Pre and post-hoc diagnosis and interpretation of malignancy from breast DCE-MRI

Automatic detection, segmentation, and classification of primary bone tumors and bone infections using an ensemble multi-task deep learning framework on multi-parametric MRIs: a multi-center study

OBJECTIVES

To develop an ensemble multi-task deep learning (DL) framework for automatic and simultaneous detection, segmentation, and classification of primary bone tumors (PBTs) and bone infections based on multi-parametric MRI from multi-center.

METHODS

This retrospective study divided 749 patients with PBTs or bone infections from two hospitals into a training set (N = 557), an internal validation set (N = 139), and an external validation set (N = 53). The ensemble framework was constructed using T1-weighted image (T1WI), T2-weighted image (T2WI), and clinical characteristics for binary (PBTs/bone infections) and three-category (benign/intermediate/malignant PBTs) classification. The detection and segmentation performances were evaluated using Intersection over Union (IoU) and Dice score. The classification performance was evaluated using the receiver operating characteristic (ROC) curve and compared with radiologist interpretations.

RESULT

On the external validation set, the single T1WI-based and T2WI-based multi-task models obtained IoUs of 0.71 ± 0.25/0.65 ± 0.30 for detection and Dice scores of 0.75 ± 0.26/0.70 ± 0.33 for segmentation. The framework achieved AUCs of 0.959 (95%CI, 0.955-1.000)/0.900 (95%CI, 0.773-0.100) and accuracies of 90.6% (95%CI, 79.7-95.9%)/78.3% (95%CI, 58.1-90.3%) for the binary/three-category classification. Meanwhile, for the three-category classification, the performance of the framework was superior to that of three junior radiologists (accuracy: 65.2%, 69.6%, and 69.6%, respectively) and comparable to that of two senior radiologists (accuracy: 78.3% and 78.3%).

CONCLUSION

The MRI-based ensemble multi-task framework shows promising performance in automatically and simultaneously detecting, segmenting, and classifying PBTs and bone infections, which was preferable to junior radiologists.

CLINICAL RELEVANCE STATEMENT

Compared with junior radiologists, the ensemble multi-task deep learning framework effectively improves differential diagnosis for patients with primary bone tumors or bone infections. This finding may help physicians make treatment decisions and enable timely treatment of patients.

KEY POINTS

• The ensemble framework fusing multi-parametric MRI and clinical characteristics effectively improves the classification ability of single-modality models. • The ensemble multi-task deep learning framework performed well in detecting, segmenting, and classifying primary bone tumors and bone infections. • The ensemble framework achieves an optimal classification performance superior to junior radiologists' interpretations, assisting the clinical differential diagnosis of primary bone tumors and bone infections.

MDF-Net for abnormality detection by fusing X-rays with clinical data

This study investigates the effects of including patients' clinical information on the performance of deep learning (DL) classifiers for disease location in chest X-ray images. Although current classifiers achieve high performance using chest X-ray images alone, consultations with practicing radiologists indicate that clinical data is highly informative and essential for interpreting medical images and making proper diagnoses. In this work, we propose a novel architecture consisting of two fusion methods that enable the model to simultaneously process patients' clinical data (structured data) and chest X-rays (image data). Since these data modalities are in different dimensional spaces, we propose a spatial arrangement strategy, spatialization, to facilitate the multimodal learning process in a Mask R-CNN model. We performed an extensive experimental evaluation using MIMIC-Eye, a dataset comprising different modalities: MIMIC-CXR (chest X-ray images), MIMIC IV-ED (patients' clinical data), and REFLACX (annotations of disease locations in chest X-rays). Results show that incorporating patients' clinical data in a DL model together with the proposed fusion methods improves the disease localization in chest X-rays by 12% in terms of Average Precision compared to a standard Mask R-CNN using chest X-rays alone. Further ablation studies also emphasize the importance of multimodal DL architectures and the incorporation of patients' clinical data in disease localization. In the interest of fostering scientific reproducibility, the architecture proposed within this investigation has been made publicly accessible( https://github.com/ChihchengHsieh/multimodal-abnormalities-detection ).

