Graph Embedding Techniques Research Articles

Multi-scale locality preserving projection for partial multi-view incomplete multi-label learning

Amidst advancements in feature extraction techniques, research on multi-view multi-label classifications has attracted widespread interest in recent years. However, real-world scenarios often pose a challenge where the completeness of multiple views and labels cannot be ensured. At present, only a handful of techniques have attempted to address the complex issue of partial multi-view incomplete multi-label classification, and the majority of these approaches overlook the significance of manifold structures between instances. To tackle these challenges, we propose a novel partial multi-view incomplete multi-label learning model, termed MSLPP. Differing from existing studies, MSLPP emphasizes retaining the effective inherent structure of data during the feature extraction process, thereby facilitating a richer semantic information extraction. Specifically, MSLPP captures and integrates four types of information: the distance and similarity information in the original feature space, and the distance and similarity information in the extracted feature space. Further, by adopting the graph embedding technique, it simultaneously preserves the intrinsic structure with multi-scale information through a constraint term. Moreover, taking into account the negative impact of the missing views on the model and the possible impact of missing views on the data inherent structure, we further propose a shielding strategy for missing views, which not only eliminates the negative effects of missing views on the model but also more accurately captures the inherent data structure. The experimental results on five widely recognized datasets indicate that the model performs better than many excellent methods.

Research Progresses and Applications of Knowledge Graph Embedding Technique in Chemistry.

A knowledge graph (KG) is a technique for modeling entities and their interrelations. Knowledge graph embedding (KGE) translates these entities and relationships into a continuous vector space to facilitate dense and efficient representations. In the domain of chemistry, applying KG and KGE techniques integrates heterogeneous chemical information into a coherent and user-friendly framework, enhances the representation of chemical data features, and is beneficial for downstream tasks, such as chemical property prediction. This paper begins with a comprehensive review of classical and contemporary KGE methodologies, including distance-based models, semantic matching models, and neural network-based approaches. We then catalogue the primary databases employed in chemistry and biochemistry that furnish the KGs with essential chemical data. Subsequently, we explore the latest applications of KG and KGE in chemistry, focusing on risk assessment, property prediction, and drug discovery. Finally, we discuss the current challenges to KG and KGE techniques and provide a perspective on their potential future developments.

Graph Attention Networks: A Comprehensive Review of Methods and Applications

Real-world problems often exhibit complex relationships and dependencies, which can be effectively captured by graph learning systems. Graph attention networks (GATs) have emerged as a powerful and versatile framework in this direction, inspiring numerous extensions and applications in several areas. In this review, we present a thorough examination of GATs, covering both diverse approaches and a wide range of applications. We examine the principal GAT-based categories, including Global Attention Networks, Multi-Layer Architectures, graph-embedding techniques, Spatial Approaches, and Variational Models. Furthermore, we delve into the diverse applications of GATs in various systems such as recommendation systems, image analysis, medical domain, sentiment analysis, and anomaly detection. This review seeks to act as a navigational reference for researchers and practitioners aiming to emphasize the capabilities and prospects of GATs.

Finding Efficient Graph Embeddings and Processing them by a CNN-based Tool

We introduce new tools to support finding efficient graph embedding techniques for graph databases and to process their outputs using deep learning for classification scenarios. Accordingly, we investigate the possibility of creating an ensemble of different graph embedding methods to raise accuracy and present an interconnected neural network-based ensemble to increase the efficiency of the member classification algorithms. We also introduce a new convolutional neural network-based architecture that can be generally proposed to process vectorized graph data provided by various graph embedding methods and compare it with other architectures in the literature to show the competitiveness of our approach. We also exhibit a statistical-based inhomogeneity level estimation procedure to select the optimal embedding for a given graph database efficiently. The efficiency of our framework is exhaustively tested using several publicly available graph datasets and numerous state-of-the-art graph embedding techniques. Our experimental results for classification tasks have proved the competitiveness of our approach by outperforming the state-of-the-art frameworks.

