{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,12]],"date-time":"2026-03-12T23:30:55Z","timestamp":1773358255277,"version":"3.50.1"},"publisher-location":"New York, NY, USA","reference-count":61,"publisher":"ACM","content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2025,11,16]]},"DOI":"10.1145\/3712285.3759782","type":"proceedings-article","created":{"date-parts":[[2025,11,12]],"date-time":"2025-11-12T16:05:39Z","timestamp":1762963539000},"page":"1524-1538","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["SIGMo: High-Throughput Batched Subgraph Isomorphism on GPUs for Molecular Matching"],"prefix":"10.1145","author":[{"ORCID":"https:\/\/orcid.org\/0009-0004-9909-6440","authenticated-orcid":false,"given":"Antonio","family":"De Caro","sequence":"first","affiliation":[{"name":"University of Salerno, Fisciano, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9148-9769","authenticated-orcid":false,"given":"Gennaro","family":"Cordasco","sequence":"additional","affiliation":[{"name":"University of Salerno, Fisciano, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1447-8278","authenticated-orcid":false,"given":"Federico","family":"Ficarelli","sequence":"additional","affiliation":[{"name":"CINECA, Casalecchio di Reno, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8869-6705","authenticated-orcid":false,"given":"Biagio","family":"Cosenza","sequence":"additional","affiliation":[{"name":"University of Salerno, Fisciano, Italy"}]}],"member":"320","published-online":{"date-parts":[[2025,11,15]]},"reference":[{"key":"e_1_3_3_3_2_2","doi-asserted-by":"publisher","unstructured":"M.\u00a0A. Abdulrahim and M. Misra. 1998. A Graph Isomorphism Algorithm for Object Recognition. Pattern Analysis and Applications 1 3 (1998) 189\u2013201. 10.1007\/BF01259368","DOI":"10.1007\/BF01259368"},{"key":"e_1_3_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1706.06654"},{"key":"e_1_3_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1145\/2897518.2897542"},{"key":"e_1_3_3_3_5_2","doi-asserted-by":"crossref","unstructured":"John\u00a0A Barnes and Frank Harary. 1983. Graph theory in network analysis. Social networks 5 2 (1983) 235\u2013244.","DOI":"10.1016\/0378-8733(83)90026-6"},{"key":"e_1_3_3_3_6_2","doi-asserted-by":"publisher","unstructured":"Vincenzo Bonnici Rosalba Giugno Alfredo Pulvirenti Dennis Shasha and Alfredo Ferro. 2013. A Subgraph Isomorphism Algorithm and Its Application to Biochemical Data. BMC Bioinformatics 14 S7 (2013) S13. 10.1186\/1471-2105-14-S7-S13","DOI":"10.1186\/1471-2105-14-S7-S13"},{"key":"e_1_3_3_3_7_2","doi-asserted-by":"crossref","unstructured":"Vincenzo Bonnici Rosalba Giugno Alfredo Pulvirenti Dennis Shasha and Alfredo Ferro. 2013. A subgraph isomorphism algorithm and its application to biochemical data. BMC bioinformatics 14 (2013) 1\u201313.","DOI":"10.1186\/1471-2105-14-S7-S13"},{"key":"e_1_3_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-58961-9_12"},{"key":"e_1_3_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-18224-7_17"},{"key":"e_1_3_3_3_10_2","doi-asserted-by":"publisher","unstructured":"Matthew Clark Richard\u00a0D. Cramer and Nicole Van\u00a0Opdenbosch. 1989. Validation of the General Purpose Tripos 5.2 Force Field. Journal of Computational Chemistry 10 8 (1989) 982\u20131012. 10.1002\/jcc.540100804","DOI":"10.1002\/jcc.540100804"},{"key":"e_1_3_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/hesc\/9780199270293.001.0001"},{"key":"e_1_3_3_3_12_2","doi-asserted-by":"crossref","unstructured":"Luigi\u00a0P Cordella Pasquale Foggia Carlo Sansone and Mario Vento. 