The method implemented by the winning team.

<p>Schematic overview of the data processing, feature selection, and prediction modeling workflow. (a) The workflow begins with raw experimental data, including training and challenge datasets from plasma antibody levels, PBMC gene expression, PBMC cell frequency, and plasma cytokine concentra...

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Main Author:	Pramod Shinde (20968597) (author)
Other Authors:	Lisa Willemsen (12067970) (author), Michael Anderson (3396614) (author), Minori Aoki (20968600) (author), Saonli Basu (28868) (author), Julie G. Burel (14378658) (author), Peng Cheng (153428) (author), Souradipto Ghosh Dastidar (20968603) (author), Aidan Dunleavy (20968606) (author), Tal Einav (2629669) (author), Jamie Forschmiedt (20968609) (author), Slim Fourati (221387) (author), Javier Garcia (709874) (author), William Gibson (3017370) (author), Jason A. Greenbaum (10287146) (author), Leying Guan (4720269) (author), Weikang Guan (20968612) (author), Jeremy P. Gygi (17346673) (author), Brendan Ha (20968615) (author), Joe Hou (20968618) (author), Jason Hsiao (20968621) (author), Yunda Huang (235282) (author), Rick Jansen (198642) (author), Bhargob Kakoty (20968624) (author), Zhiyu Kang (2821910) (author), James J. Kobie (7365761) (author), Mari Kojima (832141) (author), Anna Konstorum (20968627) (author), Jiyeun Lee (20968630) (author), Sloan A. Lewis (11304747) (author), Aixin Li (2332534) (author), Eric F. Lock (4573135) (author), Jarjapu Mahita (807956) (author), Marcus Mendes (20968633) (author), Hailong Meng (19806) (author), Aidan Neher (20968636) (author), Somayeh Nili (20968639) (author), Lars Rønn Olsen (1633549) (author), Shelby Orfield (20968642) (author), James A. Overton (2634355) (author), Nidhi Pai (20968645) (author), Cokie Parker (20968648) (author), Brian Qian (20968651) (author), Mikkel Rasmussen (20968654) (author), Joaquin Reyna (20968657) (author), Eve Richardson (16561164) (author), Sandra Safo (4241968) (author), Josey Sorenson (20968660) (author), Aparna Srinivasan (4479640) (author), Nicola Thrupp (20968663) (author), Rashmi Tippalagama (14378646) (author), Raphael Trevizani (3639214) (author), Steffen Ventz (4594945) (author), Jiuzhou Wang (7818911) (author), Cheng-Chang Wu (20968666) (author), Ferhat Ay (368912) (author), Barry Grant (21679) (author), Steven H. Kleinstein (8219844) (author), Bjoern Peters (19131) (author)
Published:	2025
Subjects:	Immunology Science Policy Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified systems vaccinology studies settings performed poorly generate experimental data div >< p benchmarked 49 algorithms advanced data preprocessing open model evaluations successful models stood compare models predicting putting computational models build computational models computational models model evaluation models adopted built models vaccination responses test — study designs representative subsets pertussis </ invited challenge generated datasets factors contributing challenging due booster responses 53 scientists
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author	Pramod Shinde (20968597)
author2	Lisa Willemsen (12067970) Michael Anderson (3396614) Minori Aoki (20968600) Saonli Basu (28868) Julie G. Burel (14378658) Peng Cheng (153428) Souradipto Ghosh Dastidar (20968603) Aidan Dunleavy (20968606) Tal Einav (2629669) Jamie Forschmiedt (20968609) Slim Fourati (221387) Javier Garcia (709874) William Gibson (3017370) Jason A. Greenbaum (10287146) Leying Guan (4720269) Weikang Guan (20968612) Jeremy P. Gygi (17346673) Brendan Ha (20968615) Joe Hou (20968618) Jason Hsiao (20968621) Yunda Huang (235282) Rick Jansen (198642) Bhargob Kakoty (20968624) Zhiyu Kang (2821910) James J. Kobie (7365761) Mari Kojima (832141) Anna Konstorum (20968627) Jiyeun Lee (20968630) Sloan A. Lewis (11304747) Aixin Li (2332534) Eric F. Lock (4573135) Jarjapu Mahita (807956) Marcus Mendes (20968633) Hailong Meng (19806) Aidan Neher (20968636) Somayeh Nili (20968639) Lars Rønn Olsen (1633549) Shelby Orfield (20968642) James A. Overton (2634355) Nidhi Pai (20968645) Cokie Parker (20968648) Brian Qian (20968651) Mikkel Rasmussen (20968654) Joaquin Reyna (20968657) Eve Richardson (16561164) Sandra Safo (4241968) Josey Sorenson (20968660) Aparna Srinivasan (4479640) Nicola Thrupp (20968663) Rashmi Tippalagama (14378646) Raphael Trevizani (3639214) Steffen Ventz (4594945) Jiuzhou Wang (7818911) Cheng-Chang Wu (20968666) Ferhat Ay (368912) Barry Grant (21679) Steven H. Kleinstein (8219844) Bjoern Peters (19131)
