Mask Enhanced Deeply Supervised Prostate Cancer Detection on B-mode Micro-Ultrasound

Prostate cancer is a leading cause of cancer-related deaths among men. The recent development of high frequency, micro-ultrasound imaging offers improved resolution compared to conventional ultrasound and potentially a better ability to differentiate clinically significant cancer from normal tissue. However, the features of prostate cancer remain subtle, with ambiguous borders with normal tissue and large variations in appearance, making it challenging for both machine learning and humans to localize it on micro-ultrasound images. We propose a novel Mask Enhanced Deeply-supervised Micro-US network, termed MedMusNet, to automatically and more accurately segment prostate cancer to be used as potential targets for biopsy procedures. MedMusNet leverages predicted masks of prostate cancer to enforce the learned features layer-wisely within the network, reducing the influence of noise and improving overall consistency across frames. MedMusNet successfully detected 76% of clinically significant cancer with a Dice Similarity Coefficient of 0.365, significantly outperforming the baseline Swin-M2F in specificity and accuracy (Wilcoxon test, Bonferroni correction, p-value<0.05). While the lesion-level and patient-level analyses showed improved performance compared to human experts and different baseline, the improvements did not reach statistical significance, likely on account of the small cohort. We have presented a novel approach to automatically detect and segment clinically significant prostate cancer on B-mode micro-ultrasound images. Our MedMusNet model outperformed other models, surpassing even human experts. These preliminary results suggest the potential for aiding urologists in prostate cancer diagnosis via biopsy and treatment decision-making.

Sound event detection based on auxiliary decoder and maximum probability aggregation for DCASE Challenge 2024 Task 4

In this report, we propose three novel methods for developing a sound event detection (SED) model for the DCASE 2024 Challenge Task 4. First, we propose an auxiliary decoder attached to the final convolutional block to improve feature extraction capabilities while reducing dependency on embeddings from pre-trained large models. The proposed auxiliary decoder operates independently from the main decoder, enhancing performance of the convolutional block during the initial training stages by assigning a different weight strategy between main and auxiliary decoder losses. Next, to address the time interval issue between the DESED and MAESTRO datasets, we propose maximum probability aggregation (MPA) during the training step. The proposed MPA method enables the model's output to be aligned with soft labels of 1 s in the MAESTRO dataset. Finally, we propose a multi-channel input feature that employs various versions of logmel and MFCC features to generate time-frequency pattern. The experimental results demonstrate the efficacy of these proposed methods in a view of improving SED performance by achieving a balanced enhancement across different datasets and label types. Ultimately, this approach presents a significant step forward in developing more robust and flexible SED models

ProsDectNet: Bridging the Gap in Prostate Cancer Detection via Transrectal B-mode Ultrasound Imaging

Interpreting traditional B-mode ultrasound images can be challenging due to image artifacts (e.g., shadowing, speckle), leading to low sensitivity and limited diagnostic accuracy. While Magnetic Resonance Imaging (MRI) has been proposed as a solution, it is expensive and not widely available. Furthermore, most biopsies are guided by Transrectal Ultrasound (TRUS) alone and can miss up to 52% cancers, highlighting the need for improved targeting. To address this issue, we propose ProsDectNet, a multi-task deep learning approach that localizes prostate cancer on B-mode ultrasound. Our model is pre-trained using radiologist-labeled data and fine-tuned using biopsy-confirmed labels. ProsDectNet includes a lesion detection and patch classification head, with uncertainty minimization using entropy to improve model performance and reduce false positive predictions. We trained and validated ProsDectNet using a cohort of 289 patients who underwent MRI-TRUS fusion targeted biopsy. We then tested our approach on a group of 41 patients and found that ProsDectNet outperformed the average expert clinician in detecting prostate cancer on B-mode ultrasound images, achieving a patient-level ROC-AUC of 82%, a sensitivity of 74%, and a specificity of 67%. Our results demonstrate that ProsDectNet has the potential to be used as a computer-aided diagnosis system to improve targeted biopsy and treatment planning.

