{"doi":"10.1101/2024.12.03.626631","title":"Tokenvizz: GraphRAG-Inspired Tokenization Tool for Genomic Data Discovery and Visualization","abstract":"ABSTRACT Summary One of the primary challenges in biomedical research is the interpretation of complex genomic relationships and the prediction of functional interactions across the genome. Tokenvizz is a novel tool for genomic analysis that enhances data discovery and visualization by combining GraphRAG-inspired tokenization with graph-based modeling. In Tokenvizz, genomic sequences are represented as graphs, where sequence k-mers (tokens) serve as nodes and attention scores as edge weights, enabling researchers to visually interpret complex, non-linear relationships within DNA sequences. Through a web-based visualization interface, researchers can interactively explore these genomic relationships and extract biologically meaningful insights about regulatory patterns and functional elements. Applied to promoter-enhancer interaction prediction tasks, Tokenvizz outperformed traditional sequential models while providing interpretable insights into genomic features, demonstrating the advantage of graph-based representations for biological discovery. Availability and Implementation Tokenvizz, along with its user guide, is freely accessible on GitHub at: https://github.com/ceragoguztuzun/tokenvizz . ACM Reference Format Çerağ Oğuztüzün, Zhenxiang Gao, and Rong Xu. 2024. Tokenvizz: GraphRAG Inspired Tokenization Tool for Genomic Data Discovery and Visualization. In Proceedings of (Bioinformatics) . ACM, New York, NY, USA, 7 pages. https://doi.org/XXXXXXX.XXXXXXX","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":492556,"datarank":0.10397207708399181,"base_score":0.6931471805599453,"endowment":0.6931471805599453,"self_citation_contribution":0.10397207708399181,"citation_network_contribution":0.0,"self_endowment_contribution":0.10397207708399181,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":1,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9526,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":1078942,"name":"Zhenxiang Gao","orcid":"0000-0002-2223-5092","position":1,"is_corresponding":false},{"id":109147,"name":"Rong Xu","orcid":"0000-0003-3127-4795","position":2,"is_corresponding":false},{"id":1133299,"name":"Çerağ Oğuztüzün","orcid":"0009-0008-3134-3379","position":0,"is_corresponding":true}],"reference_count":13,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T02:08:56.210382Z","pmid":"39677617","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}