Enhancing Histopathological Lung Cancer Diagnosis Through Explainable Deep Learning Models: A Methodological Framework Proposal
Abstract
1. Introduction
1.1. Contextualization
1.2. Aim
1.3. Research Paradigm
1.4. Research Design
1.5. Dataset Requirements
1.6. Document Structure
2. Materials and Methods
2.1. Dataset Acquisition
2.2. Dataset Preparation
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- Patch resampling from minority groups to increase intra-class diversity.
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- Geometric data augmentation will include normalization by rescaling pixel values by a factor of 1/255, the application of shear transformations with an intensity of 0.2, random rotations up to an angle of 0.2 radians, zooming in or out within a 0.5 range, and horizontal flipping. These transformations are designed to expand the variability of tissue presentation.
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- Stain normalization to reduce color domain shifts.
2.3. Training
2.3.1. Model Selection
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2.3.2. Training Configuration
2.3.3. Hardware and Software Configuration
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- Central Process Unit(s): 2 × AMD EPYC ROME 7452 (32 cores, 64 threads, 2.35 GHz).
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- Random Access Memory: 16 × 32 GB DDR4 RAM @ 3200 MHz (ECC Registered).
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- Graphical Process Unit(s): 4 × NVIDIA TESLA A100 40 GB.
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- Physical Memory: 2 × 3.84 TB NVMe PCIe SSDs (Western Digital DC SN640).
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- Operating System: Ubuntu 20.04 LTS with CUDA 11.6 and cuDNN 8.2.
2.4. Explainability Techniques’ Application
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- Saliency and Gradient-Based Visualization: This highlights the spatial regions of input histopathological patches that contribute most to the model’s classification. Grad-CAM will be used to generate class-discriminative heatmaps by projecting gradients onto the final convolutional layer.
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- Occlusion Sensitivity: This involves masking parts of the image and observing changes in the output prediction. This helps to identify regions where the model is most sensitive.
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- Shapley Additive Explanations (SHAP): Values will be computed to quantify the contribution of each input feature toward the final decision.
2.5. Evaluation
2.5.1. Model Validation
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- Accuracy: Represents the overall correctness of the model by calculating the proportion of correctly classified instances (both positive and negative) over the total number of instances.
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- Sensitivity: Measures the model’s ability to correctly identify positive tumoral cases. It is defined as the ratio of true positives to the sum of true positives and false negatives.
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- Specificity: Assesses the model’s ability to correctly identify negative cases (benign tissue). It is calculated as the ratio of true negatives to the sum of true negatives and false positives.
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- F1-score: Measures a weighted mean of Specificity and Sensitivity, balancing the trade-off between over-detection and under-detection.
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- AUC: Measures the model’s ability to distinguish between classes across varying classification thresholds. It plots the true positive rate against the false positive rate, with values closer to 1.0 indicating superior discriminative capability.
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- Cohen’s Kappa: Quantifies the inter-rater agreement between the predicted labels and the true labels, adjusting for agreement that could occur by chance.
2.5.2. Explainability Methods’ Validation
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- Localization Accuracy: Assesses whether saliency-based methods such as Grad-CAM correctly localize cancerous tissue. Metrics such as the Intersection Over Union (IoU) will be used to quantify the alignment between the highlighted heatmaps and annotated tumor regions.
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- Sensitivity to Input Perturbation: Measures how significantly the prediction changes with systematic masking.
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- Reliability: Each interpretability method will be measured across multiple augmentations (e.g., flipped or rotated patches). A stable explanation method should generate consistent attribution maps regardless of minor transformations.
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- Pathologists’ Evaluation: Pathologists will be asked to rate the clinical acceptability and diagnostic utility of the model explanations.