Domain Generalization for Prostate Segmentation in Transrectal Ultrasound Images: A Multi-center Study

Prostate biopsy and image-guided treatment procedures are often performed under the guidance of ultrasound fused with magnetic resonance images (MRI). Accurate image fusion relies on accurate segmentation of the prostate on ultrasound images. Yet, the reduced signal-to-noise ratio and artifacts (e.g., speckle and shadowing) in ultrasound images limit the performance of automated prostate segmentation techniques and generalizing these methods to new image domains is inherently difficult. In this study, we address these challenges by introducing a novel 2.5D deep neural network for prostate segmentation on ultrasound images. Our approach addresses the limitations of transfer learning and finetuning methods (i.e., drop in performance on the original training data when the model weights are updated) by combining a supervised domain adaptation technique and a knowledge distillation loss. The knowledge distillation loss allows the preservation of previously learned knowledge and reduces the performance drop after model finetuning on new datasets. Furthermore, our approach relies on an attention module that considers model feature positioning information to improve the segmentation accuracy. We trained our model on 764 subjects from one institution and finetuned our model using only ten subjects from subsequent institutions. We analyzed the performance of our method on three large datasets encompassing 2067 subjects from three different institutions. Our method achieved an average Dice Similarity Coefficient (Dice) of $94.0\pm0.03$ and Hausdorff Distance (HD95) of 2.28 $mm$ in an independent set of subjects from the first institution. Moreover, our model generalized well in the studies from the other two institutions (Dice: $91.0\pm0.03$; HD95: 3.7$mm$ and Dice: $82.0\pm0.03$; HD95: 7.1 $mm$).

ConFUDA: Contrastive Fewshot Unsupervised Domain Adaptation for Medical Image Segmentation

Unsupervised domain adaptation (UDA) aims to transfer knowledge learned from a labeled source domain to an unlabeled target domain. Contrastive learning (CL) in the context of UDA can help to better separate classes in feature space. However, in image segmentation, the large memory footprint due to the computation of the pixel-wise contrastive loss makes it prohibitive to use. Furthermore, labeled target data is not easily available in medical imaging, and obtaining new samples is not economical. As a result, in this work, we tackle a more challenging UDA task when there are only a few (fewshot) or a single (oneshot) image available from the target domain. We apply a style transfer module to mitigate the scarcity of target samples. Then, to align the source and target features and tackle the memory issue of the traditional contrastive loss, we propose the centroid-based contrastive learning (CCL) and a centroid norm regularizer (CNR) to optimize the contrastive pairs in both direction and magnitude. In addition, we propose multi-partition centroid contrastive learning (MPCCL) to further reduce the variance in the target features. Fewshot evaluation on MS-CMRSeg dataset demonstrates that ConFUDA improves the segmentation performance by 0.34 of the Dice score on the target domain compared with the baseline, and 0.31 Dice score improvement in a more rigorous oneshot setting.

Few-shot Unsupervised Domain Adaptation for Multi-modal Cardiac Image Segmentation

Unsupervised domain adaptation (UDA) methods intend to reduce the gap between source and target domains by using unlabeled target domain and labeled source domain data, however, in the medical domain, target domain data may not always be easily available, and acquiring new samples is generally time-consuming. This restricts the development of UDA methods for new domains. In this paper, we explore the potential of UDA in a more challenging while realistic scenario where only one unlabeled target patient sample is available. We call it Few-shot Unsupervised Domain adaptation (FUDA). We first generate target-style images from source images and explore diverse target styles from a single target patient with Random Adaptive Instance Normalization (RAIN). Then, a segmentation network is trained in a supervised manner with the generated target images. Our experiments demonstrate that FUDA improves the segmentation performance by 0.33 of Dice score on the target domain compared with the baseline, and it also gives 0.28 of Dice score improvement in a more rigorous one-shot setting. Our code is available at \url{https://github.com/MingxuanGu/Few-shot-UDA}.

Learn2Reg: comprehensive multi-task medical image registration challenge, dataset and evaluation in the era of deep learning

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks, in part because of the lack of availability of such diverse data. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration benchmark for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, and the results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias.

