ProtNN: fast and accurate protein 3D-structure classification in structural and topological space

Background

Studying the functions and structures of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the classification of a protein structure remains a difficult, costly, and time consuming task. The difficulties are often due to the essential role of spatial and topological structures in the classification of protein structures.

Results

We propose ProtNN, a novel classification approach for protein 3D-structures. Given an unannotated query protein structure and a set of annotated proteins, ProtNN assigns to the query protein the class with the highest number of votes across the k nearest neighbor reference proteins, where k is a user-defined parameter. The search of the nearest neighbor annotated structures is based on a protein-graph representation model and pairwise similarities between vector embedding of the query and the reference protein structures in structural and topological spaces.

Conclusions

We demonstrate through an extensive experimental evaluation that ProtNN is able to accurately classify several datasets in an extremely fast runtime compared to state-of-the-art approaches. We further show that ProtNN is able to scale up to a whole PDB dataset in a single-process mode with no parallelization, with a gain of thousands order of magnitude in runtime compared to state-of-the-art approaches.

CommPOOL: An interpretable graph pooling framework for hierarchical graph representation learning

Recent years have witnessed the emergence and flourishing of hierarchical graph pooling neural networks (HGPNNs) which are effective graph representation learning approaches for graph level tasks such as graph classification. However, current HGPNNs do not take full advantage of the graph's intrinsic structures (e.g., community structure). Moreover, the pooling operations in existing HGPNNs are difficult to be interpreted. In this paper, we propose a new interpretable graph pooling framework - CommPOOL, that can capture and preserve the hierarchical community structure of graphs in the graph representation learning process. Specifically, the proposed community pooling mechanism in CommPOOL utilizes an unsupervised approach for capturing the inherent community structure of graphs in an interpretable manner. CommPOOL is a general and flexible framework for hierarchical graph representation learning that can further facilitate various graph-level tasks. Evaluations on five public benchmark datasets and one synthetic dataset demonstrate the superior performance of CommPOOL in graph representation learning for graph classification compared to the state-of-the-art baseline methods, and its effectiveness in capturing and preserving the community structure of graphs.

GraphTar: applying word2vec and graph neural networks to miRNA target prediction

BACKGROUND

MicroRNAs (miRNAs) are short, non-coding RNA molecules that regulate gene expression by binding to specific mRNAs, inhibiting their translation. They play a critical role in regulating various biological processes and are implicated in many diseases, including cardiovascular, oncological, gastrointestinal diseases, and viral infections. Computational methods that can identify potential miRNA-mRNA interactions from raw data use one-dimensional miRNA-mRNA duplex representations and simple sequence encoding techniques, which may limit their performance.

RESULTS

We have developed GraphTar, a new target prediction method that uses a novel graph-based representation to reflect the spatial structure of the miRNA-mRNA duplex. Unlike existing approaches, we use the word2vec method to accurately encode RNA sequence information. In conjunction with the novel encoding method, we use a graph neural network classifier that can accurately predict miRNA-mRNA interactions based on graph representation learning. As part of a comparative study, we evaluate three different node embedding approaches within the GraphTar framework and compare them with other state-of-the-art target prediction methods. The results show that the proposed method achieves similar performance to the best methods in the field and outperforms them on one of the datasets.

CONCLUSIONS

In this study, a novel miRNA target prediction approach called GraphTar is introduced. Results show that GraphTar is as effective as existing methods and even outperforms them in some cases, opening new avenues for further research. However, the expansion of available datasets is critical for advancing the field towards real-world applications.

Locality preserving dense graph convolutional networks with graph context-aware node representations

Graph convolutional networks (GCNs) have been widely used for representation learning on graph data, which can capture structural patterns on a graph via specifically designed convolution and readout operations. In many graph classification applications, GCN-based approaches have outperformed traditional methods. However, most of the existing GCNs are inefficient to preserve local information of graphs - a limitation that is especially problematic for graph classification. In this work, we propose a locality-preserving dense GCN with graph context-aware node representations. Specifically, our proposed model incorporates a local node feature reconstruction module to preserve initial node features into node representations, which is realized via a simple but effective encoder-decoder mechanism. To capture local structural patterns in neighborhoods representing different ranges of locality, dense connectivity is introduced to connect each convolutional layer and its corresponding readout with all previous convolutional layers. To enhance node representativeness, the output of each convolutional layer is concatenated with the output of the previous layer's readout to form a global context-aware node representation. In addition, a self-attention module is introduced to aggregate layer-wise representations to form the final graph-level representation. Experiments on benchmark datasets demonstrate the superiority of the proposed model over state-of-the-art methods in terms of classification accuracy.

