EliasHossain/CancerAbstracts huggingface dataset:
Category: Generic
In drug development, unexpected side effects are the main reason for the failure of candidate drug trials. Discovering potential side effects of drugsin silicocan improve the success rate of drug screening. However, most previous works extracted and utilized an effective representation of drugs from a single perspective. These methods merely considered the topological information of drug in the biological entity network, or combined the association information (e.g. knowledge graph KG) between drug and other biomarkers, or only used the chemical structure or sequence information of drug. Consequently, to jointly learn drug features from both the macroscopic biological network and the microscopic drug molecules. We propose a hybrid embedding graph neural network model named idse-HE, which integrates graph embedding module and node embedding module. idse-HE can fuse the drug chemical structure information, the drug substructure sequence information and the drug network topology information. Our model deems the final representation of drugs and side effects as two implicit factors to reconstruct the original matrix and predicts the potential side effects of drugs. In the robustness experiment, idse-HE shows stable performance in all indicators. We reproduce the baselines under the same conditions, and the experimental results indicate that idse-HE is superior to other advanced methods. Finally, we also collect evidence to confirm several real drug side effect pairs in the predicted results, which were previously regarded as negative samples. More detailed information, scientific researchers can access the user-friendly web-server of idse-HE at http://bioinfo.jcu.edu.cn/idse-HE. In this server, users can obtain the original data and source code, and will be guided to reproduce the model results.
Category: Generic
Identifying the potential compound-protein interactions (CPIs) plays an essential role in drug development. The computational approaches for CPI prediction can reduce time and costs of experimental methods and have benefited from the continuously improved graph representation learning. However, most of the network-based methods use heterogeneous graphs, which is challenging due to their complex structures and heterogeneous attributes. Therefore, in this work, we transformed the compound-protein heterogeneous graph to a homogeneous graph by integrating the ligand-based protein representations and overall similarity associations. We then proposed an Inductive Graph AggrEgator-based framework, named CPI-IGAE, for CPI prediction. CPI-IGAE learns the low-dimensional representations of compounds and proteins from the homogeneous graph in an end-to-end manner. The results show that CPI-IGAE performs better than some state-of-the-art methods. Further ablation study and visualization of embeddings reveal the advantages of the model architecture and its role in feature extraction, and some of the top ranked CPIs by CPI-IGAE have been validated by a review of recent literature. The data and source codes are available at https://github.com/wanxiaozhe/CPI-IGAE.
Category: Generic
The utilization of web search activity for pandemic forecasting has significant implications for managing disease spread and informing policy decisions. However, web search records tend to be noisy and influenced by geographical location, making it difficult to develop large-scale models. While regularized linear models have been effective in predicting the spread of respiratory illnesses like COVID-19, they are limited to specific locations. The lack of incorporation of neighboring areas' data and the inability to transfer models to new locations with limited data has impeded further progress. To address these limitations, this study proposes a novel self-supervised message-passing neural network (SMPNN) framework for modeling local and cross-location dynamics in pandemic forecasting. The SMPNN framework utilizes an MPNN module to learn cross-location dependencies through self-supervised learning and improve local predictions with graph-generated features. The framework is designed as an end-to-end solution and is compared with state-of-the-art statistical and deep learning models using COVID-19 data from England and the US. The results of the study demonstrate that the SMPNN model outperforms other models by achieving up to a 6.9% improvement in prediction accuracy and lower prediction errors during the early stages of disease outbreaks. This approach represents a significant advancement in disease surveillance and forecasting, providing a novel methodology, datasets, and insights that combine web search data and spatial information. The proposed SMPNN framework offers a promising avenue for modeling the spread of pandemics, leveraging both local and cross-location information, and has the potential to inform public health policy decisions.
Category: Generic
With the help of convolutional neural networks (CNNs), deep learning-based methods have achieved remarkable performance in face super-resolution (FSR) task. Despite their success, most of the existing methods neglect non-local correlations of face images, leaving much room for improvement. In this paper, we introduce a novel end-to-end trainable attention-driven graph neural network (AD-GNN) for more discriminative feature extraction and feature relation modeling. This is achieved by two major components. The first component is a cross-scale dynamic graph (CDG) block. The CDG block considers cross-scale relationships of patches in distant areas and employs two dynamic graphs to construct enhanced features. The second component is a series of channel attention and spatial dynamic graph (CASDG) blocks. A CASDG block has a channel-wise attention unit and a spatial-aware dynamic graph (SDG) unit. The SDG unit extracts informative features by exploring spatial non-local self-similarity information of the patches using dynamic graph convolution. Using these two components, facial details can be effectively reconstructed with the help of information supplemented by similar but spatially remote patches and structural information of faces. Extensive experiments on two public benchmarks demonstrate the superiority of AD-GNN over the state-of-the-art FSR methods.
