{"id":"https://openalex.org/W7160942236","doi":"https://doi.org/10.48550/arxiv.2605.08924","title":"PPI2Text: Captioning Protein-Protein Interactions with Coordinate-Aligned Pair-Map Decoding","display_name":"PPI2Text: Captioning Protein-Protein Interactions with Coordinate-Aligned Pair-Map Decoding","publication_year":2026,"publication_date":"2026-05-09","ids":{"openalex":"https://openalex.org/W7160942236","doi":"https://doi.org/10.48550/arxiv.2605.08924"},"language":"en","primary_location":{"id":"pmh:oai:HAL:hal-05670461v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05670461","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2026","raw_type":"info:eu-repo/semantics/preprint"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://hal.science/hal-05670461","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5135938058","display_name":"Xiao Fei","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fei, Xiao","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001449160","display_name":"Sarah Almeida Carneiro","orcid":"https://orcid.org/0000-0001-7653-8614"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Carneiro, Sarah Almeida","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5135927600","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-7219-3409"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Zhang, Yang","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043002859","display_name":"Lawrence P. Petalidis","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Petalidis, Lawrence P.","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043755134","display_name":"Achilleas Tsortos","orcid":"https://orcid.org/0000-0003-4598-4624"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Tsortos, Achilleas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5023347965","display_name":"Costas Bouyioukos","orcid":"https://orcid.org/0000-0002-7443-3736"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Bouyioukos, Costas","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5135951416","display_name":"Michalis Vazirgiannis","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Vazirgiannis, Michalis","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.42969998717308044,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.42969998717308044,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2313999980688095,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.18649999797344208,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/closed-captioning","display_name":"Closed captioning","score":0.8896999955177307},{"id":"https://openalex.org/keywords/decoding-methods","display_name":"Decoding methods","score":0.6498000025749207},{"id":"https://openalex.org/keywords/vocabulary","display_name":"Vocabulary","score":0.6035000085830688},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.47119998931884766},{"id":"https://openalex.org/keywords/binary-number","display_name":"Binary number","score":0.43700000643730164},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.43540000915527344}],"concepts":[{"id":"https://openalex.org/C157657479","wikidata":"https://www.wikidata.org/wiki/Q2367247","display_name":"Closed captioning","level":3,"score":0.8896999955177307},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7454000115394592},{"id":"https://openalex.org/C57273362","wikidata":"https://www.wikidata.org/wiki/Q576722","display_name":"Decoding methods","level":2,"score":0.6498000025749207},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.6140000224113464},{"id":"https://openalex.org/C2777601683","wikidata":"https://www.wikidata.org/wiki/Q6499736","display_name":"Vocabulary","level":2,"score":0.6035000085830688},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5540000200271606},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.47119998931884766},{"id":"https://openalex.org/C48372109","wikidata":"https://www.wikidata.org/wiki/Q3913","display_name":"Binary number","level":2,"score":0.43700000643730164},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.43540000915527344},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.3400999903678894},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.30550000071525574},{"id":"https://openalex.org/C155092808","wikidata":"https://www.wikidata.org/wiki/Q182557","display_name":"Computational linguistics","level":2,"score":0.29409998655319214},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.26840001344680786},{"id":"https://openalex.org/C2777200299","wikidata":"https://www.wikidata.org/wiki/Q52943","display_name":"Conversation","level":2,"score":0.26249998807907104},{"id":"https://openalex.org/C195324797","wikidata":"https://www.wikidata.org/wiki/Q33742","display_name":"Natural language","level":2,"score":0.2549000084400177}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:HAL:hal-05670461v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05670461","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2026","raw_type":"info:eu-repo/semantics/preprint"},{"id":"doi:10.48550/arxiv.2605.08924","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.08924","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"pmh:oai:HAL:hal-05670461v1","is_oa":true,"landing_page_url":"https://hal.science/hal-05670461","pdf_url":null,"source":{"id":"https://openalex.org/S4306402512","display_name":"HAL (Le Centre pour la Communication Scientifique Directe)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1294671590","host_organization_name":"Centre National de la Recherche Scientifique","host_organization_lineage":["https://openalex.org/I1294671590"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"2026","raw_type":"info:eu-repo/semantics/preprint"},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.7282722592353821,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Protein-protein":[0],"interaction":[1],"(PPI)":[2],"modeling":[3],"has":[4],"been":[5],"widely":[6],"studied":[7],"as":[8],"a":[9,67,86,105,113,138],"binary":[10],"or":[11],"multi-label":[12],"classification":[13],"task.":[14],"While":[15],"emerging":[16],"multimodal":[17,68],"large":[18],"language":[19,107],"models":[20],"(LLMs)":[21],"can":[22],"now":[23],"describe":[24],"single":[25],"proteins,":[26],"they":[27],"remain":[28],"unable":[29],"to":[30,46,93],"generate":[31],"free-form":[32,71,142],"descriptions":[33,103,144],"of":[34,121,129,141],"interactions":[35,95],"between":[36],"protein":[37,81],"pairs.":[38],"Moving":[39],"beyond":[40],"controlled":[41],"vocabulary":[42],"annotations,":[43],"we":[44,135],"propose":[45],"model":[47],"PPI":[48,72,143],"using":[49,82,104],"free-text":[50],"description,":[51],"enabling":[52],"richer":[53],"expressiveness,":[54],"improved":[55],"interpretability,":[56],"and":[57,100,151,168],"better":[58],"integration":[59],"with":[60,125,154],"literature":[61],"knowledge":[62],"base.":[63],"We":[64,109],"present":[65],"PPI2Text,":[66],"LLM":[69],"for":[70],"captioning":[73],"from":[74,89,146],"amino":[75],"acid":[76],"sequences,":[77],"that":[78,117],"encodes":[79],"each":[80,119],"ESM3":[83],"encoder,":[84],"constructs":[85],"pair":[87,123],"map":[88],"the":[90,122,126,130],"two":[91],"representations":[92],"capture":[94],"across":[96,164],"all":[97],"residue":[98,127],"pairs,":[99],"autoregressively":[101],"generates":[102],"Qwen3":[106],"decoder.":[108],"further":[110,152],"introduce":[111],"PaCo-RoPE,":[112],"coordinate-aligned":[114],"positional":[115],"encoding":[116],"aligns":[118],"axis":[120],"grid":[124],"positions":[128],"corresponding":[131],"protein.":[132],"In":[133],"addition,":[134],"release":[136],"PPI2Text-Dataset,":[137],"351k-pair":[139],"corpus":[140],"aggregated":[145],"ten":[147],"curated":[148],"biological":[149,197],"databases":[150],"synthesized":[153,181],"Gemini":[155],"under":[156],"evidence-tiered":[157],"prompting.":[158],"PPI2Text":[159],"consistently":[160],"outperforms":[161],"strong":[162],"baselines":[163],"multiple":[165],"ablation":[166],"settings":[167],"evaluation":[169],"protocols.":[170],"It":[171],"not":[172],"only":[173],"achieves":[174],"higher":[175],"scores":[176],"on":[177,186],"linguistic":[178],"metrics":[179],"against":[180,195],"references,":[182],"but":[183],"also":[184],"excels":[185],"factuality":[187],"metrics,":[188],"where":[189],"an":[190],"LLM-based":[191],"judge":[192],"evaluates":[193],"outputs":[194],"raw":[196],"evidence.":[198]},"counts_by_year":[],"updated_date":"2026-07-28T07:46:37.118299","created_date":"2026-05-13T00:00:00"}