3. Ethical Considerations
4. Data Analysis
4.1. Data Preparation
4.2. First-Order Coding and Evaluation
4.3. Second-Order Coding and Modeling
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
ADC | Adenocarcinoma |
AI | Artificial Intelligence |
AUC | Area Under the Curve |
DL | Deep Learning |
Grad-CAM | Gradient-Weighted Class Activation Mapping |
H&E | Haematoxylin and Eosin |
HIPAA | Health Insurance Portability and Accountability Act |
IoU | Intersection over Union |
LC25000 | Lung and Colon Cancer Histopathological Image Dataset |
ROI | Region of Interest |
SCC | Squamous Cell Carcinoma |
SHAP | Shapley Additive Explanations |
TCGA | The Cancer Genome Atlas |
WSI | Whole Slide Image |
References
- Faria, N.; Campelos, S.; Carvalho, V. A Novel Convolutional Neural Network Algorithm for Histopathological Lung Cancer Detection. Appl. Sci. 2023, 13, 6571. [Google Scholar] [CrossRef]
- Bera, K.; Schalper, K.A.; Rimm, D.L.; Velcheti, V.; Madabhushi, A. Artificial Intelligence in Digital Pathology—New Tools for Diagnosis and Precision Oncology. Nat. Rev. Clin. Oncol. 2019, 16, 703–715. [Google Scholar] [CrossRef] [PubMed]
- Faria, N.; Campelos, S.; Carvalho, V. Lorenz, R., Fred, A., Gamboa, H., Eds.; Cancer Detec-Lung Cancer Diagnosis Support System: First Insights. In Bioinformatics; Proceedings of the 15th International Joint Conference on Biomedical Engineering Systems and Technologies—Vol 3: Bioinformatics, Virtual Event, February 9–11, 2022; Scitepress: Setubal, Portugal, 2021; pp. 81–88. [Google Scholar]
- Gour, M.; Jain, S.; Sunil Kumar, T. Residual Learning Based CNN for Breast Cancer Histopathological Image Classification. Int. J. Imaging Syst. Tech. 2020, 30, 621–635. [Google Scholar] [CrossRef]
- Litjens, G.; Kooi, T.; Bejnordi, B.E.; Setio, A.A.A.; Ciompi, F.; Ghafoorian, M.; van der Laak, J.A.W.M.; van Ginneken, B.; Sánchez, C.I. A Survey on Deep Learning in Medical Image Analysis. Med. Image Anal. 2017, 42, 60–88. [Google Scholar] [CrossRef] [PubMed]
- Chaddad, A.; Peng, J.; Xu, J.; Bouridane, A. Survey of Explainable AI Techniques in Healthcare. Sensors 2023, 23, 634. [Google Scholar] [CrossRef] [PubMed]
- Patrício, C.; Neves, J.C.; Teixeira, L.F. Explainable Deep Learning Methods in Medical Image Classification: A Survey. ACM Comput. Surv. 2023, 56, 1–41. [Google Scholar] [CrossRef]
- Salahuddin, Z.; Woodruff, H.C.; Chatterjee, A.; Lambin, P. Transparency of Deep Neural Networks for Medical Image Analysis: A Review of Interpretability Methods. Comput. Biol. Med. 2022, 140, 105111. [Google Scholar] [CrossRef]
- Latha, M.; Kumar, P.S.; Chandrika, R.R.; Mahesh, T.R.; Kumar, V.V.; Guluwadi, S. Revolutionizing Breast Ultrasound Diagnostics with EfficientNet-B7 and Explainable AI. BMC Med. Imaging 2024, 24, 230. [Google Scholar] [CrossRef]
- Tian, L.; Wu, J.; Song, W.; Hong, Q.; Liu, D.; Ye, F.; Gao, F.; Hu, Y.; Wu, M.; Lan, Y.; et al. Precise and Automated Lung Cancer Cell Classification Using Deep Neural Network with Multiscale Features and Model Distillation. Sci. Rep. 2024, 14, 10471. [Google Scholar] [CrossRef]
- Creswell, J.W.; Creswell, J.D. Research Design: Qualitative, Quantitative, and Mixed Methods Approaches; SAGE Publications: London, UK, 2017; ISBN 978-1-5063-8669-0. [Google Scholar]
- Ghassemi, M.; Oakden-Rayner, L.; Beam, A.L. The False Hope of Current Approaches to Explainable Artificial Intelligence in Health Care. Lancet Digit. Health 2021, 3, e745–e750. [Google Scholar] [CrossRef]
- Lincoln, Y.S.; Lynham, S.A.; Guba, E.G. Paradigmatic Controversies, Contradictions, and Emerging Confluences, Revisited. Sage Handb. Qual. Res. 2011, 4, 97–128. [Google Scholar]
- Mertens, D.M. Transformative Research: Personal and Societal. Int. J. Transform. Res. 2017, 4, 18–24. [Google Scholar] [CrossRef]
