Advances in the application of deep learning in computed tomography imaging analysis of rare lung diseases

Bingyi Liu , Min Xie

Rare Disease and Orphan Drugs Journal ›› 2026, Vol. 5 ›› Issue (3) : 26

PDF
Rare Disease and Orphan Drugs Journal ›› 2026, Vol. 5 ›› Issue (3) :26 DOI: 10.20517/rdodj.2025.88
Review
Advances in the application of deep learning in computed tomography imaging analysis of rare lung diseases
Author information +
History +
PDF

Abstract

Diagnosis and management of rare lung diseases remain challenging owing to their low incidence, heterogeneous manifestations, and limited therapeutic options. High-resolution computed tomography (CT) is central to imaging assessment, yet conventional visual interpretation is subjective and lacks good reproducibility. Recent advances in artificial intelligence, especially deep learning, provide new approaches for automated, quantitative and objective chest computed tomography image analysis. This review summarizes deep learning applications across core stages of CT imaging analysis for rare respiratory diseases: image reconstruction and generation, lesion segmentation and detection, disease classification and diagnosis, and treatment response and prognosis prediction. With typical cases of rare lung diseases, we illustrate that deep learning models enable accurate quantification of imaging biomarkers, elevated diagnostic accuracy and optimized outcome stratification. Despite notable progress, key challenges remain in model generalization, interpretability, and clinical validation.

Keywords

Deep learning / artificial intelligence / computed tomography / rare lung diseases

Cite this article

Download citation ▾
Bingyi Liu, Min Xie. Advances in the application of deep learning in computed tomography imaging analysis of rare lung diseases. Rare Disease and Orphan Drugs Journal, 2026, 5 (3) : 26 DOI:10.20517/rdodj.2025.88

登录浏览全文

4963

注册一个新账户 忘记密码

References

[1]

Stoller JK.The challenge of rare diseases.Chest2018;153:1309-14

[2]

McCarthy C,Trapnell BC.Epidemiology of rare lung diseases: The challenges and opportunities to improve research and knowledge. In: Posada de la Paz M, Taruscio D, Groft SC, Editors. Rare diseases epidemiology: update and overview. Cham: Springer International Publishing; 2017. pp. 419-42.

[3]

Willemink MJ.The evolution of image reconstruction for CT-from filtered back projection to artificial intelligence.Eur Radiol2019;29:2185-95 PMCID:PMC6443602

[4]

Chen H,Zhang W.Low-dose CT via convolutional neural network.Biomed Opt Express2017;8:679-94

[5]

Chen H,Kalra MK.Low-dose CT with a residual encoder-decoder convolutional neural network.IEEE Trans Med Imaging2017;36:2524-35 PMCID:PMC5727581

[6]

Goodfellow IJ,Mirza M.Generative adversarial networks.arXiv2014;arXiv:1406.2661Available from: https://arxiv.org/abs/1406.2661 [Last accessed on 20 Jul 2026]

[7]

Pan J,Wu W,Wu W.Multi-domain integrative swin transformer network for sparse-view tomographic reconstruction.Patterns2022;3:100498 PMCID:PMC9214338

[8]

Hu J,Wang B,Huang W.Super-resolution swin transformer and attention network for medical CT imaging.Biomed Res Int2022;2022:4431536

[9]

Tan Z,Tao H,Hu Y.XctNet: Reconstruction network of volumetric images from a single X-ray image.Comput Med Imaging Graph2022;98:102067

[10]

Ying X,Ma K.X2CT-GAN: reconstructing CT from biplanar X-rays with generative adversarial networks. In: 2019 IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR); 2019 Jun 15-20; Long Beach, CA, USA. IEEE; 2019. pp. 10611-20.

[11]

Jiang J,Tyagi N.Cross-modality (CT-MRI) prior augmented deep learning for robust lung tumor segmentation from small MR datasets.Med Phys2019;46:4392-404

[12]

Jue J,Neelam T.Integrating cross-modality hallucinated MRI with CT to aid mediastinal lung tumor segmentation. In: Shen D, Liu T, Peters TM, et al. Editors. Medical image computing and computer assisted intervention-MICCAI 2019. Cham: Springer International Publishing; 2019. pp. 221-9. PMCID:PMC7225573

[13]

Ho J,Abbeel P. Denoising diffusion probabilistic models. In: Proceedings of the 34th International Conference on Neural Information Processing Systems; Red Hook, NY, USA. Curran Associates Inc.; 2020. pp. 6840-51. Available from: https://dl.acm.org/doi/abs/10.5555/3495724.3496298 [Last accessed on 20 Jul 2026]