BrainTGL: A dynamic graph representation learning model for brain network analysis

Modeling the dynamics characteristics in functional brain networks (FBNs) is important for understanding the functional mechanism of the human brain. However, the current works do not fully consider the potential complex spatial and temporal correlations in human brain. To solve this problem, we propose a temporal graph representation learning framework for brain networks (BrainTGL). The framework involves a temporal graph pooling for eliminating the noisy edges as well as data inconsistency, and a dual temporal graph learning for capturing the spatio-temporal features of the temporal graphs. The proposed method has been evaluated in both tasks of brain disease (ASD, MDD and BD) diagnosis/gender classification (classification task) and subtype identification (clustering task) on the four datasets: Human Connectome Project (HCP), Autism Brain Imaging Data Exchange (ABIDE), NMU-MDD and NMU-BD. A large improvement is achieved for the ASD diagnosis. Specifically, our model outperforms the GroupINN and ST-GCN by an average increase of 4.2% and 8.6% on accuracy, respectively, demonstrating its advantages in comparison to the state-of-the-art methods based on functional connectivity features or learned spatio-temporal features. The results demonstrate that learning the spatial-temporal brain network representation for modeling dynamics characteristics in FBNs can improve the model's performance on both disease diagnosis and subtype identification tasks for multiple disorders. Apart from performance, the improvements of computational efficiency and convergence speed reduce training costs.

On exploring node-feature and graph-structure diversities for node drop graph pooling

Graph Neural Networks (GNNs) have been successfully applied to graph-level tasks in various fields such as biology, social networks, computer vision, and natural language processing. For the graph-level representations learning of GNNs, graph pooling plays an essential role. Among many pooling techniques, node drop pooling has garnered significant attention and is considered as a leading approach. However, existing node drop pooling methods, which typically retain the top-k nodes based on their significance scores, often overlook the diversity inherent in node features and graph structures. This limitation leads to suboptimal graph-level representations. To overcome this, we introduce a groundbreaking plug-and-play score scheme, termed MID. MID comprises a Multidimensional score space and two key operations: flIpscore and Dropscore. The multidimensional score space depicts the significance of nodes by multiple criteria; the flipscore process promotes the preservation of distinct node features; the dropscore compels the model to take into account a range of graph structures rather than focusing on local structures. To evaluate the effectiveness of our proposed MID, we have conducted extensive experiments by integrating it with a broad range of recent node drop pooling methods, such as TopKPool, SAGPool, GSAPool, and ASAP. In particular, MID has proven to bring a significant average improvement of approximately 2.8% over the four aforementioned methods when tested on 17 real-world graph classification datasets. Code is available at https://github.com/whuchuang/mid.

SP-GNN: Learning structure and position information from graphs

Graph neural network (GNN) is a powerful model for learning from graph data. However, existing GNNs may have limited expressive power, especially in terms of capturing adequate structural and positional information of input graphs. Structure properties and node position information are unique to graph-structured data, but few GNNs are capable of capturing them. This paper proposes Structure- and Position-aware Graph Neural Networks (SP-GNN), a new class of GNNs offering generic and expressive power of graph data. SP-GNN enhances the expressive power of GNN architectures by incorporating a near-isometric proximity-aware position encoder and a scalable structure encoder. Further, given a GNN learning task, SP-GNN can be used to analyze positional and structural awareness of GNN tasks using the corresponding embeddings computed by the encoders. The awareness scores can guide fusion strategies of the extracted positional and structural information with raw features for better performance of GNNs on downstream tasks. We conduct extensive experiments using SP-GNN on various graph datasets and observe significant improvement in classification over existing GNN models.

