Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data
Jo T, Kim J, Bice P, Huynh K, Wang T, Arnold M, Meikle P, Giles C, Kaddurah-Daouk R, Saykin A, Nho K, Kaddurah-Daouk R, Kueider-Paisley A, Doraiswamy P, Blach C, Moseley A, Thompson W, St John-Williams L, Mahmoudiandehkhordi S, Tenenbaum J, Welsh-Balmer K, Plassman B, Saykin A, Nho K, Risacher S, Kastenmüller G, Arnold M, Han X, Baillie R, Knight R, Dorrestein P, Brewer J, Mayer E, Labus J, Baldi P, Gupta A, Fiehn O, Barupal D, Meikle P, Mazmanian S, Rader D, Kling M, Shaw L, Trojanowski J, van Duijin C, Nevado-Holgado A, Bennett D, Krishnan R, Keshavarzian A, Vogt R, Ikram A, Hankemeier T, Thiele I, Price N, Funk C, Baloni P, Jia W, Wishart D, Brinton R, Chang R, Farrer L, Au R, Qiu W, Würtz P, Koal T, Mangravite L, Krumsiek J, Suhre K, Newman J, Moreno H, Foroud T, Sacks F, Jansson J, Weiner M, Aisen P, Petersen R, Jack C, Jagust W, Trojanowki J, Toga A, Beckett L, Green R, Saykin A, Morris J, Perrin R, Shaw L, Khachaturian Z, Carrillo M, Potter W, Barnes L, Bernard M, Gonzalez H, Ho C, Hsiao J, Jackson J, Masliah E, Masterman D, Okonkwo O, Perrin R, Ryan L, Silverberg N, Fleisher A, Sacrey D, Fockler J, Conti C, Veitch D, Neuhaus J, Jin C, Nosheny R, Ashford M, Flenniken D, Kormos A, Montine T, Rafii M, Raman R, Jimenez G, Donohue M, Gessert D, Salazar J, Zimmerman C, Cabrera Y, Walter S, Miller G, Coker G, Clanton T, Hergesheimer L, Smith S, Adegoke O, Mahboubi P, Moore S, Pizzola J, Shaffer E, Sloan B, Harvey D, Forghanian-Arani A, Borowski B, Ward C, Schwarz C, Jones D, Gunter J, Kantarci K, Senjem M, Vemuri P, Reid R, Fox N, Malone I, Thompson P, Thomopoulos S, Nir T, Jahanshad N, DeCarli C, Knaack A, Fletcher E, Tosun-Turgut D, Chen S, Choe M, Crawford K, Yushkevich P, Das S, Koeppe R, Reiman E, Chen K, Mathis C, Landau S, Cairns N, Householder E, Franklin E, Bernhardt H, Taylor-Reinwald L, Korecka M, Figurski M, Neu S, Nho K, Risacher S, Apostolova L, Shen L, Foroud T, Nudelman K, Faber K, Wilmes K, Thal L, Silbert L, Lind B, Crissey R, Kaye J, Carter R, Dolen S, Quinn J, Schneider L, Pawluczyk S, Becerra M, Teodoro L, Dagerman K, Spann B, Brewer J, Vanderswag H, Ziolkowski J, Heidebrink J, Zbizek-Nulph L, Lord J, Mason S, Albers C, Knopman D, Johnson K, Villanueva-Meyer J, Pavlik V, Pacini N, Lamb A, Kass J, Doody R, Shibley V, Chowdhury M, Rountree S, Dang M, Stern Y, Honig L, Mintz A, Ances B, Winkfield D, Carroll M, Stobbs-Cucchi G, Oliver A, Creech M, Mintun M, Schneider S, Geldmacher D, Love M, Griffith R, Clark D, Brockington J, Marson D, Grossman H, Goldstein M, Greenberg J, Mitsis E, Shah R, Lamar M, Samuels P, Duara R, Greig-Custo M, Rodriguez R, Albert M, Onyike C, Farrington L, Rudow S, Brichko R, Kielb S, Smith A, Raj B, Fargher K, Sadowski M, Wisniewski T, Shulman M, Faustin A, Rao J, Castro K, Ulysse A, Chen S, Sheikh M, Singleton-Garvin J, Doraiswamy P, Petrella J, James