Evidence map›Paper›PMID 32755895›Full record

ArticleJournal of medical Internet research2020

Reproducible Machine Learning Methods for Lung Cancer Detection Using Computed Tomography Images: Algorithm Development and Validation.

Kun-Hsing Yu, Tsung-Lu Michael Lee, Ming-Hsuan Yen, S C Kou, Bruce Rosen, Jung-Hsien Chiang, Isaac S Kohane

Abstract readValidation Study
In one paragraph

Article in Journal of medical Internet research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed, 1 pooled it
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
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  8. Medical Artificial Intelligence and Human Values.The New England journal of medicine · 2024
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

7 authors.

Kun-Hsing YuDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.ORCID 0000-0001-9892-8218
Tsung-Lu Michael LeeDepartment of Information Engineering, Kun Shan University, Tainan, Taiwan.ORCID 0000-0003-4453-3151
Ming-Hsuan YenGraduate Program of Multimedia Systems and Intelligent Computing, National Cheng Kung University and Academia Sinica, Tainan, Taiwan.ORCID 0000-0003-1644-950X
S C KouDepartment of Statistics, Harvard University, Cambridge, MA, United States.ORCID 0000-0002-1774-3316
Bruce RosenDepartment of Radiology, Athinoula A Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Boston, MA, United States.ORCID 0000-0002-8576-0839
Jung-Hsien ChiangDepartment of Computer Science and Information Engineering, National Cheng Kung University, Tainan, Taiwan.ORCID 0000-0002-4657-6705
Isaac S KohaneDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.ORCID 0000-0003-2192-5160

Funding

Patient-Centric Information Commons under FAIR Principles (PIC-FAIR)OT3OD025466 · OD · HARVARD MEDICAL SCHOOL · PI AVILLACH, PAUL, KOHANE, ISAAC S. · 2017 to 2018
$771k
NIH HHS OT3 OD025466
6 · The paper itself

Abstract

backgroundChest computed tomography (CT) is crucial for the detection of lung cancer, and many automated CT evaluation methods have been proposed. Due to the divergent software dependencies of the reported approaches, the developed methods are rarely compared or reproduced.

objectiveThe goal of the research was to generate reproducible machine learning modules for lung cancer detection and compare the approaches and performances of the award-winning algorithms developed in the Kaggle Data Science Bowl.

methodsWe obtained the source codes of all award-winning solutions of the Kaggle Data Science Bowl Challenge, where participants developed automated CT evaluation methods to detect lung cancer (training set n=1397, public test set n=198, final test set n=506). The performance of the algorithms was evaluated by the log-loss function, and the Spearman correlation coefficient of the performance in the public and final test sets was computed.

resultsMost solutions implemented distinct image preprocessing, segmentation, and classification modules. Variants of U-Net, VGGNet, and residual net were commonly used in nodule segmentation, and transfer learning was used in most of the classification algorithms. Substantial performance variations in the public and final test sets were observed (Spearman correlation coefficient = .39 among the top 10 teams). To ensure the reproducibility of results, we generated a Docker container for each of the top solutions.

conclusionsWe compared the award-winning algorithms for lung cancer detection and generated reproducible Docker images for the top solutions. Although convolutional neural networks achieved decent accuracy, there is plenty of room for improvement regarding model generalizability.

Indexed as

AlgorithmsHumansLung NeoplasmsMachine LearningReproducibility of ResultsTomography, X-Ray Computedcomputed tomography, spiralearly detection of cancerlung cancermachine learningreproducibility of results

Identifiers

PMID32755895
PMCPMC7439139

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.