# On the Interplay of Subset Selection and Informed Graph Neural Networks

arXiv: https://arxiv.org/abs/2306.10066 · HTML: https://mlsanity.com/paper/2306.10066/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 33 of its 67 references that are in the map.
- First posted on arXiv 15 Jun 2023.

## Builds on (most cited first, 30 of 33)

- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [Fast Graph Representation Learning with PyTorch Geometric](https://mlsanity.com/paper/1903.02428/) (2019)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [The Concrete Distribution: A Continuous Relaxation of Discrete Random Variables](https://mlsanity.com/paper/1611.00712/) (2016)
- [SmoothGrad: removing noise by adding noise](https://mlsanity.com/paper/1706.03825/) (2017)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [GNNExplainer: Generating Explanations for Graph Neural Networks](https://mlsanity.com/paper/1903.03894/) (2019)
- [E(3)-Equivariant Graph Neural Networks for Data-Efficient and Accurate Interatomic Potentials](https://mlsanity.com/paper/2101.03164/) (2021)
- [Scientific Machine Learning through Physics-Informed Neural Networks: Where we are and What's next](https://mlsanity.com/paper/2201.05624/) (2022)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Parameterized Explainer for Graph Neural Network](https://mlsanity.com/paper/2011.04573/) (2020)
- [Explainability in Graph Neural Networks: A Taxonomic Survey](https://mlsanity.com/paper/2012.15445/) (2020)
- [On Explainability of Graph Neural Networks via Subgraph Explorations](https://mlsanity.com/paper/2102.05152/) (2021)
- [Geometric and Physical Quantities Improve E(3) Equivariant Message Passing](https://mlsanity.com/paper/2110.02905/) (2021)
- [XGNN: Towards Model-Level Explanations of Graph Neural Networks](https://mlsanity.com/paper/2006.02587/) (2020)
- [GraphLIME: Local Interpretable Model Explanations for Graph Neural Networks](https://mlsanity.com/paper/2001.06216/) (2020)
- [Informed Machine Learning -- A Taxonomy and Survey of Integrating Knowledge into Learning Systems](https://mlsanity.com/paper/1903.12394/) (2019)
- [Explainable Machine Learning for Scientific Insights and Discoveries](https://mlsanity.com/paper/1905.08883/) (2019)
- [Interpreting Graph Neural Networks for NLP With Differentiable Edge Masking](https://mlsanity.com/paper/2010.00577/) (2020)
- [Evaluating Explainability for Graph Neural Networks](https://mlsanity.com/paper/2208.09339/) (2022)
- [Physics-informed neural network for ultrasound nondestructive quantification of surface breaking cracks](https://mlsanity.com/paper/2005.03596/) (2020)
- [GraphSVX: Shapley Value Explanations for Graph Neural Networks](https://mlsanity.com/paper/2104.10482/) (2021)
- [New Frameworks for Offline and Streaming Coreset Constructions](https://mlsanity.com/paper/1612.00889/) (2016)
- [GCExplainer: Human-in-the-Loop Concept-based Explanations for Graph Neural Networks](https://mlsanity.com/paper/2107.11889/) (2021)
- [Thermodynamics-informed graph neural networks](https://mlsanity.com/paper/2203.01874/) (2022)
- [A Rate-Distortion Framework for Explaining Neural Network Decisions](https://mlsanity.com/paper/1905.11092/) (2019)
- [Directional Message Passing on Molecular Graphs via Synthetic Coordinates](https://mlsanity.com/paper/2111.04718/) (2021)

## Abstract (arXiv)

Machine learning techniques paired with the availability of massive datasets dramatically enhance our ability to explore the chemical compound space by providing fast and accurate predictions of molecular properties. However, learning on large datasets is strongly limited by the availability of computational resources and can be infeasible in some scenarios. Moreover, the instances in the datasets may not yet be labelled and generating the labels can be costly, as in the case of quantum chemistry computations. Thus, there is a need to select small training subsets from large pools of unlabelled data points and to develop reliable ML methods that can effectively learn from small training sets. This work focuses on predicting the molecules atomization energy in the QM9 dataset. We investigate the advantages of employing domain knowledge-based data sampling methods for an efficient training set selection combined with informed ML techniques. In particular, we show how maximizing molecular diversity in the training set selection process increases the robustness of linear and nonlinear regression techniques such as kernel methods and graph neural networks. We also check the reliability of the predictions made by the graph neural network with a model-agnostic explainer based on the rate distortion explanation framework.