| Literature DB >> 33125051 |
Zhi Qiao1, Austin Bae2, Lucas M Glass2, Cao Xiao1, Jimeng Sun3.
Abstract
OBJECTIVE: The study sought to test the possibility of differentiating chest x-ray images of coronavirus disease 2019 (COVID-19) against other pneumonia and healthy patients using deep neural networks.Entities:
Keywords: COVID-19 detection; class imbalance; computer-assisted radiographic image interpretation; neural network ensemble
Mesh:
Year: 2021 PMID: 33125051 PMCID: PMC7665533 DOI: 10.1093/jamia/ocaa280
Source DB: PubMed Journal: J Am Med Inform Assoc ISSN: 1067-5027 Impact factor: 4.497
Experimental data description
| Source | Total | COVID-19 | Viral | Bacterial | Normal | |
|---|---|---|---|---|---|---|
| Original data | CCX data | 119 | 100 | 11 | 7 | 1 |
| KCX data | 5389 | 0 | 1492 | 2780 | 1117 | |
| View distribution | AP view | 5413 | 24 | 1492 | 2780 | 1117 |
| PA view | 95 | 76 | 11 | 7 | 1 | |
| Training/test splits | Training | 4406 | 77 | 1194 | 2237 | 898 |
| Testing | 1102 | 23 | 309 | 550 | 220 | |
| Total | 5508 | 100 | 1503 | 2787 | 1118 | |
AP: anteroposterior; CCX: COVID Chest X-ray; COVID-19: coronavirus disease 2019; KCX: COVID Chest X-ray; PA: posteroanterior.
Figure 1.Framework of FLANNEL (Focal Loss bAsed Neural Network EnsembLe).
Performance comparison on F1 score: Class-specific F1 score is calculated using 1 class vs the rest strategy
| COVID-19 | Pneumonia virus | Pneumonia bacteria | Normal | Macro-F1 | |
|---|---|---|---|---|---|
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| |||||
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| 0.5904 (0.27) | 0.5864 (0.05) | 0.8056 (0.01) | 0.8771 (0.04) | 0.7149 (0.09) |
|
| 0.6160 (0.06) | 0.5349 (0.04) | 0.7967 (0.02) | 0.8691 (0.03) | 0.7042 (0.02) |
|
| 0.6378 (0.12) | 0.5649 (0.03) | 0.7959 (0.01) | 0.8537 (0.02) | 0.7140 (0.03) |
|
| 0.6277 (0.11) | 0.5506 (0.02) | 0.7988 (0.01) | 0.8700 (0.01) | 0.7110 (0.03) |
|
| 0.6880 (0.07) | 0.5930 (0.02) | 0.8017 (0.01) | 0.8953 (0.01) | 0.7445 (0.02) |
|
| |||||
|
| 0.7179 (0.13) | 0.5592 (0.04) | 0.8095 (0.02) | 0.8787 (0.03) | 0.7413 (0.03) |
|
| 0.6391 (0.16) | 0.5238 (0.07) | 0.7504 (0.02) | 0.7223 (0.03) | 0.6589 (0.07) |
|
| |||||
|
| 0.7684 (0.04) | 0.6005 (0.03) | 0.8214 (0.03) | 0.9079 (0.01) | 0.7745 (0.01) |
|
| 0.6247 (0.07) | 0.6042 (0.03) | 0.8185 (0.01) | 0.9161 (0.01) | 0.7409 (0.02) |
|
| 0.3735 (0.23) | 0.6030 (0.02) | 0.8206 (0.00) | 0.9128 (0.01) | 0.6775 (0.05) |
| Variant FLANNEL | |||||
|
| 0.7671 (0.06) | 0.6001 (0.03) | 0.8238 (0.01) | 0.9135 (0.01) | 0.7761 (0.01) |
|
| 0.7837 (0.04) | 0.5953 (0.04) | 0.8245 (0.01) | 0.9131 (0.01) | 0.7791 (0.02) |
|
| 0.8168 (0.03) | 0.6063 (0.02) | 0.8267 (0.00) | 0.9144 (0.01) | 0.7910 (0.01) |
The values in parentheses are the standard deviations.
Figure 2.Illustrates the COVID-19 (coronavirus disease 2019) F1 score vs rest comparing different models. The error bars are from 5-fold cross-validation.
Figure 3.The diagnostic ability of the compared models for COVID-19 (coronavirus disease 2019) classification. Panel A shows the precision-recall curve, while Panel B shows the receiver-operating characteristic curve. FLANNEL: Focal Loss bAsed Neural Network EnsembLe; PR: precision-recall; ROC: receiver-operating characteristic.
Figure 4.Confusion matrix (instance counts). COVID-19: coronavirus disease 2019.
Figure 5.Performance verification (F1 score for COVID-19 [coronavirus disease 2019] vs rest) on anteroposterior view images comparing different models. FLANNEL: Focal Loss bAsed Neural Network EnsembLe.
Figure 6.Visual explanations for the classification results. FLANNEL: Focal Loss bAsed Neural Network EnsembLe;
The FLANNEL algorithm
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X-ray Images, Class Labels Base Models {Learner1, Learner2, …, Learnern}
Fine-tune all base models with respect to inputs images and labels.
(where Loss = Back-propagate on Loss and update parameters End For |