- Elder-Vass, D. Pragmatism, Critical Realism and the Study of Value. J. Crit. Realism 2022, 21, 261–287. [Google Scholar] [CrossRef]
- Lawani, A. Critical Realism: What You Should Know and How to Apply It. Qual. Res. J. 2020, 21, 320–333. [Google Scholar] [CrossRef]
- Topol, E. Deep Medicine: How Artificial Intelligence Can Make Healthcare Human Again; Basic Books: New York, NY, USA, 2019; ISBN 978-1-5416-4464-9. [Google Scholar]
- Haibe-Kains, B.; Adam, G.A.; Hosny, A.; Khodakarami, F.; Waldron, L.; Wang, B.; McIntosh, C.; Goldenberg, A.; Kundaje, A.; Greene, C.S.; et al. Transparency and Reproducibility in Artificial Intelligence. Nature 2020, 586, E14–E16. [Google Scholar] [CrossRef]
- Holzinger, A.; Langs, G.; Denk, H.; Zatloukal, K.; Müller, H. Causability and Explainability of Artificial Intelligence in Medicine. WIREs Data Min. Knowl. Discov. 2019, 9, e1312. [Google Scholar] [CrossRef]
- Dawadi, S.; Shrestha, S.; Giri, R.A. Mixed-Methods Research: A Discussion on Its Types, Challenges, and Criticisms. JPSE 2021, 2, 25–36. [Google Scholar] [CrossRef]
- Cohen, L.; Manion, L.; Morrison, K. Research Methods in Education, 8th ed.; Routledge: London, UK, 2017; ISBN 978-1-315-45653-9. [Google Scholar]
- LeCun, Y.; Bengio, Y.; Hinton, G. Deep Learning. Nature 2015, 521, 436–444. [Google Scholar] [CrossRef] [PubMed]
- Goodfellow, I.; Bengio, Y.; Courville, A. Deep Learning; MIT Press: Cambridge, MA, USA, 2016. [Google Scholar]
- Yamashita, R.; Nishio, M.; Do, R.K.G.; Togashi, K. Convolutional Neural Networks: An Overview and Application in Radiology. Insights Imaging 2018, 9, 611–629. [Google Scholar] [CrossRef] [PubMed]
- Goldenholz, D.M.; Sun, H.; Ganglberger, W.; Westover, M.B. Sample Size Analysis for Machine Learning Clinical Validation Studies. Biomedicines 2023, 11, 685. [Google Scholar] [CrossRef]
- Collins, G.S.; Ogundimu, E.O.; Altman, D.G. Sample Size Considerations for the External Validation of a Multivariable Prognostic Model: A Resampling Study. Stat. Med. 2016, 35, 214–226. [Google Scholar] [CrossRef] [PubMed]
- Suri, H. Purposeful Sampling in Qualitative Research Synthesis. Qual. Res. J. 2011, 11, 63–75. [Google Scholar] [CrossRef]
- Chen, I.Y.; Joshi, S.; Ghassemi, M. Treating Health Disparities with Artificial Intelligence. Nat. Med. 2020, 26, 16–17. [Google Scholar] [CrossRef]
- National Cancer Institute. The Cancer Genome Atlas Program (TCGA). Available online: https://www.cancer.gov/ccg/research/genome-sequencing/tcga (accessed on 10 April 2025).
- Albertina, B.; Watson, M.; Holback, C.; Jarosz, R.; Kirk, S.; Lee, Y.; Rieger-Christ, K.; Lemmerman, J. The Cancer Genome Atlas Lung Adenocarcinoma Collection (TCGA-LUAD); The Cancer Imaging Archive: Palo Alto, CA, USA, 2016. [Google Scholar]
- Kirk, S.; Lee, Y.; Kumar, P.; Filippini, J.; Albertina, B.; Watson, M.; Rieger-Christ, K.; Lemmerman, J. The Cancer Genome Atlas Lung Squamous Cell Carcinoma Collection (TCGA-LUSC); The Cancer Imaging Archive: Palo Alto, CA, USA, 2016. [Google Scholar]
- Borkowski, A.A.; Bui, M.M.; Thomas, L.B.; Wilson, C.P.; DeLand, L.A.; Mastorides, S.M. Lung and Colon Cancer Histopathological Image Dataset (LC25000). arXiv 2019, arXiv:1912.12142. [Google Scholar] [CrossRef]
- cBioPortal for Cancer Genomics—Lung Adenocarcinoma (TCGA, GDC). Available online: https://www.cbioportal.org/study/summary?id=luad_tcga_gdc (accessed on 3 May 2025).
- Coudray, N.; Ocampo, P.S.; Sakellaropoulos, T.; Narula, N.; Snuderl, M.; Fenyö, D.; Moreira, A.L.; Razavian, N.; Tsirigos, A. Classification and Mutation Prediction from Non-Small Cell Lung Cancer Histopathology Images Using Deep Learning. Nat. Med. 2018, 24, 1559–1567. [Google Scholar] [CrossRef]
- cBioPortal for Cancer Genomics—Lung Squamous Cell Carcinoma (TCGA, GDC). Available online: https://www.cbioportal.org/study/summary?id=lusc_tcga_gdc (accessed on 3 May 2025).
