Leveraging explainable AI for gut microbiome-based colorectal cancer classification

被引：18

作者：

Rynazal, Ryza ^{[1
]}

Fujisawa, Kota ^{[1
]}

Shiroma, Hirotsugu ^{[1
]}

Salim, Felix ^{[1
]}

Mizutani, Sayaka ^{[1
]}

Shiba, Satoshi ^{[5
]}

Yachida, Shinichi ^{[5
,6
]}

Yamada, Takuji ^{[1
,2
,3
,4
]}

机构：

[1] Tokyo Inst Technol, Sch Life Sci & Technol, Tokyo, Japan

[2] Metagen Inc, Yamagata, Japan

[3] Metagen Theurapeut Inc, Yamagata, Japan

[4] Digzyme Inc, Tokyo, Japan

[5] Natl Canc Ctr, Div Genom Med, Tokyo, Japan

[6] Osaka Univ, Grad Sch Med, Dept Canc Genome Informat, Osaka, Japan

来源：

GENOME BIOLOGY | 2023年 / 24卷 / 01期

基金：

日本学术振兴会;

关键词：

D O I：

10.1186/s13059-023-02858-4

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Studies have shown a link between colorectal cancer (CRC) and gut microbiome compositions. In these studies, machine learning is used to infer CRC biomarkers using global explanation methods. While these methods allow the identification of bacteria generally correlated with CRC, they fail to recognize species that are only influential for some individuals. In this study, we investigate the potential of Shapley Additive Explanations (SHAP) for a more personalized CRC biomarker identification. Analyses of five independent datasets show that this method can even separate CRC subjects into subgroups with distinct CRC probabilities and bacterial biomarkers.

引用

页数：13

共 50 条

[1] Leveraging explainable AI for gut microbiome-based colorectal cancer classification
Ryza Rynazal
Kota Fujisawa
Hirotsugu Shiroma
Felix Salim
Sayaka Mizutani
Satoshi Shiba
Shinichi Yachida
Takuji Yamada
Genome Biology, 24
[2] Explainable AI for gut microbiome-based diagnostics: colorectal cancer as a case study
Acharjee, Animesh
DIAGNOSIS, 2023, 10 (04) : 448 - 449
[3] A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer
Armour, Courtney R.
Topcuoglu, Begum D.
Garretto, Andrea
Schloss, Patrick D.
MBIO, 2022, 13 (01):
[4] Human Fecal Microbiome-Based Biomarkers for Colorectal Cancer
Narayanan, Vilvapathy
Peppelenbosch, Maikel P.
Konstantinov, Sergey R.
CANCER PREVENTION RESEARCH, 2014, 7 (11) : 1108 - 1111
[5] Human Gut Microbiome-Based Knowledgebase as a Biomarker Screening Tool to Improve the Predicted Probability for Colorectal Cancer
Zhou, Zhongkun
Ge, Shiqiang
Li, Yang
Ma, Wantong
Liu, Yuheng
Hu, Shujian
Zhang, Rentao
Ma, Yunhao
Du, Kangjia
Syed, Ashikujaman
Chen, Peng
FRONTIERS IN MICROBIOLOGY, 2020, 11
[6] Gut microbiome-based strategies for host health and disease
Wang, Chen
Bai, Junying
Chen, Xiaoyong
Song, Jiajia
Zhang, Yu
Wang, Hongwei
Suo, Huayi
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION, 2024, 64 (19) : 6834 - 6849
[7] Gut microbiome-based therapeutics in inflammatory bowel disease
Hu, Kelly A.
Gubatan, John
CLINICAL AND TRANSLATIONAL DISCOVERY, 2023, 3 (02):
[8] Gut Microbiome and Colorectal Cancer
Gweon, Tae-Geun
KOREAN JOURNAL OF GASTROENTEROLOGY, 2023, 82 (02): : 56 - 62
[9] The Gut Microbiome in Colorectal Cancer
Piawah, Sorbarikor
Walker, Evan J.
Van Blarigan, Erin L.
Atreya, Chloe E.
HEMATOLOGY-ONCOLOGY CLINICS OF NORTH AMERICA, 2022, 36 (03) : 491 - 506
[10] The gut microbiome in colorectal cancer
Atreya, Chloe E.
CANCER RESEARCH, 2022, 82 (23) : 8 - 8

← 1 2 3 4 5 →