BreastDM: A DCE-MRI dataset for breast tumor image segmentation and classification

Dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI) has shown high sensitivity to diagnose breast cancer. However, few computer-aided algorithms focus on employing DCE-MR images for breast cancer diagnosis due to the lack of publicly available DCE-MRI datasets. To address this issue, our work releases a new DCE-MRI dataset called BreastDM for breast tumor segmentation and classification. In particular, a dataset of 232 patients selected with DCE-MR images for benign and malignant cases is established. Each case consists of three types of sequences: pre-contrast, post-contrast, and subtraction sequences. To show the difficulty of breast DCE-MRI tumor image segmentation and classification tasks, benchmarks are achieved by state-of-the-art image segmentation and classification algorithms, including conventional hand-crafted based methods and recently-emerged deep learning-based methods. More importantly, a local-global cross attention fusion network (LG-CAFN) is proposed to further improve the performance of breast tumor images classification. Specifically, LG-CAFN achieved the highest accuracy (88.20%, 83.93%) and AUC value (0.9154,0.8826) in both groups of experiments. Extensive experiments are conducted to present strong baselines based on various typical image segmentation and classification algorithms. Experiment results also demonstrate the superiority of the proposed LG-CAFN to other breast tumor images classification methods. The related dataset and evaluation codes are publicly available at smallboy-code/Breast-cancer-dataset.

Clinical applications of deep learning in breast MRI

Deep learning (DL) is one of the most powerful data-driven machine-learning techniques in artificial intelligence (AI). It can automatically learn from raw data without manual feature selection. DL models have led to remarkable advances in data extraction and analysis for medical imaging. Magnetic resonance imaging (MRI) has proven useful in delineating the characteristics and extent of breast lesions and tumors. This review summarizes the current state-of-the-art applications of DL models in breast MRI. Many recent DL models were examined in this field, along with several advanced learning approaches and methods for data normalization and breast and lesion segmentation. For clinical applications, DL-based breast MRI models were proven useful in five aspects: diagnosis of breast cancer, classification of molecular types, classification of histopathological types, prediction of neoadjuvant chemotherapy response, and prediction of lymph node metastasis. For subsequent studies, further improvement in data acquisition and preprocessing is necessary, additional DL techniques in breast MRI should be investigated, and wider clinical applications need to be explored.

A review of the current state of the computer-aided diagnosis (CAD) systems for breast cancer diagnosis

Breast cancer is one of the most common cancers affecting females worldwide. Early detection and diagnosis of breast cancer may aid in timely treatment, reducing the mortality rate to a great extent. To diagnose breast cancer, computer-aided diagnosis (CAD) systems employ a variety of imaging modalities such as mammography, computerized tomography, magnetic resonance imaging, ultrasound, and histological imaging. CAD and breast-imaging specialists are in high demand for early detection and diagnosis. This system has the potential to enhance the partiality of traditional histopathological image analysis. This review aims to highlight the recent advancements and the current state of CAD systems for breast cancer detection using different modalities.

Deep reinforcement learning in medical imaging: A literature review

Deep reinforcement learning (DRL) augments the reinforcement learning framework, which learns a sequence of actions that maximizes the expected reward, with the representative power of deep neural networks. Recent works have demonstrated the great potential of DRL in medicine and healthcare. This paper presents a literature review of DRL in medical imaging. We start with a comprehensive tutorial of DRL, including the latest model-free and model-based algorithms. We then cover existing DRL applications for medical imaging, which are roughly divided into three main categories: (i) parametric medical image analysis tasks including landmark detection, object/lesion detection, registration, and view plane localization; (ii) solving optimization tasks including hyperparameter tuning, selecting augmentation strategies, and neural architecture search; and (iii) miscellaneous applications including surgical gesture segmentation, personalized mobile health intervention, and computational model personalization. The paper concludes with discussions of future perspectives.

