Fully Automatic Atrial Fibrosis Assessment Using a Multilabel Convolutional Neural Network
Bibliographic record
Abstract
BACKGROUND: Pathological atrial fibrosis is a major contributor to sustained atrial fibrillation. Currently, late gadolinium enhancement (LGE) scans provide the only noninvasive estimate of atrial fibrosis. However, widespread adoption of atrial LGE has been hindered partly by nonstandardized image processing techniques, which can be operator and algorithm dependent. Minimal validation and limited access to transparent software platforms have also exacerbated the problem. This study aims to estimate atrial fibrosis from cardiac magnetic resonance scans using a reproducible operator-independent fully automatic open-source end-to-end pipeline. METHODS: A multilabel convolutional neural network was designed to accurately delineate atrial structures including the blood pool, pulmonary veins, and mitral valve. The output from the network removed the operator dependent steps in a reproducible pipeline and allowed for automated estimation of atrial fibrosis from LGE-cardiac magnetic resonance scans. The pipeline results were compared against manual fibrosis burdens, calculated using published thresholds: image intensity ratio 0.97, image intensity ratio 1.61, and mean blood pool signal +3.3 SD. RESULTS: We validated our methods on a large 3-dimensional LGE-cardiac magnetic resonance data set from 207 labeled scans. Automatic atrial segmentation achieved a 91% Dice score, compared with the mutual agreement of 85% in Dice seen in the interobserver analysis of operators. Intraclass correlation coefficients of the automatic pipeline with manually generated results were excellent and better than or equal to interobserver correlations for all 3 thresholds: 0.94 versus 0.88, 0.99 versus 0.99, 0.99 versus 0.96 for image intensity ratio 0.97, image intensity ratio 1.61, and +3.3 SD thresholds, respectively. Automatic analysis required 3 minutes per case on a standard workstation. The network and the analysis software are publicly available. CONCLUSIONS: Our pipeline provides a fully automatic estimation of fibrosis burden from LGE-cardiac magnetic resonance scans that is comparable to manual analysis. This removes one key source of variability in the measurement of atrial fibrosis.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".