O, Wong T, Borges-Neto S, Karlawish J, Wolk D, Vaishnavi S, Clark C, Arnold S, Smith C, Jicha G, Raslau F, Lopez O, Oakley M, Simpson D, Porsteinsson A, Martin K, Kowalski N, Keltz M, Goldstein B, Makino K, Ismail M, Brand C, Thai G, Pierce A, Yanez B, Sosa E, Witbracht M, Kelley B, Nguyen T, Womack K, Mathews D, Quiceno M, Levey A, Lah J, Hajjar I, Cellar J, Burns J, Swerdlow R, Brooks W, Silverman D, Kremen S, Apostolova L, Tingus K, Lu P, Bartzokis G, Woo E, Teng E, Graff-Radford N, Parfitt F, Poki-Walker K, Farlow M, Hake A, Matthews B, Brosch J, Herring S, van C, Mecca A, Good S, MacAvoy M, Carson R, Varma P, Chertkow H, Vaitekunis S, Hosein C, Black S, Stefanovic B, Heyn C, Hsiung G, Kim E, Mudge B, Sossi V, Feldman H, Assaly M, Finger E, Pasternak S, Rachinsky I, Kertesz A, Drost D, Rogers J, Grant I, Muse B, Rogalski E, Robson J, Mesulam M, Kerwin D, Wu C, Johnson N, Lipowski K, Weintraub S, Bonakdarpour B, Pomara N, Hernando R, Sarrael A, Rosen H, Miller B, Perry D, Turner R, Johnson K, Reynolds B, MCCann K, Poe J, Sperling R, Johnson K, Marshall G, Yesavage J, Taylor J, Chao S, Coleman J, White J, Lane B, Rosen A, Tinklenberg J, Belden C, Atri A, Clark K, Zamrini E, Sabbagh M, Killiany R, Stern R, Mez J, Kowall N, Budson A, Obisesan T, Ntekim O, Wolday S, Khan J, Nwulia E, Nadarajah S, Lerner A, Ogrocki P, Tatsuoka C, Fatica P, Maillard P, Olichney J, Carmichael O, Bates V, Capote H, Rainka M, Borrie M, Lee T, Bartha R, Johnson S, Asthana S, Carlsson C, Perrin A, Burke A, Scharre D, Kataki M, Tarawneh R, Hart D, Zimmerman E, Celmins D, Miller D, BolesPonto L, Smith K, Koleva H, Shim H, Nam K, Schultz S, Williamson J, Craft S, Cleveland J, Yang M, Sink K, Ott B, Drake J, Tremont G, Daiello L, Drake J, Ritter A, Bernick C, Munic D, O'Connelll A, Mintzer J, Wiliams A, Masdeu J, Shi J, Garcia A, Newhouse P, Potkin S, Salloway S, Malloy P, Correia S, Kittur S, Pearlson G, Blank K, Anderson K, Flashman L, Seltzer M, Hynes M, Santulli R, Relkin N, Chiang G, Lee A, Lin M, Ravdin L, Petersen R, Neylan T, Grafman J, Danowski S, Nguyen-Barrera C, Hayes J, Finley S, Bernstein M, Senjem M, Foster N, Kim S, Sood A, Blanchard K, Fleischman D, Arfanakis K, Varon D, Greig M, Petrella J, Goldstein B, Martin K, Reist C, Sadowsky C, Martinez W, Villena T, Rosen H, Marshall G, Peskind E, Petrie E, Li G, Mackin S, Jimenez-Maggiora G, Drake E, Donohue M, Nelson C, Bickford D, Butters M, Zmuda M, Reyes D, Faber K, Nudelman K, Au Y, Scherer K, Catalinotto D, Stark S, Ong E, Fernandez D. Circular-SWAT for deep learning based diagnostic classification of Alzheimer's disease: application to metabolome data. EBioMedicine 2023, 97: 104820. PMID: 37806288, PMCID: PMC10579282, DOI: 10.1016/j.ebiom.2023.104820.Peer-Reviewed Original ResearchMeSH KeywordsAgedAlzheimer DiseaseCognitive DysfunctionDeep LearningHumansLipidsMagnetic Resonance ImagingMetabolomeNeuroimagingEvaluation of boundaries between mood and psychosis disorder using dynamic functional network connectivity (dFNC) via deep learning classification
