{"paper":{"title":"HonestAffinity: Leak-Aware Evaluation of Protein and Pocket Priors for Binding Affinity Prediction","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.CE","authors_text":"Baili Lu, Dexing Yao, Haochen Li, Junhao Wei, Sio-Kei Im, Wanyan Li, Xudong Ye, Xu Yang, Yanxiao Li, Yapeng Wang, Yifu Zhao, Zhenhong Peng, Zhirong Huang","submitted_at":"2026-06-02T10:08:22Z","abstract_excerpt":"Sequence-based deep learning offers a scalable alternative to structure-based scoring for protein-ligand binding affinity prediction. However, progress is hard to interpret when architectural priors are evaluated on canonical PDBbind-style splits that leak similarity classes across folds. We present HonestAffinity, a compact 1D-input predictor to isolate two priors under a leak-aware protocol: frozen ESM-2 (650M) protein embeddings and a learned binary pocket-position marker. We evaluate a multi-scale convolutional/Transformer template in three variants: HonestAffinity-Pocket, HonestAffinity-N"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2606.03422","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2606.03422/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}