M2PSC: Multilingual sentiment analysis using improved multi-attention based Deep Learning model

Sentiment analysis, which involves determining the emotional polarity positivity, negativity, or neutrality in the source texts, is a crucial task. Multilingual sentiment analysis techniques were developed to analyze data in several languages; a notable deficiency of resources in multilingual sentiment analysis is one of the primary issues. Furthermore, the developed methods for multilingual sentiment analysis have some limitations such as data dependency, reliability, robustness, and computational complexity. To tackle these shortcomings, this research proposed a multilingual improved multi-attention Deep Learning model (M2PSC-DL), which leverages the advantages of the Bi-directional Long Short Term Memory (BiLSTM) classifier with improved attention mechanisms. The Multi-metric graph embedding technique encodes the data to provide more contextual information representation. Additionally, the combination of improved Positional Spatial Channel (SPC) attention increases the capability of the model to extract relevant features in the training process which leads to getting accurate results in sentiment analysis tasks. Furthermore, the research proposed an improved sigmoid activation for solving the vanishing gradient issues that help the model avoid gradient saturations. The validation results demonstrate that the M2PSC-DL model attains 96.26% accuracy, 96.06% precision, and 96.18% recall for the XED dataset which is far better than the traditional methods.

Multi-Site Wind Speed Prediction Based on Graph Embedding and Cyclic Graph Isomorphism Network (GIN-GRU)

Accurate and reliable wind speed prediction is conducive to improving the power generation efficiency of electrical systems. Due to the lack of adequate consideration of spatial feature extraction, the existing wind speed prediction models have certain limitations in capturing the rich neighborhood information of multiple sites. To address the previously mentioned constraints, our study introduces a graph isomorphism-based gated recurrent unit (GIN-GRU). Initially, the model utilizes a hybrid mechanism of random forest and principal component analysis (PCA-RF) to discuss the feature data from different sites. This process not only preserves the primary features but also extracts critical information by performing dimensionality reduction on the residual features. Subsequently, the model constructs graph networks by integrating graph embedding techniques with the Mahalanobis distance metric to synthesize the correlation information among features from multiple sites. This approach effectively consolidates the interrelated feature data and captures the complex interactions across multiple sites. Ultimately, the graph isomorphism network (GIN) delves into the intrinsic relationships within the graph networks and the gated recurrent unit (GRU) integrates these relationships with temporal correlations to address the challenges of wind speed prediction effectively. The experiments conducted on wind farm datasets for offshore California in 2019 have demonstrated that the proposed model has higher prediction accuracy compared to the comparative model such as CNN-LSTM and GAT-LSTM. Specifically, by modifying the network layers, we achieved higher precision, with the mean square error (MSE) and root mean square error (RMSE) of wind speed at a height of 10 m being 0.8457 m/s and 0.9196 m/s, respectively.

Construction of a large-scale maritime element semantic schema based on knowledge graph models for unmanned automated decision-making

In maritime logistics optimization, considerable research efforts are focused on the extraction of deep behavioral characteristics from comprehensive shipping data to discern patterns in maritime vessel behavior. The effective linkage of these characteristics with maritime infrastructure, such as berths, is critical for the enhancement of ship navigation systems. This endeavor is paramount not only as a research focus within maritime information science but also for the progression of intelligent maritime systems. Traditional methodologies have primarily emphasized the analysis of navigational paths of vessels without an extensive consideration of the geographical dynamics between ships and port infrastructure. However, the introduction of knowledge graphs has enabled the integration of disparate data sources, facilitating new insights that propel the development of intelligent maritime systems. This manuscript presents a novel framework using knowledge graph technology for profound analysis of maritime data. Utilizing automatic identification system (AIS) data alongside spatial information from port facilities, the framework forms semantic triplet connections among ships, anchorages, berths, and waterways. This enables the semantic modeling of maritime behaviors, offering precise identification of ships through their diverse semantic information. Moreover, by exploiting the semantic relations between ships and berths, a reverse semantic knowledge graph for berths is constructed, which is specifically tailored to ship type, size, and category. The manuscript critically evaluates a range of graph embedding techniques, dimensionality reduction methods, and classification strategies through experimental frameworks to determine the most efficacious methodologies. The findings reveal that the maritime knowledge graph significantly enhances the semantic understanding of unmanned maritime equipment, thereby improving decision-making capabilities. Additionally, it establishes a semantic foundation for the development of expansive maritime models, illustrating the potential of knowledge graph technology in advancing intelligent maritime systems.

