Self-supervised learning for classifying paranasal anomalies in the maxillary sinus.

PURPOSE: Paranasal anomalies, frequently identified in routine radiological screenings, exhibit diverse morphological characteristics. Due to the diversity of anomalies, supervised learning methods require large labelled dataset exhibiting diverse anomaly morphology. Self-supervised learning (SSL) can be used to learn representations from unlabelled data. However, there are no SSL methods designed for the downstream task of classifying paranasal anomalies in the maxillary sinus (MS). METHODS: Our approach uses a 3D convolutional autoencoder (CAE) trained in an unsupervised anomaly detection (UAD) framework. Initially, we train the 3D CAE to reduce reconstruction errors when reconstructing normal maxillary sinus (MS) image. Then, this CAE is applied to an unlabelled dataset to generate coarse anomaly locations by creating residual MS images. Following this, a 3D convolutional neural network (CNN) reconstructs these residual images, which forms our SSL task. Lastly, we fine-tune the encoder part of the 3D CNN on a labelled dataset of normal and anomalous MS images. RESULTS: The proposed SSL technique exhibits superior performance compared to existing generic self-supervised methods, especially in scenarios with limited annotated data. When trained on just 10% of the annotated dataset, our method achieves an area under the precision-recall curve (AUPRC) of 0.79 for the downstream classification task. This performance surpasses other methods, with BYOL attaining an AUPRC of 0.75, SimSiam at 0.74, SimCLR at 0.73 and masked autoencoding using SparK at 0.75. CONCLUSION: A self-supervised learning approach that inherently focuses on localizing paranasal anomalies proves to be advantageous, particularly when the subsequent task involves differentiating normal from anomalous maxillary sinuses. Access our code at https://github.com/mtec-tuhh/self-supervised-paranasal-anomaly .

BrainLossNet: a fast, accurate and robust method to estimate brain volume loss from longitudinal MRI.

PURPOSE: MRI-derived brain volume loss (BVL) is widely used as neurodegeneration marker. SIENA is state-of-the-art for BVL measurement, but limited by long computation time. Here we propose "BrainLossNet", a convolutional neural network (CNN)-based method for BVL-estimation. METHODS: BrainLossNet uses CNN-based non-linear registration of baseline(BL)/follow-up(FU) 3D-T1w-MRI pairs. BVL is computed by non-linear registration of brain parenchyma masks segmented in the BL/FU scans. The BVL estimate is corrected for image distortions using the apparent volume change of the total intracranial volume. BrainLossNet was trained on 1525 BL/FU pairs from 83 scanners. Agreement between BrainLossNet and SIENA was assessed in 225 BL/FU pairs from 94 MS patients acquired with a single scanner and 268 BL/FU pairs from 52 scanners acquired for various indications. Robustness to short-term variability of 3D-T1w-MRI was compared in 354 BL/FU pairs from a single healthy men acquired in the same session without repositioning with 116 scanners (Frequently-Traveling-Human-Phantom dataset, FTHP). RESULTS: Processing time of BrainLossNet was 2-3 min. The median [interquartile range] of the SIENA-BrainLossNet BVL difference was 0.10% [- 0.18%, 0.35%] in the MS dataset, 0.08% [- 0.14%, 0.28%] in the various indications dataset. The distribution of apparent BVL in the FTHP dataset was narrower with BrainLossNet (p = 0.036; 95th percentile: 0.20% vs 0.32%). CONCLUSION: BrainLossNet on average provides the same BVL estimates as SIENA, but it is significantly more robust, probably due to its built-in distortion correction. Processing time of 2-3 min makes BrainLossNet suitable for clinical routine. This can pave the way for widespread clinical use of BVL estimation from intra-scanner BL/FU pairs.

Computer-Aided Diagnosis of Maxillary Sinus Anomalies: Validation and Clinical Correlation.

OBJECTIVE: Computer aided diagnostics (CAD) systems can automate the differentiation of maxillary sinus (MS) with and without opacification, simplifying the typically laborious process and aiding in clinical insight discovery within large cohorts. METHODS: This study uses Hamburg City Health Study (HCHS) a large, prospective, long-term, population-based cohort study of participants between 45 and 74 years of age. We develop a CAD system using an ensemble of 3D Convolutional Neural Network (CNN) to analyze cranial MRIs, distinguishing MS with opacifications (polyps, cysts, mucosal thickening) from MS without opacifications. The system is used to find correlations of participants with and without MS opacifications with clinical data (smoking, alcohol, BMI, asthma, bronchitis, sex, age, leukocyte count, C-reactive protein, allergies). RESULTS: The evaluation metrics of CAD system (Area Under Receiver Operator Characteristic: 0.95, sensitivity: 0.85, specificity: 0.90) demonstrated the effectiveness of our approach. MS with opacification group exhibited higher alcohol consumption, higher BMI, higher incidence of intrinsic asthma and extrinsic asthma. Male sex had higher prevalence of MS opacifications. Participants with MS opacifications had higher incidence of hay fever and house dust allergy but lower incidence of bee/wasp venom allergy. CONCLUSION: The study demonstrates a 3D CNN's ability to distinguish MS with and without opacifications, improving automated diagnosis and aiding in correlating clinical data in population studies. LEVEL OF EVIDENCE: 3 Laryngoscope, 2024.

