Search to Fine-tune Pre-trained Graph Neural Networks for Graph-level Tasks

Recently, graph neural networks (GNNs) have shown its unprecedented success in many graph-related tasks. However, GNNs face the label scarcity issue as other neural networks do. Thus, recent efforts try to pre-train GNNs on a large-scale unlabeled graph and adapt the knowledge from the unlabeled graph to the target downstream task. The adaptation is generally achieved by fine-tuning the pre-trained GNNs with a limited number of labeled data. Despite the importance of fine-tuning, current GNNs pre-training works often ignore designing a good fine-tuning strategy to better leverage transferred knowledge and improve the performance on downstream tasks. Only few works start to investigate a better fine-tuning strategy for pre-trained GNNs. But their designs either have strong assumptions or overlook the data-aware issue for various downstream datasets. Therefore, we aim to design a better fine-tuning strategy for pre-trained GNNs to improve the model performance in this paper. Given a pre-trained GNN, we propose to search to fine-tune pre-trained graph neural networks for graph-level tasks (S2PGNN), which adaptively design a suitable fine-tuning framework for the given labeled data on the downstream task. To ensure the improvement brought by searching fine-tuning strategy, we carefully summarize a proper search space of fine-tuning framework that is suitable for GNNs. The empirical studies show that S2PGNN can be implemented on the top of 10 famous pre-trained GNNs and consistently improve their performance. Besides, S2PGNN achieves better performance than existing fine-tuning strategies within and outside the GNN area. Our code is publicly available at \url{https://anonymous.4open.science/r/code_icde2024-A9CB/}

Pore-GNN: A graph neural network-based framework for predicting flow properties of porous media from micro-CT images

This paper presents a hybrid deep learning framework that combines graph neural networks with convolutional neural networks to predict porous media properties. This approach capitalizes on the capabilities of pre-trained convolutional neural networks to extract n-dimensional feature vectors from processed three dimensional micro computed tomography porous media images obtained from seven different sandstone rock samples. Subsequently, two strategies for embedding the computed feature vectors into graphs were explored: extracting a single feature vector per sample (image) and treating each sample as a node in the training graph, and representing each sample as a graph by extracting a fixed number of feature vectors, which form the nodes of each training graph. Various types of graph convolutional layers were examined to evaluate the capabilities and limitations of spectral and spatial approaches. The dataset was divided into 70/20/10 for training, validation, and testing. The models were trained to predict the absolute permeability of porous media. Notably, the proposed architectures further reduce the selected objective loss function to values below 35 mD, with improvements in the coefficient of determination reaching 9%. Moreover, the generalizability of the networks was evaluated by testing their performance on unseen sandstone and carbonate rock samples that were not encountered during training. Finally, a sensitivity analysis is conducted to investigate the influence of various hyperparameters on the performance of the models. The findings highlight the potential of graph neural networks as promising deep learning-based alternatives for characterizing porous media properties. The proposed architectures efficiently predict the permeability, which is more than 500 times faster than that of numerical solvers.Document Type: Original articleCited as: Alzahrani, M. K., Shapoval, A., Chen, Z., Rahman, S. S. Pore-GNN: A graph neural network-based framework for predicting flow properties of porous media from micro-CT images. Advances in Geo-Energy Research, 2023, 10(1):39-55. https://doi.org/10.46690/ager.2023.10.0

Motif-aware Attribute Masking for Molecular Graph Pre-training

Attribute reconstruction is used to predict node or edge features in the pre-training of graph neural networks. Given a large number of molecules, they learn to capture structural knowledge, which is transferable for various downstream property prediction tasks and vital in chemistry, biomedicine, and material science. Previous strategies that randomly select nodes to do attribute masking leverage the information of local neighbors However, the over-reliance of these neighbors inhibits the model's ability to learn from higher-level substructures. For example, the model would learn little from predicting three carbon atoms in a benzene ring based on the other three but could learn more from the inter-connections between the functional groups, or called chemical motifs. In this work, we propose and investigate motif-aware attribute masking strategies to capture inter-motif structures by leveraging the information of atoms in neighboring motifs. Once each graph is decomposed into disjoint motifs, the features for every node within a sample motif are masked. The graph decoder then predicts the masked features of each node within the motif for reconstruction. We evaluate our approach on eight molecular property prediction datasets and demonstrate its advantages

Efficient Deep Feature Learning and Extraction via StochasticNets

Deep neural networks are a powerful tool for feature learning and extraction given their ability to model high-level abstractions in highly complex data. One area worth exploring in feature learning and extraction using deep neural networks is efficient neural connectivity formation for faster feature learning and extraction. Motivated by findings of stochastic synaptic connectivity formation in the brain as well as the brain's uncanny ability to efficiently represent information, we propose the efficient learning and extraction of features via StochasticNets, where sparsely-connected deep neural networks can be formed via stochastic connectivity between neurons. To evaluate the feasibility of such a deep neural network architecture for feature learning and extraction, we train deep convolutional StochasticNets to learn abstract features using the CIFAR-10 dataset, and extract the learned features from images to perform classification on the SVHN and STL-10 datasets. Experimental results show that features learned using deep convolutional StochasticNets, with fewer neural connections than conventional deep convolutional neural networks, can allow for better or comparable classification accuracy than conventional deep neural networks: relative test error decrease of ~4.5% for classification on the STL-10 dataset and ~1% for classification on the SVHN dataset. Furthermore, it was shown that the deep features extracted using deep convolutional StochasticNets can provide comparable classification accuracy even when only 10% of the training data is used for feature learning. Finally, it was also shown that significant gains in feature extraction speed can be achieved in embedded applications using StochasticNets. As such, StochasticNets allow for faster feature learning and extraction performance while facilitate for better or comparable accuracy performances.Comment: 10 pages. arXiv admin note: substantial text overlap with arXiv:1508.0546