Graph-based multi-agent reinforcement learning for large-scale UAVs swarm system control

In this study, a novel graph-embedding technique based on a graph neural network (GNN) is proposed to identify the topology in the motion of a unmanned aerial vehicles (UAV) swarm and quickly obtain local information around each agent. We also propose a model reference reinforcement learning method to learn the potential field function and determine an appropriate strategy for each agent that can satisfy the requirements of collaborative motion and obstacle avoidance for large-scale UAV swarms. First, a new swarm structure is proposed to provide reserved maneuvering space for UAVs during flight. After encoding the obstacle avoidance behavior of multiple UAVs into spatial graphs, a graph attention mechanism (GAT) was employed to extract the dynamic information from them. Consequently, each individual autonomously generate actions based on its local data. Second, a new distributed control algorithm based on multi-agent reinforcement learning (MARL) is proposed to learn the potential field function from the local information. Each individual can repel and cooperate with the target within a short range and attract objects over a long distance. Finally, simulation results demonstrate the effectiveness and superiority of the proposed method, which has great potential for application in online autonomous collaboration.

Clinical trial recommendations using Semantics-Based inductive inference and knowledge graph embeddings

ObjectiveDesigning a new clinical trial entails many decisions, such as defining a cohort and setting the study objectives to name a few, and therefore can benefit from recommendations based on exhaustive mining of past clinical trial records. This study proposes an approach based on knowledge graph embeddings and semantics-driven inductive inference for generating such recommendations. MethodThe proposed recommendation methodology is based on neural embeddings trained on first-of-its-kind knowledge graph constructed from clinical trials data. The methodology includes design of a knowledge graph for clinical trial data, evaluation of various knowledge graph embedding techniques for it, application of a novel inductive inference method using these embeddings, and generation of recommendations for clinical trial design. The study uses freely available data from clinicaltrials.gov and related sources. ResultsThe proposed approach for recommendations obtained relevance scores ranging from 70% to 83%. These scores were determined by evaluating the text similarity of recommended elements to actual elements used in clinical trials that are in progress. Furthermore, the most pertinent recommendations were consistently located towards the top of the list, indicating the effectiveness of our method. ConclusionOur study suggests that inductive inference using node semantics is a viable approach for generating recommendations using graphs neural embeddings, and that there is a potential for improvement in training graph embeddings using node semantics.

Biomedical Knowledge Graph Embedding with Householder Projection (Student Abstract)

Researchers have applied knowledge graph embedding (KGE) techniques with advanced neural network techniques, such as capsule networks, for predicting drug-drug interactions (DDIs) and achieved remarkable results. However, most ignore molecular structure and position features between drug pairs. They cannot model the biomedical field's significant relational mapping properties (RMPs,1-N, N-1, N-N) relation. To solve these problems, we innovatively propose CDHse that consists of two crucial modules: 1) Entity embedding module, we obtain position feature obtained by PubMedBERT and Convolutional Neural Network (CNN), obtain molecular structure feature with Graphic Nuaral Network (GNN), obtain entity embedding feature of drug pairs, and then incorporate these features into one synthetic feature. 2) Knowledge graph embedding module, the synthetic feature is Householder projections and then embedded in the complex vector space for training. In this paper, we have selected several advanced models for the DDIs task and performed experiments on three standard BioKG to validate the effectiveness of CDHse.

