Neural Network for Graphs: A Contextual Constructive Approach
Abstract
This paper presents a new approach for learning in structured domains (SDs) using a constructive neural network for graphs (NN4G). The new model allows the extension of the input domain for supervised neural networks to a general class of graphs including both acyclic/cyclic, directed/undirected labeled graphs. In particular, the model can realize adaptive contextual transductions, learning the mapping from graphs for both classification and regression tasks. In contrast to previous neural networks for structures that had a recursive dynamics, NN4G is based on a constructive feedforward architecture with state variables that uses neurons with no feedback connections. The neurons are applied to the input graphs by a general traversal process that relaxes the constraints of previous approaches derived by the causality assumption over hierarchical input data. Moreover, the incremental approach eliminates the need to introduce cyclic dependencies in the definition of the system state variables. In the traversal process, the NN4G units exploit (local) contextual information of the graphs vertices. In spite of the simplicity of the approach, we show that, through the compositionality of the contextual information developed by the learning, the model can deal with contextual information that is incrementally extended according to the graphs topology. The effectiveness and the generality of the new approach are investigated by analyzing its theoretical properties and providing experimental results.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In 2009, Micheli et al. first addressed graph mutual dependency by architecturally composite nonrecursive layers while inheriting ideas of message passing from RecGNNs.
“In 2009, Micheli et al. [24] first addressed graph mutual dependency by architecturally composite nonrecursive layers while inheriting ideas of message passing from RecGNNs.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
NN4G performs graph convolutions by summing up a node's neighborhood information directly.
“NN4G performs graph convolutions by summing up a node's neighborhood information directly.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
NN4G is the first work towards spatial-based ConvGNNs.
“Neural Network for Graphs (NN4G) [24], proposed in parallel with GNN*, is the first work towards spatial-based ConvGNNs.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
NN4G uses the unnormalized adjacency matrix, which may potentially cause hidden node states to have extremely different scales.
“One difference is that NN4G uses the unnormalized adjacency matrix which may potentially cause hidden node states to have extremely different scales.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
Distinctively different from RecGNNs, NN4G learns graph mutual dependency through a compositional neural architecture with independent parameters at each layer.
“Distinctively different from RecGNNs, NN4G learns graph mutual dependency through a compositional neural architecture with independent parameters at each layer.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
Micheli proves that a finite number of spatial graph convolutional layers exists such that for each node v, the receptive field of node v covers all nodes in the graph.
“Micheli [24] prove that a finite number of spatial graph convolutional layers exists such that for each node v ∈ V the receptive field of node v covers all nodes in the graph.”
From A Comprehensive Survey on Graph Neural Networks (2021) · cites this paper as [24]
Cites
Neural Networks: A Comprehensive Foundation
Haykin, S. (1998) · Cited by 30,070 · see citing works
Numerical recipes in C: the art of scientific computing
(1993) · Choice Reviews Online · doi:10.5860/choice.30-5638 · Cited by 17,933 · see citing works
Elman, J. L. (1990) · Cognitive Science · doi:10.1207/s15516709cog1402_1 · Cited by 11,212 · see citing works
Kernel Methods for Pattern Analysis
Shawe-Taylor, J. S., & Cristianini, N. (2004) · Cambridge University Press eBooks · doi:10.1017/cbo9780511809682 · Cited by 6,610 · see citing works
The Handbook of brain theory and neural networks
(1996) · Choice Reviews Online · doi:10.5860/choice.33-4484 · Cited by 3,913 · see citing works
