{"id":"https://openalex.org/W2808680821","doi":"https://doi.org/10.32657/10356/75771","title":"Challenges and solutions in drug-target interaction prediction","display_name":"Challenges and solutions in drug-target interaction prediction","publication_year":2018,"publication_date":"2018-01-01","ids":{"openalex":"https://openalex.org/W2808680821","doi":"https://doi.org/10.32657/10356/75771","mag":"2808680821"},"language":"en","primary_location":{"id":"doi:10.32657/10356/75771","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/75771","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/75771/1/THESIS_Aly_Ezzat_Hard_Bound_Thesis_version.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},"type":"dissertation","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://dr.ntu.edu.sg/bitstream/10356/75771/1/THESIS_Aly_Ezzat_Hard_Bound_Thesis_version.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5003922274","display_name":"Ali Ezzat","orcid":"https://orcid.org/0000-0002-7426-3888"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Ezzat, Ali","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5003922274"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":2,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.993399977684021,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9882000088691711,"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/drug","display_name":"Drug","score":0.5606562495231628},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4023861587047577},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3947005271911621},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.2614837884902954},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.2244609296321869}],"concepts":[{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.5606562495231628},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4023861587047577},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3947005271911621},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.2614837884902954},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.2244609296321869}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.32657/10356/75771","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/75771","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/75771/1/THESIS_Aly_Ezzat_Hard_Bound_Thesis_version.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},{"id":"pmh:oai:dr.ntu.edu.sg:10356/75771","is_oa":false,"landing_page_url":"http://hdl.handle.net/10356/75771","pdf_url":null,"source":{"id":"https://openalex.org/S4306402609","display_name":"DR-NTU (Nanyang Technological University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I172675005","host_organization_name":"Nanyang Technological University","host_organization_lineage":["https://openalex.org/I172675005"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Thesis"}],"best_oa_location":{"id":"doi:10.32657/10356/75771","is_oa":true,"landing_page_url":"https://doi.org/10.32657/10356/75771","pdf_url":"https://dr.ntu.edu.sg/bitstream/10356/75771/1/THESIS_Aly_Ezzat_Hard_Bound_Thesis_version.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nanyang Technological University","raw_type":"dissertation"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320334744","display_name":"Institute for Infocomm Research","ror":"https://ror.org/053rfa017"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2808680821.pdf","grobid_xml":"https://content.openalex.org/works/W2808680821.grobid-xml"},"referenced_works_count":202,"referenced_works":["https://openalex.org/W122274013","https://openalex.org/W134582654","https://openalex.org/W146100937","https://openalex.org/W188755909","https://openalex.org/W331119053","https://openalex.org/W436863597","https://openalex.org/W571200655","https://openalex.org/W576428146","https://openalex.org/W579521957","https://openalex.org/W605727707","https://openalex.org/W1034357721","https://openalex.org/W1466286227","https://openalex.org/W1494068210","https://openalex.org/W1499921085","https://openalex.org/W1568521728","https://openalex.org/W1580948147","https://openalex.org/W1605923270","https://openalex.org/W1775897493","https://openalex.org/W1832221731","https://openalex.org/W1941659294","https://openalex.org/W1952825535","https