Abstract 902: Explainable AI: Graph machine learning for response prediction and biomarker discovery

Abstract Accurately predicting drug sensitivity and understanding what is driving it are major challenges in drug discovery. Graphs are a natural framework for capturing diverse pharmacological data for efficacy predictions, thanks to their ability to integrate multimodal data and represent relationships such as gene-gene or drug-target interactions as edges. They have also had proven success across a range of other drug discovery tasks including repositioning and target identification. In this study, we sought to address the explainability challenges of drug response predictions. Recent developments in the field of Graph AI have led to improvements in interpretability mechanisms that highlight parts of a graph which are driving predictions. We have conducted a comprehensive review of multiple major approaches for tackling drug efficacy prediction using graph methods, benchmarking the performance and interpretability of these algorithms across indications. Methods: We assembled a combined dataset of GDSC1 and GDSC2 drug response data in cell lines, with multiomic cell line data and drug target and chemical structure data. We then applied graph-based approaches for the prediction of binarized IC50 on an indication-by-indication basis. Approach 1 involved the creation of a ‘GDSC knowledge graph’, where drug response and cell line ‘omic information is represented in an unweighted knowledge graph: cell lines are connected to genes expressed in them, drugs are connected to genes they target, and so on. We then used state-of-the-art graph embedding techniques to predict IC50 using paired drug and cell line embeddings. In Approach 2 we used a weighted knowledge graph instead, and generated embeddings using heterogeneous graph neural networks (HGNNs). In Approach 3, we modelled response prediction as a graph classification task, where one single graph captures one drug-cell line interaction. The graph classifier and HGNN models both have in-built interpretability mechanisms, including graph attention, that can signify the genes in the cell line which were most important for the eventual prediction. We can also integrate biomedical prior knowledge with all these models by capturing gene-pathway and gene-gene data in the graphs. Results: Our models outperformed benchmark models including DNNs and GBMs, and identified both established and novel response biomarkers in NSCLC cell lines (AUC = 0.94, Accuracy = 89%). We have also applied our models to Breast Cancer, Pancreatic Cancer, Colorectal Cancer and Haematological malignancies with similar predictive performance and explainability. Conclusions:Our graph analytical framework for response predictions showed better performance than benchmarking models and provided insights from explainability. This framework is easily extendable to response and ‘omic data from any disease model and patient studies. Citation Format: Jake Cohen-Setton, Krishna Bulusu, Jonathan Dry, Ben Sidders. Explainable AI: Graph machine learning for response prediction and biomarker discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 902.

Emerging technologies for drug repurposing: Harnessing the potential of text and graph embedding approaches

Drug repurposing is an approach to identifying new uses for existing drugs, where advanced computational methods, such as text and graph embedding techniques, are playing an ever-increasing role. This review provides a timely overview of these embedding methods for drug repurposing and discusses their integration with machine learning. Text embedding techniques, such as Word2Vec, FastText, BERT, and Doc2Vec, enable the analysis of biomedical literature and clinical data to discover potential drug-disease relationships. These methods convert textual data into numerical representations, allowing for similarity calculations and predictive modeling. Several successful applications of text embedding for drug repurposing are highlighted. In addition, graph embedding methods, such as Node2Vec and GraphSAGE, are being employed to convert complex biological knowledge graphs into vector representations. These representations facilitate various network analysis tasks, including predicting drug-target interactions and identifying hidden associations between drugs and diseases. Case studies in both technologies demonstrate their effectiveness in drug repurposing. The advantages and limitations of both text and graph embedding technologies, and their complementarity with traditional structure-based approaches have been discussed. Finally, text and graph embedding methods can be employed in conjunction with traditional approaches of computational methods, which can offer a promising path to identifying novel drug repurposing opportunities, particularly for rare diseases.

