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With the rise of multi-modal methods, multi-modal knowledge graphs have become a better choice for storing human knowledge. However, knowledge graphs often suffer from the problem of incompleteness due to the infinite and constantly updating nature of knowledge, and thus the task of knowledge graph completion has been proposed. Existing multi-modal knowledge graph completion methods mostly rely on either embedding-based representations or graph neural networks, and there is still room for improvement in terms of interpretability and the ability to handle multi-hop tasks. Therefore, we propose a new method for multi-modal knowledge graph completion. Our method aims to learn multi-level graph structural features to fully explore hidden relationships within the knowledge graph and to improve reasoning accuracy. Specifically, we first use a Transformer architecture to separately learn about data representations for both the image and text modalities. Then, with the help of multimodal gating units, we filter out irrelevant information and perform feature fusion to obtain a unified encoding of knowledge representations. Furthermore, we extract multi-level path features using a width-adjustable sliding window and learn about structural feature information in the knowledge graph using graph convolutional operations. Finally, we use a scoring function to evaluate the probability of the truthfulness of encoded triplets and to complete the prediction task. To demonstrate the effectiveness of the model, we conduct experiments on two publicly available datasets, FB15K-237-IMG and WN18-IMG, and achieve improvements of 1.8 and 0.7%, respectively, in the Hits@1 metric.
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http://dx.doi.org/10.3934/mbe.2023630 | DOI Listing |
PLoS One
September 2025
School of Mechanical and Automotive Engineering, Qingdao University of Technology, Qingdao, Shandong, China.
Drug-target interaction (DTI) prediction is essential for the development of novel drugs and the repurposing of existing ones. However, when the features of drug and target are applied to biological networks, there is a lack of capturing the relational features of drug-target interactions. And the corresponding multimodal models mainly depend on shallow fusion strategies, which results in suboptimal performance when trying to capture complex interaction relationships.
View Article and Find Full Text PDFCurr Microbiol
September 2025
Department of Health Sciences, Università del Piemonte Orientale UPO, Corso Trieste 15/A, 28100, Novara, Italy.
A Python-scripted software tool has been developed to help study the heterogeneity of gene changes, markedly or moderately expressed, when several experimental conditions are compared. The analysis workflow encloses a scorecard that groups genes based on relative fold-change and statistical significance, providing additional functions that facilitate knowledge extraction. The scorecard reports highlight unique patterns of gene regulation, such as genes whose expression is consistently up- or down-regulated across experiments, all of which are supported by graphs and summaries to characterize the dataset under investigation.
View Article and Find Full Text PDFNucleic Acids Res
September 2025
School of Software, Shandong University, Jinan 250101, Shandong, China.
Spatial transcriptomics (ST) reveals gene expression distributions within tissues. Yet, predicting spatial gene expression from histological images still faces the challenges of limited ST data that lack prior knowledge, and insufficient capturing of inter-slice heterogeneity and intra-slice complexity. To tackle these challenges, we introduce FmH2ST, a foundation model-based method for spatial gene expression prediction.
View Article and Find Full Text PDFIEEE Trans Comput Biol Bioinform
September 2025
Artificial intelligence (AI) based anticancer drug recommendation systems have emerged as powerful tools for precision dosing. Although existing methods have advanced in terms of predictive accuracy, they encounter three significant obstacles, including the "black-box" problem resulting in unexplainable reasoning, the computational difficulty for graphbased structures, and the combinatorial explosion during multistep reasoning. To tackle these issues, we introduce a novel Macro-Micro agent Drug sensitivity inference (MarMirDrug).
View Article and Find Full Text PDFBioinformatics
September 2025
Centre National de Recherche en Génomique Humaine, Institut François Jacob CEA Université Paris-Saclay.
Motivation: Graph Neural Network (GNN) models have emerged in many fields and notably for biological networks constituted by genes or proteins and their interactions. The majority of enrichment study methods apply over-representation analysis and gene/protein set scores according to the existing overlap between pathways. Such methods neglect knowledges coming from the interactions between the gene/protein sets.
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