{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/generalist-equivariant-transformer-towards-3d","title":"Generalist Equivariant Transformer Towards 3D Molecular Interaction Learning","arxiv_id":"2306.01474","date":"2023-06-02","proceeding":null,"authors":["Xiangzhe Kong","Wenbing Huang","Yang Liu"],"abstract":"Many processes in biology and drug discovery involve various 3D interactions between molecules, such as protein and protein, protein and small molecule, etc. Given that different molecules are usually represented in different granularity, existing methods usually encode each type of molecules independently with different models, leaving it defective to learn the various underlying interaction physics. In this paper, we first propose to universally represent an arbitrary 3D complex as a geometric graph of sets, shedding light on encoding all types of molecules with one model. We then propose a Generalist Equivariant Transformer (GET) to effectively capture both domain-specific hierarchies and domain-agnostic interaction physics. To be specific, GET consists of a bilevel attention module, a feed-forward module and a layer normalization module, where each module is E(3) equivariant and specialized for handling sets of variable sizes. Notably, in contrast to conventional pooling-based hierarchical models, our GET is able to retain fine-grained information of all levels. Extensive experiments on the interactions between proteins, small molecules and RNA/DNAs verify the effectiveness and generalization capability of our proposed method across different domains.","url_abs":"https://arxiv.org/abs/2306.01474v6","url_pdf":"https://arxiv.org/pdf/2306.01474v6.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"generalist-equivariant-transformer-towards-3d","repo_url":"https://github.com/thunlp-mt/get","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"drug-discovery","task_name":"Drug Discovery"}],"methods":[{"method_slug":"absolute-position-encodings","method_name":"Absolute Position Encodings"},{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"position-wise-feed-forward-layer","method_name":"Position-Wise Feed-Forward Layer"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"transformer","method_name":"Transformer"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/2306.01474","atlas_url":"https://app.syntology.ai/?focus=2306.01474","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2306.01474"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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