[14]

Kazerouni A,Heidari M.Diffusion models in medical imaging: a comprehensive survey.Med Image Anal2023;88:102846

[15]

Jiang Y,Loew M.COVID-19 CT image synthesis with a conditional generative adversarial network.IEEE J Biomed Health Inform2021;25:441-52 PMCID:PMC8545178

[16]

Onishi Y,Tsujimoto M.Automated pulmonary nodule classification in computed tomography images using a deep convolutional neural network trained by generative adversarial networks.Biomed Res Int2019;2019:6051939 PMCID:PMC6334309

[17]

Apostolopoulos ID,Panayiotakis GS.Classification of lung nodule malignancy in computed tomography imaging utilising generative adversarial networks and semi-supervised transfer learning.Biocybern Biomed Eng2021;41:1243-57

[18]

Ronneberger O,Brox T.U-net: Convolutional networks for biomedical image segmentation. In: Navab N, Hornegger J, Wells WM, et al. Editors. Medical Image Computing and Computer-Assisted Intervention-MICCAI 2015. Cham: Springer International Publishing; 2015. pp. 234-41.

[19]

Milletari F,Ahmadi S-A.V-net: fully convolutional neural networks for volumetric medical image segmentation. In: 2016 Fourth International Conference on 3D Vision (3DV); 2016 Oct 25-28; Stanford, CA, USA. IEEE; 2016. pp. 565-71.

[20]

Hu H,Zhao Y.Parallel deep learning algorithms with hybrid attention mechanism for image segmentation of lung tumors.IEEE Trans Ind Inf2021;17:2880-9

[21]

Nan Y,Tang Z.Fuzzy attention neural network to tackle discontinuity in airway segmentation.IEEE Trans Neural Netw Learn Syst2024;35:7391-404

[22]

Abdalaoui Slimani F.Improving deep learning U-Net++ by discrete wavelet and attention gate mechanisms for effective pathological lung segmentation in chest X-ray imaging.Phys Eng Sci Med2025;48:59-73

[23]

Isensee F,Kohl SAA,Maier-Hein KH.nnU-Net: a self-configuring method for deep learning-based biomedical image segmentation.Nat Methods2021;18:203-11

[24]

Wasserthal J,Meyer MT.TotalSegmentator: robust segmentation of 104 anatomic structures in CT images.Radiol Artif Intell2023;5:e230024 PMCID:PMC10546353

[25]

Diaz-Pinto A,Nath V.MONAI label: a framework for AI-assisted interactive labeling of 3D medical images.Med Image Anal2024;95:103207

[26]

Shelhamer E,Darrell T.Fully convolutional networks for semantic segmentation.IEEE Trans Pattern Anal Mach Intell2017;39:640-51

[27]

Dosovitskiy A,Kolesnikov A.An image is worth 16x16 words: transformers for image recognition at scale.arXiv2021;arXiv:2010.11929Available from: http://arxiv.org/abs/2010.11929 [Last accessed on 20 Jul 2026]

[28]

Liu Z,Cao Y.Swin transformer: hierarchical vision transformer using shifted windows. In: 2021 IEEE/CVF International Conference on Computer Vision (ICCV); 2021 Oct 10-17; Montreal, QC, Canada. IEEE; 2021. pp. 9992-10002.

[29]

Chen J,Yu Q.TransUNet: transformers make strong encoders for medical image segmentation.arXiv2021;arXiv:2102.04306Available from: http://arxiv.org/abs/2102.04306 [Last accessed on 20 Jul 2026]

[30]

Raza R,Khan MO.Lung-EffNet: Lung cancer classification using EfficientNet from CT-scan images.Eng Appl Artif Intell2023;126:106902

[31]

Huang ML.A lightweight CNN-based network on COVID-19 detection using X-ray and CT images.Comput Biol Med2022;146:105604 PMCID:PMC9090861

[32]

Kathamuthu ND,Le QH.A deep transfer learning-based convolution neural network model for COVID-19 detection using computed tomography scan images for medical applications.Adv Eng Softw2023;175:103317 PMCID:PMC9595382

[33]

Jiang H,Liu W.Deep learning for COVID-19 chest CT (computed tomography) image analysis: a lesson from lung cancer.Comput Struct Biotechnol J2021;19:1391-9 PMCID:PMC7923948

[34]

