Universal Readout for Graph Convolutional Neural Networks

Several machine learning problems can be naturally defined over graph data. Recently, many researchers have been focusing on the definition of neural networks for graphs. The core idea is to learn a hidden representation for the graph vertices, with a convolutive or recurrent mechanism. When considering discriminative tasks on graphs, such as classification or regression, one critical component to design is the readout function, i.e. the mapping from the set of vertex representations to a fixed-size vector (or the output). Different approaches have been presented in literature, but recent approaches tend to be complex, making the training of the whole network harder. In this paper, we frame the problem in the setting of learning over sets. Adopting recently proposed theorems over functions defined on sets, we propose a simple but powerful formulation for a readout layer that can encode or approximate arbitrarily well any continuous permutation-invariant function over sets. Experimental results on real-world graph datasets show that, compared to other approaches, the proposed readout architecture can improve the predictive performance of Graph Neural Networks while being computationally more efficient.

[1]  Mathias Niepert,et al.  Learning Convolutional Neural Networks for Graphs , 2016, ICML.

[2]  George Karypis,et al.  Comparison of descriptor spaces for chemical compound retrieval and classification , 2006, Sixth International Conference on Data Mining (ICDM'06).

[3]  Alessandro Sperduti,et al.  Supervised neural networks for the classification of structures , 1997, IEEE Trans. Neural Networks.

[4]  Jian Sun,et al.  Deep Residual Learning for Image Recognition , 2015, 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[5]  Max Welling,et al.  Semi-Supervised Classification with Graph Convolutional Networks , 2016, ICLR.

[6]  Kurt Mehlhorn,et al.  Weisfeiler-Lehman Graph Kernels , 2011, J. Mach. Learn. Res..

[7]  Hannu Toivonen,et al.  Statistical evaluation of the predictive toxicology challenge , 2000 .

[8]  Alessio Micheli,et al.  Neural Network for Graphs: A Contextual Constructive Approach , 2009, IEEE Transactions on Neural Networks.

[9]  Samuel S. Schoenholz,et al.  Neural Message Passing for Quantum Chemistry , 2017, ICML.

[10]  Xavier Bresson,et al.  Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering , 2016, NIPS.

[11]  Jure Leskovec,et al.  How Powerful are Graph Neural Networks? , 2018, ICLR.

[12]  Alán Aspuru-Guzik,et al.  Convolutional Networks on Graphs for Learning Molecular Fingerprints , 2015, NIPS.

[13]  A. Debnath,et al.  Structure-activity relationship of mutagenic aromatic and heteroaromatic nitro compounds. Correlation with molecular orbital energies and hydrophobicity. , 1991, Journal of medicinal chemistry.

[14]  P. Dobson,et al.  Distinguishing enzyme structures from non-enzymes without alignments. , 2003, Journal of molecular biology.

[15]  Ashwin Srinivasan,et al.  Statistical Evaluation of the Predictive Toxicology Challenge 2000-2001 , 2003, Bioinform..

[16]  Nikos Komodakis,et al.  Dynamic Edge-Conditioned Filters in Convolutional Neural Networks on Graphs , 2017, 2017 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[17]  Donald F. Towsley,et al.  Diffusion-Convolutional Neural Networks , 2015, NIPS.

[18]  Samy Bengio,et al.  Order Matters: Sequence to sequence for sets , 2015, ICLR.

[19]  Alessandro Sperduti,et al.  On Filter Size in Graph Convolutional Networks , 2018, 2018 IEEE Symposium Series on Computational Intelligence (SSCI).

[20]  Kurt Mehlhorn,et al.  Efficient graphlet kernels for large graph comparison , 2009, AISTATS.

[21]  Jure Leskovec,et al.  Hierarchical Graph Representation Learning with Differentiable Pooling , 2018, NeurIPS.

[22]  Yixin Chen,et al.  An End-to-End Deep Learning Architecture for Graph Classification , 2018, AAAI.

[23]  Tomaso A. Poggio,et al.  Bridging the Gaps Between Residual Learning, Recurrent Neural Networks and Visual Cortex , 2016, ArXiv.

[24]  Xavier Bresson,et al.  An Experimental Study of Neural Networks for Variable Graphs , 2018, ICLR.

[25]  Ji Wan,et al.  Deep Learning for Content-Based Image Retrieval: A Comprehensive Study , 2014, ACM Multimedia.

[26]  Ah Chung Tsoi,et al.  The Graph Neural Network Model , 2009, IEEE Transactions on Neural Networks.

[27]  Alessandro Sperduti,et al.  Multiple Graph-Kernel Learning , 2015, 2015 IEEE Symposium Series on Computational Intelligence.

[28]  Alessandro Sperduti,et al.  A Tree-Based Kernel for Graphs , 2012, SDM.

[29]  Brendan D. McKay,et al.  Practical graph isomorphism, II , 2013, J. Symb. Comput..

[30]  Davide Bacciu,et al.  Contextual Graph Markov Model: A Deep and Generative Approach to Graph Processing , 2018, ICML.

[31]  Brian Kingsbury,et al.  New types of deep neural network learning for speech recognition and related applications: an overview , 2013, 2013 IEEE International Conference on Acoustics, Speech and Signal Processing.

[32]  Roman Garnett,et al.  Efficient Graph Kernels by Randomization , 2012, ECML/PKDD.

[33]  Giorgio Valle,et al.  Scuba: scalable kernel-based gene prioritization , 2018, BMC Bioinformatics.

[34]  Pietro Liò,et al.  Towards Sparse Hierarchical Graph Classifiers , 2018, ArXiv.

[35]  Richard S. Zemel,et al.  Gated Graph Sequence Neural Networks , 2015, ICLR.