Graph structure reforming framework enhanced by commute time distance for graph classification

As a graph data mining task, graph classification has high academic value and wide practical application. Among them, the graph neural network-based method is one of the mainstream methods. Most graph neural networks (GNNs) follow the message passing paradigm and can be called Message Passing Neural Networks (MPNNs), achieving good results in structural data-related tasks. However, it has also been reported that these methods suffer from over-squashing and limited expressive power. In recent years, many works have proposed different solutions to these problems separately, but none has yet considered these shortcomings in a comprehensive way. After considering these several aspects comprehensively, we identify two specific defects: information loss caused by local information aggregation, and an inability to capture higher-order structures. To solve these issues, we propose a plug-and-play framework based on Commute Time Distance (CTD), in which information is propagated in commute time distance neighborhoods. By considering both local and global graph connections, the commute time distance between two nodes is evaluated with reference to the path length and the number of paths in the whole graph. Moreover, the proposed framework CTD-MPNNs (Commute Time Distance-based Message Passing Neural Networks) can capture higher-order structural information by utilizing commute paths to enhance the expressive power of GNNs. Thus, our proposed framework can propagate and aggregate messages from defined important neighbors and model more powerful GNNs. We conduct extensive experiments using various real-world graph classification benchmarks. The experimental performance demonstrates the effectiveness of our framework. Codes are released on https://github.com/Haldate-Yu/CTD-MPNNs.

Graph explicit pooling for graph-level representation learning

Graph pooling has been increasingly recognized as crucial for Graph Neural Networks (GNNs) to facilitate hierarchical graph representation learning. Existing graph pooling methods commonly consist of two stages: selecting top-ranked nodes and discarding the remaining to construct coarsened graph representations. However, this paper highlights two key issues with these methods: (1) The process of selecting nodes to discard frequently employs additional Graph Convolutional Networks or Multilayer Perceptrons, lacking a thorough evaluation of each node's impact on the final graph representation and subsequent prediction tasks. (2) Current graph pooling methods tend to directly discard the noise segment (dropped) of the graph without accounting for the latent information contained within these elements. To address the first issue, we introduce a novel Graph explicit Pooling (GrePool) method, which selects nodes by explicitly leveraging the relationships between the nodes and final representation vectors crucial for classification. The second issue is addressed using an extended version of GrePool (i.e., GrePool+), which applies a uniform loss on the discarded nodes. This addition is designed to augment the training process and improve classification accuracy. Furthermore, we conduct comprehensive experiments across 12 widely used datasets to validate our proposed method's effectiveness, including the Open Graph Benchmark datasets. Our experimental results uniformly demonstrate that GrePool outperforms 14 baseline methods for most datasets. Likewise, implementing GrePool+ enhances GrePool's performance without incurring additional computational costs. The code is available at https://github.com/LiuChuang0059/GrePool.

Lurker: Backdoor attack-based explainable rumor detection on online media

Because of their proficiency in capturing the category characteristics of graphs, graph neural networks have shown remarkable advantages for graph-level classification tasks, that is, rumor detection and anomaly detection. Due to the manipulation of special means (e.g. bots) on online media, rumors may spread across the whole network at an overwhelming speed. Compared with normal information, popular rumors usually have a special propagation structure, especially in the early stage of information dissemination. More specifically, the special propagation structure determines whether rumors can be spread successfully. Namely, online users and their interaction that constitute the special propagation structure play a key role in the spread of rumors. Therefore, the problem of rumor detection can be transformed into detecting the existence of a special propagation structure. Inspired by backdoor attacks, we propose an interpretable rumor detection algorithm based on backdoor. Firstly, based on causal analysis, the causal sub-graph that determines the category of the graph (rumor vs. normal information) is obtained, that is, the critical online users in the rumor spreading effect are found, and then the specific propagation structure is explored. Finally, the special propagation structure is planted into the rumor detection model as a trigger. Experimental results and performance analysis on three real-world datasets demonstrate the effectiveness of our proposed algorithm in the special propagation structure detection of rumors. Compared with two baselines, Lurker achieves up to 33.1% and 61.8% performance improvement in terms of attack success rate and clean accuracy drop.