author2_role	author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author author
author_facet	Pramod Shinde (20968597) Lisa Willemsen (12067970) Michael Anderson (3396614) Minori Aoki (20968600) Saonli Basu (28868) Julie G. Burel (14378658) Peng Cheng (153428) Souradipto Ghosh Dastidar (20968603) Aidan Dunleavy (20968606) Tal Einav (2629669) Jamie Forschmiedt (20968609) Slim Fourati (221387) Javier Garcia (709874) William Gibson (3017370) Jason A. Greenbaum (10287146) Leying Guan (4720269) Weikang Guan (20968612) Jeremy P. Gygi (17346673) Brendan Ha (20968615) Joe Hou (20968618) Jason Hsiao (20968621) Yunda Huang (235282) Rick Jansen (198642) Bhargob Kakoty (20968624) Zhiyu Kang (2821910) James J. Kobie (7365761) Mari Kojima (832141) Anna Konstorum (20968627) Jiyeun Lee (20968630) Sloan A. Lewis (11304747) Aixin Li (2332534) Eric F. Lock (4573135) Jarjapu Mahita (807956) Marcus Mendes (20968633) Hailong Meng (19806) Aidan Neher (20968636) Somayeh Nili (20968639) Lars Rønn Olsen (1633549) Shelby Orfield (20968642) James A. Overton (2634355) Nidhi Pai (20968645) Cokie Parker (20968648) Brian Qian (20968651) Mikkel Rasmussen (20968654) Joaquin Reyna (20968657) Eve Richardson (16561164) Sandra Safo (4241968) Josey Sorenson (20968660) Aparna Srinivasan (4479640) Nicola Thrupp (20968663) Rashmi Tippalagama (14378646) Raphael Trevizani (3639214) Steffen Ventz (4594945) Jiuzhou Wang (7818911) Cheng-Chang Wu (20968666) Ferhat Ay (368912) Barry Grant (21679) Steven H. Kleinstein (8219844) Bjoern Peters (19131)
author_role	author
dc.creator.none.fl_str_mv	Pramod Shinde (20968597) Lisa Willemsen (12067970) Michael Anderson (3396614) Minori Aoki (20968600) Saonli Basu (28868) Julie G. Burel (14378658) Peng Cheng (153428) Souradipto Ghosh Dastidar (20968603) Aidan Dunleavy (20968606) Tal Einav (2629669) Jamie Forschmiedt (20968609) Slim Fourati (221387) Javier Garcia (709874) William Gibson (3017370) Jason A. Greenbaum (10287146) Leying Guan (4720269) Weikang Guan (20968612) Jeremy P. Gygi (17346673) Brendan Ha (20968615) Joe Hou (20968618) Jason Hsiao (20968621) Yunda Huang (235282) Rick Jansen (198642) Bhargob Kakoty (20968624) Zhiyu Kang (2821910) James J. Kobie (7365761) Mari Kojima (832141) Anna Konstorum (20968627) Jiyeun Lee (20968630) Sloan A. Lewis (11304747) Aixin Li (2332534) Eric F. Lock (4573135) Jarjapu Mahita (807956) Marcus Mendes (20968633) Hailong Meng (19806) Aidan Neher (20968636) Somayeh Nili (20968639) Lars Rønn Olsen (1633549) Shelby Orfield (20968642) James A. Overton (2634355) Nidhi Pai (20968645) Cokie Parker (20968648) Brian Qian (20968651) Mikkel Rasmussen (20968654) Joaquin Reyna (20968657) Eve Richardson (16561164) Sandra Safo (4241968) Josey Sorenson (20968660) Aparna Srinivasan (4479640) Nicola Thrupp (20968663) Rashmi Tippalagama (14378646) Raphael Trevizani (3639214) Steffen Ventz (4594945) Jiuzhou Wang (7818911) Cheng-Chang Wu (20968666) Ferhat Ay (368912) Barry Grant (21679) Steven H. Kleinstein (8219844) Bjoern Peters (19131)
dc.date.none.fl_str_mv	2025-03-31T18:00:09Z
dc.identifier.none.fl_str_mv	10.1371/journal.pcbi.1012927.g003
dc.relation.none.fl_str_mv	https://figshare.com/articles/figure/The_method_implemented_by_the_winning_team_/28700382
dc.rights.none.fl_str_mv	CC BY 4.0 info:eu-repo/semantics/openAccess