UrbanAgriKG: A knowledge graph on urban agriculture and its embeddings

Abstract This research article outlines a study that examines the creation of a comprehensive knowledge graph specifically designed for the domain of urban agriculture. The research centers on the acquisition, synthesis, and arrangement of pertinent information from various origins in order to establish a specialized knowledge graph tailored for urban agricultural systems. The graph depicts the interrelationships and attributes of various entities, including urban farms, crops, farming methods, environmental factors, and economic elements. Moreover, this study investigates the efficacy of different graph embedding methodologies in the domain of urban agriculture. The aforementioned techniques are utilized in the context of the urban agriculture knowledge graph in order to extract significant representations of entities and their relationships. The primary objective of the experimental study is to investigate and reveal semantic relationships, patterns, and predictions that have the potential to improve decision-making processes and optimize practices in the field of urban agriculture. The results of this study make a significant contribution to the existing body of knowledge in the area of urban agriculture. Additionally, they offer valuable insights into the potential uses of graph embedding techniques within this field.

Graph embedding approach to analyze sentiments on cryptocurrency

This paper presents a comprehensive exploration of graph embedding techniques for sentiment analysis. The objective of this study is to enhance the accuracy of sentiment analysis models by leveraging the rich contextual relationships between words in text data. We investigate the application of graph embedding in the context of sentiment analysis, focusing on it is effectiveness in capturing the semantic and syntactic information of text. By representing text as a graph and employing graph embedding techniques, we aim to extract meaningful insights and improve the performance of sentiment analysis models. To achieve our goal, we conduct a thorough comparison of graph embedding with traditional word embedding and simple embedding layers. Our experiments demonstrate that the graph embedding model outperforms these conventional models in terms of accuracy, highlighting it is potential for sentiment analysis tasks. Furthermore, we address two limitations of graph embedding techniques: handling out-of-vocabulary words and incorporating sentiment shift over time. The findings of this study emphasize the significance of graph embedding techniques in sentiment analysis, offering valuable insights into sentiment analysis within various domains. The results suggest that graph embedding can capture intricate relationships between words, enabling a more nuanced understanding of the sentiment expressed in text data.

Account credibility inference based on news-sharing networks

The spread of misinformation poses a threat to the social media ecosystem. Effective countermeasures to mitigate this threat require that social media platforms be able to accurately detect low-credibility accounts even before the content they share can be classified as misinformation. Here we present methods to infer account credibility from information diffusion patterns, in particular leveraging two networks: the reshare network, capturing an account’s trust in other accounts, and the bipartite account-source network, capturing an account’s trust in media sources. We extend network centrality measures and graph embedding techniques, systematically comparing these algorithms on data from diverse contexts and social media platforms. We demonstrate that both kinds of trust networks provide useful signals for estimating account credibility. Some of the proposed methods yield high accuracy, providing promising solutions to promote the dissemination of reliable information in online communities. Two kinds of homophily emerge from our results: accounts tend to have similar credibility if they reshare each other’s content or share content from similar sources. Our methodology invites further investigation into the relationship between accounts and news sources to better characterize misinformation spreaders.

An evolving learning style detection approach for online education using bipartite graph embedding

The increasingly widespread online education recently enabled a new form of teaching, learning, and overall educational outcome. However, the need of personalization is required as learners learn differently and learning follows a one-size-fits-all approach. Learning style is the most used personalization that plays an important role in learning. This learning style is a changeable trait that is influenced by the learner's behavior based on past experiences. As a result, knowing it over time helps to point learners in the right direction, motivate them, and enhance their learning outcomes. Research done so far does not take into account the changes in the behavior of learners, and the behavioral data is at large volume, making the existing approaches fail to capture and extract the behavior of learners efficiently. Inspired by these constraints, we propose an incremental learning style detection approach for online education with a bipartite graph embedding technique. We first construct a dynamic bipartite graph to represent the incremental interaction between learners and learning resources while learning. Then, introduce a dynamic bipartite graph embedding to learn the low dimensional representation of the constructed graph from the current and previous time. Finally, the low dimensional features are mapped to the selected Felder-Silverman learning style model (FSLSM) dimension each time to identify and group similar learners using the k-means clustering algorithm. The proposed approach can be integrated into different educational systems. Extensive experiments conducted using three datasets from 2015 KDD Cup courses demonstrate the effectiveness of our approach. Average of 93.19%, 95.76%, and 98.48% are achieved across the three datasets in accuracy compared to the existing approaches.