Category: Generic
Cancer prognosis prediction and analysis can help patients understand expected life and help clinicians provide correct therapeutic guidance. Thanks to the development of sequencing technology, multi-omics data, and biological networks have been used for cancer prognosis prediction. Besides, graph neural networks can simultaneously consider multi-omics features and molecular interactions in biological networks, becoming mainstream in cancer prognosis prediction and analysis. However, the limited number of neighboring genes in biological networks restricts the accuracy of graph neural networks. To solve this problem, a local augmented graph convolutional network named LAGProg is proposed in this paper for cancer prognosis prediction and analysis. The process follows: first, given a patient's multi-omics data features and biological network, the corresponding augmented conditional variational autoencoder generates features. Then, the generated augmented features and the original features are fed into a cancer prognosis prediction model to complete the cancer prognosis prediction task. The conditional variational autoencoder consists of two parts: encoder-decoder. In the encoding phase, an encoder learns the conditional distribution of the multi-omics data. As a generative model, a decoder takes the conditional distribution and the original feature as inputs to generate the enhanced features. The cancer prognosis prediction model consists of a two-layer graph convolutional neural network and a Cox proportional risk network. The Cox proportional risk network consists of fully connected layers. Extensive experiments on 15 real-world datasets from TCGA demonstrated the effectiveness and efficiency of the proposed method in predicting cancer prognosis. LAGProg improved the C-index values by an average of 8.5% over the state-of-the-art graph neural network method. Moreover, we confirmed that the local augmentation technique could enhance the model's ability to represent multi-omics features, improve the model's robustness to missing multi-omics features, and prevent the model's over-smoothing during training. Finally, based on genes identified through differential expression analysis, we discovered 13 prognostic markers highly associated with breast cancer, among which ten genes have been proved by literature review.
Category: Generic
Sequential recommendation uses contrastive learning to randomly augment user sequences and alleviate the data sparsity problem. However, there is no guarantee that the augmented positive or negative views remain semantically similar. To address this issue, we propose graph neural network-guided contrastive learning for sequential recommendation (GC4SRec). The guided process employs graph neural networks to obtain user embeddings, an encoder to determine the importance score of each item, and various data augmentation methods to construct a contrast view based on the importance score. Experimental validation is conducted on three publicly available datasets, and the experimental results demonstrate that GC4SRec improves the hit rate and normalized discounted cumulative gain metrics by 1.4% and 1.7%, respectively. The model can enhance recommendation performance and mitigate the data sparsity problem.
Category: Generic
Medication combination prediction (MCP) can provide assistance for experts in the more thorough comprehension of complex mechanisms behind health and disease. Many recent studies focus on the patient representation from the historical medical records, but neglect the value of the medical knowledge, such as the prior knowledge and the medication knowledge. This article develops a medical-knowledge-based graph neural network (MK-GNN) model which incorporates the representation of patients and the medical knowledge into the neural network. More specifically, the features of patients are extracted from their medical records in different feature subspaces. Then these features are concatenated to obtain the feature representation of patients. The prior knowledge, which is calculated according to the mapping relationship between medications and diagnoses, provides heuristic medication features according to the diagnosis results. Such medication features can help the MK-GNN model learn optimal parameters. Moreover, the medication relationship in prescriptions is formulated as a drug network to integrate the medication knowledge into medication representation vectors. The results reveal the superior performance of the MK-GNN model compared with the state-of-the-art baselines on different evaluation metrics. The case study manifests the application potential of the MK-GNN model.
Category: Generic
Signed graph neural networks learn low-dimensional representations for nodes in signed networks with positive and negative links, which helps with many downstream tasks like link prediction. However, most existing signed graph neural networks ignore individual characteristics of nodes and thus limit the ability to learn the underlying structure of real signed graphs. To address this limitation, a deep graph neural network framework SiNP to learn Signed network embedding with Node Polarity is proposed. To be more explicit, a node-signed property metric mechanism is developed to encode the individual characteristics of the nodes. In addition, a graph convolution layer is added so that both positive and negative information from neighboring nodes can be combined. The final embedding of nodes is produced by concatenating the outcomes of these two portions. Finally, extensive experiments have been conducted on four significant real-world signed network datasets to demonstrate the efficiency and superiority of the proposed method in comparison to the state-of-the-art.
