Graph-in-Graph Convolutional Network for Hyperspectral Image Classification

T-HyperGNNs: Hypergraph Neural Networks via Tensor Representations

Hypergraph neural networks (HyperGNNs) are a family of deep neural networks designed to perform inference on hypergraphs. HyperGNNs follow either a spectral or a spatial approach, in which a convolution or message-passing operation is conducted based on a hypergraph algebraic descriptor. While many HyperGNNs have been proposed and achieved state-of-the-art performance on broad applications, there have been limited attempts at exploring high-dimensional hypergraph descriptors (tensors) and joint node interactions carried by hyperedges. In this article, we depart from hypergraph matrix representations and present a new tensor-HyperGNN (T-HyperGNN) framework with cross-node interactions (CNIs). The T-HyperGNN framework consists of T-spectral convolution, T-spatial convolution, and T-message-passing HyperGNNs (T-MPHN). The T-spectral convolution HyperGNN is defined under the t-product algebra that closely connects to the spectral space. To improve computational efficiency for large hypergraphs, we localize the T-spectral convolution approach to formulate the T-spatial convolution and further devise a novel tensor-message-passing algorithm for practical implementation by studying a compressed adjacency tensor representation. Compared to the state-of-the-art approaches, our T-HyperGNNs preserve intrinsic high-order network structures without any hypergraph reduction and model the joint effects of nodes through a CNI layer. These advantages of our T-HyperGNNs are demonstrated in a wide range of real-world hypergraph datasets. The implementation code is available at https://github.com/wangfuli/T-HyperGNNs.git.

Masked Spatial-Spectral Autoencoders Are Excellent Hyperspectral Defenders

Deep learning (DL) methodology contributes a lot to the development of hyperspectral image (HSI) analysis community. However, it also makes HSI analysis systems vulnerable to adversarial attacks. To this end, we propose a masked spatial-spectral autoencoder (MSSA) in this article under self-supervised learning theory, for enhancing the robustness of HSI analysis systems. First, a masked sequence attention learning (MSAL) module is conducted to promote the inherent robustness of HSI analysis systems along spectral channel. Then, we develop a graph convolutional network (GCN) with learnable graph structure to establish global pixel-wise combinations. In this way, the attack effect would be dispersed by all the related pixels among each combination, and a better defense performance is achievable in spatial aspect. Finally, to improve the defense transferability and address the problem of limited labeled samples, MSSA employs spectra reconstruction as a pretext task and fits the datasets in a self-supervised manner. Comprehensive experiments over three benchmarks verify the effectiveness of MSSA in comparison with the state-of-the-art hyperspectral classification methods and representative adversarial defense strategies.

High-Accuracy Identification and Structure-Activity Analysis of Antioxidant Peptides via Deep Learning and Quantum Chemistry

Antioxidant peptides (AOPs) hold great promise for mitigating oxidative-stress-related diseases, but their discovery is hindered by inefficient and time-consuming traditional methods. To address this, we developed an innovative framework combining machine learning and quantum chemistry to accelerate AOP identification and analyze structure-activity relationships. A Bi-LSTM-based model, AOPP, achieved superior performance with accuracies of 0.9043 and 0.9267, precisions of 0.9767 and 0.9848, and Matthews correlation coefficients (MCCs) of 0.818 and 0.859 on two data sets, outperforming existing methods. Compared with XGBoost and LightGBM, AOPP demonstrated a 4.67% improvement in accuracy. Feature fusion significantly enhanced classification, as validated by UMAP visualization. Experimental validation of ten peptides confirmed the antioxidant activity, with LLA exhibiting the highest DPPH and ABTS scavenging rates (0.108 and 0.437 mmol/g, respectively). Quantum chemical calculations identified LLA's lowest HOMO-LUMO gap (ΔE = 0.26 eV) and C3-H26 as the key active site contributing to its superior antioxidant potential. This study highlights the synergy of machine learning and quantum chemistry, offering an efficient framework for AOP discovery with broad applications in therapeutics and functional foods.

Multiresolution Interpretable Contourlet Graph Network for Image Classification

Modeling contextual relationships in images as graph inference is an interesting and promising research topic. However, existing approaches only perform graph modeling of entities, ignoring the intrinsic geometric features of images. To overcome this problem, a novel multiresolution interpretable contourlet graph network (MICGNet) is proposed in this article. MICGNet delicately balances graph representation learning with the multiscale and multidirectional features of images, where contourlet is used to capture the hyperplanar directional singularities of images and multilevel sparse contourlet coefficients are encoded into graph for further graph representation learning. This process provides interpretable theoretical support for optimizing the model structure. Specifically, first, the superpixel-based region graph is constructed. Then, the region graph is applied to code the nonsubsampled contourlet transform (NSCT) coefficients of the image, which are considered as node features. Considering the statistical properties of the NSCT coefficients, we calculate the node similarity, i.e., the adjacency matrix, using Mahalanobis distance. Next, graph convolutional networks (GCNs) are employed to further learn more abstract multilevel NSCT-enhanced graph representations. Finally, the learnable graph assignment matrix is designed to get the geometric association representations, which accomplish the assignment of graph representations to grid feature maps. We conduct comparative experiments on six publicly available datasets, and the experimental analysis shows that MICGNet is significantly more effective and efficient than other algorithms of recent years.