://openalex.org/W1965895350","https://openalex.org/W1966631994","https://openalex.org/W1968217711","https://openalex.org/W1971106435","https://openalex.org/W1975147762","https://openalex.org/W1976251851","https://openalex.org/W1976526581","https://openalex.org/W1978370150","https://openalex.org/W1979104937","https://openalex.org/W1979537657","https://openalex.org/W1981088884","https://openalex.org/W1984014392","https://openalex.org/W1984020445","https://openalex.org/W1984084871","https://openalex.org/W1984673823","https://openalex.org/W1986684432","https://openalex.org/W1987027200","https://openalex.org/W1991646180","https://openalex.org/W1991681722","https://openalex.org/W1991919669","https://openalex.org/W1993220166","https://openalex.org/W1996850420","https://openalex.org/W1997453506","https://openalex.org/W1998767819","https://openalex.org/W1998898494","https://openalex.org/W2001141328","https://openalex.org/W2003516452","https://openalex.org/W2007965730","https://openalex.org/W2008731781","https://openalex.org/W2008840001","https://openalex.org/W2009113274","https://openalex.org/W2011242261","https://openalex.org/W2012438480","https://openalex.org/W2012746420","https://openalex.org/W2015393683","https://openalex.org/W2018340784","https://openalex.org/W2018408116","https://openalex.org/W2018661561","https://openalex.org/W2019707847","https://openalex.org/W2025577942","https://openalex.org/W2029348196","https://openalex.org/W2029980980","https://openalex.org/W2033591223","https://openalex.org/W2037022423","https://openalex.org/W2038122249","https://openalex.org/W2040022355","https://openalex.org/W2043398720","https://openalex.org/W2044002635","https://openalex.org/W2053186076","https://openalex.org/W2055147198","https://openalex.org/W2060851522","https://openalex.org/W2062941476","https://openalex.org/W2065812641","https://openalex.org/W2066201825","https://openalex.org/W2068351024","https://openalex.org/W2069293737","https://openalex.org/W2073459066","https://openalex.org/W2075426299","https://openalex.org/W2075692164","https://openalex.org/W2079745490","https://openalex.org/W2081193615","https://openalex.org/W2081526643","https://openalex.org/W2083042679","https://openalex.org/W2085789144","https://openalex.org/W2086286404","https://openalex.org/W2087064593","https://openalex.org/W2088632292","https://openalex.org/W2093117046","https://openalex.org/W2095867585","https://openalex.org/W2096541451","https://openalex.org/W2098318720","https://openalex.org/W2098464924","https://openalex.org/W2100128988","https://openalex.org/W2100672820","https://openalex.org/W2102750386","https://openalex.org/W2103017472","https://openalex.org/W2104290444","https://openalex.org/W2104950117","https://openalex.org/W2106029302","https://openalex.org/W2108119513","https://openalex.org/W2109743529","https://openalex.org/W2109991441","https://openalex.org/W2111078532","https://openalex.org/W2113951828","https://openalex.org/W2115584760","https://openalex.org/W2118978333","https://openalex.org/W2122863289","https://openalex.org/W2124185479","https://openalex.org/W2125125731","https://openalex.org/W2125200271","https://openalex.org/W2125414037","https://openalex.org/W2126671570","https://openalex.org/W2131573225","https://openalex.org/W2132582966","https://openalex.org/W2133864802","https://openalex.org/W2135007932","https://openalex.org/W2135125546","https://openalex.org/W2135209350","https://openalex.org/W2136865157","https://openalex.org/W2136903812","https://openalex.org/W2137052779","https://openalex.org/W2138512826","https://openalex.org/W2139736926","https://openalex.org/W2139932193","https://openalex.org/W2142572836","https://openalex.org/W2144769066","https://openalex.org/W2147526198","https://openalex.org/W2148143831","https://openalex.org/W2148145769","https://openalex.org/W2152800101","https://openalex.org/W2153838454","https://openalex.org/W2154053567","https://openalex.org/W2156718197","https://openalex.org/W2157748890","https://openalex.org/W2158698691","https://openalex.org/W2160400421","https://openalex.org/W2161607603","https://openalex.org/W2162011385","https://openalex.org/W2163891305","https://openalex.org/W2165253681","https://openalex.org/W2166550586","https://openalex.org/W2169678694","https://