{"doi":"10.1101/2024.04.01.587631","title":"A versatile information retrieval framework for evaluating profile strength and similarity","abstract":"In profiling assays, thousands of biological properties are measured across many samples, yielding biological discoveries by capturing the state of a cell population, often at the single-cell level. However, for profiling datasets, it has been challenging to evaluate the phenotypic activity of a sample and the phenotypic consistency among samples, due to profiles' high dimensionality, heterogeneous nature, and non-linear properties. Existing methods leave researchers uncertain where to draw boundaries between meaningful biological response and technical noise. Here, we developed a statistical framework that uses the well-established mean average precision (mAP) as a single, data-driven metric to bridge this gap. We validated the mAP framework against established metrics through simulations and real-world data applications, revealing its ability to capture subtle and meaningful biological differences in cell state. Specifically, we used mAP to assess both phenotypic activity for a given perturbation (or a sample) as well as consistency within groups of perturbations (or samples) across diverse high-dimensional datasets. We evaluated the framework on different profile types (image, protein, and mRNA profiles), perturbation types (CRISPR gene editing, gene overexpression, and small molecules), and profile resolutions (single-cell and bulk). Our open-source software allows this framework to be applied to identify interesting biological phenomena and promising therapeutics from large-scale profiling data.","journal":"bioRxiv (Cold Spring Harbor Laboratory)","year":2024,"id":484140,"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":15,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.918,"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":809160,"name":"John Arévalo","orcid":"0000-0002-1138-5036","position":1,"is_corresponding":false},{"id":971314,"name":"Erik Serrano","orcid":"0000-0003-4188-9080","position":2,"is_corresponding":false},{"id":815164,"name":"Loan Vulliard","orcid":"0000-0002-2260-4935","position":3,"is_corresponding":false},{"id":1161059,"name":"Hillary Tsang","orcid":null,"position":4,"is_corresponding":false},{"id":805069,"name":"Michael Bornholdt","orcid":null,"position":5,"is_corresponding":false},{"id":1325745,"name":"Alán F. Muñoz","orcid":"0000-0001-8698-5477","position":6,"is_corresponding":false},{"id":692873,"name":"Suganya Sivagurunathan","orcid":"0000-0002-9778-5400","position":7,"is_corresponding":false},{"id":411823,"name":"Bartek Rajwa","orcid":"0000-0001-7540-8236","position":8,"is_corresponding":false},{"id":11498,"name":"Anne E. Carpenter","orcid":"0000-0003-1555-8261","position":9,"is_corresponding":false},{"id":301,"name":"Gregory P. Way","orcid":"0000-0002-0503-9348","position":10,"is_corresponding":false},{"id":18821,"name":"Shantanu Singh","orcid":"0000-0003-3150-3025","position":11,"is_corresponding":false},{"id":63496,"name":"Alexandr A. Kalinin","orcid":"0000-0003-4563-3226","position":0,"is_corresponding":true}],"reference_count":66,"raw_metadata":null,"created_at":"2026-07-19T02:07:38.055693Z","pmid":"38617315","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":[]}