Explainable artificial intelligence (XAI) in deep learning-based medical image analysis

With an increase in deep learning-based methods, the call for explainability of such methods grows, especially in high-stakes decision making areas such as medical image analysis. This survey presents an overview of eXplainable Artificial Intelligence (XAI) used in deep learning-based medical image analysis. A framework of XAI criteria is introduced to classify deep learning-based medical image analysis methods. Papers on XAI techniques in medical image analysis are then surveyed and categorized according to the framework and according to anatomical location. The paper concludes with an outlook of future opportunities for XAI in medical image analysis.Comment: Submitted for publication. Comments welcome by email to first autho

Volumetric breast density estimation on MRI using explainable deep learning regression

To purpose of this paper was to assess the feasibility of volumetric breast density estimations on MRI without segmentations accompanied with an explainability step. A total of 615 patients with breast cancer were included for volumetric breast density estimation. A 3-dimensional regression convolutional neural network (CNN) was used to estimate the volumetric breast density. Patients were split in training (N = 400), validation (N = 50), and hold-out test set (N = 165). Hyperparameters were optimized using Neural Network Intelligence and augmentations consisted of translations and rotations. The estimated densities were evaluated to the ground truth using Spearman's correlation and Bland-Altman plots. The output of the CNN was visually analyzed using SHapley Additive exPlanations (SHAP). Spearman's correlation between estimated and ground truth density was ρ = 0.81 (N = 165, P < 0.001) in the hold-out test set. The estimated density had a median bias of 0.70% (95% limits of agreement = - 6.8% to 5.0%) to the ground truth. SHAP showed that in correct density estimations, the algorithm based its decision on fibroglandular and fatty tissue. In incorrect estimations, other structures such as the pectoral muscle or the heart were included. To conclude, it is feasible to automatically estimate volumetric breast density on MRI without segmentations, and to provide accompanying explanations

Multi-modal volumetric concept activation to explain detection and classification of metastatic prostate cancer on PSMA-PET/CT

Explainable artificial intelligence (XAI) is increasingly used to analyze the behavior of neural networks. Concept activation uses human-interpretable concepts to explain neural network behavior. This study aimed at assessing the feasibility of regression concept activation to explain detection and classification of multi-modal volumetric data. Proof-of-concept was demonstrated in metastatic prostate cancer patients imaged with positron emission tomography/computed tomography (PET/CT). Multi-modal volumetric concept activation was used to provide global and local explanations. Sensitivity was 80% at 1.78 false positive per patient. Global explanations showed that detection focused on CT for anatomical location and on PET for its confidence in the detection. Local explanations showed promise to aid in distinguishing true positives from false positives. Hence, this study demonstrated feasibility to explain detection and classification of multi-modal volumetric data using regression concept activation.Comment: Accepted as: Kraaijveld, R.C.J., Philippens, M.E.P., Eppinga, W.S.C., J\"urgenliemk-Schulz, I.M., Gilhuijs, K.G.A., Kroon, P.S., van der Velden, B.H.M. "Multi-modal volumetric concept activation to explain detection and classification of metastatic prostate cancer on PSMA-PET/CT." MICCAI workshop on Interpretability of Machine Intelligence in Medical Image Computing (iMIMIC), 202

Computer-Aided Diagnosis in Multiparametric Magnetic Resonance Imaging Screening of Women With Extremely Dense Breasts to Reduce False-Positive Diagnoses