dc.subject.none.fl_str_mv	Immunology Science Policy Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified systems vaccinology studies settings performed poorly generate experimental data div >< p benchmarked 49 algorithms advanced data preprocessing open model evaluations successful models stood compare models predicting putting computational models build computational models computational models model evaluation models adopted built models vaccination responses test — study designs representative subsets pertussis </ invited challenge generated datasets factors contributing challenging due booster responses 53 scientists
dc.title.none.fl_str_mv	The method implemented by the winning team.
dc.type.none.fl_str_mv	Image Figure info:eu-repo/semantics/publishedVersion image
description	<p>Schematic overview of the data processing, feature selection, and prediction modeling workflow. (a) The workflow begins with raw experimental data, including training and challenge datasets from plasma antibody levels, PBMC gene expression, PBMC cell frequency, and plasma cytokine concentration assays. The common features across these datasets are identified, followed by batch-effect correction and timepoint-wise imputation. (b) Feature selection was performed using various dimension reduction techniques, including LASSO, Ridge, PLS, PCA, and Multiple Co-inertia Analysis (MCIA). MCIA outperformed the other models and was selected for further analysis. MCIA integrates different data types (e.g., X1, X2, X3, X4) and their associated weights (A1, A2, A3, A4) to produce MCIA factors (G) that represent the combined data structure. (c) These MCIA factors were then used in a Linear Mixed Effects (LME) model to predict the outcome. The model was trained on 80% of the data (train set) using 5-fold cross-validation and evaluated on the remaining 20% (test set). The trained model was then applied to the challenge baseline data to generate predictions, which were used to rank subjects according to their predicted outcomes. Figure is created in <a href="https://BioRender.com" target="_blank">https://BioRender.com</a>.</p>
eu_rights_str_mv	openAccess
id	Manara_a320dda831bb49ff7e196fa7bfb97bd0
identifier_str_mv	10.1371/journal.pcbi.1012927.g003
network_acronym_str	Manara
network_name_str	ManaraRepo
oai_identifier_str	oai:figshare.com:article/28700382
publishDate	2025
repository.mail.fl_str_mv
repository.name.fl_str_mv
repository_id_str
rights_invalid_str_mv	CC BY 4.0
spelling	The method implemented by the winning team.Pramod Shinde (20968597)Lisa Willemsen (12067970)Michael Anderson (3396614)Minori Aoki (20968600)Saonli Basu (28868)Julie G. Burel (14378658)Peng Cheng (153428)Souradipto Ghosh Dastidar (20968603)Aidan Dunleavy (20968606)Tal Einav (2629669)Jamie Forschmiedt (20968609)Slim Fourati (221387)Javier Garcia (709874)William Gibson (3017370)Jason A. Greenbaum (10287146)Leying Guan (4720269)Weikang Guan (20968612)Jeremy P. Gygi (17346673)Brendan Ha (20968615)Joe Hou (20968618)Jason Hsiao (20968621)Yunda Huang (235282)Rick Jansen (198642)Bhargob Kakoty (20968624)Zhiyu Kang (2821910)James J. Kobie (7365761)Mari Kojima (832141)Anna Konstorum (20968627)Jiyeun Lee (20968630)Sloan A. Lewis (11304747)Aixin Li (2332534)Eric F. Lock (4573135)Jarjapu Mahita (807956)Marcus Mendes (20968633)Hailong Meng (19806)Aidan Neher (20968636)Somayeh Nili (20968639)Lars Rønn Olsen (1633549)Shelby Orfield (20968642)James A. Overton (2634355)Nidhi Pai (20968645)Cokie Parker (20968648)Brian Qian (20968651)Mikkel Rasmussen (20968654)Joaquin Reyna (20968657)Eve Richardson (16561164)Sandra Safo (4241968)Josey Sorenson (20968660)Aparna Srinivasan (4479640)Nicola Thrupp (20968663)Rashmi Tippalagama (14378646)Raphael Trevizani (3639214)Steffen Ventz (4594945)Jiuzhou Wang (7818911)Cheng-Chang Wu (20968666)Ferhat Ay (368912)Barry Grant (21679)Steven H. Kleinstein (8219844)Bjoern Peters (19131)ImmunologyScience PolicyEnvironmental Sciences not elsewhere classifiedBiological Sciences not elsewhere classifiedMathematical Sciences not elsewhere classifiedInformation Systems not elsewhere classifiedsystems vaccinology