{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T20:06:52Z","timestamp":1784318812768,"version":"3.55.0"},"reference-count":49,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T00:00:00Z","timestamp":1784246400000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["12404263"],"award-info":[{"award-number":["12404263"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["82203868"],"award-info":[{"award-number":["82203868"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"High-Level Talents Innovation Team Project of the Guangdong-Macao In-Depth Cooperation Zone in Hengqin","award":["2630004018925"],"award-info":[{"award-number":["2630004018925"]}]},{"name":"Guangdong High-Level Innovation Research Institute","award":["2021B0909050004"],"award-info":[{"award-number":["2021B0909050004"]}]},{"name":"Macau Polytechnic University","award":["fca.d9b0.10de.9"],"award-info":[{"award-number":["fca.d9b0.10de.9"]}]},{"DOI":"10.13039\/501100002858","name":"China Postdoctoral Science Foundation","doi-asserted-by":"publisher","award":["2022M721409"],"award-info":[{"award-number":["2022M721409"]}],"id":[{"id":"10.13039\/501100002858","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Research Project of Jiangsu Cancer Hospital","award":["ZJ202101"],"award-info":[{"award-number":["ZJ202101"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,7,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Rare-cell identification is essential for dissecting disease mechanisms and developmental programs. Existing methods mostly rely on fixed-size neighbourhood graphs to separate rare-cell populations in single-cell expression data, which may embed rare cells into dominant clusters under varying sampling densities. This paper proposes the RAG method for identifying rare cells based on regularized adaptive graphs, which can better separate rare cells. Specifically, the regularized adaptive graph is constructed by estimating cell-specific radii from Euclidean\u2013cosine hybrid dissimilarity to constrain effective neighbours and stabilize the adjacency, and then, assigning locally scaled hybrid affinities to make affinity magnitudes comparable across density-varying regions. Across 10 real single-cell RNA sequencing datasets, RAG overall outperformed six state-of-the-art methods, improving precision, F1 score, and rare-type coverage rate over the second-ranked baseline by 42%, 26%, and 35%, respectively. A case study on colorectal tumour tissue shows that RAG is more accurate in recovering annotated rare-cell populations and separating the substructure from the major population than the other evaluated methods. Further analyses on mouse airway epithelium and two pancreas datasets showed that about half of RAG-resolved small clusters corresponded to known annotated populations or marker-supported subpopulations.<\/jats:p>\n                  <jats:p>The source code is available at https:\/\/github.com\/wangxingsu\/RAG.<\/jats:p>","DOI":"10.1093\/bib\/bbag379","type":"journal-article","created":{"date-parts":[[2026,7,7]],"date-time":"2026-07-07T11:42:36Z","timestamp":1783424556000},"source":"Crossref","is-referenced-by-count":0,"title":["RAG: a regularized adaptive graph-based method for rare-cell identification from single-cell expression data"],"prefix":"10.1093","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0009-0009-6911-3947","authenticated-orcid":false,"given":"Xingsu","family":"Wang","sequence":"first","affiliation":[{"name":"College of Applied Sciences, Macau Polytechnic University , Gomes Street, Macau 999078,","place":["China"]},{"name":"Laboratory of High-Performance Intelligent Computing, Guangdong Institute of Intelligence Science and Technology , Building 6, 2515 North Huandao Road, Hengqin Guangdong-Macao In-Depth Cooperation Zone, Zhuhai, Guangdong 519031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanyan","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Oncology, Jiangsu Cancer Hospital , 42th, Baiziting Road, Nanjing, Jiangsu 230031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4833-2376","authenticated-orcid":false,"given":"Dian","family":"Huang","sequence":"additional","affiliation":[{"name":"Laboratory of High-Performance Intelligent Computing, Guangdong