3,728 research outputs found
Surface Networks
We study data-driven representations for three-dimensional triangle meshes,
which are one of the prevalent objects used to represent 3D geometry. Recent
works have developed models that exploit the intrinsic geometry of manifolds
and graphs, namely the Graph Neural Networks (GNNs) and its spectral variants,
which learn from the local metric tensor via the Laplacian operator. Despite
offering excellent sample complexity and built-in invariances, intrinsic
geometry alone is invariant to isometric deformations, making it unsuitable for
many applications. To overcome this limitation, we propose several upgrades to
GNNs to leverage extrinsic differential geometry properties of
three-dimensional surfaces, increasing its modeling power.
In particular, we propose to exploit the Dirac operator, whose spectrum
detects principal curvature directions --- this is in stark contrast with the
classical Laplace operator, which directly measures mean curvature. We coin the
resulting models \emph{Surface Networks (SN)}. We prove that these models
define shape representations that are stable to deformation and to
discretization, and we demonstrate the efficiency and versatility of SNs on two
challenging tasks: temporal prediction of mesh deformations under non-linear
dynamics and generative models using a variational autoencoder framework with
encoders/decoders given by SNs
A generative model for protein contact networks
In this paper we present a generative model for protein contact networks. The
soundness of the proposed model is investigated by focusing primarily on
mesoscopic properties elaborated from the spectra of the graph Laplacian. To
complement the analysis, we study also classical topological descriptors, such
as statistics of the shortest paths and the important feature of modularity.
Our experiments show that the proposed model results in a considerable
improvement with respect to two suitably chosen generative mechanisms,
mimicking with better approximation real protein contact networks in terms of
diffusion properties elaborated from the Laplacian spectra. However, as well as
the other considered models, it does not reproduce with sufficient accuracy the
shortest paths structure. To compensate this drawback, we designed a second
step involving a targeted edge reconfiguration process. The ensemble of
reconfigured networks denotes improvements that are statistically significant.
As a byproduct of our study, we demonstrate that modularity, a well-known
property of proteins, does not entirely explain the actual network architecture
characterizing protein contact networks. In fact, we conclude that modularity,
intended as a quantification of an underlying community structure, should be
considered as an emergent property of the structural organization of proteins.
Interestingly, such a property is suitably optimized in protein contact
networks together with the feature of path efficiency.Comment: 18 pages, 67 reference
Encoding Robust Representation for Graph Generation
Generative networks have made it possible to generate meaningful signals such
as images and texts from simple noise. Recently, generative methods based on
GAN and VAE were developed for graphs and graph signals. However, the
mathematical properties of these methods are unclear, and training good
generative models is difficult. This work proposes a graph generation model
that uses a recent adaptation of Mallat's scattering transform to graphs. The
proposed model is naturally composed of an encoder and a decoder. The encoder
is a Gaussianized graph scattering transform, which is robust to signal and
graph manipulation. The decoder is a simple fully connected network that is
adapted to specific tasks, such as link prediction, signal generation on graphs
and full graph and signal generation. The training of our proposed system is
efficient since it is only applied to the decoder and the hardware requirements
are moderate. Numerical results demonstrate state-of-the-art performance of the
proposed system for both link prediction and graph and signal generation.Comment: 9 pages, 7 figures, 6 table
Metrics for Graph Comparison: A Practitioner's Guide
Comparison of graph structure is a ubiquitous task in data analysis and
machine learning, with diverse applications in fields such as neuroscience,
cyber security, social network analysis, and bioinformatics, among others.
Discovery and comparison of structures such as modular communities, rich clubs,
hubs, and trees in data in these fields yields insight into the generative
mechanisms and functional properties of the graph.
Often, two graphs are compared via a pairwise distance measure, with a small
distance indicating structural similarity and vice versa. Common choices
include spectral distances (also known as distances) and distances
based on node affinities. However, there has of yet been no comparative study
of the efficacy of these distance measures in discerning between common graph
topologies and different structural scales.
In this work, we compare commonly used graph metrics and distance measures,
and demonstrate their ability to discern between common topological features
found in both random graph models and empirical datasets. We put forward a
multi-scale picture of graph structure, in which the effect of global and local
structure upon the distance measures is considered. We make recommendations on
the applicability of different distance measures to empirical graph data
problem based on this multi-scale view. Finally, we introduce the Python
library NetComp which implements the graph distances used in this work
Anomaly Detection on Graph Time Series
In this paper, we use variational recurrent neural network to investigate the
anomaly detection problem on graph time series. The temporal correlation is
modeled by the combination of recurrent neural network (RNN) and variational
inference (VI), while the spatial information is captured by the graph
convolutional network. In order to incorporate external factors, we use feature
extractor to augment the transition of latent variables, which can learn the
influence of external factors. With the target function as accumulative ELBO,
it is easy to extend this model to on-line method. The experimental study on
traffic flow data shows the detection capability of the proposed method
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