Amogel: a multi-omics classification framework using associative graph neural networks with prior knowledge for biomarker identification

The advent of high-throughput sequencing technologies, such as DNA microarray and DNA sequencing, has enabled effective analysis of cancer subtypes and targeted treatment. Furthermore, numerous studies have highlighted the capability of graph neural networks (GNN) to model complex biological systems and capture non-linear interactions in high-throughput data. GNN has proven to be useful in leveraging multiple types of omics data, including prior biological knowledge from various sources, such as transcriptomics, genomics, proteomics, and metabolomics, to improve cancer classification. However, current works do not fully utilize the non-linear learning potential of GNN and lack of the integration ability to analyse high-throughput multi-omics data simultaneously with prior biological knowledge. Nevertheless, relying on limited prior knowledge in generating gene graphs might lead to less accurate classification due to undiscovered significant gene-gene interactions, which may require expert intervention and can be time-consuming. Hence, this study proposes a graph classification model called associative multi-omics graph embedding learning (AMOGEL) to effectively integrate multi-omics datasets and prior knowledge through GNN coupled with association rule mining (ARM). AMOGEL employs an early fusion technique using ARM to mine intra-omics and inter-omics relationships, forming a multi-omics synthetic information graph before the model training. Moreover, AMOGEL introduces multi-dimensional edges, with multi-omics gene associations or edges as the main contributors and prior knowledge edges as auxiliary contributors. Additionally, it uses a gene ranking technique based on attention scores, considering the relationships between neighbouring genes. Several experiments were performed on BRCA and KIPAN cancer subtypes to demonstrate the integration of multi-omics datasets (miRNA, mRNA, and DNA methylation) with prior biological knowledge of protein-protein interactions, KEGG pathways and Gene Ontology. The experimental results showed that the AMOGEL outperformed the current state-of-the-art models in terms of classification accuracy, F1 score and AUC score. The findings of this study represent a crucial step forward in advancing the effective integration of multi-omics data and prior knowledge to improve cancer subtype classification.

Graph Geometric Algebra networks for graph representation learning

Graph neural networks (GNNs) have emerged as a prominent approach for capturing graph topology and modeling vertex-to-vertex relationships. They have been widely used in pattern recognition tasks including node and graph label prediction. However, when dealing with graphs from non-Euclidean domains, the relationships, and interdependencies between objects become more complex. Existing GNNs face limitations in handling a large number of model parameters in such complex graphs. To address this, we propose the integration of Geometric Algebra into graph neural networks, enabling the generalization of GNNs within the geometric space to learn geometric embeddings for nodes and graphs. Our proposed Graph Geometric Algebra Network (GGAN) enhances correlations among nodes by leveraging relations within the Geometric Algebra space. This approach reduces model complexity and improves the learning of graph representations. Through extensive experiments on various benchmark datasets, we demonstrate that our models, utilizing the properties of Geometric Algebra operations, outperform state-of-the-art methods in graph classification and semi-supervised node classification tasks. Our theoretical findings are empirically validated, confirming that our model achieves state-of-the-art performance.

Exploring sparsity in graph transformers

Graph Transformers (GTs) have achieved impressive results on various graph-related tasks. However, the huge computational cost of GTs hinders their deployment and application, especially in resource-constrained environments. Therefore, in this paper, we explore the feasibility of sparsifying GTs, a significant yet under-explored topic. We first discuss the redundancy of GTs based on the characteristics of existing GT models, and then propose a comprehensive Graph Transformer SParsification (GTSP) framework that helps to reduce the computational complexity of GTs from four dimensions: the input graph data, attention heads, model layers, and model weights. Specifically, GTSP designs differentiable masks for each individual compressible component, enabling effective end-to-end pruning. We examine our GTSP through extensive experiments on prominent GTs, including GraphTrans, Graphormer, and GraphGPS. The experimental results demonstrate that GTSP effectively reduces computational costs, with only marginal decreases in accuracy or, in some instances, even improvements. For example, GTSP results in a 30% reduction in Floating Point Operations while contributing to a 1.8% increase in Area Under the Curve accuracy on the OGBG-HIV dataset. Furthermore, we provide several insights on the characteristics of attention heads and the behavior of attention mechanisms, all of which have immense potential to inspire future research endeavors in this domain. Our code is available at https://github.com/LiuChuang0059/GTSP.