VisCARS: Knowledge Graph-based Context-Aware Recommender System for Time-Series Data Visualization and Monitoring Dashboards.

Data visualization recommendation aims to assist the user in creating visualizations from a given dataset. The process of creating appropriate visualizations requires expert knowledge of the available data model as well as the dashboard application that is used. To relieve the user from requiring this knowledge and from the manual process of creating numerous visualizations or dashboards, we present a context-aware visualization recommender system (VisCARS) for monitoring applications that automatically recommends a personalized dashboard to the user, based on the system they are monitoring and the task they are trying to achieve. Through a knowledge graph-based approach, expert knowledge about the data and the application is included as contextual features to improve the recommendation process. A dashboard ontology is presented that describes key components in a dashboard ecosystem in order to semantically annotate all the knowledge in the graph. The recommender system leverages knowledge graph embedding and comparison techniques in combination with a context-aware collaborative filtering approach to derive recommendations based on the context, i.e., the state of the monitored system, and the end-user preferences. The proposed methodology is implemented and integrated in a dynamic dashboard solution. The resulting recommender system is evaluated on a smart healthcare use-case through a quantitative performance and scalability analysis as well as a qualitative user study. The results highlight the performance of the proposed solution compared to the state-of-the-art and its potential for time-critical monitoring applications.

Identification of oral therapeutics using an AI platform against the virus responsible for COVID-19, SARS-CoV-2.

Purpose: This study introduces a sophisticated computational pipeline, eVir, designed for the discovery of antiviral drugs based on their interactions within the human protein network. There is a pressing need for cost-effective therapeutics for infectious diseases (e.g., COVID-19), particularly in resource-limited countries. Therefore, our team devised an Artificial Intelligence (AI) system to explore repurposing opportunities for currently used oral therapies. The eVir system operates by identifying pharmaceutical compounds that mirror the effects of antiviral peptides (AVPs)-fragments of human proteins known to interfere with fundamental phases of the viral life cycle: entry, fusion, and replication. eVir extrapolates the probable antiviral efficacy of a given compound by analyzing its established and predicted impacts on the human protein-protein interaction network. This innovative approach provides a promising platform for drug repurposing against SARS-CoV-2 or any virus for which peptide data is available. Methods: The eVir AI software pipeline processes drug-protein and protein-protein interaction networks generated from open-source datasets. eVir uses Node2Vec, a graph embedding technique, to understand the nuanced connections among drugs and proteins. The embeddings are input a Siamese Network (SNet) and MLPs, each tailored for the specific mechanisms of entry, fusion, and replication, to evaluate the similarity between drugs and AVPs. Scores generated from the SNet and MLPs undergo a Platt probability calibration and are combined into a unified score that gauges the potential antiviral efficacy of a drug. This integrated approach seeks to boost drug identification confidence, offering a potential solution for detecting therapeutic candidates with pronounced antiviral potency. Once identified a number of compounds were tested for efficacy and toxicity in lung carcinoma cells (Calu-3) infected with SARS-CoV-2. A lead compound was further identified to determine its efficacy and toxicity in K18-hACE2 mice infected with SARS-CoV-2. Computational Predictions: The SNet confidently differentiated between similar and dissimilar drug pairs with an accuracy of 97.28% and AUC of 99.47%. Key compounds identified through these networks included Zinc, Mebendazole, Levomenol, Gefitinib, Niclosamide, and Imatinib. Notably, Mebendazole and Zinc showcased the highest similarity scores, while Imatinib, Levemenol, and Gefitinib also ranked within the top 20, suggesting their significant pharmacological potentials. Further examination of protein binding analysis using explainable AI focused on reverse engineering the causality of the networks. Protein interaction scores for Mebendazole and Imatinib revealed their effects on notable proteins such as CDPK1, VEGF2, ABL1, and several tyrosine protein kinases. Laboratory Studies: This study determined that Mebendazole, Gefitinib, Topotecan and to some extent Carfilzomib showed conventional drug-response curves, with IC50 values near or below that of Remdesivir with excellent confidence all above R2>0.91, and no cytotoxicity at the IC50 concentration in Calu-3 cells. Cyclosporine A showed antiviral activity, but also unconventional drug-response curves and low R2 which are explained by the non-dose dependent toxicity of the compound. Additionally, Niclosamide demonstrated a conventional drug-response curve with high confidence; however, its inherent cytotoxicity may be a confounding element that misrepresents true antiviral efficacy, by reflecting cellular damage rather than a genuine antiviral action. Remdesivir was used as a control compound and was evaluated in parallel with the submitted test article and had conventional drug-response curves validating the overall results of the assay. Mebendazole was identified from the cell studies to have efficacy at non-toxic concentrations and were further evaluated in mice infected with SARS-CoV-2. Mebendazole administered to K18-hACE2 mice infected with SARS-CoV-2, resulted in a 44.2% reduction in lung viral load compared to non-treated placebo control respectively. There were no significant differences in body weight and all clinical chemistry determinations evaluated (i.e., kidney and liver enzymes) between the different treatment groups. Conclusion: This research underscores the potential of repurposing existing compounds for treating COVID-19. Our preliminary findings underscore the therapeutic promise of several compounds, notably Mebendazole, in both in vitro and in vivo settings against SARS-CoV-2. Several of the drugs explored, especially Mebendazole, are off-label medication; their cost-effectiveness position them as economical therapies against SARS-CoV-2.

