{"id":"https://openalex.org/W4292656745","doi":"https://doi.org/10.1021/acs.jctc.1c01241","title":"Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol","display_name":"Graph Theoretic Molecular Fragmentation for Multidimensional Potential Energy Surfaces Yield an Adaptive and General Transfer Machine Learning Protocol","publication_year":2022,"publication_date":"2022-08-22","ids":{"openalex":"https://openalex.org/W4292656745","doi":"https://doi.org/10.1021/acs.jctc.1c01241","pmid":"https://pubmed.ncbi.nlm.nih.gov/35994592"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jctc.1c01241","doi":"https://doi.org/10.1021/acs.jctc.1c01241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jctc.1c01241","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},"volume":null,"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/A5101866538","display_name":"Xiao Zhu","orcid":"https://orcid.org/0000-0001-6257-6740","observed_orcids":["https://orcid.org/0000-0001-6257-6740","https://orcid.org/0009-0007-8646-8040"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiao Zhu","raw_affiliation_strings":["Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5019081599","display_name":"Srinivasan S. Iyengar","orcid":"https://orcid.org/0000-0001-6526-2907","observed_orcids":["https://orcid.org/0000-0001-6526-2907"]},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]},{"id":"https://openalex.org/I592451","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98","country_code":"US","type":"education","lineage":["https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Srinivasan S. Iyengar","raw_affiliation_strings":["Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States"],"raw_orcid":"https://orcid.org/0000-0001-6526-2907","affiliations":[{"raw_affiliation_string":"Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington 47405, Indiana, United States","institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5019081599"],"corresponding_institution_ids":["https://openalex.org/I4210119109","https://openalex.org/I592451"],"apc_list":{"value":5000,"currency":"USD","value_usd":5000},"apc_paid":null,"fwci":1.0187,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.73170129,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"18","issue":"9","first_page":"5125","last_page":"5144"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.9872999787330627,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.007600000128149986,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12044","display_name":"Advanced Physical and Chemical Molecular Interactions","score":0.0005000000237487257,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/multidimensional-potential-energy-surfaces","display_name":"multidimensional potential energy surfaces","score":0.9290000200271606},{"id":"https://openalex.org/keywords/transfer-learning","display_name":"transfer learning","score":0.5720000267028809},{"id":"https://openalex.org/keywords/neural-network","display_name":"artificial neural networks","score":0.4869999885559082},{"id":"https://openalex.org/keywords/many-body-expansion","display_name":"many-body expansion","score":0.6729999780654907},{"id":"https://openalex.org/keywords/oniom","display_name":"ONIOM","score":0.9179999828338623},{"id":"https://openalex.org/keywords/ab-initio-molecular-dynamics","display_name":"ab initio molecular dynamics","score":0.9369999766349792},{"id":"https://openalex.org/keywords/coupled-cluster-theory","display_name":"coupled-cluster theory","score":0.5759999752044678},{"id":"https://openalex.org/keywords/training-set-reduction","display_name":"training data reduction","score":0.6980000138282776},{"id":"https://openalex.org/keywords/complete-basis-set-extrapolation","display_name":"basis set extrapolation","score":0.6790000200271606},{"id":"https://openalex.org/keywords/quantum-algorithms","display_name":"quantum algorithms","score":0.5239999890327454}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6199926733970642},{"id":"https://openalex.org/C86025842","wikidata":"https://www.wikidata.org/wiki/Q5358432","display_name":"Electronic structure","level":2,"score":0.5404137372970581},{"id":"https://openalex.org/C62438384","wikidata":"https://www.wikidata.org/wiki/Q331350","display_name":"Simplex","level":2,"score":0.46932217478752136},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.43298470973968506},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.33971595764160156},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.32108360528945923},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2114260494709015},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.19733116030693054},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.15544554591178894},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D011789","descriptor_name":"Quantum Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jctc.1c01241","doi":"https://doi.org/10.1021/acs.jctc.1c01241","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jctc.1c01241","pdf_url":null,"source":{"id":"https://openalex.org/S189701308","display_name":"Journal of Chemical Theory and