The Cascade-Correlation learning architecture
Fahlman, S. E., & Lebiere, C. J. (2018) · doi:10.1184/r1/6610403 · Cited by 2,391 · see citing works
Introduction to Statistical Relational Learning
(2007) · doi:10.7551/mitpress/7432.001.0001 · Cited by 1,643 · see citing works
Kernel Methods in Computational Biology
Vert, J., & 阿久津, 達. (2004) · The MIT Press eBooks · doi:10.7551/mitpress/4057.001.0001 · Cited by 1,051 · see citing works
On Graph Kernels: Hardness Results and Efficient Alternatives
Gärtner, T., Flach, P. A., & Wrobel, S. (2003) · Lecture notes in computer science · doi:10.1007/978-3-540-45167-9_11 · Cited by 887 · see citing works
Supervised neural networks for the classification of structures
Sperduti, A., & Starita, A. (1997) · IEEE Transactions on Neural Networks · doi:10.1109/72.572108 · Cited by 666 · see citing works
Džeroski, S. (2006) · Springer eBooks · doi:10.1007/0-387-25465-x_41 · Cited by 523 · see citing works
Introduction to Statistical Relational Learning (Adaptive Computation and Machine Learning)
Getoor, L., & Taskar, B. (2007) · The MIT Press eBooks · Cited by 502 · see citing works
Exploiting the past and the future in protein secondary structure prediction
Baldi, P., Brunak, S., Frasconi, P., Soda, G., & Pollastri, G. (1999) · Bioinformatics · doi:10.1093/bioinformatics/15.11.937 · Cited by 495 · see citing works
A general framework for adaptive processing of data structures
Frasconi, P., Gori, M., & Sperduti, A. (1998) · IEEE Transactions on Neural Networks · doi:10.1109/72.712151 · Cited by 481 · see citing works
A survey of kernels for structured data
Gärtner, T. (2003) · ACM SIGKDD Explorations Newsletter · doi:10.1145/959242.959248 · Cited by 451 · see citing works
A Field Guide to Dynamical Recurrent Networks
Kolen, J. F., & Kremer, S. C. (2009) · Institute of Electrical and Electronics Engineers eBooks · doi:10.1109/9780470544037 · Cited by 338 · see citing works
(2001) · Springer eBooks · doi:10.1007/978-3-662-04599-2 · Cited by 317 · see citing works
Dězeroski, S. (2001) · Springer eBooks · Cited by 221 · see citing works
Backpropagation Algorithms for a Broad Class of Dynamic Networks
Jesus, O. D., & Hagan, M. (2007) · IEEE Transactions on Neural Networks · doi:10.1109/tnn.2006.882371 · Cited by 148 · see citing works
Expressivity versus efficiency of graph kernels
Ramon, J., & Gaertner, T. (2003) · Lirias · Cited by 148 · see citing works
On the Theory of the Analytical Forms called Trees
Cayley, A. (2009) · The Collected Mathematical Papers · doi:10.1017/cbo9780511703690.046 · Cited by 140 · see citing works
Use of a neural network to determine the boiling point of alkanes
Cherqaoui, D., & Villemin, D. (1994) · Journal of the Chemical Society Faraday Transactions · doi:10.1039/ft9949000097 · Cited by 97 · see citing works
Ilin, R., Kozma, R., & Werbos, P. J. (2008) · IEEE Transactions on Neural Networks · doi:10.1109/tnn.2008.2000396 · Cited by 93 · see citing works
Application of Cascade Correlation Networks for Structures to Chemistry
Bianucci, A. M., Micheli, A., Sperduti, A., & Starita, A. (2000) · Applied Intelligence · doi:10.1023/a:1008368105614 · Cited by 80 · see citing works
Self-citationContextual Processing of Structured Data by Recursive Cascade Correlation
Micheli, A., Sona, D., & Sperduti, A. (2004) · IEEE Transactions on Neural Networks · doi:10.1109/tnn.2004.837783 · Cited by 66 · see citing works
Self-citationLearning with recurrent neural networks
Hammer, B. (2000) · Lecture notes in control and information sciences · doi:10.1007/bfb0110016 · Cited by 66 · see citing works
(2000) · Applied Physics Letters · doi:10.1162/153244304773936054 · Cited by 62 · see citing works
Universal Approximation Capability of Cascade Correlation for Structures
Hammer, B., Micheli, A., & Sperduti, A. (2005) · Neural Computation · doi:10.1162/0899766053491878 · Cited by 51 · see citing works
Self-citationA Comparison between Recursive Neural Networks and Graph Neural Networks
Massa, V. D., Monfardini, G., Sarti, L., Scarselli, F., Maggini, M., & Gori, M. (2006) · International Joint Conference on Neural Networks (IJCNN) · doi:10.1109/ijcnn.2006.246763 · Cited by 41 · see citing works
Learning protein secondary structure from sequential and relational data
Ceroni, A., Frasconi, P., & Pollastri, G. (2005) · Neural Networks · doi:10.1016/j.neunet.2005.07.001 · Cited by 35 · see citing works
