{"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/gigamae-generalizable-graph-masked","title":"GiGaMAE: Generalizable Graph Masked Autoencoder via Collaborative Latent Space Reconstruction","arxiv_id":"2308.09663","date":"2023-08-18","proceeding":null,"authors":["Yucheng Shi","Yushun Dong","Qiaoyu Tan","Jundong Li","Ninghao Liu"],"abstract":"Self-supervised learning with masked autoencoders has recently gained popularity for its ability to produce effective image or textual representations, which can be applied to various downstream tasks without retraining. However, we observe that the current masked autoencoder models lack good generalization ability on graph data. To tackle this issue, we propose a novel graph masked autoencoder framework called GiGaMAE. Different from existing masked autoencoders that learn node presentations by explicitly reconstructing the original graph components (e.g., features or edges), in this paper, we propose to collaboratively reconstruct informative and integrated latent embeddings. By considering embeddings encompassing graph topology and attribute information as reconstruction targets, our model could capture more generalized and comprehensive knowledge. Furthermore, we introduce a mutual information based reconstruction loss that enables the effective reconstruction of multiple targets. This learning objective allows us to differentiate between the exclusive knowledge learned from a single target and common knowledge shared by multiple targets. We evaluate our method on three downstream tasks with seven datasets as benchmarks. Extensive experiments demonstrate the superiority of GiGaMAE against state-of-the-art baselines. We hope our results will shed light on the design of foundation models on graph-structured data. Our code is available at: https://github.com/sycny/GiGaMAE.","url_abs":"https://arxiv.org/abs/2308.09663v1","url_pdf":"https://arxiv.org/pdf/2308.09663v1.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":"gigamae-generalizable-graph-masked","repo_url":"https://github.com/sycny/gigamae","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"attribute","task_name":"Attribute"},{"task_slug":"self-supervised-learning","task_name":"Self-Supervised Learning"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2308.09663","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2308.09663"}},"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. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/sycny/gigamae","reach":{"status":"ok"}}],"summary":{"ran":8,"unverified":2},"by_repo_kind":{"official":{"samples":10,"ran":8,"repositories":1}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":10,"samples":[{"code_sha256_prefix":"3f64b20e9795c842","entry":"PCA","repo":"sycny/gigamae","repo_kind":"official","path":"teacher.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/teacher.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"3f64b20e9795c842"}},{"code_sha256_prefix":"c676fbf50ad6244c","entry":"do_edge_split_direct","repo":"sycny/gigamae","repo_kind":"official","path":"datasets.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/datasets.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"c676fbf50ad6244c"}},{"code_sha256_prefix":"ec2ae2a3f6a2ca9c","entry":"dropout_edge","repo":"sycny/gigamae","repo_kind":"official","path":"data_aug.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/data_aug.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"ec2ae2a3f6a2ca9c"}},{"code_sha256_prefix":"dc3d32425b372023","entry":"filter_adj","repo":"sycny/gigamae","repo_kind":"official","path":"data_aug.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/data_aug.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"dc3d32425b372023"}},{"code_sha256_prefix":"3b4f7ab3eed498e6","entry":"link_decoder","repo":"sycny/gigamae","repo_kind":"official","path":"main_lp.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/main_lp.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"3b4f7ab3eed498e6"}},{"code_sha256_prefix":"ec28b9776bd950c5","entry":"mask_feature","repo":"sycny/gigamae","repo_kind":"official","path":"data_aug.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/data_aug.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"ec28b9776bd950c5"}},{"code_sha256_prefix":"4eab2ff901bf063b","entry":"sim","repo":"sycny/gigamae","repo_kind":"official","path":"main_lp.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/main_lp.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"4eab2ff901bf063b"}},{"code_sha256_prefix":"2db7a1575c22b0ca","entry":"svd_flip","repo":"sycny/gigamae","repo_kind":"official","path":"teacher.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/teacher.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"2db7a1575c22b0ca"}},{"code_sha256_prefix":"be622abe7c2c1836","entry":"get_dataset","repo":"sycny/gigamae","repo_kind":"official","path":"datasets.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/datasets.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"be622abe7c2c1836"}},{"code_sha256_prefix":"77b7b6ea81a4291f","entry":"postprocess","repo":"sycny/gigamae","repo_kind":"official","path":"teacher.py","file_url":"https://github.com/sycny/gigamae/blob/HEAD/teacher.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"77b7b6ea81a4291f"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}