Sabir M,Almalki NS,Sampedro GA.FibroVit-Vision transformer-based framework for detection and classification of pulmonary fibrosis from chest CT images.Front Med2023;10:1282200 PMCID:PMC10666764

[35]

UrRehman Z,Wang L.Effective lung nodule detection using deep CNN with dual attention mechanisms.Sci Rep2024;14:3934 PMCID:PMC10873370

[36]

Sangeetha SKB,Karthikeyan P.An enhanced multimodal fusion deep learning neural network for lung cancer classification.Syst Soft Comput2024;6:200068

[37]

Huang SC,Zamanian R,Lungren MP.Multimodal fusion with deep neural networks for leveraging CT imaging and electronic health record: a case-study in pulmonary embolism detection.Sci Rep2020;10:22147 PMCID:PMC7746687

[38]

Hasenstab KA,Retson T.Automated CT staging of chronic obstructive pulmonary disease severity for predicting disease progression and mortality with a deep learning convolutional neural network.Radiol Cardiothorac Imaging2021;3:e200477

[39]

González G,Vegas-Sánchez-Ferrero G.Disease staging and prognosis in smokers using deep learning in chest computed tomography.Am J Respir Crit Care Med2018;197:193-203 PMCID:PMC5768902

[40]

Mukherjee P,Lee E.A shallow convolutional neural network predicts prognosis of lung cancer patients in multi-institutional CT-image data.Nat Mach Intell2020;2:274-82

[41]

Katzman JL,Cloninger A,Jiang T.DeepSurv: personalized treatment recommender system using a Cox proportional hazards deep neural network.BMC Med Res Methodol2018;18:24 PMCID:PMC5828433

[42]

Mei X,Singh A.Interstitial lung disease diagnosis and prognosis using an AI system integrating longitudinal data.Nat Commun2023;14:2272 PMCID:PMC10119160

[43]

Han J,Yang W.MS-ResNet: disease-specific survival prediction using longitudinal CT images and clinical data.Int J Comput Assist Radiol Surg2022;17:1049-57 PMCID:PMC9020752

[44]

Aslani S,Gudmundsson E.Enhancing cancer prediction in challenging screen-detected incident lung nodules using time-series deep learning.Comput Med Imaging Graph2024;116:102399

[45]

Zhang S,Zhou L.Intelligent prognosis evaluation system for stage I-III resected non-small-cell lung cancer patients on CT images: a multi-center study.EClinicalMedicine2023;65:102270 PMCID:PMC10725055

[46]

Gong J,Ma X.Hybrid deep multi-task learning radiomics approach for predicting EGFR mutation status of non-small cell lung cancer in CT images.Phys Med Biol2023;68:245021

[47]

Ye G,Qi Y.Non-invasive multimodal CT deep learning biomarker to predict pathological complete response of non-small cell lung cancer following neoadjuvant immunochemotherapy: a multicenter study.J Immunother Cancer2024;12:e009348

[48]

Niu Y,Li XM.Deep learning radiomics and mediastinal adipose tissue-based nomogram for preoperative prediction of postoperative‌ brain metastasis risk in non-small cell lung cancer.BMC Cancer2025;25:1133 PMCID:PMC12219950

[49]

Ortiz A,Desbiens J.Effective deep learning approaches for predicting COVID-19 outcomes from chest computed tomography volumes.Sci Rep2022;12:1716 PMCID:PMC8810911

[50]

She Y,Wang F.Deep learning for predicting major pathological response to neoadjuvant chemoimmunotherapy in non-small cell lung cancer: a multicentre study.EBioMedicine2022;86:104364 PMCID:PMC9672965

[51]

Raghu G,Richeldi L.Idiopathic pulmonary fibrosis (an update) and progressive pulmonary fibrosis in adults: an official ATS/ERS/JRS/ALAT clinical practice guideline.Am J Respir Crit Care Med2022;205:e18-47

[52]

Refaee T,Frix AN.Diagnosis of idiopathic pulmonary fibrosis in high-resolution computed tomography scans using a combination of handcrafted radiomics and deep learning.Front Med2022;9:915243 PMCID:PMC9259876

[53]

Bratt A,Liu G.Predicting usual interstitial pneumonia histopathology from chest CT imaging with deep learning.Chest2022;162:815-23

[54]

Huang X,Ye X.Novel 3D-based deep learning for classification of acute exacerbation of idiopathic pulmonary fibrosis using high-resolution CT.BMJ Open Respir Res2024;11:e002226 PMCID:PMC10928777

[55]

