An Interpretable Machine Learning Model to Predict Cortical Atrophy in Multiple Sclerosis
Abstract
:1. Introduction
2. Materials and Methods
2.1. Patient Population
2.2. MRI Protocol
2.3. Image Processing
2.4. Lesion Identification
2.5. Predictive Model
- (i)
- We randomly divided the data set in a stratified manner into training and test sets (70% and 30%, respectively).
- (ii)
- We used a grid search (5-fold cross-validation) during training to optimize model hyperparameters (maximum depth of a tree; step size shrinkage used in update to prevent overfitting; the minimum sum of instance weight needed in a child).
- (iii)
- We evaluated model performances by calculating, through the same Python script, the Pearson correlation (r) and p value between the real and predicted values in the test set.
- (iv)
- The individual and cumulative contribution of each feature to the final prediction was assessed by calculating the Shapley additive explanations (SHAP) values [20].
- (v)
- By repeating 50 times all the procedure on different 70/30 randomly split training and test sets, it was possible to obtain a confidence interval for both r- and p-values, as well as average SHAP values across repetitions.
3. Results
4. Discussion
Limitations of the Study
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Mean Thickness | r-Value | p Value |
---|---|---|
Right Hemisphere | 0.47 (0.15) | 0.009 (0.0013) |
Left Hemisphere | 0.44 (0.18) | 0.016 (0.020) |
Whole Brain | 0.48 (0.17) | 0.008 (0.011) |
LEFT HEMISPHERE | RIGHT HEMISPHERE | ||||
---|---|---|---|---|---|
REGION | r Value (SD) | p-Pearson (SD) | REGION | r Value (SD) | p-Pearson (SD) |
Superior frontal gyrus (F1) | 0.436 (0.149) | 0.016 (0.023) | Superior frontal gyrus (F1) | 0.480 (0.125) | 0.007 (0.011) |
Medial occipitotemporal sulcus (collateral sulcus) and lingual sulcus | 0.537 (0.131) | 0.002 (0.003) | Medial occipitotemporal sulcus (collateral sulcus) and lingual sulcus | 0.539 (0.125) | 0.002 (0.003) |
Superior temporal sulcus (parallel sulcus) | 0.444 (0.121) | 0.014 (0.019) | Superior temporal sulcus (parallel sulcus | 0.388 (0.212) | 0.034 (0.050) |
Opercular part of the inferior frontal gyrus | 0.420 (0.157) | 0.021 (0.030) | Middle-posterior part of the cingulate gyrus and sulcus (pMCC) | 0.374 (0.227) | 0.042 (0.060) |
Long insular gyrus and central sulcus of the insula | 0.371 (0.137) | 0.044 (0.055) | Middle frontal gyrus (F2) | 0.443 (0.178) | 0.014 (0.020) |
Middle temporal gyrus (T2) | 0.396 (0.134) | 0.030 (0.042) | Anterior transverse collateral sulcus | 0.377 (0.163) | 0.040 (0.056) |
Medial orbital sulcus (olfactory sulcus) | 0.387 (0.104) | 0.034 (0.043) | Superior occipital sulcus and transverse occipital sulcus | 0.439 (0.116) | 0.015 (0.020) |
Lateral occipito-temporal sulcus | 0.413 (0.165) | 0.023 (0.033) |
G1 | G2 | |||
---|---|---|---|---|
Mean Thickness | r-Value | p Value | r-Value | p Value |
Right Hemisphere | 0.46 | 0.0006 | 0.19 | 0.21 |
Left Hemisphere | 0.41 | 0.002 | 0.12 | 0.43 |
Whole Brain | 0.45 | 0.0007 | 0.19 | 0.21 |
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Conti, A.; Treaba, C.A.; Mehndiratta, A.; Barletta, V.T.; Mainero, C.; Toschi, N. An Interpretable Machine Learning Model to Predict Cortical Atrophy in Multiple Sclerosis. Brain Sci. 2023, 13, 198. https://doi.org/10.3390/brainsci13020198
Conti A, Treaba CA, Mehndiratta A, Barletta VT, Mainero C, Toschi N. An Interpretable Machine Learning Model to Predict Cortical Atrophy in Multiple Sclerosis. Brain Sciences. 2023; 13(2):198. https://doi.org/10.3390/brainsci13020198
Chicago/Turabian StyleConti, Allegra, Constantina Andrada Treaba, Ambica Mehndiratta, Valeria Teresa Barletta, Caterina Mainero, and Nicola Toschi. 2023. "An Interpretable Machine Learning Model to Predict Cortical Atrophy in Multiple Sclerosis" Brain Sciences 13, no. 2: 198. https://doi.org/10.3390/brainsci13020198
APA StyleConti, A., Treaba, C. A., Mehndiratta, A., Barletta, V. T., Mainero, C., & Toschi, N. (2023). An Interpretable Machine Learning Model to Predict Cortical Atrophy in Multiple Sclerosis. Brain Sciences, 13(2), 198. https://doi.org/10.3390/brainsci13020198