Processing directed acyclic graphs with recursive neural networks
Bianchini, M., Gori, M., & Scarselli, F. (2001) · IEEE Transactions on Neural Networks · doi:10.1109/72.963781 · Cited by 33 · see citing works
A Novel Approach to QSPR/QSAR Based on Neural Networks for Structures
Bianucci, A. M., Micheli, A., Sperduti, A., & Starita, A. (2003) · Studies in fuzziness and soft computing · doi:10.1007/978-3-540-36213-5_10 · Cited by 32 · see citing works
Self-citationLearning and Generalization in Cascade Network Architectures
Littmann, E., & Ritter, H. J. (1996) · Neural Computation · doi:10.1162/neco.1996.8.7.1521 · Cited by 30 · see citing works
Neural methods for non-standard data
Hammer, B., & Jain, B. J. (2004) · Cited by 28 · see citing works
Recursive Processing of Cyclic Graphs
Bianchini, M., Gori, M., Sarti, L., & Scarselli, F. (2006) · IEEE Transactions on Neural Networks · doi:10.1109/tnn.2005.860873 · Cited by 28 · see citing works
Clustering documents into a web directory for bootstrapping a supervised classification
Adami, G., Avesani, P., & Sona, D. (2004) · Data & Knowledge Engineering · doi:10.1016/j.datak.2004.11.003 · Cited by 28 · see citing works
From Sequences to Data Structures: Theory and Applications
Kolen, J. F., & Kremer, S. C. (2009) · Institute of Electrical and Electronics Engineers eBooks · doi:10.1109/9780470544037.ch19 · Cited by 25 · see citing works
Micheli, A., Portera, F., & Sperduti, A. (2005) · Neurocomputing · doi:10.1016/j.neucom.2004.11.013 · Cited by 21 · see citing works
Self-citationMenchetti, S., Costa, F., Frasconi, P., et al. (2005) · Pattern Recognition Letters · doi:10.1016/j.patrec.2005.03.011 · Cited by 19 · see citing works
A Normalized Adaptive Training of Recurrent Neural Networks With Augmented Error Gradient
Wu, Y., Qing, S., & Liu, S. (2008) · IEEE Transactions on Neural Networks · doi:10.1109/tnn.2007.908647 · Cited by 16 · see citing works
An Introduction to Recursive Neural Networks and Kernel Methods for Cheminformatics
Micheli, A., Sperduti, A., & Starita, A. (2007) · Current Pharmaceutical Design · doi:10.2174/138161207780765981 · Cited by 15 · see citing works
Self-citationSchleif, F.-M., Clauss, U., Villmann, T., et al. (2005) · International Conference on Machine Learning and Applications · doi:10.1109/icmla.2004.1383538 · Cited by 9 · see citing works
Tutorial: Perspectives on Learning with RNNs
Hammer, B., & Steil, J. J. (2002) · Cited by 9 · see citing works
Statistical Relational Learning: An Inductive Logic Programming Perspective
Raedt, L. D. (2005) · Lecture notes in computer science · doi:10.1007/11564096_3 · Cited by 6 · see citing works
Kernels on prolog ground terms
Passerini, A., & Frasconi, P. (2005) · Cited by 4 · see citing works
A New Neural Network Model for Contextual Processing of Graphs
Micheli, A., & Sestito, A. S. (2006) · Lecture notes in computer science · doi:10.1007/11731177_2 · Cited by 4 · see citing works
Self-citationDealing with Graphs by Neural Networks
Micheli, A., & Sestito, A. S. (2005) · CINECA IRIS Institutial research information system (University of Pisa) · Cited by 3 · see citing works
Self-citationStatistical Relational Learning: An Inductive Logic Programming Perspective
Raedt, L. D. (2005) · Lecture notes in computer science · doi:10.1007/11564126_3 · Cited by 3 · see citing works
Menchetti, S., Costa, F., Frasconi, P., et al. (2003) · Cited by 2 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
A Comprehensive Survey on Graph Neural Networks
Wu, Z., Pan, S., Chen, F., Long, G., Zhang, C., & Yu, P. S. (2021) · IEEE Transactions on Neural Networks and Learning Systems · doi:10.1109/tnnls.2020.2978386 · Cited by 11,000 · see citing works
Graph neural networks: A review of methods and applications
Zhou, J., Cui, G., Hu, S., Zhang, Z., Yang, C., Liu, Z., Wang, L., Li, C., & Sun, M. (2020) · AI Open · doi:10.1016/j.aiopen.2021.01.001 · Cited by 6,880 · see citing works
A Survey of Convolutional Neural Networks: Analysis, Applications, and Prospects
Li, Z., Liu, F., Yang, W., Peng, S., & Zhou, J. (2022) · IEEE Transactions on Neural Networks and Learning Systems · doi:10.1109/tnnls.2021.3084827 · Cited by 5,273 · see citing works
“To record each layer’s features, NN4G [55] uses residual structure and skip connections.”
