Integrating machine learning with SHAP to uncover multi-tissue molecular signatures in Osteoarthritis progression

Jifeng Zhao; Jiasheng Tao; Yizhe Song; Jiyong Yang; Xiaodong Lin; Zhilong Ye; Chao Lu; Mingzhu Zeng; Weijian Chen; Wengang Liu

doi:10.1371/journal.pone.0343226

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Open Access

Peer-reviewed

Research Article

Integrating machine learning with SHAP to uncover multi-tissue molecular signatures in Osteoarthritis progression

Jifeng Zhao ,

Contributed equally to this work with: Jifeng Zhao, Jiasheng Tao, Yizhe Song

Roles Writing – original draft

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Jiasheng Tao ,

Contributed equally to this work with: Jifeng Zhao, Jiasheng Tao, Yizhe Song

Roles Data curation

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Yizhe Song ,

Contributed equally to this work with: Jifeng Zhao, Jiasheng Tao, Yizhe Song

Roles Formal analysis

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Jiyong Yang,

Roles Investigation

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Xiaodong Lin,

Roles Project administration

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Zhilong Ye,

Roles Software

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Chao Lu,

Roles Supervision

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Mingzhu Zeng ,

Roles Supervision

* E-mail: zmz_sezgyk@163.com (MZ); Dr.WJ_Chan@hotmail.com (WJC); wengangliu_gyk@126.com (WL)

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Weijian Chen ,

Roles Validation

* E-mail: zmz_sezgyk@163.com (MZ); Dr.WJ_Chan@hotmail.com (WJC); wengangliu_gyk@126.com (WL)

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China
⨯
Wengang Liu

Roles Writing – review & editing

* E-mail: zmz_sezgyk@163.com (MZ); Dr.WJ_Chan@hotmail.com (WJC); wengangliu_gyk@126.com (WL)

Affiliations The Fifth Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, Guangdong, China, Guangdong Provincial Second Hospital of Traditional Chinese Medicine (Guangdong Provincial Engineering Technology Research Institute of Traditional Chinese Medicine), Guangzhou, Guangdong, China, Guangdong Provincial Key Laboratory of Research and Development in Traditional Chinese Medicine, Guangzhou, Guangdong, China

https://orcid.org/0000-0002-8887-8429

⨯

Integrating machine learning with SHAP to uncover multi-tissue molecular signatures in Osteoarthritis progression

Jifeng Zhao,
Jiasheng Tao,
Yizhe Song,
Jiyong Yang,
Xiaodong Lin,
Zhilong Ye,
Chao Lu,
Mingzhu Zeng,
Weijian Chen,
Wengang Liu

Published: March 9, 2026
https://doi.org/10.1371/journal.pone.0343226

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