Category: Generic
Single-cell data analysis has been at forefront of development in biology and medicine since sequencing data have been made available. An important challenge in single-cell data analysis is the identification of cell types. Several methods have been proposed for cell-type identification. However, these methods do not capture the higher-order topological relationship between different samples. In this work, we propose an attention-based graph neural network that captures the higher-order topological relationship between different samples and performs transductive learning for predicting cell types. The evaluation of our method on both simulation and publicly available datasets demonstrates the superiority of our method, scAGN, in terms of prediction accuracy. In addition, our method works best for highly sparse datasets in terms of F1 score, precision score, recall score, and Matthew's correlation coefficients as well. Further, our method's runtime complexity is consistently faster compared to other methods.
Category: Generic
Graph Neural Networks (GNNs) are powerful architectures for learning on graphs. They are efficient for predicting nodes, links and graphs properties. Standard GNN variants follow a message passing schema to update nodes representations using information from higher-order neighborhoods iteratively. Consequently, deeper GNNs make it possible to define high-level nodes representations generated based on local as well as distant neighborhoods. However, deeper networks are prone to suffer from over-smoothing. To build deeper GNN architectures and avoid losing the dependency between lower (the layers closer to the input) and higher (the layers closer to the output) layers, networks can integrate residual connections to connect intermediate layers. We propose the Augmented Graph Neural Network (AGNN) model with hierarchical global-based residual connections. Using the proposed residual connections, the model generates high-level nodes representations without the need for a deeper architecture. We disclose that the nodes representations generated through our proposed AGNN model are able to define an expressive all-encompassing representation of the entire graph. As such, the graph predictions generated through the AGNN model surpass considerably state-of-the-art results. Moreover, we carry out extensive experiments to identify the best global pooling strategy and attention weights to define the adequate hierarchical and global-based residual connections for different graph property prediction tasks. Furthermore, we propose a reversible variant of the AGNN model to address the extensive memory consumption problem that typically arises from training networks on large and dense graph datasets. The proposed Reversible Augmented Graph Neural Network (R-AGNN) only stores the nodes representations acquired from the output layer as opposed to saving all representations from intermediate layers as it is conventionally done when optimizing the parameters of other GNNs. We further refine the definition of the backpropagation algorithm to fit the R-AGNN model. We evaluate the proposed models AGNN and R-AGNN on benchmark Molecular, Bioinformatics and Social Networks datasets for graph classification and achieve state-of-the-art results. For instance the AGNN model realizes improvements of +39% on IMDB-MULTI reaching 91.7% accuracy and +16% on COLLAB reaching 96.8% accuracy compared to other GNN variants.
Category: Generic
As a critical indicator of how easily the human immune system recognizes tumour cells, tumour mutational burden (TMB) is widely used to identify the potential effectiveness of immune checkpoint inhibitor therapy. However, the difficulties associated with the whole exome sequencing (WES) process, such as high tissue sampling requirements, high costs, and long turnaround times, have hindered the widespread clinical use of WES. Furthermore, the mutation landscape varies across cancer types, and the distribution of TMBs varies across cancer subtypes. Therefore, there is an urgent clinical need to develop a small cancer-specific panel to estimate TMB accurately, predict immunotherapy response cost-effectively and assist physicians in precise decision-making. This paper uses a graph neural network framework (Graph-ETMB) to address the cancer specificity problem in TMB. The correlation and tractability between mutated genes are described through message-passing and aggregation algorithms between graph networks. Then the graph neural network is trained in the lung adenocarcinoma data through a semi-supervised approach, resulting in a mutation panel containing 20 genes with a length of only 0.16 Mb. The number of genes to be detected is smaller than most commercial panels currently in clinical use. In addition, the efficacy of the designed panel in predicting immunotherapy response was further determined in an independent validation dataset, exploring the association between TMB and immunotherapy efficacy.
Category: Generic
Interval-valued data is an effective way to represent complex information where uncertainty, inaccuracy etc. are involved in the data space and they are worthy of taking into account. Interval analysis together with neural network has proven to work well on Euclidean data. However, in real-life scenarios, data follows a much more complex structure and is often represented as graphs, which is non-Euclidean in nature. Graph Neural Network is a powerful tool to handle graph like data with countable feature space. So, there is a research gap between the interval-valued data handling approaches and existing GNN model. No model in GNN literature can handle a graph with interval-valued features and, on the other hand, Multi Layer Perceptron (MLP) based on interval mathematics can not process the same due to non-Euclidean structure behind the graph. This article proposes an Interval-Valued Graph Neural Network, a novel GNN model where, for the first time, we relax the restriction of the feature space being countable without compromising the time complexity of the best performing GNN model in the literature. Our model is much more general than existing models as any countable set is always a subset of the universal set <math xmlns="http://www.w3.org/1998/Math/MathML"> <msup><mrow><mi> </mi></mrow> <mrow><mi>n</mi></mrow> </msup> </math> , which is uncountable. Here, to deal with interval-valued feature vectors, we propose a new aggregation scheme of intervals and show its expressive power to capture different interval structures. We validate our theoretical findings about our model for graph classification task by comparing its performance with those of the state-of-the-art models on several benchmark and synthetic network datasets.