Rokham H, Falakshahi H, Fu Z, Pearlson G, Calhoun V. Evaluation of boundaries between mood and psychosis disorder using dynamic functional network connectivity (dFNC) via deep learning classification. Human Brain Mapping 2023, 44: 3180-3195. PMID: 36919656, PMCID: PMC10171526, DOI: 10.1002/hbm.26273.Peer-Reviewed Original ResearchConceptsDynamic functional network connectivityFunctional network connectivityDSM-IVFMRI-based measuresResting-state fMRI dataBiomarker-based approachPsychosis disordersClinical courseBipolar-Schizophrenia NetworkClinical evaluationSymptomatic measuresHealthy controlsPsychotic illnessHealthy individualsNeurological observationsMental disordersReliability of diagnosisStatistical group differencesMental healthNeuroimaging techniquesStatistical ManualDiagnostic problemsGroup differencesIntermediate phenotypesDisordersAnatomically interpretable deep learning of brain age captures domain-specific cognitive impairment
Yin C, Imms P, Cheng M, Amgalan A, Chowdhury N, Massett R, Chaudhari N, Chen X, Thompson P, Bogdan P, Irimia A, Initiative T, Weiner M, Aisen P, Petersen R, Weiner M, Aisen P, Petersen R, Jack C, Jagust W, Trojanowki J, Toga A, Beckett L, Green R, Saykin A, Morris J, Perrin R, Shaw L, Khachaturian Z, Carrillo M, Potter W, Barnes L, Bernard M, González H, Ho C, Hsiao J, Jackson J, Masliah E, Masterman D, Okonkwo O, Perrin R, Ryan L, Silverberg N, Fleisher A, Lilly E, Weiner M, Sacrey D, Fockler J, Conti C, Veitch D, Neuhaus J, Jin C, Nosheny R, Ashford M, Flenniken D, Kormos A, Green R, Montine T, Conti C, Petersen R, Aisen P, Rafii M, Raman R, Jimenez G, Donohue M, Gessert D, Salazar J, Zimmerman C, Cabrera Y, Walter S, Miller G, Coker G, Clanton T, Hergesheimer L, Smith S, Adegoke O, Mahboubi P, Moore S, Pizzola J, Shaffer E, Sloan B, Beckett L, Harvey D, Donohue M, Jack C, Forghanian-Arani A, Borowski B, Ward C, Schwarz C, Jones D, Gunter J, Kantarci K, Senjem M, Vemuri P, Reid R, Fox N, Malone I, Thompson P, Thomopoulos S, Nir T, Jahanshad N, DeCarli C, Knaack A, Fletcher E, Harvey D, Tosun-Turgut D, Chen S, Choe M, Crawford K, Yushkevich P, Das S, Jagust W, Koeppe R, Reiman E, Chen K, Mathis C, Landau S, Morris J, Perrin R, Cairns N, Householder E, Franklin E, Bernhardt H, Taylor-Reinwald L, Shaw L, Trojanowki J, Korecka M, Figurski M, Toga A, Crawford K, Neu S, Saykin A, Nho K, Risacher S, Apostolova L, Shen L, Foroud T, Nudelman K, Faber K, Wilmes K, Weiner M, Thal L, Khachaturian Z, Hsiao J, Silbert L, Lind B, Crissey R, Kaye J, Carter R, Dolen S, Quinn J, Schneider L, Pawluczyk S, Becerra M, Teodoro L, Dagerman K, Spann B, Brewer J, Vanderswag H, Fleisher A, Ziolkowski J, Heidebrink J, Zbizek-Nulph L, Lord J, Zbizek-Nulph L, Petersen R, Mason S, Albers C, Knopman D, Johnson