Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob; Tomiko T. Oskotsky; Alice S. Tang; Alennie Roldan; Verena Chung; Connie W.Y. Ha; Ronald J. Wong; Kaitlin J. Flynn; Rong Chai; Claire Dubin; Antonio Parraga-Leo; Camilla Wibrand; Samuel S. Minot; Boris Oskotsky; Gaia Andreoletti; Idit Kosti; Julie Bletz; Amber Nelson; Jifan Gao; Zhoujingpeng Wei; Guanhua Chen; Zheng Zheng Tang; Pierfrancesco Novielli; Donato Romano; Ester Pantaleo; Nicola Amoroso; Alfonso Monaco; Mirco Vacca; Maria De Angelis; Roberto Bellotti; Sabina Tangaro; Zehua Wang; Jiaming Yao; Akhil Goel; Jiangyue Mao; Huiqian Wang; Yuci Zhang; Ambuj Tewari; Abigail Kuntzleman; Isaac Bigcraft; Stephen Techtmann; Daehun Bae; Eunyoung Kim; Jongbum Jeon; Soobok Joe; Kevin R. Theis; Sherrianne Ng; Yun S. Lee; Patricia Diaz-Gimeno; Phillip R. Bennett; David A. MacIntyre; Gustavo Stolovitzky; Susan V. Lynch; Jake Albrecht; Nardhy Gomez-Lopez; Roberto Romero; David K. Stevenson; Nima Aghaeepour; Adi L. Tarca; James C. Costello; Marina Sirota

doi:10.1016/j.xcrm.2025.102428

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Jonathan L. Golob
, Tomiko T. Oskotsky
, Alice S. Tang
, Alennie Roldan
, Verena Chung
, Connie W.Y. Ha
, Ronald J. Wong
, Kaitlin J. Flynn
, Rong Chai
, Claire Dubin
, Antonio Parraga-Leo
, Camilla Wibrand
, Samuel S. Minot
, Boris Oskotsky
, Gaia Andreoletti
, Idit Kosti
, Julie Bletz
, Amber Nelson
, Jifan Gao
, Zhoujingpeng Wei

Guanhua Chen, Zheng Zheng Tang, Pierfrancesco Novielli, Donato Romano, Ester Pantaleo, Nicola Amoroso, Alfonso Monaco, Mirco Vacca, Maria De Angelis, Roberto Bellotti, Sabina Tangaro, Zehua Wang, Jiaming Yao, Akhil Goel, Jiangyue Mao, Huiqian Wang, Yuci Zhang, Ambuj Tewari, Abigail Kuntzleman, Isaac Bigcraft, Stephen Techtmann, Daehun Bae, Eunyoung Kim, Jongbum Jeon, Soobok Joe, Kevin R. Theis, Sherrianne Ng, Yun S. Lee, Patricia Diaz-Gimeno, Phillip R. Bennett, David A. MacIntyre, Gustavo Stolovitzky, Susan V. Lynch, Jake Albrecht, Nardhy Gomez-Lopez, Roberto Romero, David K. Stevenson, Nima Aghaeepour, Adi L. Tarca, James C. Costello, Marina Sirota

Research output: Contribution to journal › Comment/debate

Abstract

In the originally published version of this article, 12 individuals were inadvertently represented in both the training dataset as well as the validation dataset for evaluating the models (different samples, but still a potential source of data leakage). The authors have updated their validation dataset (specifically, Project S) to exclude these 12 individuals and their samples (https://www.immport.org/shared/study/SDY2187).

Original language	English
Article number	102428
Journal	Cell Reports Medicine
DOIs	https://doi.org/10.1016/j.xcrm.2025.102428
State	Accepted/In press - 2025

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Golob, J. L., Oskotsky, T. T., Tang, A. S., Roldan, A., Chung, V., Ha, C. W. Y., Wong, R. J., Flynn, K. J., Chai, R., Dubin, C., Parraga-Leo, A., Wibrand, C., Minot, S. S., Oskotsky, B., Andreoletti, G., Kosti, I., Bletz, J., Nelson, A., Gao, J., ... Sirota, M. (Accepted/In press). Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research. Cell Reports Medicine, Article 102428. https://doi.org/10.1016/j.xcrm.2025.102428

@article{a8c292403f7849839d5fafe3eb197c5b,

title = "Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research",

abstract = "In the originally published version of this article, 12 individuals were inadvertently represented in both the training dataset as well as the validation dataset for evaluating the models (different samples, but still a potential source of data leakage). The authors have updated their validation dataset (specifically, Project S) to exclude these 12 individuals and their samples (https://www.immport.org/shared/study/SDY2187).",

author = "Golob, \{Jonathan L.\} and Oskotsky, \{Tomiko T.\} and Tang, \{Alice S.\} and Alennie Roldan and Verena Chung and Ha, \{Connie W.Y.\} and Wong, \{Ronald J.\} and Flynn, \{Kaitlin J.\} and Rong Chai and Claire Dubin and Antonio Parraga-Leo and Camilla Wibrand and Minot, \{Samuel S.\} and Boris Oskotsky and Gaia Andreoletti and Idit Kosti and Julie Bletz and Amber Nelson and Jifan Gao and Zhoujingpeng Wei and Guanhua Chen and Tang, \{Zheng Zheng\} and Pierfrancesco Novielli and Donato Romano and Ester Pantaleo and Nicola Amoroso and Alfonso Monaco and Mirco Vacca and \{De Angelis\}, Maria and Roberto Bellotti and Sabina Tangaro and Zehua Wang and Jiaming Yao and Akhil Goel and Jiangyue Mao and Huiqian Wang and Yuci Zhang and Ambuj Tewari and Abigail Kuntzleman and Isaac Bigcraft and Stephen Techtmann and Daehun Bae and Eunyoung Kim and Jongbum Jeon and Soobok Joe and Theis, \{Kevin R.\} and Sherrianne Ng and Lee, \{Yun S.\} and Patricia Diaz-Gimeno and Bennett, \{Phillip R.\} and MacIntyre, \{David A.\} and Gustavo Stolovitzky and Lynch, \{Susan V.\} and Jake Albrecht and Nardhy Gomez-Lopez and Roberto Romero and Stevenson, \{David K.\} and Nima Aghaeepour and Tarca, \{Adi L.\} and Costello, \{James C.\} and Marina Sirota",