Location-aware convolutional neural networks for graph classification

Graph patterns play a critical role in various graph classification tasks, e.g., chemical patterns often determine the properties of molecular graphs. Researchers devote themselves to adapting Convolutional Neural Networks (CNNs) to graph classification due to their powerful capability in pattern learning. The varying numbers of neighbor nodes and the lack of canonical order of nodes on graphs pose challenges in constructing receptive fields for CNNs. Existing methods generally follow a heuristic ranking-based framework, which constructs receptive fields by selecting a fixed number of nodes and dropping the others according to predetermined rules. However, such methods may lose important structure information through dropping nodes, and they also cannot learn task-oriented graph patterns. In this paper, we propose a Location learning-based Convolutional Neural Networks (LCNN) for graph classification. LCNN constructs receptive fields by learning the location of each node according to its embedding that contains structures and features information, then standard CNNs are applied to capture graph patterns. Such a location learning mechanism not only retains the information of all nodes, but also provides the ability for task-oriented pattern learning. Experimental results show the effectiveness of the proposed LCNN, and visualization results further illustrate the valid pattern learning ability of our method for graph classification.

Breast cancer image classification based on H&E staining using a causal attention graph neural network model

Breast cancer image classification remains a challenging task due to the high-resolution nature of pathological images and their complex feature distributions. Graph neural networks (GNNs) offer promising capabilities to capture local structural information but often suffer from limited generalization and reliance on shortcut features. This study proposes a novel causal discovery attention-based graph neural network (CDA-GNN) model. The model converts high-resolution image data into graph data using superpixel segmentation and employs a causal attention mechanism to identify and utilize key causal features. A backdoor adjustment strategy further disentangles causal features from shortcut features, enhancing model interpretability and robustness. Experimental evaluations on the 2018 BACH breast cancer image dataset demonstrate that CDA-GNN achieves a classification accuracy of 86.36%. Additional metrics, including F1-score and ROC, validate the superior performance and generalization of the proposed approach. The CDA-GNN model, with its powerful automated cancer image analysis capabilities and strong interpretability, provides an effective tool for clinical applications. It significantly reduces the workload of healthcare professionals while facilitating the early detection and diagnosis of breast cancer, thereby improving diagnostic efficiency and accuracy.

A drug molecular classification model based on graph structure generation

Molecular property prediction based on artificial intelligence technology has significant prospects in speeding up drug discovery and reducing drug discovery costs. Among them, molecular property prediction based on graph neural networks (GNNs) has received extensive attention in recent years. However, the existing graph neural networks still face the following challenges in node representation learning. First, the number of nodes increases exponentially with the expansion of the perception field, which limits the exploration ability of the model in the depth direction. Secondly, the large number of nodes in the perception field brings noise, which is not conducive to the model's representation learning of the key structures. Therefore, a graph neural network model based on structure generation is proposed in this paper. The model adopts the depth-first strategy to generate the key structures of the graph, to solve the problem of insufficient exploration ability of the graph neural network in the depth direction. A tendentious node selection method is designed to gradually select nodes and edges to generate the key structures of the graph, to solve the noise problem caused by the excessive number of nodes. In addition, the model skillfully realizes forward propagation and iterative optimization of structure generation by using an attention mechanism and random bias. Experimental results on public data sets show that the proposed model achieves better classification results than the existing best models.

Graph global attention network with memory: A deep learning approach for fake news detection

With the proliferation of social media, the detection of fake news has become a critical issue that poses a significant threat to society. The dissemination of fake information can lead to social harm and damage the credibility of information. To address this issue, deep learning has emerged as a promising approach, especially with the development of Natural Language Processing (NLP). This study introduces a novel approach called Graph Global Attention Network with Memory (GANM) for detecting fake news. This approach leverages NLP techniques to encode nodes with news context and user content. It employs three graph convolutional networks to extract informative features from the news propagation network and aggregates endogenous and exogenous user information. This methodology aims to address the challenge of identifying fake news within the context of social media. Innovatively, the GANM combines two strategies. First, a novel global attention mechanism with memory is employed in the GANM to learn the structural homogeneity of news propagation networks, which is the attention mechanism of a single graph with a history of all graphs. Second, we design a module for partial key information learning aggregation to emphasize the acquisition of partial key information in the graph and merge node-level embeddings with graph-level embeddings into fine-grained joint information. Our proposed method provides a new direction in news detection research with a combination of global and partial information and achieves promising performance on real-world datasets.