K, Villanueva-Meyer J, Pavlik V, Pacini N, Lamb A, Kass J, Doody R, Shibley V, Chowdhury M, Rountree S, Dang M, Stern Y, Honig L, Mintz A, Ances B, Morris J, Winkfield D, Carroll M, Stobbs-Cucchi G, Oliver A, Creech M, Mintun M, Schneider S, Geldmacher D, Love M, Griffith R, Clark D, Brockington J, Marson D, Grossman H, Goldstein M, Greenberg J, Mitsis E, Shah R, Lamar M, Samuels P, Duara R, Greig-Custo M, Rodriguez R, Albert M, Onyike C, Farrington L, Rudow S, Brichko R, Kielb S, Smith A, Raj B, Fargher K, Sadowski M, Wisniewski T, Shulman M, Faustin A, Rao J, Castro K, Ulysse A, Chen S, Sheikh M, Singleton-Garvin J, Doraiswamy P, Petrella J, James O, Wong T, Borges-Neto S, Karlawish J, Wolk D, Vaishnavi S, Clark C, Arnold S, Smith C, Jicha G, Khouli R, Raslau F, Lopez O, Oakley M, Simpson D, Porsteinsson A, Martin K, Kowalski N, Keltz M, Goldstein B, Makino K, Ismail M, Brand C, Thai G, Pierce A, Yanez B, Sosa E, Witbracht M, Kelley B, Nguyen T, Womack K, Mathews D, Quiceno M, Levey A, Lah J, Hajjar I, Cellar J, Burns J, Swerdlow R, Brooks W, Silverman D, Kremen S, Apostolova L, Tingus K, Lu P, Bartzokis G, Woo E, Teng E, Graff-Radford N, Parfitt F, Poki-Walker K, Farlow M, Hake A, Matthews B, Brosch J, Herring S, van Dyck C, Mecca A, MacAvoy M, Carson R, Varma P, Chertkow H, Vaitekunis S, Hosein C, Black S, Stefanovic B, Heyn C, Hsiung G, Kim E, Mudge B, Sossi V, Feldman H, Assaly M, Finger E, Pasternak S, Rachinsky I, Kertesz A, Drost D, Rogers J, Grant I, Muse B, Rogalski E, Robson J, Mesulam M, Kerwin D, Wu C, Johnson N, Lipowski K, Weintraub S, Bonakdarpour B, Pomara N, Hernando R, Sarrael A, Rosen H, Miller B, Perry D, Turner R, Johnson K, Reynolds B, MCCann K, Poe J, Sperling R, Johnson K, Marshall G, Yesavage J, Taylor J, Chao S, Coleman J, White J, Lane B, Rosen A, Tinklenberg J, Belden C, Spann B, Clark K, Zamrini E, Sabbagh M, Killiany R, Stern R, Mez J, Kowall N, Budson A, Obisesan T, Ntekim O, Wolday S, Khan J, Nwulia E, Nadarajah S, Lerner A, Ogrocki P, Tatsuoka C, Fatica P, Fletcher E, Maillard P, Olichney J, DeCarli C, Carmichael O, Bates V, Capote H, Rainka M, Borrie M, Lee T, Bartha R, Johnson S, Asthana S, Carlsson C, Perrin A, Burke A, Scharre D, Kataki M, Tarawneh R, Kelley B, Hart D, Zimmerman E, Celmins D, Miller D, Ponto L, Smith K, Koleva H, Shim H, Nam K, Schultz S, Williamson J, Craft S, Cleveland J, Yang M, Sink K, Ott B, Drake J, Tremont G, Daiello L, Drake J, Sabbagh M, Ritter A, Bernick C, Munic D, Mintz A, O’Connelll A, Mintzer J, Wiliams A, Masdeu J, Shi J, Garcia A, Sabbagh M, Newhouse P, Potkin S, Salloway S, Malloy P, Correia S, Kittur S, Pearlson G, Blank K, Anderson K, Flashman L, Seltzer M, Hynes M, Santulli R, Relkin N, Chiang G, Lee A, Lin M, Ravdin L, Weiner M, Aisen P, Petersen R, Weiner M, Aisen P, Petersen R, Green R, Harvey D, Jack C, Jagust W, Morris J, Saykin A, Shaw L, Toga A, Trojanowki J, Neylan