{"paper":{"title":"Computing Gram Matrix for SMILES Strings using RDKFingerprint and Sinkhorn-Knopp Algorithm","license":"http://creativecommons.org/licenses/by-nc-nd/4.0/","headline":"","cross_cats":[],"primary_cat":"cs.LG","authors_text":"Haris Mansoor, Imdad Ullah Khan, Murray Patterson, Prakash Chourasia, Sarwan Ali","submitted_at":"2024-12-19T10:31:25Z","abstract_excerpt":"In molecular structure data, SMILES (Simplified Molecular Input Line Entry System) strings are used to analyze molecular structure design. Numerical feature representation of SMILES strings is a challenging task. This work proposes a kernel-based approach for encoding and analyzing molecular structures from SMILES strings. The proposed approach involves computing a kernel matrix using the Sinkhorn-Knopp algorithm while using kernel principal component analysis (PCA) for dimensionality reduction. The resulting low-dimensional embeddings are then used for classification and regression analysis. "},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2412.14717","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/2412.14717/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"}