{"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/topology-informed-graph-transformer","title":"Topology-Informed Graph Transformer","arxiv_id":"2402.02005","date":"2024-02-03","proceeding":null,"authors":["Yun Young Choi","Sun Woo Park","Minho Lee","Youngho Woo"],"abstract":"Transformers have revolutionized performance in Natural Language Processing and Vision, paving the way for their integration with Graph Neural Networks (GNNs). One key challenge in enhancing graph transformers is strengthening the discriminative power of distinguishing isomorphisms of graphs, which plays a crucial role in boosting their predictive performances. To address this challenge, we introduce 'Topology-Informed Graph Transformer (TIGT)', a novel transformer enhancing both discriminative power in detecting graph isomorphisms and the overall performance of Graph Transformers. TIGT consists of four components: A topological positional embedding layer using non-isomorphic universal covers based on cyclic subgraphs of graphs to ensure unique graph representation: A dual-path message-passing layer to explicitly encode topological characteristics throughout the encoder layers: A global attention mechanism: And a graph information layer to recalibrate channel-wise graph features for better feature representation. TIGT outperforms previous Graph Transformers in classifying synthetic dataset aimed at distinguishing isomorphism classes of graphs. Additionally, mathematical analysis and empirical evaluations highlight our model's competitive edge over state-of-the-art Graph Transformers across various benchmark datasets.","url_abs":"https://arxiv.org/abs/2402.02005v1","url_pdf":"https://arxiv.org/pdf/2402.02005v1.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":"topology-informed-graph-transformer","repo_url":"https://github.com/leemingo/tigt","is_official":1,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}},{"paper_slug":"topology-informed-graph-transformer","repo_url":"https://github.com/leemingo/cy2mixer","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}}],"tasks":[{"task_slug":"graph-classification","task_name":"Graph Classification"},{"task_slug":"graph-regression","task_name":"Graph Regression"},{"task_slug":"inductive-bias","task_name":"Inductive Bias"},{"task_slug":"node-classification","task_name":"Node Classification"}],"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":"graph-transformer","method_name":"Graph Transformer"},{"method_slug":"label-smoothing","method_name":"Label Smoothing"},{"method_slug":"lapeigen","method_name":"LapEigen"},{"method_slug":"laplacian-pe","method_name":"Laplacian PE"},{"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":[{"leaderboard":"/sota/graph-classification-on-cifar10-100k","task":"Graph Classification","dataset":"CIFAR10 100k","model":"TIGT","rank_in_archive_order":8,"of":20,"metrics":{"Accuracy (%)":"73.955"},"uses_additional_data":false},{"leaderboard":"/sota/graph-classification-on-mnist","task":"Graph Classification","dataset":"MNIST","model":"TIGT","rank_in_archive_order":9,"of":13,"metrics":{"Accuracy":"98.230±0.133"},"uses_additional_data":false},{"leaderboard":"/sota/graph-classification-on-peptides-func","task":"Graph Classification","dataset":"Peptides-func","model":"TIGT","rank_in_archive_order":25,"of":44,"metrics":{"AP":"0.6679"},"uses_additional_data":false},{"leaderboard":"/sota/graph-regression-on-pcqm4mv2-lsc","task":"Graph Regression","dataset":"PCQM4Mv2-LSC","model":"TIGT","rank_in_archive_order":7,"of":20,"metrics":{"Validation MAE":"0.0826"},"uses_additional_data":false},{"leaderboard":"/sota/graph-regression-on-peptides-struct","task":"Graph Regression","dataset":"Peptides-struct","model":"TIGT","rank_in_archive_order":19,"of":39,"metrics":{"MAE":"0.2485"},"uses_additional_data":false},{"leaderboard":"/sota/graph-regression-on-zinc","task":"Graph Regression","dataset":"ZINC","model":"TIGT","rank_in_archive_order":3,"of":27,"metrics":{"MAE":"0.057"},"uses_additional_data":false},{"leaderboard":"/sota/graph-regression-on-zinc-full","task":"Graph Regression","dataset":"ZINC-full","model":"TIGT","rank_in_archive_order":3,"of":19,"metrics":{"Test MAE":"0.014"},"uses_additional_data":false},{"leaderboard":"/sota/node-classification-on-cluster","task":"Node Classification","dataset":"CLUSTER","model":"TIGT","rank_in_archive_order":8,"of":12,"metrics":{"Accuracy":"78.033"},"uses_additional_data":false},{"leaderboard":"/sota/node-classification-on-pattern","task":"Node Classification","dataset":"PATTERN","model":"TIGT","rank_in_archive_order":10,"of":11,"metrics":{"Accuracy":"86.680"},"uses_additional_data":false}],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2402.02005","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2402.02005"}},"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/leemingo/tigt","reach":{"status":"ok"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/leemingo/cy2mixer","reach":{"status":"ok"}}],"summary":{"ran":12,"ran_violates":2,"unverified":7},"by_repo_kind":{"official":{"samples":11,"ran":5,"repositories":1},"listed":{"samples":10,"ran":9,"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":21,"samples":[{"code_sha256_prefix":"561509b199175ea9","entry":"MAE","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/metrics.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/metrics.py","link_basis":"harvester_set","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":"561509b199175ea9"}},{"code_sha256_prefix":"0a7d2992d05685eb","entry":"MSE","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/metrics.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/metrics.py","link_basis":"harvester_set","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":"0a7d2992d05685eb"}},{"code_sha256_prefix":"602913d134538363","entry":"RMSE","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/metrics.