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Additionally, class imbalance in protein complexes, where binding residues constitute a small fraction of all residues, hinders model performance. To address these challenges, we constructed a training dataset 9$\\times $ larger than previous benchmarks by filtering the latest protein\u2013protein complex data, improving diversity and generalization. We propose Gated-GPS, a Graph Transformer model with a novel gating mechanism designed to effectively leverage this expanded dataset. Additionally, we integrate cross-entropy loss with Tversky Loss to adjust sensitivity to positive and negative samples, mitigating class imbalance by emphasizing underrepresented binding residues. Experimental results show that Gated-GPS outperforms state-of-the-art (SOTA) models across four test sets. Notably, on the UBTest dataset, designed to evaluate generalization on unbounded proteins, our method improves MCC and AUPRC by 18.5% and 21.4%, respectively, over the previous SOTA. In a case study of snake venom toxin\u2013protein interactions, our model accurately identified interaction sites, demonstrating its potential for therapeutic design and advancing the understanding of complex protein interactions.<\/jats:p>","DOI":"10.1093\/bib\/bbaf248","type":"journal-article","created":{"date-parts":[[2025,6,4]],"date-time":"2025-06-04T05:14:34Z","timestamp":1749014074000},"source":"Crossref","is-referenced-by-count":1,"title":["Gated-GPS: enhancing protein\u2013protein interaction site prediction with scalable learning and imbalance-aware optimization"],"prefix":"10.1093","volume":"26","author":[{"given":"Xin","family":"Gao","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering, University of California San Diego , 9500 Gilman Drive, La Jolla, California 92093 ,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hanqun","family":"Cao","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jinpeng","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiezhong","family":"Qiu","sequence":"additional","affiliation":[{"name":"Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guangyong","family":"Chen","sequence":"additional","affiliation":[{"name":"Zhejiang Lab, Kechu ang Avenue , Hangzhou Zhejiang 311121 ,","place":["China"]},{"name":"Hangzhou Institute of Medicine, Chinese Academy of Sciences , 150 Dongfang Street Xiasha, Hangzhou, Zhejiang, 310000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pheng-Ann","family":"Heng","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","place":["China"]},{"name":"Institute of Medical Intelligence and XR, The Chinese University of Hong Kong, Ma Liu Shui , Shatin, Hong Kong SAR, Hong Kong SAR 000000 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,4]]},"reference":[{"key":"2025060401142496400_ref1","doi-asserted-by":"publisher","first-page":"2833","DOI":"10.1002\/pmic.200700131","article-title":"Methods for the detection and analysis of protein\u2013protein interactions","volume":"7","author":"Bergg\u00e5rd","year":"2007","journal-title":"Proteomics"},{"key":"2025060401142496400_ref2","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/nature06526","article-title":"Reaching for high-hanging fruit in drug discovery at protein\u2013protein interfaces","volume":"450","author":"Wells","year":"2007","journal-title":"Nature"},{"key":"2025060401142496400_ref3","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1186\/s40425-015-0078-9","article-title":"Pembrolizumab","volume":"3","author":"Khoja","year":"2015","journal-title":"J Immunother Cancer"},{"key":"2025060401142496400_ref4","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/gm441","article-title":"Protein-protein interaction networks: probing disease mechanisms using model systems","volume":"5","author":"Kuzmanov","year":"2013","journal-title":"Genome Med"},{"key":"2025060401142496400_ref5","doi-asserted-by":"publisher","first-page":"e42","DOI":"10.1371\/journal.pcbi.0030042","article-title":"Deciphering protein\u2013protein interactions. 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