note = "Publisher Copyright: {\textcopyright} 2025 The Author(s). Published by Elsevier Inc.",

year = "2025",

doi = "10.1016/j.xcrm.2025.102428",

language = "English",

journal = "Cell Reports Medicine",

issn = "2666-3791",

}

Golob, JL, Oskotsky, TT, Tang, AS, Roldan, A, Chung, V, Ha, CWY, Wong, RJ, Flynn, KJ, Chai, R, Dubin, C, Parraga-Leo, A, Wibrand, C, Minot, SS, Oskotsky, B, Andreoletti, G, Kosti, I, Bletz, J, Nelson, A, Gao, J, Wei, Z, Chen, G, Tang, ZZ, Novielli, P, Romano, D, Pantaleo, E, Amoroso, N, Monaco, A, Vacca, M, De Angelis, M, Bellotti, R, Tangaro, S, Wang, Z, Yao, J, Goel, A, Mao, J, Wang, H, Zhang, Y, Tewari, A, Kuntzleman, A, Bigcraft, I, Techtmann, S, Bae, D, Kim, E, Jeon, J, Joe, S, Theis, KR, Ng, S, Lee, YS, Diaz-Gimeno, P, Bennett, PR, MacIntyre, DA, Stolovitzky, G, Lynch, SV, Albrecht, J, Gomez-Lopez, N, Romero, R, Stevenson, DK, Aghaeepour, N, Tarca, AL, Costello, JC & Sirota, M 2025, 'Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research', Cell Reports Medicine. https://doi.org/10.1016/j.xcrm.2025.102428

TY - JOUR

T1 - Microbiome preterm birth DREAM challenge

T2 - Crowdsourcing machine learning approaches to advance preterm birth research

AU - Golob, Jonathan L.

AU - Oskotsky, Tomiko T.

AU - Tang, Alice S.

AU - Roldan, Alennie

AU - Chung, Verena

AU - Ha, Connie W.Y.

AU - Wong, Ronald J.

AU - Flynn, Kaitlin J.

AU - Chai, Rong

AU - Dubin, Claire

AU - Parraga-Leo, Antonio

AU - Wibrand, Camilla

AU - Minot, Samuel S.

AU - Oskotsky, Boris

AU - Andreoletti, Gaia

AU - Kosti, Idit

AU - Bletz, Julie

AU - Nelson, Amber

AU - Gao, Jifan

AU - Wei, Zhoujingpeng

AU - Chen, Guanhua

AU - Tang, Zheng Zheng

AU - Novielli, Pierfrancesco

AU - Romano, Donato

AU - Pantaleo, Ester

AU - Amoroso, Nicola

AU - Monaco, Alfonso

AU - Vacca, Mirco

AU - De Angelis, Maria

AU - Bellotti, Roberto

AU - Tangaro, Sabina

AU - Wang, Zehua

AU - Yao, Jiaming

AU - Goel, Akhil

AU - Mao, Jiangyue

AU - Wang, Huiqian

AU - Zhang, Yuci

AU - Tewari, Ambuj

AU - Kuntzleman, Abigail

AU - Bigcraft, Isaac

AU - Techtmann, Stephen

AU - Bae, Daehun

AU - Kim, Eunyoung

AU - Jeon, Jongbum

AU - Joe, Soobok

AU - Theis, Kevin R.

AU - Ng, Sherrianne

AU - Lee, Yun S.

AU - Diaz-Gimeno, Patricia

AU - Bennett, Phillip R.

AU - MacIntyre, David A.

AU - Stolovitzky, Gustavo

AU - Lynch, Susan V.

AU - Albrecht, Jake

AU - Gomez-Lopez, Nardhy

AU - Romero, Roberto

AU - Stevenson, David K.

AU - Aghaeepour, Nima

AU - Tarca, Adi L.

AU - Costello, James C.

AU - Sirota, Marina

PY - 2025

Y1 - 2025

N2 - In the originally published version of this article, 12 individuals were inadvertently represented in both the training dataset as well as the validation dataset for evaluating the models (different samples, but still a potential source of data leakage). The authors have updated their validation dataset (specifically, Project S) to exclude these 12 individuals and their samples (https://www.immport.org/shared/study/SDY2187).

AB - In the originally published version of this article, 12 individuals were inadvertently represented in both the training dataset as well as the validation dataset for evaluating the models (different samples, but still a potential source of data leakage). The authors have updated their validation dataset (specifically, Project S) to exclude these 12 individuals and their samples (https://www.immport.org/shared/study/SDY2187).

UR - https://www.scopus.com/pages/publications/105024094099

U2 - 10.1016/j.xcrm.2025.102428

DO - 10.1016/j.xcrm.2025.102428

M3 - Comment/debate

C2 - 41205590

AN - SCOPUS:105024094099

SN - 2666-3791

JO - Cell Reports Medicine

JF - Cell Reports Medicine

M1 - 102428

ER -

Microbiome preterm birth DREAM challenge: Crowdsourcing machine learning approaches to advance preterm birth research

Abstract

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