{"id":"https://openalex.org/W4387129749","doi":"https://doi.org/10.1371/journal.pcbi.1011511","title":"Evaluating a large language model\u2019s ability to solve programming exercises from an introductory bioinformatics course","display_name":"Evaluating a large language model\u2019s ability to solve programming exercises from an introductory bioinformatics course","publication_year":2023,"publication_date":"2023-09-28","ids":{"openalex":"https://openalex.org/W4387129749","doi":"https://doi.org/10.1371/journal.pcbi.1011511","pmid":"https://pubmed.ncbi.nlm.nih.gov/37769024"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1011511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011511&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005005415","display_name":"Stephen Piccolo","orcid":"https://orcid.org/0000-0003-2001-5640"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Stephen R. Piccolo","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, Utah, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, Utah, United States of America","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032890999","display_name":"Paul Denny","orcid":"https://orcid.org/0000-0002-5150-9806"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Paul Denny","raw_affiliation_strings":["School of Computer Science, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061895558","display_name":"Andrew Luxton-Reilly","orcid":"https://orcid.org/0000-0001-8269-2909"},"institutions":[{"id":"https://openalex.org/I154130895","display_name":"University of Auckland","ror":"https://ror.org/03b94tp07","country_code":"NZ","type":"education","lineage":["https://openalex.org/I154130895"]}],"countries":["NZ"],"is_corresponding":true,"raw_author_name":"Andrew Luxton-Reilly","raw_affiliation_strings":["School of Computer Science, The University of Auckland, Auckland, New Zealand"],"affiliations":[{"raw_affiliation_string":"School of Computer Science, The University of Auckland, Auckland, New Zealand","institution_ids":["https://openalex.org/I154130895"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040201243","display_name":"Samuel Payne","orcid":"https://orcid.org/0000-0002-8351-1994"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Samuel H. Payne","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, Utah, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, Utah, United States of America","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046268336","display_name":"Perry G. Ridge","orcid":"https://orcid.org/0000-0001-6944-2753"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Perry G. Ridge","raw_affiliation_strings":["Department of Biology, Brigham Young University, Provo, Utah, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Brigham Young University, Provo, Utah, United States of America","institution_ids":["https://openalex.org/I100005738"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5005005415","https://openalex.org/A5032890999","https://openalex.org/A5040201243","https://openalex.org/A5046268336","https://openalex.org/A5061895558"],"corresponding_institution_ids":["https://openalex.org/I100005738","https://openalex.org/I154130895"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":6.9334,"has_fulltext":true,"cited_by_count":44,"citation_normalized_percentile":{"value":0.97578972,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"19","issue":"9","first_page":"e1011511","last_page":"e1011511"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9951000213623047,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9951000213623047,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9587000012397766,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T13280","display_name":"Biomedical and Engineering Education","score":0.9294000267982483,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/course","display_name":"Course (navigation)","score":0.686495840549469},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5977450013160706},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.45951569080352783},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3766995072364807},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3723164200782776},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33372732996940613},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19405993819236755},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.11818951368331909}],"concepts":[{"id":"https://openalex.org/C2777552389","wikidata":"https://www.wikidata.org/wiki/Q1962728","display_name":"Course (navigation)","level":2,"score":0.686495840549469},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5977450013160706},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.45951569080352783},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3766995072364807},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3723164200782776},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33372732996940613},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19405993819236755},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.11818951368331909},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000098342","descriptor_name":"Large Language Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003479","descriptor_name":"Curriculum","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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1011511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:37769024","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37769024","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10564134","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10564134","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10564134/pdf/pcbi.1011511.