Diagnosis of Infantile Hip Dysplasia with B-mode Ultrasound via Two-stage Meta-learning Based Deep Exclusivity Regularized Machine

The B-mode ultrasound (BUS) based computer-aided diagnosis (CAD) has shown its effectiveness for developmental dysplasia of the hip (DDH) in infants. In this work, a two-stage meta-learning based deep exclusivity regularized machine (TML-DERM) is proposed for the BUS-based CAD of DDH. TML-DERM integrates deep neural network (DNN) and exclusivity regularized machine into a unified framework to simultaneously improve the feature representation and classification performance. Moreover, the first-stage meta-learning is mainly conducted on the DNN module to alleviate the overfitting issue caused by the significantly increased parameters in DNN, and a random sampling strategy is adopted to self-generate the meta-tasks; while the second-stage meta-learning mainly learns the combination of multiple weak classifiers by a weight vector to improve the classification performance, and also optimizes the unified framework again. The experimental results on a DDH ultrasound dataset show the proposed TML-DERM achieves the superior classification performance with the mean accuracy of 85.89%, sensitivity of 86.54%, and specificity of 85.23%.

Patient-level Prediction of Multi-classification Task at Prostate MRI based on End-to-End Framework learning from Diagnostic Logic of Radiologists

The grade groups (GGs) of Gleason scores (Gs) is the most critical indicator in the clinical diagnosis and treatment system of prostate cancer. End-to-end method for stratifying the patient-level pathological appearance of prostate cancer (PCa) in magnetic resonance (MRI) are of high demand for clinical decision. Existing methods typically employ a statistical method for integrating slice-level results to a patient-level result, which ignores the asymmetric use of ground truth (GT) and overall optimization. Therefore, more domain knowledge (e.g. diagnostic logic of radiologists) needs to be incorporated into the design of the framework. The patient-level GT is necessary to be logically assigned to each slice of a MRI to achieve joint optimization between slice-level analysis and patient-level decision-making. In this paper, we propose a framework (PCa-GGNet-v2) that learns from radiologists to capture signs in a separate two-dimensional (2-D) space of MRI and further associate them for the overall decision, where all steps are optimized jointly in an end-to-end trainable way. In the training phase, patient-level prediction is transferred from weak supervision to supervision with GT. An association route records the attentional slice for reweighting loss of MRI slices and interpretability. We evaluate our method in an in-house multi-center dataset (N=570) and PROSTATEx (N=204), which yields five-classification accuracy over 80% and AUC of 0.804 at patient-level respectively. Our method reveals the state-of-the-art performance for patient-level multi-classification task to personalized medicine.

Automatic lesion detection, segmentation and characterization via 3D multiscale morphological sifting in breast MRI

Previous studies on computer aided detection/diagnosis (CAD) in 4D breast magnetic resonance imaging (MRI) usually regard lesion detection, segmentation and characterization as separate tasks, and typically require users to manually select 2D MRI slices or regions of interest as the input. In this work, we present a breast MRI CAD system that can handle 4D multimodal breast MRI data, and integrate lesion detection, segmentation and characterization with no user intervention. The proposed CAD system consists of three major stages: region candidate generation, feature extraction and region candidate classification. Breast lesions are firstly extracted as region candidates using the novel 3D multiscale morphological sifting (MMS). The 3D MMS, which uses linear structuring elements to extract lesion-like patterns, can segment lesions from breast images accurately and efficiently. Analytical features are then extracted from all available 4D multimodal breast MRI sequences, including T1-, T2-weighted and DCE sequences, to represent the signal intensity, texture, morphological and enhancement kinetic characteristics of the region candidates. The region candidates are lastly classified as lesion or normal tissue by the random under-sampling boost (RUSboost), and as malignant or benign lesion by the random forest. Evaluated on a breast MRI dataset which contains a total of 117 cases with 141 biopsy-proven lesions (95 malignant and 46 benign lesions), the proposed system achieves a true positive rate (TPR) of 0.90 at 3.19 false positives per patient (FPP) for lesion detection and a TPR of 0.91 at a FPP of 2.95 for identifying malignant lesions without any user intervention. The average dice similarity index (DSI) is0.72±0.15for lesion segmentation. Compared with previously proposed lesion detection, detection-segmentation and detection-characterization systems evaluated on the same breast MRI dataset, the proposed CAD system achieves a favourable performance in breast lesion detection and characterization.