Nodule detection and generation on chest X-rays: NODE21 Challenge.

Pulmonary nodules may be an early manifestation of lung cancer, the leading cause of cancer-related deaths among both men and women. Numerous studies have established that deep learning methods can yield high-performance levels in the detection of lung nodules in chest X-rays. However, the lack of gold-standard public datasets slows down the progression of the research and prevents benchmarking of methods for this task. To address this, we organized a public research challenge, NODE21, aimed at the detection and generation of lung nodules in chest X-rays. While the detection track assesses state-of-the-art nodule detection systems, the generation track determines the utility of nodule generation algorithms to augment training data and hence improve the performance of the detection systems. This paper summarizes the results of the NODE21 challenge and performs extensive additional experiments to examine the impact of the synthetically generated nodule training images on the detection algorithm performance.

Multiple instance ensembling for paranasal anomaly classification in the maxillary sinus.

PURPOSE: Paranasal anomalies are commonly discovered during routine radiological screenings and can present with a wide range of morphological features. This diversity can make it difficult for convolutional neural networks (CNNs) to accurately classify these anomalies, especially when working with limited datasets. Additionally, current approaches to paranasal anomaly classification are constrained to identifying a single anomaly at a time. These challenges necessitate the need for further research and development in this area. METHODS: We investigate the feasibility of using a 3D convolutional neural network (CNN) to classify healthy maxillary sinuses (MS) and MS with polyps or cysts. The task of accurately localizing the relevant MS volume within larger head and neck Magnetic Resonance Imaging (MRI) scans can be difficult, but we develop a strategy which includes the use of a novel sampling technique that not only effectively localizes the relevant MS volume, but also increases the size of the training dataset and improves classification results. Additionally, we employ a Multiple Instance Ensembling (MIE) prediction method to further boost classification performance. RESULTS: With sampling and MIE, we observe that there is consistent improvement in classification performance of all 3D ResNet and 3D DenseNet architecture with an average AUPRC percentage increase of 21.86 ± 11.92% and 4.27 ± 5.04% by sampling and 28.86 ± 12.80% and 9.85 ± 4.02% by sampling and MIE, respectively. CONCLUSION: Sampling and MIE can be effective techniques to improve the generalizability of CNNs for paranasal anomaly classification. We demonstrate the feasibility of classifying anomalies in the MS. We propose a data enlarging strategy through sampling alongside a novel MIE strategy that proves to be beneficial for paranasal anomaly classification in the MS.

A systematic approach to deep learning-based nodule detection in chest radiographs.

Lung cancer is a serious disease responsible for millions of deaths every year. Early stages of lung cancer can be manifested in pulmonary lung nodules. To assist radiologists in reducing the number of overseen nodules and to increase the detection accuracy in general, automatic detection algorithms have been proposed. Particularly, deep learning methods are promising. However, obtaining clinically relevant results remains challenging. While a variety of approaches have been proposed for general purpose object detection, these are typically evaluated on benchmark data sets. Achieving competitive performance for specific real-world problems like lung nodule detection typically requires careful analysis of the problem at hand and the selection and tuning of suitable deep learning models. We present a systematic comparison of state-of-the-art object detection algorithms for the task of lung nodule detection. In this regard, we address the critical aspect of class imbalance and and demonstrate a data augmentation approach as well as transfer learning to boost performance. We illustrate how this analysis and a combination of multiple architectures results in state-of-the-art performance for lung nodule detection, which is demonstrated by the proposed model winning the detection track of the Node21 competition. The code for our approach is available at https://github.com/FinnBehrendt/node21-submit.

Three-dimensional deep learning with spatial erasing for unsupervised anomaly segmentation in brain MRI.

PURPOSE: Brain Magnetic Resonance Images (MRIs) are essential for the diagnosis of neurological diseases. Recently, deep learning methods for unsupervised anomaly detection (UAD) have been proposed for the analysis of brain MRI. These methods rely on healthy brain MRIs and eliminate the requirement of pixel-wise annotated data compared to supervised deep learning. While a wide range of methods for UAD have been proposed, these methods are mostly 2D and only learn from MRI slices, disregarding that brain lesions are inherently 3D and the spatial context of MRI volumes remains unexploited. METHODS: We investigate whether using increased spatial context by using MRI volumes combined with spatial erasing leads to improved unsupervised anomaly segmentation performance compared to learning from slices. We evaluate and compare 2D variational autoencoder (VAE) to their 3D counterpart, propose 3D input erasing, and systemically study the impact of the data set size on the performance. RESULTS: Using two publicly available segmentation data sets for evaluation, 3D VAEs outperform their 2D counterpart, highlighting the advantage of volumetric context. Also, our 3D erasing methods allow for further performance improvements. Our best performing 3D VAE with input erasing leads to an average DICE score of 31.40% compared to 25.76% for the 2D VAE. CONCLUSIONS: We propose 3D deep learning methods for UAD in brain MRI combined with 3D erasing and demonstrate that 3D methods clearly outperform their 2D counterpart for anomaly segmentation. Also, our spatial erasing method allows for further performance improvements and reduces the requirement for large data sets.