{"id":"https://openalex.org/W4414564525","doi":"https://doi.org/10.1109/tcbbio.2025.3614663","title":"HiADN: Lightweight Resolution Enhancement of Hi-C Data Using High Information Attention Distillation Network","display_name":"HiADN: Lightweight Resolution Enhancement of Hi-C Data Using High Information Attention Distillation Network","publication_year":2025,"publication_date":"2025-09-25","ids":{"openalex":"https://openalex.org/W4414564525","doi":"https://doi.org/10.1109/tcbbio.2025.3614663","pmid":"https://pubmed.ncbi.nlm.nih.gov/40996990"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3614663","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3614663","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5050254080","display_name":"Pingjing Li","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Pingjing Li","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065460851","display_name":"Jiuxin Feng","orcid":null},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiuxin Feng","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112125698","display_name":"Jun Guo","orcid":"https://orcid.org/0009-0003-3864-2156"},"institutions":[{"id":"https://openalex.org/I9224756","display_name":"Northeastern University","ror":"https://ror.org/03awzbc87","country_code":"CN","type":"education","lineage":["https://openalex.org/I9224756"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jun Guo","raw_affiliation_strings":["Software College of Northeastern University, Shenyang, China"],"affiliations":[{"raw_affiliation_string":"Software College of Northeastern University, Shenyang, China","institution_ids":["https://openalex.org/I9224756"]}]},{"author_position":"last","author":{"id":null,"display_name":"Jian Liu","orcid":"https://orcid.org/0000-0001-5516-0157"},"institutions":[{"id":"https://openalex.org/I205237279","display_name":"Nankai University","ror":"https://ror.org/01y1kjr75","country_code":"CN","type":"education","lineage":["https://openalex.org/I205237279"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian Liu","raw_affiliation_strings":["College of Computer Science, Nankai University, Tianjin, China"],"affiliations":[{"raw_affiliation_string":"College of Computer Science, Nankai University, Tianjin, China","institution_ids":["https://openalex.org/I205237279"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5050254080"],"corresponding_institution_ids":["https://openalex.org/I205237279"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.3886108,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"6","first_page":"3213","last_page":"3223"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10522","display_name":"Medical Imaging Techniques and Applications","score":0.8884000182151794,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10522","display_name":"Medical Imaging Techniques and Applications","score":0.8884000182151794,"subfield":{"id":"https://openalex.org/subfields/2741","display_name":"Radiology, Nuclear Medicine and Imaging"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T14510","display_name":"Medical Imaging and Analysis","score":0.795199990272522,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12702","display_name":"Brain Tumor Detection and Classification","score":0.7753999829292297,"subfield":{"id":"https://openalex.org/subfields/2808","display_name":"Neurology"},"field":{"id":"https://openalex.org/fields/28","display_name":"Neuroscience"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/kernel","display_name":"Kernel (algebra)","score":0.564300000667572},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.4693000018596649},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4498000144958496},{"id":"https://openalex.org/keywords/decomposition","display_name":"Decomposition","score":0.38109999895095825},{"id":"https://openalex.org/keywords/chromatin","display_name":"Chromatin","score":0.37720000743865967},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.34310001134872437},{"id":"https://openalex.org/keywords/component","display_name":"Component (thermodynamics)","score":0.3237999975681305},{"id":"https://openalex.org/keywords/spatial-analysis","display_name":"Spatial analysis","score":0.31690001487731934},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.301800012588501}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7139000296592712},{"id":"https://openalex.org/C74193536","wikidata":"https://www.wikidata.org/wiki/Q574844","display_name":"Kernel (algebra)","level":2,"score":0.564300000667572},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4788999855518341},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.4693000018596649},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4498000144958496},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4388999938964844},{"id":"https://openalex.org/C124681953","wikidata":"https://www.wikidata.org/wiki/Q339062","display_name":"Decomposition","level":2,"score":0.38109999895095825},{"id":"https://openalex.org/C83640560","wikidata":"https://www.wikidata.org/wiki/Q180951","display_name":"Chromatin","level":3,"score":0.37720000743865967},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.37130001187324524},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.34310001134872437},{"id":"https://openalex.org/C168167062","wikidata":"https://www.wikidata.org/wiki/Q1117970","display_name":"Component (thermodynamics)","level":2,"score":0.3237999975681305},{"id":"https://openalex.org/C159620131","wikidata":"https://www.wikidata.org/wiki/Q1938983","display_name":"Spatial