Deep pyramid local attention neural network for cardiac structure segmentation in two-dimensional echocardiography

Automatic semantic segmentation in 2D echocardiography is vital in clinical practice for assessing various cardiac functions and improving the diagnosis of cardiac diseases. However, two distinct problems have persisted in automatic segmentation in 2D echocardiography, namely the lack of an effective feature enhancement approach for contextual feature capture and lack of label coherence in category prediction for individual pixels. Therefore, in this study, we propose a deep learning model, called deep pyramid local attention neural network (PLANet), to improve the segmentation performance of automatic methods in 2D echocardiography. Specifically, we propose a pyramid local attention module to enhance features by capturing supporting information within compact and sparse neighboring contexts. We also propose a label coherence learning mechanism to promote prediction consistency for pixels and their neighbors by guiding the learning with explicit supervision signals. The proposed PLANet was extensively evaluated on the dataset of cardiac acquisitions for multi-structure ultrasound segmentation (CAMUS) and sub-EchoNet-Dynamic, which are two large-scale and public 2D echocardiography datasets. The experimental results show that PLANet performs better than traditional and deep learning-based segmentation methods on geometrical and clinical metrics. Moreover, PLANet can complete the segmentation of heart structures in 2D echocardiography in real time, indicating a potential to assist cardiologists accurately and efficiently.

Test-retest repeatability of a deep learning architecture in detecting and segmenting clinically significant prostate cancer on apparent diffusion coefficient (ADC) maps

OBJECTIVES

To evaluate short-term test-retest repeatability of a deep learning architecture (U-Net) in slice- and lesion-level detection and segmentation of clinically significant prostate cancer (csPCa: Gleason grade group > 1) using diffusion-weighted imaging fitted with monoexponential function, ADC_m.

METHODS

One hundred twelve patients with prostate cancer (PCa) underwent 2 prostate MRI examinations on the same day. PCa areas were annotated using whole mount prostatectomy sections. Two U-Net-based convolutional neural networks were trained on three different ADC_m b value settings for (a) slice- and (b) lesion-level detection and (c) segmentation of csPCa. Short-term test-retest repeatability was estimated using intra-class correlation coefficient (ICC(3,1)), proportionate agreement, and dice similarity coefficient (DSC). A 3-fold cross-validation was performed on training set (N = 78 patients) and evaluated for performance and repeatability on testing data (N = 34 patients).

RESULTS

For the three ADC_m b value settings, repeatability of mean ADC_m of csPCa lesions was ICC(3,1) = 0.86-0.98. Two CNNs with U-Net-based architecture demonstrated ICC(3,1) in the range of 0.80-0.83, agreement of 66-72%, and DSC of 0.68-0.72 for slice- and lesion-level detection and segmentation of csPCa. Bland-Altman plots suggest that there is no systematic bias in agreement between inter-scan ground truth segmentation repeatability and segmentation repeatability of the networks.

CONCLUSIONS

For the three ADC_m b value settings, two CNNs with U-Net-based architecture were repeatable for the problem of detection of csPCa at the slice-level. The network repeatability in segmenting csPCa lesions is affected by inter-scan variability and ground truth segmentation repeatability and may thus improve with better inter-scan reproducibility.

KEY POINTS

• For the three ADC_m b value settings, two CNNs with U-Net-based architecture were repeatable for the problem of detection of csPCa at the slice-level. • The network repeatability in segmenting csPCa lesions is affected by inter-scan variability and ground truth segmentation repeatability and may thus improve with better inter-scan reproducibility.