studiessettings performed poorlygenerate experimental datadiv >< pbenchmarked 49 algorithmsadvanced data preprocessingopen model evaluationssuccessful models stoodcompare models predictingputting computational modelsbuild computational modelscomputational modelsmodel evaluationmodels adoptedbuilt modelsvaccination responsestest —study designsrepresentative subsetspertussis </invited challengegenerated datasetsfactors contributingchallenging duebooster responses53 scientists<p>Schematic overview of the data processing, feature selection, and prediction modeling workflow. (a) The workflow begins with raw experimental data, including training and challenge datasets from plasma antibody levels, PBMC gene expression, PBMC cell frequency, and plasma cytokine concentration assays. The common features across these datasets are identified, followed by batch-effect correction and timepoint-wise imputation. (b) Feature selection was performed using various dimension reduction techniques, including LASSO, Ridge, PLS, PCA, and Multiple Co-inertia Analysis (MCIA). MCIA outperformed the other models and was selected for further analysis. MCIA integrates different data types (e.g., X1, X2, X3, X4) and their associated weights (A1, A2, A3, A4) to produce MCIA factors (G) that represent the combined data structure. (c) These MCIA factors were then used in a Linear Mixed Effects (LME) model to predict the outcome. The model was trained on 80% of the data (train set) using 5-fold cross-validation and evaluated on the remaining 20% (test set). The trained model was then applied to the challenge baseline data to generate predictions, which were used to rank subjects according to their predicted outcomes. Figure is created in <a href="https://BioRender.com" target="_blank">https://BioRender.com</a>.</p>2025-03-31T18:00:09ZImageFigureinfo:eu-repo/semantics/publishedVersionimage10.1371/journal.pcbi.1012927.g003https://figshare.com/articles/figure/The_method_implemented_by_the_winning_team_/28700382CC BY 4.0info:eu-repo/semantics/openAccessoai:figshare.com:article/287003822025-03-31T18:00:09Z
spellingShingle	The method implemented by the winning team. Pramod Shinde (20968597) Immunology Science Policy Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified systems vaccinology studies settings performed poorly generate experimental data div >< p benchmarked 49 algorithms advanced data preprocessing open model evaluations successful models stood compare models predicting putting computational models build computational models computational models model evaluation models adopted built models vaccination responses test — study designs representative subsets pertussis </ invited challenge generated datasets factors contributing challenging due booster responses 53 scientists
status_str	publishedVersion
title	The method implemented by the winning team.
title_full	The method implemented by the winning team.
title_fullStr	The method implemented by the winning team.
title_full_unstemmed	The method implemented by the winning team.
title_short	The method implemented by the winning team.
title_sort	The method implemented by the winning team.
topic	Immunology Science Policy Environmental Sciences not elsewhere classified Biological Sciences not elsewhere classified Mathematical Sciences not elsewhere classified Information Systems not elsewhere classified systems vaccinology studies settings performed poorly generate experimental data div >< p benchmarked 49 algorithms advanced data preprocessing open model evaluations successful models stood compare models predicting putting computational models build computational models computational models model evaluation models adopted built models vaccination responses test — study designs representative subsets pertussis </ invited challenge generated datasets factors contributing challenging due booster responses 53 scientists

The method implemented by the winning team.

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