{"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/a-graph-is-worth-k-words-euclideanizing-graph","title":"A Graph is Worth $K$ Words: Euclideanizing Graph using Pure Transformer","arxiv_id":"2402.02464","date":"2024-02-04","proceeding":null,"authors":["Zhangyang Gao","Daize Dong","Cheng Tan","Jun Xia","Bozhen Hu","Stan Z. Li"],"abstract":"Can we model Non-Euclidean graphs as pure language or even Euclidean vectors while retaining their inherent information? The Non-Euclidean property have posed a long term challenge in graph modeling. Despite recent graph neural networks and graph transformers efforts encoding graphs as Euclidean vectors, recovering the original graph from vectors remains a challenge. In this paper, we introduce GraphsGPT, featuring an Graph2Seq encoder that transforms Non-Euclidean graphs into learnable Graph Words in the Euclidean space, along with a GraphGPT decoder that reconstructs the original graph from Graph Words to ensure information equivalence. We pretrain GraphsGPT on $100$M molecules and yield some interesting findings: (1) The pretrained Graph2Seq excels in graph representation learning, achieving state-of-the-art results on $8/9$ graph classification and regression tasks. (2) The pretrained GraphGPT serves as a strong graph generator, demonstrated by its strong ability to perform both few-shot and conditional graph generation. (3) Graph2Seq+GraphGPT enables effective graph mixup in the Euclidean space, overcoming previously known Non-Euclidean challenges. (4) The edge-centric pretraining framework GraphsGPT demonstrates its efficacy in graph domain tasks, excelling in both representation and generation. Code is available at \\href{https://github.com/A4Bio/GraphsGPT}{GitHub}.","url_abs":"https://arxiv.org/abs/2402.02464v3","url_pdf":"https://arxiv.org/pdf/2402.02464v3.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":"a-graph-is-worth-k-words-euclideanizing-graph","repo_url":"https://github.com/A4Bio/GraphsGPT","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"decoder","task_name":"Decoder"},{"task_slug":"graph-classification","task_name":"Graph Classification"},{"task_slug":"graph-generation","task_name":"Graph Generation"},{"task_slug":"graph-representation-learning","task_name":"Graph Representation Learning"},{"task_slug":"representation-learning","task_name":"Representation Learning"}],"methods":[{"method_slug":"adam","method_name":"Adam"},{"method_slug":"attention","method_name":"Attention"},{"method_slug":"attention-dropout","method_name":"Attention Dropout"},{"method_slug":"bpe","method_name":"BPE"},{"method_slug":"cosine-annealing","method_name":"Cosine Annealing"},{"method_slug":"dense-connections","method_name":"Dense Connections"},{"method_slug":"discriminative-fine-tuning","method_name":"Discriminative Fine-Tuning"},{"method_slug":"dropout","method_name":"Dropout"},{"method_slug":"gpt","method_name":"GPT"},{"method_slug":"layer-normalization","method_name":"Layer Normalization"},{"method_slug":"linear-layer","method_name":"Linear Layer"},{"method_slug":"linear-warmup-with-cosine-annealing","method_name":"Linear Warmup With Cosine Annealing"},{"method_slug":"mixup","method_name":"Mixup"},{"method_slug":"multi-head-attention","method_name":"Multi-Head Attention"},{"method_slug":"residual-connection","method_name":"Residual Connection"},{"method_slug":"softmax","method_name":"Softmax"},{"method_slug":"weight-decay","method_name":"Weight Decay"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2402.02464","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2402.02464"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+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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