2004. A (sub) graph isomorphism algorithm for matching large graphs. IEEE transactions on pattern analysis and machine intelligence 26 10 (2004) 1367\u20131372.","DOI":"10.1109\/TPAMI.2004.75"},{"key":"e_1_3_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1109\/PMBS49563.2019.00007"},{"key":"e_1_3_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1109\/IPDPS53621.2022.00025"},{"key":"e_1_3_3_3_15_2","volume-title":"NeurIPS 2021","author":"Du Yuanqi","year":"2021","unstructured":"Yuanqi Du, Shiyu Wang, Xiaojie Guo, Hengning Cao, Shujie Hu, Junji Jiang, Aishwarya Varala, Abhinav Angirekula, and Liang Zhao. 2021. GraphGT: Machine Learning Datasets for Graph Generation and Transformation. In NeurIPS 2021."},{"key":"e_1_3_3_3_16_2","doi-asserted-by":"publisher","unstructured":"Hans\u2010Christian Ehrlich and Matthias Rarey. 2011. Maximum Common Subgraph Isomorphism Algorithms and Their Applications in Molecular Science: A Review. WIREs Computational Molecular Science 1 1 (2011) 68\u201379. 10.1002\/wcms.5","DOI":"10.1002\/wcms.5"},{"key":"e_1_3_3_3_17_2","doi-asserted-by":"crossref","unstructured":"Hans-Christian Ehrlich and Matthias Rarey. 2012. Systematic benchmark of substructure search in molecular graphs-From Ullmann to VF2. Journal of cheminformatics 4 (2012) 1\u201317.","DOI":"10.1186\/1758-2946-4-13"},{"key":"e_1_3_3_3_18_2","doi-asserted-by":"publisher","unstructured":"Davide Gadioli Emanuele Vitali Federico Ficarelli Chiara Latini Candida Manelfi Carmine Talarico Cristina Silvano Carlo Cavazzoni Gianluca Palermo and Andrea\u00a0Rosario Beccari. 2022. EXSCALATE: An Extreme-Scale Virtual Screening Platform for Drug Discovery Targeting Polypharmacology to Fight SARS-CoV-2. IEEE Transactions on Emerging Topics in Computing 11 1 (2022) 1\u201312. 10.1109\/TETC.2022.3187134","DOI":"10.1109\/TETC.2022.3187134"},{"key":"e_1_3_3_3_19_2","volume-title":"SYCL 2020 Specification (revision 8) \u2014 registry.khronos.org","author":"Group The Khronos\u00ae SYCL\u2122\u00a0Working","year":"2023","unstructured":"The Khronos\u00ae SYCL\u2122\u00a0Working Group. 29-03-2023. SYCL 2020 Specification (revision 8) \u2014 registry.khronos.org. https:\/\/registry.khronos.org\/SYCL\/specs\/sycl-2020\/html\/sycl-2020.html"},{"key":"e_1_3_3_3_20_2","doi-asserted-by":"publisher","unstructured":"Thomas\u00a0A. Halgren. 1996. Merck Molecular Force Field. I. Basis Form Scope Parameterization and Performance of MMFF94. Journal of Computational Chemistry 17 5\u20136 (1996) 490\u2013519. 10.1002\/(SICI)1096-987X(199604)17:5\/6<490::AID-JCC1>3.0.CO;2-P","DOI":"10.1002\/(SICI)1096-987X(199604)17:5\/6<490::AID-JCC1>3.0.CO;2-P"},{"key":"e_1_3_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1109\/RSDHA56811.2022.00006"},{"key":"e_1_3_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1145\/2463676.2465300"},{"key":"e_1_3_3_3_23_2","doi-asserted-by":"publisher","unstructured":"Jp Hughes S Rees Sb Kalindjian and Kl Philpott. 2011. Principles of Early Drug Discovery. British Journal of Pharmacology 162 6 (2011) 1239\u20131249. 10.1111\/j.1476-5381.2010.01127.x","DOI":"10.1111\/j.1476-5381.2010.01127.x"},{"key":"e_1_3_3_3_24_2","volume-title":"oneAPI Base Toolkit","year":"2024","unstructured":"Intel\u00ae. 2024. oneAPI Base Toolkit. https:\/\/www.intel.com\/content\/www\/us\/en\/developer\/tools\/oneapi\/base-toolkit.html"},{"key":"e_1_3_3_3_25_2","doi-asserted-by":"crossref","unstructured":"John\u00a0J Irwin and Brian\u00a0K Shoichet. 