OBJECTIVES: To reduce the number of false-positive diagnoses in the screening of women with extremely dense breasts using magnetic resonance imaging (MRI), we aimed to predict which BI-RADS 3 and BI-RADS 4 lesions are benign. For this purpose, we use computer-aided diagnosis (CAD) based on multiparametric assessment. MATERIALS AND METHODS: Consecutive data were used from the first screening round of the DENSE (Dense Tissue and Early Breast Neoplasm Screening) trial. In this trial, asymptomatic women with a negative screening mammography and extremely dense breasts were screened using multiparametric MRI. In total, 4783 women, aged 50 to 75 years, enrolled and were screened in 8 participating hospitals between December 2011 and January 2016. In total, 525 lesions in 454 women were given a BI-RADS 3 (n = 202), 4 (n = 304), or 5 score (n = 19). Of these lesions, 444 were benign and 81 were malignant on histologic examination.The MRI protocol consisted of 5 different MRI sequences: T1-weighted imaging without fat suppression, diffusion-weighted imaging, T1-weighted contrast-enhanced images at high spatial resolution, T1-weighted contrast-enhanced images at high temporal resolution, and T2-weighted imaging. A machine-learning method was developed to predict, without deterioration of sensitivity, which of the BI-RADS 3- and BI-RADS 4-scored lesions are actually benign and could be prevented from being recalled. BI-RADS 5 lesions were only used for training, because the gain in preventing false-positive diagnoses is expected to be low in this group. The CAD consists of 2 stages: feature extraction and lesion classification. Two groups of features were extracted: the first based on all multiparametric sequences, the second based only on sequences that are typically used in abbreviated MRI protocols. In the first group, 49 features were used as candidate predictors: 46 were automatically calculated from the MRI scans, supplemented with 3 clinical features (age, body mass index, and BI-RADS score). In the second group, 36 image features and the same 3 clinical features were used. Each group was considered separately in a machine-learning model to differentiate between benign and malignant lesions. We developed a Ridge regression model using 10-fold cross validation. Performance of the models was analyzed using an accuracy measure curve and receiver-operating characteristic analysis. RESULTS: Of the total number of BI-RADS 3 and BI-RADS 4 lesions referred to additional MRI or biopsy, 425/487 (87.3%) were false-positive. The full multiparametric model classified 176 (41.5%) and the abbreviated-protocol model classified 111 (26.2%) of the 425 false-positive BI-RADS 3- and BI-RADS 4-scored lesions as benign without missing a malignant lesion.If the full multiparametric CAD had been used to aid in referral, recall for biopsy or repeat MRI could have been reduced from 425/487 (87.3%) to 311/487 (63.9%) lesions. For the abbreviated protocol, it could have been 376/487 (77.2%). CONCLUSIONS: Dedicated multiparametric CAD of breast MRI for BI-RADS 3 and 4 lesions in screening of women with extremely dense breasts has the potential to reduce false-positive diagnoses and consequently to reduce the number of biopsies without missing cancers

Contralateral parenchymal enhancement on breast MRI before and during neoadjuvant endocrine therapy in relation to the preoperative endocrine prognostic index

OBJECTIVES: To investigate whether contralateral parenchymal enhancement (CPE) on MRI during neoadjuvant endocrine therapy (NET) is associated with the preoperative endocrine prognostic index (PEPI) of ER+/HER2- breast cancer. METHODS: This retrospective observational cohort study included 40 unilateral ER+/HER2- breast cancer patients treated with NET. Patients received NET for 6 to 9 months with MRI response monitoring after 3 and/or 6 months. PEPI was used as endpoint. PEPI is based on surgery-derived pathology (pT- and pN-stage, Ki67, and ER-status) and stratifies patients in three groups with distinct prognoses. Mixed effects and ROC analysis were performed to investigate whether CPE was associated with PEPI and to assess discriminatory ability. RESULTS: The median patient age was 61 (interquartile interval: 52, 69). Twelve patients had PEPI-1 (good prognosis), 15 PEPI-2 (intermediate), and 13 PEPI-3 (poor). High pretreatment CPE was associated with PEPI-3: pretreatment CPE was 39.4% higher on average (95% CI = 1.3, 91.9%; p = .047) compared with PEPI-1. CPE decreased after 3 months in PEPI-2 and PEPI-3. The average reduction was 24.4% (95% CI = 2.6, 41.3%; p = .032) in PEPI-2 and 29.2% (95% CI = 7.8, 45.6%; p = .011) in PEPI-3 compared with baseline. Change in CPE was predictive of PEPI-1 vs PEPI-2+3 (AUC = 0.77; 95% CI = 0.57, 0.96). CONCLUSIONS: CPE during NET is associated with PEPI-group in ER+/HER2- breast cancer: a high pretreatment CPE and a decrease in CPE during NET were associated with a poor prognosis after NET on the basis of PEPI. KEY POINTS: • Change in contralateral breast parenchymal enhancement on MRI during neoadjuvant endocrine therapy distinguished between patients with a good and intermediate/poor prognosis at final pathology. • Patients with a poor prognosis at final pathology showed higher baseline parenchymal enhancement on average compared to patients with a good prognosis. • Patients with an intermediate/poor prognosis at final pathology showed a higher average reduction in parenchymal enhancement after 3 months of neoadjuvant endocrine therapy