BackgroundMethodMolecular graph convolutions: moving beyond fingerprints
Kearnes, S., McCloskey, K., Berndl, M., Pande, V., & Riley, P. (2016) · Journal of Computer-Aided Molecular Design · doi:10.1007/s10822-016-9938-8 · Cited by 1,631 · see citing works
A compact review of molecular property prediction with graph neural networks
Wieder, O., Kohlbacher, S., Kuenemann, M., Garon, A., Ducrot, P., Seidel, T., & Langer, T. (2020) · Drug Discovery Today: Technologies · doi:10.1016/j.ddtec.2020.11.009 · Cited by 522 · see citing works
Skeleton-based action recognition via spatial and temporal transformer networks
Plizzari, C., Cannici, M., & Matteucci, M. (2021) · Computer Vision and Image Understanding · doi:10.1016/j.cviu.2021.103219 · Cited by 409 · see citing works
Review of the State of the Art of Deep Learning for Plant Diseases: A Broad Analysis and Discussion
Hasan, R. I., Yusuf, S. M., & Alzubaidi, L. (2020) · Plants · doi:10.3390/plants9101302 · Cited by 213 · see citing works
CGC-Net: Cell Graph Convolutional Network for Grading of Colorectal Cancer Histology Images
Zhou, Y., Graham, S., Alemi Koohbanani, N., Shaban, M., Heng, P.-A., & Rajpoot, N. (2019) · 2019 IEEE/CVF International Conference on Computer Vision Workshop (ICCVW) · doi:10.1109/iccvw.2019.00050 · Cited by 225 · see citing works
Echo state graph neural networks with analogue random resistive memory arrays
Wang, S., Li, Y., Wang, D., Zhang, W., Chen, X., Dong, D., Wang, S., Zhang, X., Lin, P., Gallicchio, C., et al. (2023) · Nature Machine Intelligence · doi:10.1038/s42256-023-00609-5 · Cited by 84 · see citing works
Early prediction of dementia using fMRI data with a graph convolutional network approach
Han, S., Sun, Z., Zhao, K., Duan, F., Caiafa, C. F., Zhang, Y., & Solé-Casals, J. (2024) · Journal of Neural Engineering · doi:10.1088/1741-2552/ad1e22 · Cited by 23 · see citing works
Lin, S., & Jia, P. (2024) · GigaScience · doi:10.1093/gigascience/giae108 · Cited by 4 · see citing works
- Authors
- Micheli, A.
- Affiliations
- University of Pisa (IT)
- Corresponding author
- Micheli, A.
- ORCID
- Micheli, A.
- Venue
- IEEE Transactions on Neural Networks
- Published
- 2009-03
- Volume
- 20
- Issue
- 3
- Pages
- 498-511
- ISSN
- 1045-9227 (ISSN-L)
- 1941-0093
- OpenAlex
- W2139906443
- Cited by
- 639
- References
- 49
- Citations by year
- 2026: 31 · 2025: 76 · 2024: 91 · 2023: 93 · 2022: 97 · 2021: 107 · 2020: 76 · 2019: 12 · 2018: 12 · 2017: 2 · 2016: 7 · 2015: 6 · 2014: 6 · 2013: 8 · 2012: 6
- FWCI
- 5.40
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- IEEE Transactions on Neural Networks (publishedVersion)
- PubMed (publishedVersion)
- CINECA IRIS Institutial research information system (University of Pisa) (submittedVersion)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Neural Networks and Applications
- Physical Sciences › Computer Science › Artificial Intelligence › Advanced Graph Neural Networks
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Graph Theory and Algorithms
- Keywords
- structured domains, constructive neural networks, contextual information, graph classification, graph regression, incremental learning, cyclic graphs, directed and undirected graphs, supervised learning
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review