T, Grafman J, Green R, Montine T, Aisen P, Jimenez G, Donohue M, Gessert D, Salazar J, Zimmerman C, Walter S, Adegoke O, Mahboubi P, Danowski S, Coker G, Clanton T, Pizzola J, Shaffer E, Nguyen-Barrera C, Neylan T, Hayes J, Finley S, Harvey D, Donohue M, Jack C, Bernstein M, Borowski B, Gunter J, Senjem M, Kantarci K, Ward C, Tosun-Turgut D, Chen S, Landau S, Koeppe R, Foster N, Reiman E, Chen K, Morris J, Perrin R, Franklin E, Shaw L, Trojanowki J, Korecka M, Figurski M, Toga A, Crawford K, Neu S, Saykin A, Foroud T, Potkin S, Shen L, Faber K, Kim S, Nho K, Wilmes K, Schneider L, Pawluczyk S, Becerra M, Teodoro L, Dagerman K, Spann B, Brewer J, Vanderswag H, Fleisher A, Stern Y, Honig L, Mintz A, Shah R, Sood A, Blanchard K, Fleischman D, Arfanakis K, Duara R, Varon D, Greig M, Doraiswamy P, Petrella J, James O, Borges-Neto S, Wong T, Porsteinsson A, Martin K, Thai G, Pierce A, Reist C, Yanez B, Sosa E, Witbracht M, Sadowsky C, Martinez W, Villena T, Rosen H, Perry D, Turner R, Johnson K, Reynolds B, MCCann K, Poe J, Sperling R, Johnson K, Marshall G, Belden C, Spann B, Clark K, Zamrini E, Sabbagh M, Obisesan T, Ntekim O, Nwulia E, Nadarajah S, Asthana S, Carlsson C, Peskind E, Petrie E, Li G, Yesavage J, Taylor J, Chao S, Coleman J, White J, Lane B, Rosen A, Tinklenberg J, Lin M, Chiang G, Ravdin L, Relkin N, O’Connelll A, Mintzer J, Wiliams A, Mackin S, Aisen P, Raman R, Jimenez-Maggiora G, Donohue M, Gessert D, Salazar J, Zimmerman C, Walter S, Adegoke O, Mahboubi P, Mackin S, Weiner M, Aisen P, Raman R, Jack C, Landau S, Saykin A, Toga A, DeCarli C, Koeppe R, Green R, Drake E, Weiner M, Aisen P, Raman R, Donohue M, Mackin S, Nelson C, Bickford D, Butters M, Zmuda M, Jack C, Bernstein M, Borowski B, Gunter J, Senjem M, Kantarci K, Ward C, Reyes D, Koeppe R, Landau S, Toga A, Crawford K, Neu S, Saykin A, Foroud T, Faber K, Nho K, Nudelman K, Mackin S, Rosen H, Nelson C, Bickford D, Au Y, Scherer K, Catalinotto D, Stark S, Ong E, Fernandez D, Butters M, Zmuda M, Lopez O, Oakley M, Simpson D. Anatomically interpretable deep learning of brain age captures domain-specific cognitive impairment. Proceedings Of The National Academy Of Sciences Of The United States Of America 2023, 120: e2214634120. PMID: 36595679, PMCID: PMC9926270, DOI: 10.1073/pnas.2214634120.Peer-Reviewed Original ResearchMeSH KeywordsAdultAlzheimer DiseaseBrainCognitive DysfunctionDeep LearningHumansMagnetic Resonance ImagingConceptsChronological ageDomain-specific cognitive impairmentConvolutional neural networkCognitive impairmentBrain age estimatesExecutive functionNeurocognitive measuresNeurocognitive trajectoriesMild cognitive impairmentBrain ageNormal participantsCognitive declineCN individualsSymptom severityMagnetic resonance imagesCN participantsNeuroanatomic changesDeep learning modelsIndependent samplesBrain agingIndividual patternsParticipantsLearning modelImpairmentIndividuals