Harmonization of Quantitative Parenchymal Enhancement in T1 -Weighted Breast MRI

Background: Differences in imaging parameters influence computer-extracted parenchymal enhancement measures from breast MRI. Purpose: To investigate the effect of differences in dynamic contrast-enhanced MRI acquisition parameter settings on quantitative parenchymal enhancement of the breast, and to evaluate harmonization of contrast-enhancement values with respect to flip angle and repetition time. Study Type: Retrospective. Phantom/Populations: We modeled parenchymal enhancement using simulations, a phantom, and two cohorts (N = 398 and N = 302) from independent cancer centers. Sequence Field/Strength: 1.5T dynamic contrast-enhanced T 1-weighted spoiled gradient echo MRI. Vendors: Philips, Siemens, General Electric Medical Systems. Assessment: We assessed harmonization of parenchymal enhancement in simulations and phantom by varying the MR parameters that influence the amount of T 1-weighting: flip angle (8°–25°) and repetition time (4–12 msec). We calculated the median and interquartile range (IQR) of the enhancement values before and after harmonization. In vivo, we assessed overlap of quantitative parenchymal enhancement in the cohorts before and after harmonization using kernel density estimations. Cohort 1 was scanned with flip angle 20° and repetition time 8 msec; cohort 2 with flip angle 10° and repetition time 6 msec. Statistical Tests: Paired Wilcoxon signed-rank-test of bootstrapped kernel density estimations. Results: Before harmonization, simulated enhancement values had a median (IQR) of 0.46 (0.34–0.49). After harmonization, the IQR was reduced: median (IQR): 0.44 (0.44–0.45). In the phantom, the IQR also decreased, median (IQR): 0.96 (0.59–1.22) before harmonization, 0.96 (0.91–1.02) after harmonization. Harmonization yielded significantly (P < 0.001) better overlap in parenchymal enhancement between the cohorts: median (IQR) was 0.46 (0.37–0.58) for cohort 1 vs. 0.37 (0.30–0.44) for cohort 2 before harmonization (57% overlap); and 0.35 (0.28–0.43) vs.0.37 (0.30–0.44) after harmonization (85% overlap). Data Conclusion: The proposed practical harmonization method enables an accurate comparison between patients scanned with differences in imaging parameters. Level of Evidence: 3. Technical Efficacy Stage: 4

Long-term Survival in Breast Cancer Patients Is Associated with Contralateral Parenchymal Enhancement at MRI: Outcomes of the SELECT Study

Background Several single-center studies found that high contralateral parenchymal enhancement (CPE) at breast MRI was associated with improved long-term survival in patients with estrogen receptor (ER)-positive and human epidermal growth factor receptor 2 (HER2)-negative breast cancer. Due to varying sample sizes, population characteristics, and follow-up times, consensus of the association is currently lacking. Purpose To confirm whether CPE is associated with long-term survival in a large multicenter retrospective cohort, and to investigate if CPE is associated with endocrine therapy effectiveness. Materials and Methods This multicenter observational cohort included women with unilateral ER-positive HER2-negative breast cancer (tumor size ≤50 mm and ≤three positive lymph nodes) who underwent MRI from January 2005 to December 2010. Overall survival (OS), recurrence-free survival (RFS), and distant RFS (DRFS) were assessed. Kaplan-Meier analysis was performed to investigate differences in absolute risk after 10 years, stratified according to CPE tertile. Multivariable Cox proportional hazards regression analysis was performed to investigate whether CPE was associated with prognosis and endocrine therapy effectiveness. Results Overall, 1432 women (median age, 54 years [IQR, 47-63 years]) were included from 10 centers. Differences in absolute OS after 10 years were stratified according to CPE tertile as follows: 88.5% (95% CI: 88.1, 89.1) in tertile 1, 85.8% (95% CI: 85.2, 86.3) in tertile 2, and 85.9% (95% CI: 85.4, 86.4) in tertile 3. CPE was independently associated with OS, with a hazard ratio (HR) of 1.17 (95% CI: 1.0, 1.36; P = .047), but was not associated with RFS (HR, 1.11; P = .16) or DRFS (HR, 1.11; P = .19). The effect of endocrine therapy on survival could not be accurately assessed; therefore, the association between endocrine therapy efficacy and CPE could not reliably be estimated. Conclusion High contralateral parenchymal enhancement was associated with a marginally decreased overall survival in patients with estrogen receptor-positive and human epidermal growth factor receptor 2-negative breast cancer, but was not associated with recurrence-free survival (RFS) or distant RFS. Published under a CC BY 4.0 license. Supplemental material is available for this article. See also the editorial by Honda and Iima in this issue