Data-Efficient Molecular Generation with Hierarchical Textual Inversion

Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin
Proceedings of the 41st International Conference on Machine Learning, PMLR 235:24392-24414, 2024.

Abstract

Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and time-consuming experimental costs. To tackle this issue, we introduce Hierarchical Textual Inversion for Molecular Generation (HI-Mol), a novel data-efficient molecular generation method. HI-Mol is inspired by the importance of hierarchical information, e.g., both coarse- and fine-grained features, in understanding the molecule distribution. We propose to use multi-level embeddings to reflect such hierarchical features based on the adoption of the recent textual inversion technique in the visual domain, which achieves data-efficient image generation. Compared to the conventional textual inversion method in the image domain using a single-level token embedding, our multi-level token embeddings allow the model to effectively learn the underlying low-shot molecule distribution. We then generate molecules based on the interpolation of the multi-level token embeddings. Extensive experiments demonstrate the superiority of HI-Mol with notable data-efficiency. For instance, on QM9, HI-Mol outperforms the prior state-of-the-art method with 50x less training data. We also show the effectiveness of molecules generated by HI-Mol in low-shot molecular property prediction. Code is available at https://github.com/Seojin-Kim/HI-Mol.

Cite this Paper

BibTeX
@InProceedings{pmlr-v235-kim24z, title = {Data-Efficient Molecular Generation with Hierarchical Textual Inversion}, author = {Kim, Seojin and Nam, Jaehyun and Yu, Sihyun and Shin, Younghoon and Shin, Jinwoo}, booktitle = {Proceedings of the 41st International Conference on Machine Learning}, pages = {24392--24414}, year = {2024}, editor = {Salakhutdinov, Ruslan and Kolter, Zico and Heller, Katherine and Weller, Adrian and Oliver, Nuria and Scarlett, Jonathan and Berkenkamp, Felix}, volume = {235}, series = {Proceedings of Machine Learning Research}, month = {21--27 Jul}, publisher = {PMLR}, pdf = {https://raw.githubusercontent.com/mlresearch/v235/main/assets/kim24z/kim24z.pdf}, url = {https://proceedings.mlr.press/v235/kim24z.html}, abstract = {Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and time-consuming experimental costs. To tackle this issue, we introduce Hierarchical Textual Inversion for Molecular Generation (HI-Mol), a novel data-efficient molecular generation method. HI-Mol is inspired by the importance of hierarchical information, e.g., both coarse- and fine-grained features, in understanding the molecule distribution. We propose to use multi-level embeddings to reflect such hierarchical features based on the adoption of the recent textual inversion technique in the visual domain, which achieves data-efficient image generation. Compared to the conventional textual inversion method in the image domain using a single-level token embedding, our multi-level token embeddings allow the model to effectively learn the underlying low-shot molecule distribution. We then generate molecules based on the interpolation of the multi-level token embeddings. Extensive experiments demonstrate the superiority of HI-Mol with notable data-efficiency. For instance, on QM9, HI-Mol outperforms the prior state-of-the-art method with 50x less training data. We also show the effectiveness of molecules generated by HI-Mol in low-shot molecular property prediction. Code is available at https://github.com/Seojin-Kim/HI-Mol.} }
Endnote
%0 Conference Paper %T Data-Efficient Molecular Generation with Hierarchical Textual Inversion %A Seojin Kim %A Jaehyun Nam %A Sihyun Yu %A Younghoon Shin %A Jinwoo Shin %B Proceedings of the 41st International Conference on Machine Learning %C Proceedings of Machine Learning Research %D 2024 %E Ruslan Salakhutdinov %E Zico Kolter %E Katherine Heller %E Adrian Weller %E Nuria Oliver %E Jonathan Scarlett %E Felix Berkenkamp %F pmlr-v235-kim24z %I PMLR %P 24392--24414 %U https://proceedings.mlr.press/v235/kim24z.html %V 235 %X Developing an effective molecular generation framework even with a limited number of molecules is often important for its practical deployment, e.g., drug discovery, since acquiring task-related molecular data requires expensive and time-consuming experimental costs. To tackle this issue, we introduce Hierarchical Textual Inversion for Molecular Generation (HI-Mol), a novel data-efficient molecular generation method. HI-Mol is inspired by the importance of hierarchical information, e.g., both coarse- and fine-grained features, in understanding the molecule distribution. We propose to use multi-level embeddings to reflect such hierarchical features based on the adoption of the recent textual inversion technique in the visual domain, which achieves data-efficient image generation. Compared to the conventional textual inversion method in the image domain using a single-level token embedding, our multi-level token embeddings allow the model to effectively learn the underlying low-shot molecule distribution. We then generate molecules based on the interpolation of the multi-level token embeddings. Extensive experiments demonstrate the superiority of HI-Mol with notable data-efficiency. For instance, on QM9, HI-Mol outperforms the prior state-of-the-art method with 50x less training data. We also show the effectiveness of molecules generated by HI-Mol in low-shot molecular property prediction. Code is available at https://github.com/Seojin-Kim/HI-Mol.
APA
Kim, S., Nam, J., Yu, S., Shin, Y. & Shin, J.. (2024). Data-Efficient Molecular Generation with Hierarchical Textual Inversion. Proceedings of the 41st International Conference on Machine Learning, in Proceedings of Machine Learning Research 235:24392-24414 Available from https://proceedings.mlr.press/v235/kim24z.html.

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