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:scholarsarchive.byu.edu:facpub-8276","is_oa":true,"landing_page_url":"https://scholarsarchive.byu.edu/facpub/7370","pdf_url":null,"source":{"id":"https://openalex.org/S4377196308","display_name":"ScholarsArchive  (Brigham Young University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I100005738","host_organization_name":"Brigham Young University","host_organization_lineage":["https://openalex.org/I100005738"],"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":"Faculty Publications","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:a7bf9156ce214243af430ced07868962","is_oa":true,"landing_page_url":"https://doaj.org/article/a7bf9156ce214243af430ced07868962","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 19, Iss 9, p e1011511 (2023)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1011511","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1011511","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1011511&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4387129749.pdf","grobid_xml":"https://content.openalex.org/works/W4387129749.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1507985183","https://openalex.org/W1551385575","https://openalex.org/W1975375203","https://openalex.org/W1977384182","https://openalex.org/W2012761058","https://openalex.org/W2037237472","https://openalex.org/W2070348899","https://openalex.org/W2083612007","https://openalex.org/W2098571599","https://openalex.org/W2101234009","https://openalex.org/W2104786161","https://openalex.org/W2104916970","https://openalex.org/W2114850508","https://openalex.org/W2118258530","https://openalex.org/W2135995390","https://openalex.org/W2146292423","https://openalex.org/W2155320075","https://openalex.org/W2156251895","https://openalex.org/W2329674354","https://openalex.org/W2342249984","https://openalex.org/W2399769480","https://openalex.org/W2514664437","https://openalex.org/W2516966498","https://openalex.org/W2582743722","https://openalex.org/W2582874221","https://openalex.org/W2742478344","https://openalex.org/W2783082347","https://openalex.org/W2788436468","https://openalex.org/W2884745705","https://openalex.org/W2910880405","https://openalex.org/W2916390547","https://openalex.org/W2917832356","https://openalex.org/W2921183341","https://openalex.org/W2936416839","https://openalex.org/W2949550946","https://openalex.org/W2952156265","https://openalex.org/W2973670417","https://openalex.org/W2990427812","https://openalex.org/W2998738573","https://openalex.org/W3000240292","https://openalex.org/W3008088841","https://openalex.org/W3091798252","https://openalex.org/W3098605233","https://openalex.org/W3105247453","https://openalex.org/W3127165784","https://openalex.org/W3136918052","https://openalex.org/W3177813494","https://openalex.org/W4235243453","https://openalex.org/W4246357894","https://openalex.org/W4287024925","https://openalex.org/W4299532422","https://openalex.org/W4311887664","https://openalex.org/W4317601962","https://openalex.org/W4318263917","https://openalex.org/W4319083882","https://openalex.org/W4319301446","https://openalex.org/W4319662928","https://openalex.org/W4319827374","https://openalex.org/W4321371665","https://openalex.org/W6675354045","https://openalex.org/W6726469920","https://openalex.org/W6798182279","https://openalex.org/W6800166007","https://openalex.org/W6850300572"],"related_works":["https://openalex.org/W4318717247","https://openalex.org/W2317874921","https://openalex.org/W2736755255","https://openalex.org/W4362648715","https://openalex.org/W3180276870","https://openalex.org/W2009385780","https://openalex.org/W3082623308","https://openalex.org/W3120503679","https://openalex.org/W2359390960","https://openalex.org/W2238501609"],"abstract_inverted_index":{"Computer":[0],"programming":[1,72,90,167],"is":[2],"a":[3,28],"fundamental":[4],"tool":[5],"for":[6,31,136,154],"life":[7,64],"scientists,":[8],"allowing":[9],"them":[10],"to":[11,23,47,51,67,82,111,116,144,152,161,173,180],"carry":[12],"out":[13],"essential":[14],"research":[15],"tasks.":[16,91],"However,":[17],"despite":[18],"various":[19],"educational":[20],"efforts,":[21],"learning":[22],"write":[24,68],"code":[25],"can":[26,60],"be":[27,171],"challenging":[29],"endeavor":[30],"students":[32],"and":[33,139,149],"researchers":[34,169],"in":[35,40,175],"life-sciences":[36,137],"disciplines.":[37],"Recent":[38],"advances":[39],"artificial":[41],"intelligence":[42],"have":[43,134],"made":[44],"it":[45,115],"possible":[46],"translate":[48],"human-language":[49],"prompts":[50],"functional":[52,182],"code,":[53],"raising":[54],"questions":[55],"about":[56],"whether":[57],"these":[58,155],"technologies":[59],"aid":[61],"(or":[62],"replace)":[63],"scientists'":[65],"efforts":[66],"code.":[69,183],"Using":[70],"184":[71],"exercises":[73,98],"from":[74],"an":[75],"introductory-bioinformatics":[76],"course,":[77],"we":[78,107],"evaluated":[79],"the":[80,97,104,112,130,162],"extent":[81],"which":[83],"one":[84],"such":[85],"tool-OpenAI's":[86],"ChatGPT-could":[87],"successfully":[88],"complete":[89],"ChatGPT":[92,125],"solved":[93,126],"139":[94],"(75.5%)":[95],"of":[96,129],"on":[99],"its":[100],"first":[101],"attempt.":[102],"For":[103,165],"remaining":[105],"exercises,":[106],"provided":[108],"natural-language":[109],"feedback":[110],"model,":[113],"prompting":[114],"try":[117],"different":[118],"approaches.":[119],"Within":[120],"7":[121],"or":[122],"fewer":[123],"attempts,":[124],"179":[127],"(97.3%)":[128],"exercises.":[131],"These":[132],"findings":[133],"implications":[135],"education":[138],"research.":[140],"Instructors":[141],"may":[142,170],"need":[143],"adapt":[145],"their":[146],"pedagogical":[147],"approaches":[148],"assessment":[150],"techniques":[151],"account":[153],"new":[156],"capabilities":[157],"that":[158],"are":[159],"available":[160],"general":[163],"public.":[164],"some":[166],"tasks,":[168],"able":[172],"work":[174],"collaboration":[176],"with":[177],"machine-learning":[178],"models":[179],"produce":[181]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":20},{"year":2023,"cited_by_count":4}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