Category: Generic
The graph neural network (GNN) has demonstrated its superior power in various data mining tasks and has been widely applied in diversified fields. The core of GNN is the aggregation and combination functions, and mainstream GNN studies focus on the enhancement of these functions. However, GNNs face a common challenge, i.e., useless features contained in neighbor nodes may be integrated into the target node during the aggregation process. This leads to poor node embedding and undermines downstream tasks. To tackle this problem, this article proposes a novel GNN optimization framework GNN-MHSIC by introducing the nonparametric dependence method Hilbert-Schmidt independence criterion (HSIC) under the guidance of information bottleneck. HSIC is utilized to guide the information propagation among layers of a GNN from multiaspect views. GNN-MHSIC aims to achieve three main objectives: 1) minimizing the HSIC between the input features and the propagation layers; 2) maximizing the HSIC between the propagation layers and the ground truth; and 3) minimizing the HSIC between the propagation layers. With a multiaspect design, GNN-MHSIC can minimize the propagation of redundant information while preserving relevant information about the target node. We prove GNN-MHSIC's finite upper and lower bounds theoretically and evaluate it experimentally with four classic GNN models, including the graph convolutional network, the graph attention network (GAT), the heterogeneous GAT, and the heterogeneous graph (HG) propagation network on three widely used HGs. The results illustrate the usefulness and performance of GNN-MHSIC.
Category: Generic
The accurate extraction of wheat lodging areas can provide important technical support for post-disaster yield loss assessment and lodging-resistant wheat breeding. At present, wheat lodging assessment is facing the contradiction between timeliness and accuracy, and there is also a lack of effective lodging extraction methods. This study aims to propose a wheat lodging assessment method applicable to multiple Unmanned Aerial Vehicle (UAV) flight heights. The quadrotor UAV was used to collect high-definition images of wheat canopy at the grain filling and maturity stages, and the Unet network was evaluated and improved by introducing the Involution operator and Dense block module. The performance of the Improved_Unet was determined using the data collected from different flight heights, and the robustness of the improved network was verified with data from different years in two different geographical locations. The results of analyses show that (1) the Improved_Unet network was better than other networks (Segnet, Unet and DeeplabV3+ networks) evaluated in terms of segmentation accuracy, with the average improvement of each indicator being 3% and the maximum average improvement being 6%. The Improved_Unet network was more effective in extracting wheat lodging areas at the maturity stage. The four evaluation indicators, Precision, Dice, Recall, and Accuracy, were all the highest, which were 0.907, 0.929, 0.884, and 0.933, respectively; (2) the Improved_Unet network had the strongest robustness, and its Precision, Dice, Recall, and Accuracy reached 0.851, 0.892, 0.844, and 0.885, respectively, at the verification stage of using lodging data from other wheat production areas; and (3) the flight height had an influence on the lodging segmentation accuracy. The results of verification show that the 20-m flight height performed the best among the flight heights of 20, 40, 80 and 120 m evaluated, and the segmentation accuracy decreased with the increase of the flight height. The Precision, Dice, Recall, and Accuracy of the Improved_Unet changed from 0.907 to 0.845, from 0.929 to 0.864, from 0.884 to 0.841, and from 0.933 to 0.881, respectively. The results demonstrate the improved ability of the Improved-Unet to extract wheat lodging features. The proposed deep learning network can effectively extract the areas of wheat lodging, and the different height fusion models developed from this study can provide a more comprehensive reference for the automatic extraction of wheat lodging.
Category: Generic
To suppress the streak artifacts in images reconstructed from sparse-view projections in computed tomography (CT), a residual, attention-based, dense UNet (RAD-UNet) deep network is proposed to achieve accurate sparse reconstruction. The filtered back projection (FBP) algorithm is used to reconstruct the CT image with streak artifacts from sparse-view projections. Then, the image is processed by the RAD-UNet to suppress streak artifacts and obtain high-quality CT image. Those images with streak artifacts are used as the input of the RAD-UNet, and the output-label images are the corresponding high-quality images. Through training via the large-scale training data, the RAD-UNet can obtain the capability of suppressing streak artifacts. This network combines residual connection, attention mechanism, dense connection and perceptual loss. This network can improve the nonlinear fitting capability and the performance of suppressing streak artifacts. The experimental results show that the RAD-UNet can improve the reconstruction accuracy compared with three existing representative deep networks. It may not only suppress streak artifacts but also better preserve image details. The proposed networks may be readily applied to other image processing tasks including image denoising, image deblurring, and image super-resolution.