2005. ZINC- a free database of commercially available compounds for virtual screening. Journal of chemical information and modeling 45 1 (2005) 177\u2013182.","DOI":"10.1021\/ci049714+"},{"key":"e_1_3_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1109\/SC41404.2022.00057"},{"key":"e_1_3_3_3_27_2","doi-asserted-by":"publisher","unstructured":"William\u00a0L. Jorgensen David\u00a0S. Maxwell and Julian Tirado-Rives. 1996. Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids. Journal of the American Chemical Society 118 45 (1996) 11225\u201311236. 10.1021\/ja9621760","DOI":"10.1021\/ja9621760"},{"key":"e_1_3_3_3_28_2","doi-asserted-by":"publisher","unstructured":"Jonas H.\u00a0M\"uller Kornd\"orfer Ahmed Eleliemy Ali Mohammed and Florina\u00a0M. Ciorba. 2022. LB4OMP: A Dynamic Load Balancing Library for Multithreaded Applications. IEEE Trans. Parallel Distributed Syst. 33 4 (2022) 830\u2013841. 10.1109\/TPDS.2021.3107775","DOI":"10.1109\/TPDS.2021.3107775"},{"key":"e_1_3_3_3_29_2","doi-asserted-by":"publisher","unstructured":"Paul\u00a0D. Leeson and Brian Springthorpe. 2007. The Influence of Drug-like Concepts on Decision-Making in Medicinal Chemistry. Nature Reviews Drug Discovery 6 11 (2007) 881\u2013890. 10.1038\/nrd2445","DOI":"10.1038\/nrd2445"},{"key":"e_1_3_3_3_30_2","doi-asserted-by":"publisher","unstructured":"Matthew Leinhauser Ren\u00e9 Widera Sergei Bastrakov Alexander Debus Michael Bussmann and Sunita Chandrasekaran. 2022. Metrics and Design of an Instruction Roofline Model for AMD GPUs. ACM Trans. Parallel Comput. 9 1 (Jan. 2022). 10.1145\/3505285","DOI":"10.1145\/3505285"},{"key":"e_1_3_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1109\/SC41406.2024.00035"},{"key":"e_1_3_3_3_32_2","doi-asserted-by":"publisher","unstructured":"Candida Manelfi Valerio Tazzari Filippo Lunghini Carmen Cerchia Anna Fava Alessandro Pedretti Pieter F.\u00a0W. Stouten Giulio Vistoli and Andrea\u00a0Rosario Beccari. 2024. \u201cDompeKeys\u201d: A Set of Novel Substructure-Based Descriptors for Efficient Chemical Space Mapping Development and Structural Interpretation of Machine Learning Models and Indexing of Large Databases. Journal of Cheminformatics 16 1 (2024) 21. 10.1186\/s13321-024-00813-4","DOI":"10.1186\/s13321-024-00813-4"},{"key":"e_1_3_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-030-51372-6_19"},{"key":"e_1_3_3_3_34_2","doi-asserted-by":"publisher","unstructured":"Jeffrey Mendenhall Benjamin\u00a0P. Brown Sandeepkumar Kothiwale and Jens Meiler. 2021. BCL::Conf: Improved Open-Source Knowledge-Based Conformation Sampling Using the Crystallography Open Database. Journal of Chemical Information and Modeling 61 1 (2021) 189\u2013201. 10.1021\/acs.jcim.0c01140","DOI":"10.1021\/acs.jcim.0c01140"},{"key":"e_1_3_3_3_35_2","unstructured":"NVIDIA. 2025. NVIDIA DCGM. https:\/\/developer.nvidia.com\/dcgm."},{"key":"e_1_3_3_3_36_2","doi-asserted-by":"crossref","unstructured":"Noel\u00a0M O\u2019Boyle Michael Banck Craig\u00a0A James Chris Morley Tim Vandermeersch and Geoffrey\u00a0R Hutchison. 2011. Open Babel: An open chemical toolbox. Journal of cheminformatics 3 (2011) 1\u201314.","DOI":"10.1186\/1758-2946-3-33"},{"key":"e_1_3_3_3_37_2","volume-title":"General chemistry","author":"Pauling Linus","year":"1988","unstructured":"Linus Pauling. 1988. General chemistry. Courier Corporation."},{"key":"e_1_3_3_3_38_2","doi-asserted-by":"crossref","unstructured":"Simon\u00a0J Pennycook Jason\u00a0D Sewall and Victor\u00a0W Lee. 2019. Implications of a metric for performance portability. Future Generation Computer Systems 92 (2019) 947\u2013958.","DOI":"10.1016\/j.future.2017.08.007"},{"key":"e_1_3_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0065-3233(03)66002-X"},{"key":"e_1_3_3_3_40_2","doi-asserted-by":"publisher","unstructured":"A.