Multi-modal attention mechanisms have been successfully used in multi-modal graph learning for various tasks. However, existing attention-based multi-modal graph learning (AMGL) architectures heavily rely on manual design, requiring huge effort and expert experience. Meanwhile, graph neural architecture search (GNAS) has made great progress toward automatically designing graph-based learning architectures. However, it is challenging to directly adopt existing GNAS methods to search for better AMGL architectures because of the search spaces that only focus on designing graph neural network architectures and the search objective that ignores multi-modal interactive information between modalities and long-term content dependencies within different modalities. To address these issues, we propose an automated attention-based multi-modal graph learning architecture search (AutoAMS) framework, which can automatically design the optimal AMGL architectures for different multi-modal tasks. Specifically, we design an effective attention-based multi-modal (AM) search space consisting of four sub-spaces, which can jointly support the automatic search of multi-modal attention representation and other components of multi-modal graph learning architecture. In addition, a novel search objective based on an unsupervised multi-modal reconstruction loss and task-specific loss is introduced to search and train AMGL architectures. The search objective can extract the global features and capture multi-modal interactions from multiple modalities. The experimental results on multi-modal tasks show strong evidence that AutoAMS is capable of designing high-performance AMGL architectures.
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http://dx.doi.org/10.1016/j.neunet.2024.106427 | DOI Listing |
Brief Bioinform
November 2024
Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.
Spatially resolved transcriptomics (SRT) technologies facilitate the exploration of cell fates or states within tissue microenvironments. Despite these advances, the field has not adequately addressed the regulatory heterogeneity influenced by microenvironmental factors. Here, we propose a novel Spatially Aligned Graph Transfer Learning (SpaGTL), pretrained on a large-scale multi-modal SRT data of about 100 million cells/spots to enable inference of context-specific spatial gene regulatory networks across multiple scales in data-limited settings.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Key Laboratory for Bio-Electromagnetic Environment and Advanced Medical Theranostics, School of Biomedical Engineering and Informatics, Nanjing Medical University, Longmian Avenue No. 101, Jiangsu 211166, China.
Predicting drug-target binding affinity (DTA) is a crucial task in drug discovery research. Recent studies have demonstrated that pocket features and interactions between targets and drugs significantly improve the understanding of DTA. However, challenges remain, particularly in the detailed consideration of both global and local information and the further modeling of pocket features.
View Article and Find Full Text PDFBrief Bioinform
November 2024
College of Communication Engineering, Jilin University, No. 2699 Qianjin Street, Chaoyang District, Changchun 130012, China.
Antibiotic resistance poses a significant threat to global health, making the development of alternative strategies to combat bacterial pathogens increasingly urgent. One such promising approach is the strategic use of bacteriophages (or phages) to specifically target and eradicate antibiotic-resistant bacteria. Phages, being among the most prevalent life forms on Earth, play a critical role in maintaining ecological balance by regulating bacterial communities and driving genetic diversity.
View Article and Find Full Text PDFNeural Netw
January 2025
Harbin University of Science and Technology, Harbin, 150006, China.
Temporal Multi-Modal Knowledge Graphs (TMMKGs) can be regarded as a synthesis of Temporal Knowledge Graphs (TKGs) and Multi-Modal Knowledge Graphs (MMKGs), combining the characteristics of both. TMMKGs can effectively model dynamic real-world phenomena, particularly in scenarios involving multiple heterogeneous information sources and time series characteristics, such as e-commerce websites, scene recording data, and intelligent transportation systems. We propose a Temporal Multi-Modal Knowledge Graph Generation (TMMKGG) method that can automatically construct TMMKGs, aiming to reduce construction costs.
View Article and Find Full Text PDFNeuroimage
January 2025
College of Artificial Intelligence, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China; Key Laboratory of Brain-Machine Intelligence Technology, Ministry of Education, Nanjing University of Aeronautics and Astronautics, Nanjing, 211106, China. Electronic address:
Dynamic brain networks (DBNs) can capture the intricate connections and temporal evolution among brain regions, becoming increasingly crucial in the diagnosis of neurological disorders. However, most existing researches tend to focus on isolated brain network sequence segmented by sliding windows, and they are difficult to effectively uncover the higher-order spatio-temporal topological pattern in DBNs. Meantime, it remains a challenge to utilize the structure connectivity prior in the DBNs analysis.
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