Institute of Intelligence Science and Technology , Building 6, 2515 North Huandao Road, Hengqin Guangdong-Macao In-Depth Cooperation Zone, Zhuhai, Guangdong 519031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7720-1570","authenticated-orcid":false,"given":"Zhen","family":"Ju","sequence":"additional","affiliation":[{"name":"Laboratory of High-Performance Intelligent Computing, Guangdong Institute of Intelligence Science and Technology , Building 6, 2515 North Huandao Road, Hengqin Guangdong-Macao In-Depth Cooperation Zone, Zhuhai, Guangdong 519031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5506-0495","authenticated-orcid":false,"given":"Qi","family":"Wei","sequence":"additional","affiliation":[{"name":"Laboratory of High-Performance Intelligent Computing, Guangdong Institute of Intelligence Science and Technology , Building 6, 2515 North Huandao Road, Hengqin Guangdong-Macao In-Depth Cooperation Zone, Zhuhai, Guangdong 519031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4434-6172","authenticated-orcid":false,"given":"Shu","family":"Li","sequence":"additional","affiliation":[{"name":"College of Applied Sciences, Macau Polytechnic University , Gomes Street, Macau 999078,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shengzhong","family":"Feng","sequence":"additional","affiliation":[{"name":"Laboratory of High-Performance Intelligent Computing, Guangdong Institute of Intelligence Science and Technology , Building 6, 2515 North Huandao Road, Hengqin Guangdong-Macao In-Depth Cooperation Zone, Zhuhai, Guangdong 519031,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,7,17]]},"reference":[{"key":"2026071715540042600_ref1","doi-asserted-by":"publisher","first-page":"bbaf428","DOI":"10.1093\/bib\/bbaf428","article-title":"HiCat: a semi-supervised approach for cell type annotation","volume":"26","author":"Bi","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026071715540042600_ref2","doi-asserted-by":"publisher","first-page":"bbaf354","DOI":"10.1093\/bib\/bbaf354","article-title":"Applications and techniques of single-cell RNA sequencing across diverse species","volume":"26","author":"Woo","year":"2025","journal-title":"Brief Bioinform"},{"key":"2026071715540042600_ref3","doi-asserted-by":"publisher","first-page":"1274","DOI":"10.2215\/CJN.10031014","article-title":"A brief journey through the immune system","volume":"10","author":"Yatim","year":"2015","journal-title":"Clin J Am Soc Nephrol"},{"key":"2026071715540042600_ref4","doi-asserted-by":"publisher","first-page":"1288","DOI":"10.1017\/S0031182017000488","article-title":"The role of rare innate immune cells in type 2 immune activation against parasitic helminths","volume":"144","author":"Webb","year":"2017","journal-title":"Parasitology"},{"key":"2026071715540042600_ref5","doi-asserted-by":"publisher","first-page":"849","DOI":"10.1016\/j.ccell.2016.11.002","article-title":"Characterization of rare, dormant, and therapy-resistant cells in acute lymphoblastic leukemia","volume":"30","author":"Ebinger","year":"2016","journal-title":"Cancer Cell"},{"key":"2026071715540042600_ref6","doi-asserted-by":"publisher","first-page":"434","DOI":"10.1038\/s41568-022-00483-0","article-title":"Hunting down rare drug-tolerant cycling cells with watermelon","volume":"22","author":"Oren","year":"2022","journal-title":"Nat Rev Cancer"},{"key":"2026071715540042600_ref7","doi-asserted-by":"publisher","first-page":"1007","DOI":"10.1038\/s41590-024-01845-6","article-title":"Alternative platelet differentiation pathways initiated by nonhierarchically related hematopoietic stem cells","volume":"25","author":"Carrelha","year":"2024","journal-title":"Nat Immunol"},{"key":"2026071715540042600_ref8","doi-asserted-by":"publisher","first-page":"170","DOI":"10.1038\/s41392-024-01851-y","article-title":"Cancer stem cells: advances in knowledge and implications for cancer therapy","volume":"9","author":"Chu","year":"2024","journal-title":"Signal Transduct Target Ther"},{"key":"2026071715540042600_ref9","doi-asserted-by":"publisher","first-page":"1628","DOI":"10.1038\/s41467-021-21884-z","article-title":"Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer","volume":"12","author":"Aissa","year":"2021","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref10","doi-asserted-by":"publisher","first-page":"809","DOI":"10.26599\/BDMA.2024.9020011","article-title":"G3DC: a gene-graph-guided selective deep clustering method for single cell RNA-seq data","volume":"7","author":"He","year":"2024","journal-title":"Big Data Min Anal"},{"key":"2026071715540042600_ref11","doi-asserted-by":"publisher","first-page":"997","DOI":"10.26599\/BDMA.2025.9020009","article-title":"A flexible data-driven framework for correcting coarsely annotated scRNA-seq data","volume":"8","author":"Zheng","year":"2025","journal-title":"Big Data Min Anal"},{"key":"2026071715540042600_ref12","doi-asserted-by":"crossref","first-page":"bbad475","DOI":"10.1093\/bib\/bbad475","article-title":"CAKE: a flexible self-supervised framework for enhancing cell visualization, clustering and rare cell identification","volume":"25","author":"Liu","year":"2023","journal-title":"Brief Bioinform"},{"key":"2026071715540042600_ref13","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1186\/s13059-023-02998-7","article-title":"SCA: recovering single-cell heterogeneity through information-based dimensionality reduction","volume":"24","author":"DeMeo","year":"2023","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref14","doi-asserted-by":"publisher","first-page":"144","DOI":"10.1186\/s13059-016-1010-4","article-title":"GiniClust: detecting rare cell types from single-cell gene expression data with Gini index","volume":"17","author":"Jiang","year":"2016","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref15","doi-asserted-by":"publisher","first-page":"58","DOI":"10.1186\/s13059-018-1431-3","article-title":"GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection","volume":"19","author":"Tsoucas","year":"2018","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref16","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1186\/s12859-020-3482-1","article-title":"GiniClust3: a fast and memory-efficient tool for rare cell type identification","volume":"21","author":"Dong","year":"2020","journal-title":"BMC Bioinformatics"},{"key":"2026071715540042600_ref17","doi-asserted-by":"publisher","first-page":"dev201264","DOI":"10.1242\/dev.201264","article-title":"CIARA: a Acluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data","volume":"150","author":"Lubatti","year":"2023","journal-title":"Development"},{"key":"2026071715540042600_ref18","doi-asserted-by":"publisher","first-page":"251","DOI":"10.1038\/nature14966","article-title":"Single-cell messenger RNA sequencing reveals rare intestinal cell types","volume":"525","author":"Gr\u00fcn","year":"2015","journal-title":"Nature"},{"key":"2026071715540042600_ref19","doi-asserted-by":"publisher","first-page":"379","DOI":"10.1038\/nmeth.4662","article-title":"Fateid infers cell fate bias in multipotent progenitors from single-cell RNA-seq data","volume":"15","author":"Herman","year":"2018","journal-title":"Nat Methods"},{"key":"2026071715540042600_ref20","doi-asserted-by":"crossref","first-page":"7561","DOI":"10.1038\/s41467-024-51891-9","article-title":"ScCAD: cluster decomposition-based anomaly detection for rare cell identification in single-cell expression data","volume":"15","author":"Yunpei","year":"2024","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref21","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1186\/s13059-019-1739-7","article-title":"CellSIUS provides sensitive and specific detection of rare cell populations from complex single-cell RNA-seq data","volume":"20","author":"Wegmann","year":"2019","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref22","doi-asserted-by":"publisher","first-page":"4719","DOI":"10.1038\/s41467-018-07234-6","article-title":"Discovery of rare cells from voluminous single cell expression data","volume":"9","author":"Jindal","year":"2018","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref23","doi-asserted-by":"publisher","first-page":"4197","DOI":"10.1038\/s41467-021-24489-8","article-title":"GapClust is a light-weight approach distinguishing rare cells from voluminous single cell expression profiles","volume":"12","author":"Fa","year":"2021","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref24","doi-asserted-by":"publisher","first-page":"5853","DOI":"10.1038\/s41467-020-19465-7","article-title":"Ensemble