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/metrics.py","link_basis":"harvester_set","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":"602913d134538363"}},{"code_sha256_prefix":"28d0813e58ab4fd5","entry":"data_load","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"model/Cy2C_utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/model/Cy2C_utils.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":"28d0813e58ab4fd5"}},{"code_sha256_prefix":"60fff7c3c400d7ff","entry":"default","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/layer/performer_layer.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/layer/performer_layer.py","link_basis":"harvester_set","language":"python","status":"ran_violates","verification_level":1,"contract_check":"VIOLATES","metamorphic_tier":"well_formed","behaviour_fingerprint":true,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"60fff7c3c400d7ff"}},{"code_sha256_prefix":"19925529d217754e","entry":"empty","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/layer/performer_layer.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/layer/performer_layer.py","link_basis":"harvester_set","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":"19925529d217754e"}},{"code_sha256_prefix":"aa5486a3650902d8","entry":"exists","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/layer/performer_layer.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/layer/performer_layer.py","link_basis":"harvester_set","language":"python","status":"ran_violates","verification_level":1,"contract_check":"VIOLATES","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"NONE","inline_ok":false,"mcp_get_code":{"code_sha256":"aa5486a3650902d8"}},{"code_sha256_prefix":"1bb331bf70a78136","entry":"get_final_pretrained_ckpt","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/finetuning.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/finetuning.py","link_basis":"harvester_set","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":"1bb331bf70a78136"}},{"code_sha256_prefix":"a1c29ec4fe872b3b","entry":"get_log_deg","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/network/tigt.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/network/tigt.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":"a1c29ec4fe872b3b"}},{"code_sha256_prefix":"cd17080a788963f3","entry":"load_pickle","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/utils.py","link_basis":"harvester_set","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":"cd17080a788963f3"}},{"code_sha256_prefix":"4a5dc6b540cf0d4f","entry":"make_cycle_adj_speed_nosl","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"model/Cy2C_utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/model/Cy2C_utils.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":"4a5dc6b540cf0d4f"}},{"code_sha256_prefix":"3c39e4ce38e253db","entry":"masked_mae_loss","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/utils.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":"3c39e4ce38e253db"}},{"code_sha256_prefix":"e5d90ec7d5feae99","entry":"max_node_dataset","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"model/Cy2C_utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/model/Cy2C_utils.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":"e5d90ec7d5feae99"}},{"code_sha256_prefix":"e7de63c9d9975208","entry":"vrange","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/utils.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/utils.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":"e7de63c9d9975208"}},{"code_sha256_prefix":"ae56bcfaae96da3c","entry":"apply_chunking_to_forward","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/layer/bigbird_layer.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/layer/bigbird_layer.py","link_basis":"harvester_set","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":"ae56bcfaae96da3c"}},{"code_sha256_prefix":"0252438018c7afc0","entry":"get_dataloaders_from_index_data","repo":"leemingo/cy2mixer","repo_kind":"listed","path":"lib/data_prepare.py","file_url":"https://github.com/leemingo/cy2mixer/blob/HEAD/lib/data_prepare.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":"0252438018c7afc0"}},{"code_sha256_prefix":"3db4474abe13fdee","entry":"init_model_from_pretrained","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/finetuning.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/finetuning.py","link_basis":"harvester_set","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":"3db4474abe13fdee"}},{"code_sha256_prefix":"c98a702be0660ac9","entry":"is_seed","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/agg_runs.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/agg_runs.py","link_basis":"harvester_set","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":"c98a702be0660ac9"}},{"code_sha256_prefix":"438635c08adfe2aa","entry":"is_split","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/agg_runs.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/agg_runs.py","link_basis":"harvester_set","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":"438635c08adfe2aa"}},{"code_sha256_prefix":"40e98e1ecbf39f34","entry":"join_list","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/agg_runs.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/agg_runs.py","link_basis":"harvester_set","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":"40e98e1ecbf39f34"}},{"code_sha256_prefix":"d796cdea5889c847","entry":"load_pretrained_model_cfg","repo":"leemingo/tigt","repo_kind":"official","path":"graphgps/finetuning.py","file_url":"https://github.com/leemingo/tigt/blob/HEAD/graphgps/finetuning.py","link_basis":"harvester_set","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":"d796cdea5889c847"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}