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基于回归的深度学习从病理切片中预测分子生物标志物。

Regression-based Deep-Learning predicts molecular biomarkers from pathology slides.

机构信息

Else Kroener Fresenius Center for Digital Health, Medical Faculty Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.

Department of Medicine 1, University Hospital and Faculty of Medicine Carl Gustav Carus, TUD Dresden University of Technology, Dresden, Germany.

出版信息

Nat Commun. 2024 Feb 10;15(1):1253. doi: 10.1038/s41467-024-45589-1.


DOI:10.1038/s41467-024-45589-1
PMID:38341402
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10858881/
Abstract

Deep Learning (DL) can predict biomarkers from cancer histopathology. Several clinically approved applications use this technology. Most approaches, however, predict categorical labels, whereas biomarkers are often continuous measurements. We hypothesize that regression-based DL outperforms classification-based DL. Therefore, we develop and evaluate a self-supervised attention-based weakly supervised regression method that predicts continuous biomarkers directly from 11,671 images of patients across nine cancer types. We test our method for multiple clinically and biologically relevant biomarkers: homologous recombination deficiency score, a clinically used pan-cancer biomarker, as well as markers of key biological processes in the tumor microenvironment. Using regression significantly enhances the accuracy of biomarker prediction, while also improving the predictions' correspondence to regions of known clinical relevance over classification. In a large cohort of colorectal cancer patients, regression-based prediction scores provide a higher prognostic value than classification-based scores. Our open-source regression approach offers a promising alternative for continuous biomarker analysis in computational pathology.

摘要

深度学习(DL)可以从癌症组织病理学中预测生物标志物。有几个经过临床批准的应用程序使用这项技术。然而,大多数方法预测的是类别标签,而生物标志物通常是连续测量值。我们假设基于回归的 DL 优于基于分类的 DL。因此,我们开发并评估了一种基于注意力的自监督弱监督回归方法,该方法可直接从 9 种癌症类型的 11671 张患者图像中预测连续的生物标志物。我们针对多个临床和生物学上相关的生物标志物测试了我们的方法:同源重组缺陷评分,一种临床应用的泛癌生物标志物,以及肿瘤微环境中关键生物学过程的标志物。使用回归显著提高了生物标志物预测的准确性,同时也提高了预测与已知临床相关区域的对应程度,优于分类。在一大群结直肠癌患者中,基于回归的预测评分比基于分类的评分具有更高的预后价值。我们的开源回归方法为计算病理学中的连续生物标志物分析提供了一种很有前途的替代方法。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/c52fa10bf615/41467_2024_45589_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/9eb862c13430/41467_2024_45589_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/f39c0f46db96/41467_2024_45589_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/0ccd9700a381/41467_2024_45589_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/c52fa10bf615/41467_2024_45589_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/9eb862c13430/41467_2024_45589_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/f39c0f46db96/41467_2024_45589_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/0ccd9700a381/41467_2024_45589_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9d35/10858881/c52fa10bf615/41467_2024_45589_Fig4_HTML.jpg

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[2]
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[3]
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[4]
Deep learning in histopathology images for prediction of oncogenic driver molecular alterations in lung cancer: a systematic review and meta-analysis.

Transl Lung Cancer Res. 2025-5-30

[5]
Breast cancer homologous recombination deficiency prediction from pathological images with a sufficient and representative Transformer.

NPJ Precis Oncol. 2025-5-30

[6]
MMRNet: Ensemble deep learning models for predicting mismatch repair deficiency in endometrial cancer from histopathological images.

Cell Rep Med. 2025-5-20

[7]
Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer.

Int J Mol Sci. 2025-3-9

[8]
Histopathology based AI model predicts anti-angiogenic therapy response in renal cancer clinical trial.

Nat Commun. 2025-3-17

[9]
Self-supervised learning reveals clinically relevant histomorphological patterns for therapeutic strategies in colon cancer.

Nat Commun. 2025-3-8

[10]
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Nat Cancer. 2025-3

本文引用的文献

[1]
A deep-learning framework to predict cancer treatment response from histopathology images through imputed transcriptomics.

Nat Cancer. 2024-9

[2]
Mutational signatures reveal mutual exclusivity of homologous recombination and mismatch repair deficiencies in colorectal and stomach tumors.

Sci Data. 2023-7-1

[3]
Prediction of heart transplant rejection from routine pathology slides with self-supervised deep learning.

Eur Heart J Digit Health. 2023-3-2

[4]
Computational pathology improves risk stratification of a multi-gene assay for early stage ER+ breast cancer.

NPJ Breast Cancer. 2023-5-17

[5]
: An Efficient Deep Learning Architecture to Predict Gene Expression from Breast Cancer Histopathology Images.

Cancers (Basel). 2023-4-30

[6]
Self-supervised attention-based deep learning for pan-cancer mutation prediction from histopathology.

NPJ Precis Oncol. 2023-3-28

[7]
Generalizable biomarker prediction from cancer pathology slides with self-supervised deep learning: A retrospective multi-centric study.

Cell Rep Med. 2023-4-18

[8]
On the 12th Day of Christmas, a Statistician Sent to Me . .

BMJ. 2022-12-20

[9]
RetCCL: Clustering-guided contrastive learning for whole-slide image retrieval.

Med Image Anal. 2023-1

[10]
Artificial intelligence in histopathology: enhancing cancer research and clinical oncology.

Nat Cancer. 2022-9

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