\u00a0K. Rappe C.\u00a0J. Casewit K.\u00a0S. Colwell W.\u00a0A. Goddard and W.\u00a0M. Skiff. 1992. UFF a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations. Journal of the American Chemical Society 114 25 (1992) 10024\u201310035. 10.1021\/ja00051a040","DOI":"10.1021\/ja00051a040"},{"key":"e_1_3_3_3_41_2","doi-asserted-by":"crossref","unstructured":"David Rogers and Mathew Hahn. 2010. Extended-connectivity fingerprints. Journal of chemical information and modeling 50 5 (2010) 742\u2013754.","DOI":"10.1021\/ci100050t"},{"key":"e_1_3_3_3_42_2","unstructured":"Yu Rong Yatao Bian Tingyang Xu Weiyang Xie Ying Wei Wenbing Huang and Junzhou Huang. 2020. Self-supervised graph transformer on large-scale molecular data. Advances in neural information processing systems 33 (2020) 12559\u201312571."},{"key":"e_1_3_3_3_43_2","doi-asserted-by":"publisher","unstructured":"Robert Schmidt Emanuel S.\u00a0R. Ehmki Farina Ohm Hans-Christian Ehrlich Andriy Mashychev and Matthias Rarey. 2019. Comparing Molecular Patterns Using the Example of SMARTS: Theory and Algorithms. Journal of Chemical Information and Modeling 59 6 (2019) 2560\u20132571. 10.1021\/acs.jcim.9b00250","DOI":"10.1021\/acs.jcim.9b00250"},{"key":"e_1_3_3_3_44_2","doi-asserted-by":"publisher","DOI":"10.1109\/HIPC.2016.021"},{"key":"e_1_3_3_3_45_2","doi-asserted-by":"crossref","unstructured":"Haichuan Shang Ying Zhang Xuemin Lin and Jeffrey\u00a0Xu Yu. 2008. Taming verification hardness: an efficient algorithm for testing subgraph isomorphism. Proceedings of the VLDB Endowment 1 1 (2008) 364\u2013375.","DOI":"10.14778\/1453856.1453899"},{"key":"e_1_3_3_3_46_2","doi-asserted-by":"publisher","unstructured":"John\u00a0C. Shelley Anuradha Cholleti Leah\u00a0L. Frye Jeremy\u00a0R. Greenwood Mathew\u00a0R. Timlin and Makoto Uchimaya. 2007. Epik: A Software Program for pK a Prediction and Protonation State Generation for Drug-like Molecules. Journal of Computer-Aided Molecular Design 21 12 (2007) 681\u2013691. 10.1007\/s10822-007-9133-z","DOI":"10.1007\/s10822-007-9133-z"},{"key":"e_1_3_3_3_47_2","doi-asserted-by":"crossref","unstructured":"Richard\u00a0A Snay. 1976. Reducing the profile of sparse symmetric matrices. Bulletin g\u00e9od\u00e9sique 50 4 (Dec. 1976) 341\u2013352.","DOI":"10.1007\/BF02521587"},{"key":"e_1_3_3_3_48_2","doi-asserted-by":"publisher","unstructured":"Yunhao Sun Guanyu Li Jingjing Du Bo Ning and Heng Chen. 2022. A Subgraph Matching Algorithm Based on Subgraph Index for Knowledge Graph. Frontiers of Computer Science 16 3 (2022) 163606. 10.1007\/s11704-020-0360-y","DOI":"10.1007\/s11704-020-0360-y"},{"key":"e_1_3_3_3_49_2","doi-asserted-by":"crossref","unstructured":"Benjamin\u00a0I Tingle Khanh\u00a0G Tang Mar Castanon John\u00a0J Gutierrez Munkhzul Khurelbaatar Chinzorig Dandarchuluun Yurii\u00a0S Moroz and John\u00a0J Irwin. 2023. ZINC-22\u2014A free multi-billion-scale database of tangible compounds for ligand discovery. Journal of chemical information and modeling 63 4 (2023) 1166\u20131176.","DOI":"10.1021\/acs.jcim.2c01253"},{"key":"e_1_3_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.1109\/HPEC.2018.8547543"},{"key":"e_1_3_3_3_51_2","volume-title":"November 2024 | TOP500","year":"2024","unstructured":"TOP500.org. 2024. November 2024 | TOP500. https:\/\/top500.org\/lists\/top500\/2024\/11\/"},{"key":"e_1_3_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1201\/9781315139111"},{"key":"e_1_3_3_3_53_2","doi-asserted-by":"crossref","unstructured":"Julian\u00a0R Ullmann. 