dimensionality reduction and feature gene extraction for single-cell RNA-seq data","volume":"11","author":"Sun","year":"2020","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref25","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-41695-z","article-title":"From Louvain to Leiden: guaranteeing well-connected communities","volume":"9","author":"Traag","year":"2019","journal-title":"Sci Rep"},{"key":"2026071715540042600_ref26","doi-asserted-by":"publisher","first-page":"2554","DOI":"10.1038\/s41467-021-22851-4","article-title":"Deep generative model embedding of single-cell RNA-seq profiles on hyperspheres and hyperbolic spaces","volume":"12","author":"Ding","year":"2021","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref27","doi-asserted-by":"publisher","first-page":"2316","DOI":"10.1093\/bib\/bby076","article-title":"Impact of similarity metrics on single-cell RNA-seq data clustering","volume":"20","author":"Kim","year":"2019","journal-title":"Brief Bioinform"},{"key":"2026071715540042600_ref28","article-title":"Self-tuning spectral clustering","volume":"17","author":"Zelnik-Manor","year":"2004","journal-title":"Adv Neural Inf Proces Syst"},{"key":"2026071715540042600_ref29","doi-asserted-by":"publisher","first-page":"293","DOI":"10.1038\/s41587-023-01767-y","article-title":"Dictionary learning for integrative, multimodal and scalable single-cell analysis","volume":"42","author":"Hao","year":"2024","journal-title":"Nat Biotechnol"},{"key":"2026071715540042600_ref30","doi-asserted-by":"publisher","first-page":"15","DOI":"10.1186\/s13059-017-1382-0","article-title":"SCANPY: large-scale single-cell gene expression data analysis","volume":"19","author":"Alexander Wolf","year":"2018","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref31","doi-asserted-by":"publisher","DOI":"10.15252\/msb.20188746","volume-title":"Current Best Practices in Single-Cell Rna-Seq Analysis: A Tutorial. Molecular Systems Biology","author":"Luecken","year":"2019"},{"key":"2026071715540042600_ref32","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1137\/090771806","article-title":"Finding structure with randomness: probabilistic algorithms for constructing approximate matrix decompositions","volume":"53","author":"Halko","year":"2011","journal-title":"SIAM Rev"},{"key":"2026071715540042600_ref33","doi-asserted-by":"publisher","first-page":"319","DOI":"10.1038\/s41586-018-0393-7","article-title":"A revised airway epithelial hierarchy includes CFTR-expressing ionocytes","volume":"560","author":"Montoro","year":"2018","journal-title":"Nature"},{"key":"2026071715540042600_ref34","doi-asserted-by":"publisher","first-page":"193","DOI":"10.1126\/science.1245316","article-title":"Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells","volume":"343","author":"Deng","year":"2014","journal-title":"Science"},{"key":"2026071715540042600_ref35","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1038\/s41593-017-0029-5","article-title":"Single-cell analysis of experience-dependent transcriptomic states in the mouse visual cortex","volume":"21","author":"Hrvatin","year":"2018","journal-title":"Nat Neurosci"},{"key":"2026071715540042600_ref36","doi-asserted-by":"publisher","first-page":"346","DOI":"10.1016\/j.cels.2016.08.011","article-title":"A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure","volume":"3","author":"Baron","year":"2016","journal-title":"Cell Syst"},{"key":"2026071715540042600_ref37","doi-asserted-by":"publisher","first-page":"14049","DOI":"10.1038\/ncomms14049","article-title":"Massively parallel digital transcriptional profiling of single cells","volume":"8","author":"Zheng","year":"2017","journal-title":"Nat Commun"},{"key":"2026071715540042600_ref38","doi-asserted-by":"publisher","first-page":"btae371","DOI":"10.1093\/bioinformatics\/btae371","article-title":"scCross: efficient search for rare subpopulations across multiple single-cell