AraPathogen2.0: An Improved Prediction of Plant-Pathogen Protein-Protein Interactions Empowered by the Natural Language Processing Technique.

Plant-pathogen protein-protein interactions (PPIs) play crucial roles in the arm race between plants and pathogens. Therefore, the identification of these interspecies PPIs is very important for the mechanistic understanding of pathogen infection and plant immunity. Computational prediction methods can complement experimental efforts, but their predictive performance still needs to be improved. Motivated by the rapid development of natural language processing and its successful applications in the field of protein bioinformatics, here we present an improved XGBoost-based plant-pathogen PPI predictor (i.e., AraPathogen2.0), in which sequence encodings from the pretrained protein language model ESM2 and Arabidopsis PPI network-related node representations from the graph embedding technique struc2vec are used as input. Stringent benchmark experiments showed that AraPathogen2.0 could achieve a better performance than its precedent version, especially for processing the test data set with novel proteins unseen in the training data.

Prokaryotic virus host prediction with graph contrastive augmentaion.

Prokaryotic viruses, also known as bacteriophages, play crucial roles in regulating microbial communities and have the potential for phage therapy applications. Accurate prediction of phage-host interactions is essential for understanding the dynamics of these viruses and their impacts on bacterial populations. Numerous computational methods have been developed to tackle this challenging task. However, most existing prediction models can be constrained due to the substantial number of unknown interactions in comparison to the constrained diversity of available training data. To solve the problem, we introduce a model for prokaryotic virus host prediction with graph contrastive augmentation (PHPGCA). Specifically, we construct a comprehensive heterogeneous graph by integrating virus-virus protein similarity and virus-host DNA sequence similarity information. As the backbone encoder for learning node representations in the virus-prokaryote graph, we employ LGCN, a state-of-the-art graph embedding technique. Additionally, we apply graph contrastive learning to augment the node representations without the need for additional labels. We further conducted two case studies aimed at predicting the host range of multi-species phages, helping to understand the phage ecology and evolution.