1976. An algorithm for subgraph isomorphism. Journal of the ACM (JACM) 23 1 (1976) 31\u201342.","DOI":"10.1145\/321921.321925"},{"key":"e_1_3_3_3_54_2","doi-asserted-by":"publisher","unstructured":"K. Vanommeslaeghe E. Hatcher C. Acharya S. Kundu S. Zhong J. Shim E. Darian O. Guvench P. Lopes I. Vorobyov and A.\u00a0D. Mackerell. 2010. CHARMM General Force Field: A Force Field for Drug\u2010like Molecules Compatible with the CHARMM All\u2010atom Additive Biological Force Fields. Journal of Computational Chemistry 31 4 (2010) 671\u2013690. 10.1002\/jcc.21367","DOI":"10.1002\/jcc.21367"},{"key":"e_1_3_3_3_55_2","doi-asserted-by":"publisher","unstructured":"Junmei Wang Romain\u00a0M. Wolf James\u00a0W. Caldwell Peter\u00a0A. Kollman and David\u00a0A. Case. 2004. Development and Testing of a General Amber Force Field. Journal of Computational Chemistry 25 9 (2004) 1157\u20131174. 10.1002\/jcc.20035","DOI":"10.1002\/jcc.20035"},{"key":"e_1_3_3_3_56_2","doi-asserted-by":"crossref","unstructured":"Yuyang Wang Jianren Wang Zhonglin Cao and Amir Barati\u00a0Farimani. 2022. Molecular contrastive learning of representations via graph neural networks. Nature Machine Intelligence 4 3 (2022) 279\u2013287.","DOI":"10.1038\/s42256-022-00447-x"},{"key":"e_1_3_3_3_57_2","doi-asserted-by":"publisher","DOI":"10.1109\/SC41404.2022.00058"},{"key":"e_1_3_3_3_58_2","doi-asserted-by":"publisher","unstructured":"E.K. Wong. 1992. Model Matching in Robot Vision by Subgraph Isomorphism. Pattern Recognition 25 3 (1992) 287\u2013303. 10.1016\/0031-3203(92)90111-U","DOI":"10.1016\/0031-3203(92)90111-U"},{"key":"e_1_3_3_3_59_2","doi-asserted-by":"publisher","DOI":"10.1145\/3458817.3476214"},{"key":"e_1_3_3_3_60_2","doi-asserted-by":"crossref","unstructured":"Xinxing Yang Genke Yang and Jian Chu. 2024. GraphCL-DTA: a graph contrastive learning with molecular semantics for drug-target binding affinity prediction. IEEE Journal of Biomedical and Health Informatics 28 8 (2024) 4544\u20134552.","DOI":"10.1109\/JBHI.2024.3350666"},{"key":"e_1_3_3_3_61_2","doi-asserted-by":"crossref","unstructured":"Li Zeng Lei Zou and M\u00a0Tamer \u00d6zsu. 2022. SGSI\u2013A Scalable GPU-friendly Subgraph Isomorphism Algorithm. IEEE Transactions on Knowledge and Data Engineering 35 11 (2022) 11899\u201311916.","DOI":"10.1109\/TKDE.2022.3230744"},{"key":"e_1_3_3_3_62_2","doi-asserted-by":"publisher","DOI":"10.1109\/ICDE48307.2020.00112"}],"event":{"name":"SC '25: The International Conference for High Performance Computing, Networking, Storage and Analysis","location":"St. Louis MO USA","acronym":"SC '25","sponsor":["SIGHPC ACM Special Interest Group on High Performance Computing, Special Interest Group on High Performance Computing"]},"container-title":["Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3712285.3759782","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,11]],"date-time":"2026-03-11T18:54:38Z","timestamp":1773255278000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3712285.3759782"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,15]]},"references-count":61,"alternative-id":["10.1145\/3712285.3759782","10.1145\/3712285"],"URL":"https:\/\/doi.org\/10.1145\/3712285.3759782","relation":{},"subject":[],"published":{"date-parts":[[2025,11,15]]},"assertion":[{"value":"2025-11-15","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}