samples","volume":"40","author":"Gerniers","year":"2024","journal-title":"Bioinformatics"},{"key":"2026071715540042600_ref39","doi-asserted-by":"publisher","first-page":"btad449","DOI":"10.1093\/bioinformatics\/btad449","article-title":"Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing","volume":"39","author":"Leary","year":"2023","journal-title":"Bioinformatics"},{"key":"2026071715540042600_ref40","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1186\/s13059-024-03339-y","article-title":"aKNNO: single-cell and spatial transcriptomics clustering with an optimized adaptive k-nearest neighbor graph","volume":"25","author":"Li","year":"2024","journal-title":"Genome Biol"},{"key":"2026071715540042600_ref41","doi-asserted-by":"publisher","first-page":"6596","DOI":"10.1021\/acs.jcim.4c00796","article-title":"Connectivity network feature sharing in single-cell RNA sequencing data identifies rare cells","volume":"64","author":"Wang","year":"2024","journal-title":"J Chem Inf Model"},{"key":"2026071715540042600_ref42","doi-asserted-by":"publisher","first-page":"3220","DOI":"10.1093\/bioinformatics\/btab239","article-title":"MicroCellClust: mining rare and highly specific subpopulations from single-cell expression data","volume":"37","author":"Gerniers","year":"2021","journal-title":"Bioinformatics"},{"key":"2026071715540042600_ref43","doi-asserted-by":"publisher","first-page":"589","DOI":"10.1016\/j.csbj.2023.12.043","article-title":"scSID: a lightweight algorithm for identifying rare cell types by capturing differential expression from single-cell sequencing data","volume":"23","author":"Wang","year":"2024","journal-title":"Comput Struct Biotechnol J"},{"key":"2026071715540042600_ref44","doi-asserted-by":"crossref","first-page":"bbad125","DOI":"10.1093\/bib\/bbad125","article-title":"A scalable unsupervised learning of scRNAseq data detects rare cells through integration of structure-preserving embedding, clustering and outlier detection","volume":"24","author":"Mallick","year":"2023","journal-title":"Brief Bioinform"},{"key":"2026071715540042600_ref45","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s42256-022-00534-z","article-title":"scBERT as a large-scale pretrained deep language model for cell type annotation of single-cell RNA-seq data","volume":"4","author":"Yang","year":"2022","journal-title":"Nat Mach Intell"},{"key":"2026071715540042600_ref46","doi-asserted-by":"publisher","first-page":"302","DOI":"10.1038\/s41392-024-02005-w","article-title":"Comprehensive snapshots of natural killer cells functions, signaling, molecular mechanisms and clinical utilization","volume":"9","author":"Chen","year":"2024","journal-title":"Signal Transduct Target Ther"},{"key":"2026071715540042600_ref47","doi-asserted-by":"crossref","first-page":"D870","DOI":"10.1093\/nar\/gkac947","article-title":"CellMarker 2.0: an updated database of manually curated cell markers in human\/mouse and web tools based on scRNA-seq data","volume":"51","author":"Congxue","year":"2023","journal-title":"Nucleic Acids Res"},{"key":"2026071715540042600_ref48","doi-asserted-by":"publisher","first-page":"1888","DOI":"10.1016\/j.cell.2019.05.031","article-title":"Comprehensive integration of single-cell data cell","volume":"177","author":"Stuart","year":"2019","journal-title":"Cell"},{"key":"2026071715540042600_ref49","doi-asserted-by":"publisher","first-page":"377","DOI":"10.1038\/s41586-018-0394-6","article-title":"A single-cell atlas of the airway epithelium reveals the CCFTR-rich pulmonary ionocyte","volume":"560","author":"Plasschaert","year":"2018","journal-title":"Nature"}],"container-title":["Briefings in Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag379\/69204726\/bbag379.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bib\/article-pdf\/27\/4\/bbag379\/69204726\/bbag379.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,17]],"date-time":"2026-07-17T19:54:10Z","timestamp":1784318050000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bib\/article\/doi\/10.1093\/bib\/bbag379\/8736956"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7]]},"references-count":49,"journal-issue":{"issue":"4","published-print":{"date-parts":[[2026,7,3]]}},"URL":"https:\/\/doi.org\/10.1093\/bib\/bbag379","relation":{},"ISSN":["1467-5463","1477-4054"],"issn-type":[{"value":"1467-5463","type":"print"},{"value":"1477-4054","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,7]]},"published":{"date-parts":[[2026,7]]},"article-number":"bbag379"}}