size would decrease computational
complexity.
Together, our results give several general recommendations for a fair
evaluation of network alignment methods.Comment: 19 pages. 10 figures. Presented at the 2014 ISMB Conference, July
13-15, Boston, M
Efficient Deformable Shape Correspondence via Kernel Matching
We present a method to match three dimensional shapes under non-isometric
deformations, topology changes and partiality. We formulate the problem as
matching between a set of pair-wise and point-wise descriptors, imposing a
continuity prior on the mapping, and propose a projected descent optimization
procedure inspired by difference of convex functions (DC) programming.
Surprisingly, in spite of the highly non-convex nature of the resulting
quadratic assignment problem, our method converges to a semantically meaningful
and continuous mapping in most of our experiments, and scales well. We provide
preliminary theoretical analysis and several interpretations of the method.Comment: Accepted for oral presentation at 3DV 2017, including supplementary
materia
Geometric Wavelet Scattering Networks on Compact Riemannian Manifolds
The Euclidean scattering transform was introduced nearly a decade ago to
improve the mathematical understanding of convolutional neural networks.
Inspired by recent interest in geometric deep learning, which aims to
generalize convolutional neural networks to manifold and graph-structured
domains, we define a geometric scattering transform on manifolds. Similar to
the Euclidean scattering transform, the geometric scattering transform is based
on a cascade of wavelet filters and pointwise nonlinearities. It is invariant
to local isometries and stable to certain types of diffeomorphisms. Empirical
results demonstrate its utility on several geometric learning tasks. Our
results generalize the deformation stability and local translation invariance
of Euclidean scattering, and demonstrate the importance of linking the used
filter structures to the underlying geometry of the data.Comment: 35 pages; 3 figures; 2 tables; v3: Revisions based on reviewer
comment
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