- CDC Health Insurance Portability and Accountability Act of 1996 (HIPAA). Available online: https://www.cdc.gov/phlp/php/resources/health-insurance-portability-and-accountability-act-of-1996-hipaa.html (accessed on 6 April 2025).
- Sumon, R.I.; Mazumdar, M.A.I.; Uddin, S.M.I.; Kim, H.-C. Exploring Deep Learning and Machine Learning Techniques for Histopathological Image Classification in Lung Cancer Diagnosis. In Proceedings of the 2024 International Conference on Electrical, Computer and Energy Technologies (ICECET), Sydney, Australia, 25–27 July 2024; pp. 1–6. [Google Scholar]
- Katar, O.; Yildirim, O.; Tan, R.-S.; Acharya, U.R. A Novel Hybrid Model for Automatic Non-Small Cell Lung Cancer Classification Using Histopathological Images. Diagnostics 2024, 14, 2497. [Google Scholar] [CrossRef]
- Tan, M.; Le, Q.V. EfficientNet: Rethinking Model Scaling for Convolutional Neural Networks. In International conference on machine learning; PMLR: Cambridge, MA, USA, 2020; pp. 6105–6114. [Google Scholar]
- Huang, G.; Liu, Z.; van der Maaten, L.; Weinberger, K.Q. Densely Connected Convolutional Networks. In Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 18–22 June 2018. [Google Scholar]
- He, K.; Zhang, X.; Ren, S.; Sun, J. Deep Residual Learning for Image Recognition. In Proceedings of the 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), Las Vegas, NV, USA, 27–30 June 2016; pp. 770–778. [Google Scholar]
- Abadi, M.; Agarwal, A.; Barham, P.; Brevdo, E.; Chen, Z.; Citro, C.; Corrado, G.S.; Davis, A.; Dean, J.; Devin, M.; et al. TensorFlow: Large-Scale Machine Learning on Heterogeneous Distributed Systems. arXiv 2016, arXiv:1603.04467. [Google Scholar]
- Müller, D.; Soto-Rey, I.; Kramer, F. Towards a Guideline for Evaluation Metrics in Medical Image Segmentation. BMC Res. Notes 2022, 15, 210. [Google Scholar] [CrossRef]
- Saldaña, J. The Coding Manual for Qualitative Researchers, 3rd ed.; SAGE: Los Angeles, CA, USA; London, UK; New Delhi, India; Singapore; Washington, DC, USA, 2016; ISBN 978-1-4739-0249-7. [Google Scholar]
- Adebayo, J.; Gilmer, J.; Muelly, M.; Goodfellow, I.; Hardt, M.; Kim, B. Sanity Checks for Saliency Maps. In Advances in Neural Information Processing Systems; Curran Associates, Inc.: Red Hook, NY, USA, 2018; Volume 31. [Google Scholar]
Characteristic | Value |
---|---|
k-fold Cross-Validation | 10 |
Dataset Ratio | 80:20 |
Epochs | Up to 100 |
Optimizer | Adam |
Loss Function | Categorical Cross-Entropy |
Early Stopping | Based on validation loss with a patience of 10 epochs |
Metric | Value |
---|---|
Accuracy | 0.92 |
Sensitivity | 0.90 |
Specificity | 0.93 |
F1-score | 0.91 |
AUC | 0.95 |
Cohen’s Kappa | 0.87 |
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Faria, N.; Campelos, S.; Carvalho, V. Enhancing Histopathological Lung Cancer Diagnosis Through Explainable Deep Learning Models: A Methodological Framework Proposal. Information 2025, 16, 740. https://doi.org/10.3390/info16090740
Faria N, Campelos S, Carvalho V. Enhancing Histopathological Lung Cancer Diagnosis Through Explainable Deep Learning Models: A Methodological Framework Proposal. Information. 2025; 16(9):740. https://doi.org/10.3390/info16090740
Chicago/Turabian StyleFaria, Nelson, Sofia Campelos, and Vítor Carvalho. 2025. "Enhancing Histopathological Lung Cancer Diagnosis Through Explainable Deep Learning Models: A Methodological Framework Proposal" Information 16, no. 9: 740. https://doi.org/10.3390/info16090740
APA StyleFaria, N., Campelos, S., & Carvalho, V. (2025). Enhancing Histopathological Lung Cancer Diagnosis Through Explainable Deep Learning Models: A Methodological Framework Proposal. Information, 16(9), 740. https://doi.org/10.3390/info16090740