analysis","level":2,"score":0.31690001487731934},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.301800012588501},{"id":"https://openalex.org/C3020199158","wikidata":"https://www.wikidata.org/wiki/Q210521","display_name":"High resolution","level":2,"score":0.3005000054836273},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2971000075340271},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.2955000102519989},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.29089999198913574},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.289900004863739},{"id":"https://openalex.org/C33676613","wikidata":"https://www.wikidata.org/wiki/Q13415176","display_name":"Dimension (graph theory)","level":2,"score":0.28929999470710754},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.28769999742507935},{"id":"https://openalex.org/C55037315","wikidata":"https://www.wikidata.org/wiki/Q5421151","display_name":"Experimental data","level":2,"score":0.2612999975681305},{"id":"https://openalex.org/C122280245","wikidata":"https://www.wikidata.org/wiki/Q620622","display_name":"Kernel method","level":3,"score":0.26010000705718994},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.25870001316070557},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.2531999945640564},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.25189998745918274},{"id":"https://openalex.org/C160920958","wikidata":"https://www.wikidata.org/wiki/Q7662746","display_name":"Synthetic data","level":2,"score":0.25029999017715454},{"id":"https://openalex.org/C2778258933","wikidata":"https://www.wikidata.org/wiki/Q16918986","display_name":"Decomposition method (queueing theory)","level":2,"score":0.2500999867916107}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D002843","descriptor_name":"Chromatin","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3614663","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3614663","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40996990","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40996990","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G6485093558","display_name":null,"funder_award_id":"23JCYBJC01740","funder_id":"https://openalex.org/F4320323993","funder_display_name":"Natural Science Foundation of Tianjin City"}],"funders":[{"id":"https://openalex.org/F4320323993","display_name":"Natural Science Foundation of Tianjin City","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":26,"referenced_works":["https://openalex.org/W1973062929","https://openalex.org/W2070021921","https://openalex.org/W2080477348","https://openalex.org/W2090037139","https://openalex.org/W2142270559","https://openalex.org/W2507209892","https://openalex.org/W2784063494","https://openalex.org/W2800216985","https://openalex.org/W2803256172","https://openalex.org/W2936970738","https://openalex.org/W2951050465","https://openalex.org/W2951559295","https://openalex.org/W2952979547","https://openalex.org/W2953462601","https://openalex.org/W3007609047","https://openalex.org/W3015754908","https://openalex.org/W3017136408","https://openalex.org/W3017323102","https://openalex.org/W3156421803","https://openalex.org/W3180346860","https://openalex.org/W4220661565","https://openalex.org/W4221095693","https://openalex.org/W4282929864","https://openalex.org/W4366602055","https://openalex.org/W4368361817","https://openalex.org/W4385613236"],"related_works":[],"abstract_inverted_index":{"Due":[0],"to":[1,32,61,79,100,114],"limitations":[2],"in":[3,8,141,169],"experimental":[4,134,155],"library":[5],"preparation":[6],"and":[7,84,97,181],"practical":[9],"sequencing":[10,39,131],"cost,":[11],"currently":[12],"available":[13],"Hi-C":[14,38,68,88],"data":[15,40],"is":[16,49,112,150],"often":[17],"sparse,":[18],"affecting":[19],"the":[20,34,43,85,127,138,158,165,171,178],"precise":[21],"characterization":[22],"of":[23,36,46,50,87,129,140,154,167,175],"complex":[24],"3D":[25,47],"chromatin":[26,48],"structures.":[27],"Providing":[28],"efficaciously":[29],"computational":[30,146],"models":[31,147],"elevate":[33],"quality":[35],"sparse":[37,67],"for":[41],"restoring":[42],"fundamental":[44],"traits":[45],"substantial":[51],"significance.":[52],"Herein,":[53],"we":[54,72,91],"introduce":[55],"HiADN,":[56,110],"a":[57,75],"deep":[58],"learning-based":[59],"approach":[60],"infer":[62],"dense":[63],"high-resolution":[64,120],"matrices":[65],"from":[66],"matrices.":[69],"In":[70],"particular,":[71],"firstly":[73],"design":[74],"specialized":[76],"architecture":[77],"HiFM":[78],"captures":[80],"local":[81],"spatial":[82,173],"structures":[83],"patterns":[86,104],"data.":[89],"Then,":[90],"develop":[92],"large":[93],"kernel":[94],"convolutional":[95],"decomposition":[96],"attention":[98],"mechanisms":[99],"effectively":[101],"explore":[102],"global":[103],"across":[105],"longer":[106],"genomic":[107],"distances.":[108],"Using":[109],"it":[111],"possible":[113],"construct":[115],"biologically":[116],"significant":[117],"regions":[118],"at":[119],"(e.g.,":[121],"10":[122],"Kb)":[123],"while":[124],"only":[125],"using":[126,148],"1/100":[128],"original":[130],"reads.":[132],"The":[133],"results":[135],"demonstrate":[136],"that":[137,153],"effect":[139],"silico":[142],"libraries":[143],"forecasted":[144],"by":[145],"HiADN":[149,168],"commensurate":[151],"with":[152],"libraries,":[156],"surpassing":[157],"state-of-the-art":[159],"(SOTA)":[160],"models.":[161],"We":[162],"further":[163],"validated":[164],"effectiveness":[166],"reconstructing":[170],"three-dimensional":[172],"structure":[174],"chromosomes":[176],"on":[177],"GM12878,":[179],"K562,":[180],"CH12-LX":[182],"cell":[183],"line":[184],"datasets.":[185]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}
