XIMP: Cross Graph Inter-Message Passing for Molecular Property Prediction
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| Main Authors: | , , , , |
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| Format: | Preprint |
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2026
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| _version_ | 1866918307706175488 |
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| author | Ehrlich, Anatol Kummer, Lorenz Voracek, Vojtech Bause, Franka Kriege, Nils M. |
| author_facet | Ehrlich, Anatol Kummer, Lorenz Voracek, Vojtech Bause, Franka Kriege, Nils M. |
| contents | Accurate molecular property prediction is central to drug discovery, yet graph neural networks often underperform in data-scarce regimes and fail to surpass traditional fingerprints. We introduce cross-graph inter-message passing (XIMP), which performs message passing both within and across multiple related graph representations. For small molecules, we combine the molecular graph with scaffold-aware junction trees and pharmacophore-encoding extended reduced graphs, integrating complementary abstractions. While prior work is either limited to a single abstraction or non-iterative communication across graphs, XIMP supports an arbitrary number of abstractions and both direct and indirect communication between them in each layer. Across ten diverse molecular property prediction tasks, XIMP outperforms state-of-the-art baselines in most cases, leveraging interpretable abstractions as an inductive bias that guides learning toward established chemical concepts, enhancing generalization in low-data settings. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2601_19037 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | XIMP: Cross Graph Inter-Message Passing for Molecular Property Prediction Ehrlich, Anatol Kummer, Lorenz Voracek, Vojtech Bause, Franka Kriege, Nils M. Machine Learning Quantitative Methods Accurate molecular property prediction is central to drug discovery, yet graph neural networks often underperform in data-scarce regimes and fail to surpass traditional fingerprints. We introduce cross-graph inter-message passing (XIMP), which performs message passing both within and across multiple related graph representations. For small molecules, we combine the molecular graph with scaffold-aware junction trees and pharmacophore-encoding extended reduced graphs, integrating complementary abstractions. While prior work is either limited to a single abstraction or non-iterative communication across graphs, XIMP supports an arbitrary number of abstractions and both direct and indirect communication between them in each layer. Across ten diverse molecular property prediction tasks, XIMP outperforms state-of-the-art baselines in most cases, leveraging interpretable abstractions as an inductive bias that guides learning toward established chemical concepts, enhancing generalization in low-data settings. |
| title | XIMP: Cross Graph Inter-Message Passing for Molecular Property Prediction |
| topic | Machine Learning Quantitative Methods |
| url | https://arxiv.org/abs/2601.19037 |