Computation","issn_l":"1549-9618","issn":["1549-9618","1549-9626"],"is_oa":false,"is_in_doaj":false,"is_core":true,"listed_in":["anvur-scientific","cwts-core","dongbi-b","jufo-2","ki-jl-2","medline","norway-2","poland-140","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Theory and Computation","raw_type":"journal-article"},{"id":"pmid:35994592","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35994592","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,"listed_in":[],"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":"Journal of chemical theory and computation","raw_type":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"sustainable_development_goals_aurora":[{"display_name":"Affordable and clean energy","score":0.9100000262260437,"id":"https://metadata.un.org/sdg/7"}],"study_designs":[],"awards":[{"id":"https://openalex.org/G3646271941","display_name":null,"funder_award_id":"CHE-2102610","funder_id":"https://openalex.org/F4320337393","funder_display_name":"Division of Chemistry"}],"funders":[{"id":"https://openalex.org/F4320337393","display_name":"Division of Chemistry","ror":"https://ror.org/01ar8dr59"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":138,"referenced_works":["https://openalex.org/W79383899","https://openalex.org/W227345765","https://openalex.org/W637208921","https://openalex.org/W1526763052","https://openalex.org/W1639564182","https://openalex.org/W1963979741","https://openalex.org/W1964474191","https://openalex.org/W1964882117","https://openalex.org/W1965163499","https://openalex.org/W1965378620","https://openalex.org/W1966241835","https://openalex.org/W1966939946","https://openalex.org/W1967005434","https://openalex.org/W1967488178","https://openalex.org/W1968344479","https://openalex.org/W1969087374","https://openalex.org/W1970585567","https://openalex.org/W1971044734","https://openalex.org/W1973565199","https://openalex.org/W1976323578","https://openalex.org/W1977556410","https://openalex.org/W1982595063","https://openalex.org/W1983309313","https://openalex.org/W1983598802","https://openalex.org/W1984862742","https://openalex.org/W1985592171","https://openalex.org/W1986113676","https://openalex.org/W1990208157","https://openalex.org/W1992942299","https://openalex.org/W1993012728","https://openalex.org/W1996649201","https://openalex.org/W1998860313","https://openalex.org/W2000411584","https://openalex.org/W2005205193","https://openalex.org/W2006176281","https://openalex.org/W2006428261","https://openalex.org/W2011745346","https://openalex.org/W2013416944","https://openalex.org/W2015078081","https://openalex.org/W2015856305","https://openalex.org/W2017592946","https://openalex.org/W2018699453","https://openalex.org/W2021031315","https://openalex.org/W2021850817","https://openalex.org/W2025444507","https://openalex.org/W2028054907","https://openalex.org/W2029042254","https://openalex.org/W2029173015","https://openalex.org/W2030756754","https://openalex.org/W2037269372","https://openalex.org/W2040685854","https://openalex.org/W2045120197","https://openalex.org/W2045659549","https://openalex.org/W2046634948","https://openalex.org/W2048195126","https://openalex.org/W2049325009","https://openalex.org/W2053018494","https://openalex.org/W2054955462","https://openalex.org/W2056286580","https://openalex.org/W2061179540","https://openalex.org/W2064882890","https://openalex.org/W2067718414","https://openalex.org/W2068758087","https://openalex.org/W2069924395","https://openalex.org/W2071973204","https://openalex.org/W2074359677","https://openalex.org/W2081315284","https://openalex.org/W2082074139","https://openalex.org/W2087102263","https://openalex.org/W2088885430","https://openalex.org/W2091253420","https://openalex.org/W2091454160","https://openalex.org/W2092289531","https://openalex.org/W2093625674","https://openalex.org/W2094371959","https://openalex.org/W2094658317","https://openalex.org/W2095148640","https://openalex.org/W2095566877","https://openalex.org/W2101001152","https://openalex.org/W2103746646","https://openalex.org/W2108671543","https://openalex.org/W2111182549","https://openalex.org/W2120145199","https://openalex.org/W2123952737","https://openalex.org/W2128672663","https://openalex.org/W2128988133","https://openalex.org/W2135373957","https://openalex.org/W2137629913","https://openalex.org/W2138395765","https://openalex.org/W2142838865","https://openalex.org/W2151319417","https://openalex.org/W2151747795","https://openalex.org/W2163453784","https://openalex.org/W2263223972","https://openalex.org/W2312497564","https://openalex.org/W2312710804","https://openalex.org/W2320465731","https://openalex.org/W2323493080","https://openalex.org/W2328081630","https://openalex.org/W2335367147","https://openalex.org/W2372530928","https://openalex.org/W2401610261","https://openalex.org/W2516937080","https://openalex.org/W2525140544","https://openalex.org/W2544518120","https://openalex.org/W2597429058","https://openalex.org/W2601420497","https://openalex.org/W2604216657","https://openalex.org/W2613386458","https://openalex.org/W2729320780","https://openalex.org/W2750647313","https://openalex.org/W2771008932","https://openalex.org/W2786721297","https://openalex.org/W2792643794","https://openalex.org/W2804194238","https://openalex.org/W2897570141","https://openalex.org/W2899519211","https://openalex.org/W2908805179","https://openalex.org/W2975672020","https://openalex.org/W2983651699","https://openalex.org/W2990174420","https://openalex.org/W2990871173","https://openalex.org/W3032315361","https://openalex.org/W3035472714","https://openalex.org/W3037871626","https://openalex.org/W3093149769","https://openalex.org/W3100571530","https://openalex.org/W3110392041","https://openalex.org/W3112852956","https://openalex.org/W3120660515","https://openalex.org/W3141927472","https://openalex.org/W3153831884","https://openalex.org/W3204269937","https://openalex.org/W4200050539","https://openalex.org/W4205940630","https://openalex.org/W4223537762","https://openalex.org/W4249103958","https://openalex.org/W4255512111"],"related_works":["https://openalex.org/W3204269937","https://openalex.org/W4390618157","https://openalex.org/W7171396237","https://openalex.org/W2406709014","https://openalex.org/W4412631765","https://openalex.org/W4404352440","https://openalex.org/W2975672020","https://openalex.org/W3189613542","https://openalex.org/W7202181444","https://openalex.org/W2526734845"],"abstract_inverted_index":{"Over":[0],"a":[1,8,15,20,38,172,185,209,336,354],"series":[2],"of":[3,22,40,55,85,175,187,226,233,288],"publications":[4],"we":[5,111,182],"have":[6,88,112],"introduced":[7],"graph-theoretic":[9,328],"description":[10],"for":[11,92,100,137,140,147,203,218,271,290,298,316,340],"molecular":[12,95,220,318],"fragmentation.":[13],"Here,":[14],"system":[16,338],"is":[17,50,62,238,245,274],"divided":[18],"into":[19],"set":[21,149],"nodes,":[23],"or":[24],"vertices,":[25],"that":[26,68,114,164,190],"are":[27,69,307,322],"then":[28,70,308,323],"connected":[29,303],"through":[30],"edges,":[31],"faces,":[32],"and":[33,43,59,87,99,116,121,145,207,222,247,280,320],"higher-order":[34],"simplexes":[35,205],"to":[36,64,159,194,214,229,254,266,276,285,293,310,330,335,353],"represent":[37],"collection":[39],"spatially":[41],"overlapping":[42],"locally":[44],"interacting":[45],"subsystems.":[46],"Each":[47],"such":[48],"subsystem":[49],"treated":[51],"at":[52,127,345],"two":[53],"levels":[54],"electronic":[56,143,177,199],"structure":[57,200],"theory,":[58],"the":[60,167,197,224,282,312,332,341,349],"result":[61],"used":[63,91,158,265,309],"construct":[65,230],"many-body":[66,80],"expansions":[67,76],"embedded":[71],"within":[72],"an":[73],"ONIOM-scheme.":[74],"These":[75,301],"converge":[77],"rapidly":[78],"with":[79],"order":[81,253],"(or":[82],"graphical":[83],"rank)":[84],"subsystems":[86],"been":[89,135,157],"previously":[90],"ab":[93],"initio":[94],"dynamics":[96],"(AIMD)":[97],"calculations":[98],"computing":[101],"multidimensional":[102,261],"potential":[103,122,313],"energy":[104,201,314,339],"surfaces.":[105],"Specifically,":[106],"in":[107,171,192,252],"all":[108,204,272,291,317],"these":[109,321],"cases":[110],"shown":[113,275],"CCSD":[115],"MP2":[117],"level":[118],"AIMD":[119,343,357],"trajectories":[120],"surfaces":[123],"may":[124],"be":[125,277],"obtained":[126],"density":[128],"functional":[129],"theory":[130],"cost.":[131],"The":[132,236,259],"approach":[133,154,237],"has":[134,155],"demonstrated":[136],"gas-phase":[138],"studies,":[139],"condensed":[141],"phase":[142],"structure,":[144],"also":[146,156],"basis":[148],"extrapolation-based":[150],"AIMD.":[151],"Recently,":[152],"this":[153,180,231],"derive":[160],"new":[161,210],"quantum-computing":[162],"algorithms":[163],"enormously":[165],"reduce":[166],"quantum":[168],"circuit":[169],"depth":[170],"circuit-based":[173],"computation":[174],"correlated":[176],"structure.":[178],"In":[179],"publication,":[181],"introduce":[183],"(a)":[184],"family":[186,232],"neural":[188,234,296,305],"networks":[189,297,306],"act":[191],"parallel":[193],"represent,":[195],"efficiently,":[196],"post-Hartree\u2013Fock":[198],"contributions":[202],"(fragments),":[206],"(b)":[208],"k-means-based":[211],"tessellation":[212],"strategy":[213],"glean":[215],"training":[216,227,269,284],"data":[217,270,289],"high-dimensional":[219],"spaces":[221],"minimize":[223],"extent":[225],"needed":[228,283],"networks.":[235],"particularly":[239],"useful":[240],"when":[241,248],"coupled":[242],"cluster":[243],"accuracy":[244],"desired":[246],"fragment":[249],"sizes":[250],"grow":[251],"capture":[255],"nonlocal":[256],"interactions":[257],"accurately.":[258],"unique":[260],"k-means":[262],"tessellation/clustering":[263],"algorithm":[264],"determine":[267],"our":[268,327],"fragments":[273,292],"extremely":[278],"efficient":[279],"reduces":[281],"only":[286],"10%":[287],"obtain":[294],"accurate":[295],"each":[299],"fragment.":[300],"fully":[302],"dense":[304],"extrapolate":[311],"surface":[315],"fragments,":[319],"combined":[324],"as":[325,351],"per":[326],"procedure":[329],"transfer":[331],"learning":[333],"process":[334],"full":[337],"entire":[342],"trajectory":[344],"less":[346],"than":[347],"one-tenth":[348],"cost":[350],"compared":[352],"regular":[355],"fragmentation-based":[356],"calculation.":[358]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2022-08-22T00:00:00"}