openalex.org/W2174011260","https://openalex.org/W2177317049","https://openalex.org/W2183717576","https://openalex.org/W2184188583","https://openalex.org/W2185227617","https://openalex.org/W2213443318","https://openalex.org/W2215019161","https://openalex.org/W2224056471","https://openalex.org/W2256119113","https://openalex.org/W2256553158","https://openalex.org/W2259538443","https://openalex.org/W2302413701","https://openalex.org/W2338318698","https://openalex.org/W2343107734","https://openalex.org/W2399335119","https://openalex.org/W2399976582","https://openalex.org/W2415153693","https://openalex.org/W2417990257","https://openalex.org/W2419892062","https://openalex.org/W2464747247","https://openalex.org/W2471196942","https://openalex.org/W2477490855","https://openalex.org/W2519019522","https://openalex.org/W2546726420","https://openalex.org/W2553681302","https://openalex.org/W2556131117","https://openalex.org/W2558698012","https://openalex.org/W2560674852","https://openalex.org/W2563206593","https://openalex.org/W2567080747","https://openalex.org/W2576544908","https://openalex.org/W2590019597","https://openalex.org/W2592742128","https://openalex.org/W2594461856","https://openalex.org/W2607497028","https://openalex.org/W2610332124","https://openalex.org/W2612467560","https://openalex.org/W2623060321","https://openalex.org/W2753588101","https://openalex.org/W2767724106","https://openalex.org/W2911964244","https://openalex.org/W2916534270","https://openalex.org/W2949231534","https://openalex.org/W2997701990","https://openalex.org/W3014813097","https://openalex.org/W3095583226","https://openalex.org/W4200351727","https://openalex.org/W4205902690","https://openalex.org/W4206251917","https://openalex.org/W4206377492","https://openalex.org/W4233253307","https://openalex.org/W4235413268","https://openalex.org/W4238433034","https://openalex.org/W4249920046","https://openalex.org/W4255003555","https://openalex.org/W4317527417","https://openalex.org/W6606363522","https://openalex.org/W6629689148","https://openalex.org/W6852048268"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W4396696052","https://openalex.org/W2382290278","https://openalex.org/W4395014643"],"abstract_inverted_index":{"When":[0],"a":[1,13,56,75,99,241,443,546,572],"drug":[2,37,57,86,164,573],"is":[3,6,28,52,123,285,289,545,603],"developed,":[4],"it":[5,10,27,64],"designed":[7],"so":[8],"that":[9,34,44,134,215,222,288,394,410,536,552,598,613],"interacts":[11,39],"with":[12,40,60,258,488,595],"specific":[14],"target":[15,165],"of":[16,120,142,224,363,366,401,442,448,490,526,560],"interest":[17],"in":[18,163,228,247,330,346,383,467,476,523,577,591,621],"order":[19],"to":[20,31,176,244,277,312,327,342,357,380,397,453,474,486,499,569,584,606],"achieve":[21],"the":[22,35,118,178,225,229,248,271,313,328,334,338,347,351,358,361,370,373,384,399,411,426,431,438,449,459,468,501,509,557,578,585,596,599,608],"desired":[23],"therapeutic":[24,70],"effect.":[25,71],"However,":[26],"quite":[29],"common":[30],"later":[32],"find":[33],"developed":[36,210,240,389],"also":[38,472],"multiple":[41,61],"other":[42],"targets":[43,107,149,198,434],"were":[45,174],"not":[46],"intended":[47],"during":[48],"its":[49],"development.":[50],"This":[51],"interesting":[53],"because":[54],"if":[55],"can":[58,297],"interact":[59],"targets,":[62],"then":[63],"may":[65,451,464,471],"have":[66,190],"more":[67,343,376,381],"than":[68,270],"one":[69],"Therefore,":[72],"this":[73,121,154,322,368,480,589],"provides":[74],"clear":[76],"motivation":[77],"for":[78,82,114,199,429,458,508],"discovering":[79,115],"new":[80,136,195],"interactions":[81,97,137,193,279],"existing":[83,143],"drugs.":[84],"In":[85,219,263,479],"discovery,":[87],"an":[88,286,390,554],"important":[89],"task":[90],"called":[91,548],"drug-target":[92,127,320,439],"interaction":[93,128,166,260],"prediction":[94,179,188,324,331,344,460,477,502,558,562,609,623],"detects":[95],"such":[96],"on":[98,125,139,556],"large":[100],"scale":[101],"by":[102,255,436],"screening":[103],"many":[104,223],"drugs":[105,144,196,432],"and":[106,145,158,181,251,274,305,318,375,405,433,493,518,530],"simultaneously.":[108],"While":[109],"there":[110,201,421,463,544],"are":[111,202,233,422,441,540],"wet-lab":[112],"techniques":[113,396],