{"doi":"10.1101/2024.01.25.577290","title":"Data-driven AI system for learning how to run transcript assemblers","abstract":"We introduce AutoTuneX, a data-driven, AI system designed to automatically predict optimal parameters for transcript assemblers - tools for reconstructing expressed transcripts from the reads in a given RNA-seq sample. AutoTuneX is built by learning parameter knowledge from existing RNA-seq samples and transferring this knowledge to unseen samples. On 1588 human RNA-seq samples tested with two transcript assemblers, AutoTuneX predicts parameters that resulted in 98% of samples achieving more accurate transcript assembly compared to using default parameter settings, with some samples experiencing up to a 600% improvement in AUC. AutoTuneX offers a new strategy for automatically optimizing use of sequence analysis tools.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":493743,"datarank":0.0,"base_score":0.0,"endowment":0.0,"self_citation_contribution":0.0,"citation_network_contribution":0.0,"self_endowment_contribution":0.0,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":0,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.956,"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":1340395,"name":"Zhiwen Yan","orcid":null,"position":1,"is_corresponding":false},{"id":58694,"name":"Carl Kingsford","orcid":null,"position":2,"is_corresponding":false},{"id":576244,"name":"Yihang Shen","orcid":"0000-0002-6161-3906","position":0,"is_corresponding":true}],"reference_count":52,"raw_metadata":null,"created_at":"2026-07-19T02:09:03.883685Z","pmid":"39554123","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":[]}