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Multimodal learning with graphs
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Artificial intelligence for graphs has achieved remarkable success in modeling complex systems, ranging from dynamic networks in biology to interacting particle systems in physics. However, the increasingly heterogeneous graph datasets call for multimodal methods that can combine different inductive biases-the set of assumptions that algorithms use to make predictions for inputs they have not encountered during training. Learning on multimodal datasets presents fundamental challenges because the inductive biases can vary by data modality and graphs might not be explicitly given in the input. To address these challenges, multimodal graph AI methods combine different modalities while leveraging cross-modal dependencies using graphs. Diverse datasets are combined using graphs and fed into sophisticated multimodal architectures, specified as image-intensive, knowledge-grounded and language-intensive models. Using this categorization, we introduce a blueprint for multimodal graph learning, use it to study existing methods and provide guidelines to design new models.
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“The “all-in-one” multimodal graph learning (MGL) architecture [67] introduced a unified framework that included entity identification, topology construction, information propagation, and representation mixing for joint learning of modalities such as images, language sequences, or biological systems.”
From Challenges in AI-driven Biomedical Multimodal Data Fusion and Analysis (2025) · cites this paper as [67]
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“For adapting GNNs into a multimodal usage [67], data points from different modalities are all well-organized in defined graphs, and in contrast to single-modal fusion architecture, GNNs can directly learn the interactions of intra- and inter-modalities simultaneously.”
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Attention-based graph neural networks: a survey
Sun, C., Li, C., Lin, X., Zheng, T., Meng, F., Rui, X., & Wang, Z. (2023) · Artificial Intelligence Review · doi:10.1007/s10462-023-10577-2 · Cited by 156
“Once complex relations between modalities can be built into a network structure, GNNs provide a powerful and flexible strategy to leverage interdependencies in multimodal datasets (Ektefaie et al. 2023).”
BackgroundGraph machine learning for integrated multi-omics analysis
Valous, N. A., Popp, F., Zörnig, I., Jäger, D., & Charoentong, P. (2024) · British Journal of Cancer · doi:10.1038/s41416-024-02706-7 · Cited by 152
“In contrast, graph machine learning can model such datasets by connecting different modalities in optimally de fi ned (but more realistically in context-de fi ned) graphs, and by building learning systems for a wide range of tasks [10].”
BackgroundCurrent and future directions in network biology
Žitnik, M., Li, M. M., Wells, A., Glass, K., Gysi, D. M., Krishnan, A., Murali, T. M., Predrag Radivojac, A., Roy, S., Baudot, A., et al. (2024) · Bioinformatics Advances · doi:10.1093/bioadv/vbae099 · Cited by 129
“Network methods can integrate multimodal data to identify patient groups with coherent genetic, genomic, physiological, and clinical profiles [92, 128, 326], even when the underlying data are incomplete and noisy [311].”
BackgroundSelf-citation
Metadata
- Authors
- Ektefaie, Y., Dasoulas, G., Noori, A., Farhat, M., & Zitnik, M.
- Affiliations
- Harvard University (US)
- Venue
- Nature Machine Intelligence
- Published
- 2023-04-03
- Volume
- 5
- Issue
- 4
- Pages
- 340-350
- ISSN
- 2522-5839 (ISSN-L)
- PMC
- PMC10704992
- OpenAlex
- W4362579348
- Cited by
- 166
- References
- 97
- Citations by year
- 2026: 44 · 2025: 72 · 2024: 37 · 2023: 13
- FWCI
- 15.65
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- Locations
- Nature Machine Intelligence (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- arXiv (Cornell University) (submittedVersion)
- arXiv (Cornell University) (cc-by)
- Funders
- AstraZeneca
- U.S. Air Force (FA8702‐15‐D‐0001)
- Harvard Data Science Initiative, Harvard University
- National Human Genome Research Institute (T32HG002295)
- National Institute of Allergy and Infectious Diseases (R01AI155765)
- Topics
- Physical Sciences › Computer Science › Artificial Intelligence › Advanced Graph Neural Networks
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Multimodal Machine Learning Applications
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Graph Theory and Algorithms
- Keywords
- graph representation learning, inductive bias, geometric relationships
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