"these":[116,171,491],"interactions,":[117,208],"focus":[119],"thesis":[122],"particularly":[124],"computational":[126],"prediction.":[129,168],"Specifically,":[130,564],"we":[131,156,173,209,239,388,482,494,511,593],"investigate":[132],"methods":[133,189,214,267,273,539],"discover":[135],"based":[138],"prior":[140,605],"knowledge":[141],"their":[146],"experimentally":[147],"confirmed":[148],"(i.e.":[150,337,350],"machine":[151],"learning).":[152],"Throughout":[153],"thesis,":[155],"identified":[157],"addressed":[159,170],"4":[160,417],"outstanding":[161],"problems":[162],"(DTI)":[167],"Having":[169],"problems,":[172],"able":[175],"enhance":[177,245],"performance":[180,325,503,559],"outperform":[182],"relevant":[183],"state-of-the-art":[184,272,418],"methods.":[185,419,563],"Firstly,":[186],"DTI":[187,231,293,423,561,622],"difficulty":[191],"predicting":[192],"involving":[194],"or":[197,236],"which":[200,470],"no":[203],"known":[204],"interactions.":[205],"To":[206],"predict":[207,278],"two":[211,301,513,524],"matrix":[212],"factorization":[213],"utilize":[216],"graph":[217],"regularization.":[218],"addition,":[220],"considering":[221],"non-occurring":[226],"edges":[227,257],"bipartite":[230],"network":[232],"actually":[234],"unknown":[235],"missing":[237],"cases,":[238],"preprocessing":[242],"step":[243],"predictions":[246,371],"\u201cnew":[249,252],"drug\u201d":[250],"target\u201d":[253],"cases":[254],"adding":[256],"intermediate":[259],"likelihood":[261],"scores.":[262],"our":[264,266,537,614],"experiments,":[265],"performed":[268],"better":[269],"was":[275],"found":[276,612],"reasonably":[280],"well.":[281],"Secondly,":[282],"class":[283,336,349,403],"imbalance":[284,296,310,314,355,359,404],"issue":[287],"prevalent":[290],"across":[291],"all":[292],"datasets.":[294],"Class":[295],"be":[298,465],"divided":[299],"into":[300],"sub-problems,":[302],"namely":[303,515],"between-class":[304],"within-class":[306,406],"7":[307],"imbalance.":[308,407],"Between-class":[309],"refers":[311,356,568],"ratio":[315],"between":[316,360,402],"interacting":[317,352],"non-interacting":[319,339],"pairs;":[321],"degrades":[323],"due":[326],"bias":[329,551,567],"results":[332,415,534],"towards":[333,372],"majority":[335],"pairs),":[340],"leading":[341,379],"errors":[345,382],"minority":[348],"pairs).":[353],"Withinclass":[354],"sizes":[362],"sub-groups":[364],"(types)":[365],"interactions;":[367],"biases":[369],"bigger":[374],"well-represented":[377],"sub-groups,":[378],"smaller":[385],"groups.":[386],"Here,":[387],"ensemble":[391,497,527],"learning":[392,498],"method":[393,413],"incorporates":[395],"address":[398],"issues":[400],"Experiments":[408],"show":[409,535],"proposed":[412,538],"improves":[414],"over":[416],"Thirdly,":[420],"datasets":[424],"where":[425],"feature":[427],"sets":[428],"representing":[430],"(and,":[435],"extension,":[437],"pairs)":[440],"high":[444],"dimensionality.":[445],"High":[446],"dimensionality":[447,484],"data":[450,581,602],"lead":[452,473],"much":[454,571],"longer":[455],"running":[456],"times":[457],"models.":[461],"Furthermore,":[462],"redundancy":[466],"features":[469],"degradation":[475],"performance.":[478,624],"work,":[481],"used":[483,496],"reduction":[485],"deal":[487],"both":[489],"issues,":[492],"additionally":[495],"improve":[500],"further.":[504],"As":[505],"base":[506],"learners":[507],"ensemble,":[510],"selected":[512],"classifiers,":[514],"Decision":[516],"Tree":[517],"Kernel":[519],"Ridge":[520],"Regression,":[521],"resulting":[522],"variants":[525],"models,":[528],"EnsemDT":[529],"EnsemKRR,":[531],"respectively.":[532],"Experimental":[533],"indeed":[541],"successful.":[542],"Lastly,":[543],"concept":[547,590],"differential":[549,565],"representation":[550,566],"has":[553],"impact":[555],"how":[570],"(or":[574],"target)":[575],"appears":[576],"positive":[579],"training":[580,601,607],"as":[582],"opposed":[583],"negative":[586,600],"data.":[587],"Bearing":[588],"mind,":[592],"experimented":[594],"way":[597],"sampled":[604],"model.":[610],"We":[611],"modified":[615],"sampling":[616],"procedure":[617],"produced":[618],"significant":[619],"improvements":[620]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-03-25T13:04:00.132906","created_date":"2025-10-10T00:00:00"}