Comprehensive Graph Gradual Pruning for Sparse Training in Graph Neural Networks

Graph neural networks (GNNs) tend to suffer from high computation costs due to the exponentially increasing scale of graph data and a large number of model parameters, which restricts their utility in practical applications. To this end, some recent works focus on sparsifying GNNs (including graph structures and model parameters) with the lottery ticket hypothesis (LTH) to reduce inference costs while maintaining performance levels. However, the LTH-based methods suffer from two major drawbacks: 1) they require exhaustive and iterative training of dense models, resulting in an extremely large training computation cost, and 2) they only trim graph structures and model parameters but ignore the node feature dimension, where vast redundancy exists. To overcome the above limitations, we propose a comprehensive graph gradual pruning framework termed CGP. This is achieved by designing a during-training graph pruning paradigm to dynamically prune GNNs within one training process. Unlike LTH-based methods, the proposed CGP approach requires no retraining, which significantly reduces the computation costs. Furthermore, we design a cosparsifying strategy to comprehensively trim all the three core elements of GNNs: graph structures, node features, and model parameters. Next, to refine the pruning operation, we introduce a regrowth process into our CGP framework, to reestablish the pruned but important connections. The proposed CGP is evaluated over a node classification task across six GNN architectures, including shallow models [graph convolutional network (GCN) and graph attention network (GAT)], shallow-but-deep-propagation models [simple graph convolution (SGC) and approximate personalized propagation of neural predictions (APPNP)], and deep models [GCN via initial residual and identity mapping (GCNII) and residual GCN (ResGCN)], on a total of 14 real-world graph datasets, including large-scale graph datasets from the challenging Open Graph Benchmark (OGB). Experiments reveal that the proposed strategy greatly improves both training and inference efficiency while matching or even exceeding the accuracy of the existing methods.

Dense Multi-Scale Graph Convolutional Network for Knee Joint Cartilage Segmentation

In this paper, we propose a dense multi-scale adaptive graph convolutional network (DMA-GCN) method for automatic segmentation of the knee joint cartilage from MR images. Under the multi-atlas setting, the suggested approach exhibits several novelties, as described in the following. First, our models integrate both local-level and global-level learning simultaneously. The local learning task aggregates spatial contextual information from aligned spatial neighborhoods of nodes, at multiple scales, while global learning explores pairwise affinities between nodes, located globally at different positions in the image. We propose two different structures of building models, whereby the local and global convolutional units are combined by following an alternating or a sequential manner. Secondly, based on the previous models, we develop the DMA-GCN network, by utilizing a densely connected architecture with residual skip connections. This is a deeper GCN structure, expanded over different block layers, thus being capable of providing more expressive node feature representations. Third, all units pertaining to the overall network are equipped with their individual adaptive graph learning mechanism, which allows the graph structures to be automatically learned during training. The proposed cartilage segmentation method is evaluated on the entire publicly available Osteoarthritis Initiative (OAI) cohort. To this end, we have devised a thorough experimental setup, with the goal of investigating the effect of several factors of our approach on the classification rates. Furthermore, we present exhaustive comparative results, considering traditional existing methods, six deep learning segmentation methods, and seven graph-based convolution methods, including the currently most representative models from this field. The obtained results demonstrate that the DMA-GCN outperforms all competing methods across all evaluation measures, providing DSC=95.71% and DSC=94.02% for the segmentation of femoral and tibial cartilage, respectively.

Identifying Candidate Gene-Disease Associations via Graph Neural Networks

Real-world objects are usually defined in terms of their own relationships or connections. A graph (or network) naturally expresses this model though nodes and edges. In biology, depending on what the nodes and edges represent, we may classify several types of networks, gene-disease associations (GDAs) included. In this paper, we presented a solution based on a graph neural network (GNN) for the identification of candidate GDAs. We trained our model with an initial set of well-known and curated inter- and intra-relationships between genes and diseases. It was based on graph convolutions, making use of multiple convolutional layers and a point-wise non-linearity function following each layer. The embeddings were computed for the input network built on a set of GDAs to map each node into a vector of real numbers in a multidimensional space. Results showed an AUC of 95% for training, validation, and testing, that in the real case translated into a positive response for 93% of the Top-15 (highest dot product) candidate GDAs identified by our solution. The experimentation was conducted on the DisGeNET dataset, while the DiseaseGene Association Miner (DG-AssocMiner) dataset by Stanford's BioSNAP was also processed for performance evaluation only.

Graph Convolutional Network Using Adaptive Neighborhood Laplacian Matrix for Hyperspectral Images with Application to Rice Seed Image Classification

Graph convolutional neural network architectures combine feature extraction and convolutional layers for hyperspectral image classification. An adaptive neighborhood aggregation method based on statistical variance integrating the spatial information along with the spectral signature of the pixels is proposed for improving graph convolutional network classification of hyperspectral images. The spatial-spectral information is integrated into the adjacency matrix and processed by a single-layer graph convolutional network. The algorithm employs an adaptive neighborhood selection criteria conditioned by the class it belongs to. Compared to fixed window-based feature extraction, this method proves effective in capturing the spectral and spatial features with variable pixel neighborhood sizes. The experimental results from the Indian Pines, Houston University, and Botswana Hyperion hyperspectral image datasets show that the proposed AN-GCN can significantly improve classification accuracy. For example, the overall accuracy for Houston University data increases from 81.71% (MiniGCN) to 97.88% (AN-GCN). Furthermore, the AN-GCN can classify hyperspectral images of rice seeds exposed to high day and night temperatures, proving its efficacy in discriminating the seeds under increased ambient temperature treatments.