Sun H,Kang H.Quantitative analysis of high-resolution computed tomography features of idiopathic pulmonary fibrosis: a structure-function correlation study.Quant Imaging Med Surg2022;12:3655-65

[56]

Thillai M,Ruggiero A.Deep learning-based segmentation of computed tomography scans predicts disease progression and mortality in idiopathic pulmonary fibrosis.Am J Respir Crit Care Med2024;210:465-72

[57]

Maetani T,Tanizawa K.Computed tomography morphological assessments of central airways in interstitial lung abnormalities and idiopathic pulmonary fibrosis.Respir Res2024;25:404 PMCID:PMC11550523

[58]

Nan Y,Humphries S.Prognostication in patients with idiopathic pulmonary fibrosis using quantitative airway analysis from HRCT: a retrospective study.Eur Respir J2025;66:2500981 PMCID:PMC12528776

[59]

Humphries SM,Jo HE.Quantitative computed tomography predicts outcomes in idiopathic pulmonary fibrosis.Respirology2022;27:1045-53 PMCID:PMC9796832

[60]

Humphries SM,Baraghoshi D.Deep learning classification of usual interstitial pneumonia predicts outcomes.Am J Respir Crit Care Med2024;209:1121-31

[61]

Shteinberg M,Polineni D.Cystic fibrosis.Lancet2021;397:2195-211

[62]

Nezamabadi K,Moghaddam HA,Pak N.Lung HRCT pattern classification for cystic fibrosis using convolutional neural network.SIViP2019;13:1225-32

[63]

Zucker EJ,Lungren MP.Deep learning to automate brasfield chest radiographic scoring for cystic fibrosis.J Cyst Fibros2020;19:131-8

[64]

Dournes G,Willmering MM.Artificial intelligence in computed tomography for quantifying lung changes in the era of CFTR modulators.Eur Respir J2022;59:2100844

[65]

Hadj Bouzid AI,Benlala I.Artificial intelligence-driven volumetric CT outcome score in cystic fibrosis: longitudinal and multicenter validation with/without modulators treatment.Eur Radiol2025;35:815-27

[66]

Hadj Bouzid AI,Benlala I.Quantitative CT evaluation of bronchiectasis improvement in cystic fibrosis after CFTR-modulator therapy.Radiol Cardiothorac Imaging2025;7:e250116

[67]

McCormack FX,Finlay GR.Official American Thoracic Society/Japanese Respiratory Society clinical practice guidelines: lymphangioleiomyomatosis diagnosis and management.Am J Respir Crit Care Med2016;194:748-61

[68]

Jonas A,Gupta N.Machine learning to distinguish lymphangioleiomyomatosis from other diffuse cystic lung diseases.Respir Investig2022;60:430-3

[69]

Golbus AE,Schuzer JL.Ultra-low dose chest CT with silver filter and deep learning reconstruction significantly reduces radiation dose and retains quantitative information in the investigation and monitoring of lymphangioleiomyomatosis (LAM).Eur Radiol2024;34:5613-20 PMCID:PMC11364713

[70]

Zhang L,Lu L.Self-learning to detect and segment cysts in lung CT images without manual annotation. In: 2018 IEEE 15th International Symposium on Biomedical Imaging (ISBI 2018); 2018 Apr 4-7; Washington, DC, USA. IEEE; 2018. pp. 1100-3.

[71]

McCarthy C,O'Callaghan M.European Respiratory Society guidelines for the diagnosis and management of pulmonary alveolar proteinosis.Eur Respir J2024;64:2400725

[72]

Shi S,Chen L.Quantitative chest CT assessment of pulmonary alveolar proteinosis with deep learning: a real-world longitudinal study.Quant Imaging Med Surg2022;12:5394-403 PMCID:PMC9703118

[73]

Shi S,Ding J.Assessment of statin treatment for pulmonary alveolar proteinosis without hypercholesterolemia: a 12-month prospective, longitudinal, and observational study.Biomed Res Int2022;2022:1589660

[74]

Gao Z,Liang H.A lung CT vision foundation model facilitating disease diagnosis and medical imaging.Nat Commun2025;17:35 PMCID:PMC12764816

[75]

Castro DC,Glocker B.Causality matters in medical imaging.Nat Commun2020;11:3673 PMCID:PMC7376027

[76]

Roberts M,Thorpe M. Common pitfalls and recommendations for using machine learning to detect and prognosticate for COVID-19 using chest radiographs and CT scans.Nat Mach Intell2021;3:199-217

PDF

2

Accesses

0

Citation

Detail

Sections
Recommended

/

〈 〉