Adapt Everywhere: Unsupervised Adaptation of Point-Clouds and Entropy Minimisation for Multi-modal Cardiac Image Segmentation

Deep learning models are sensitive to domain shift phenomena. A model trained on images from one domain cannot generalise well when tested on images from a different domain, despite capturing similar anatomical structures. It is mainly because the data distribution between the two domains is different. Moreover, creating annotation for every new modality is a tedious and time-consuming task, which also suffers from high inter- and intra- observer variability. Unsupervised domain adaptation (UDA) methods intend to reduce the gap between source and target domains by leveraging source domain labelled data to generate labels for the target domain. However, current state-of-the-art (SOTA) UDA methods demonstrate degraded performance when there is insufficient data in source and target domains. In this paper, we present a novel UDA method for multi-modal cardiac image segmentation. The proposed method is based on adversarial learning and adapts network features between source and target domain in different spaces. The paper introduces an end-to-end framework that integrates: a) entropy minimisation, b) output feature space alignment and c) a novel point-cloud shape adaptation based on the latent features learned by the segmentation model. We validated our method on two cardiac datasets by adapting from the annotated source domain, bSSFP-MRI (balanced Steady-State Free Procession-MRI), to the unannotated target domain, LGE-MRI (Late-gadolinium enhance-MRI), for the multi-sequence dataset; and from MRI (source) to CT (target) for the cross-modality dataset. The results highlighted that by enforcing adversarial learning in different parts of the network, the proposed method delivered promising performance, compared to other SOTA methods.

Spatio-temporal Multi-task Learning for Cardiac MRI Left Ventricle Quantification

Quantitative assessment of cardiac left ventricle (LV) morphology is essential to assess cardiac function and improve the diagnosis of different cardiovascular diseases. In current clinical practice, LV quantification depends on the measurement of myocardial shape indices, which is usually achieved by manual contouring of the endo- and epicardial. However, this process subjected to inter and intra-observer variability, and it is a time-consuming and tedious task. In this paper, we propose a spatio-temporal multi-task learning approach to obtain a complete set of measurements quantifying cardiac LV morphology, regional-wall thickness (RWT), and additionally detecting the cardiac phase cycle (systole and diastole) for a given 3D Cine-magnetic resonance (MR) image sequence. We first segment cardiac LVs using an encoder-decoder network and then introduce a multitask framework to regress 11 LV indices and classify the cardiac phase, as parallel tasks during model optimization. The proposed deep learning model is based on the 3D spatio-temporal convolutions, which extract spatial and temporal features from MR images. We demonstrate the efficacy of the proposed method using cine-MR sequences of 145 subjects and comparing the performance with other state-of-the-art quantification methods. The proposed method obtained high prediction accuracy, with an average mean absolute error (MAE) of 129 $mm^2$, 1.23 $mm$, 1.76 $mm$, Pearson correlation coefficient (PCC) of 96.4%, 87.2%, and 97.5% for LV and myocardium (Myo) cavity regions, 6 RWTs, 3 LV dimensions, and an error rate of 9.0\% for phase classification. The experimental results highlight the robustness of the proposed method, despite varying degrees of cardiac morphology, image appearance, and low contrast in the cardiac MR sequences.

Cardiac Segmentation on Late Gadolinium Enhancement MRI: A Benchmark Study from Multi-Sequence Cardiac MR Segmentation Challenge

Accurate computing, analysis and modeling of the ventricles and myocardium from medical images are important, especially in the diagnosis and treatment management for patients suffering from myocardial infarction (MI). Late gadolinium enhancement (LGE) cardiac magnetic resonance (CMR) provides an important protocol to visualize MI. However, automated segmentation of LGE CMR is still challenging, due to the indistinguishable boundaries, heterogeneous intensity distribution and complex enhancement patterns of pathological myocardium from LGE CMR. Furthermore, compared with the other sequences LGE CMR images with gold standard labels are particularly limited, which represents another obstacle for developing novel algorithms for automatic segmentation of LGE CMR. This paper presents the selective results from the Multi-Sequence Cardiac MR (MS-CMR) Segmentation challenge, in conjunction with MICCAI 2019. The challenge offered a data set of paired MS-CMR images, including auxiliary CMR sequences as well as LGE CMR, from 45 patients who underwent cardiomyopathy. It was aimed to develop new algorithms, as well as benchmark existing ones for LGE CMR segmentation and compare them objectively. In addition, the paired MS-CMR images could enable algorithms to combine the complementary information from the other sequences for the segmentation of LGE CMR. Nine representative works were selected for evaluation and comparisons, among which three methods are unsupervised methods and the other six are supervised. The results showed that the average performance of the nine methods was comparable to the inter-observer variations. The success of these methods was mainly attributed to the inclusion of the auxiliary sequences from the MS-CMR images, which provide important label information for the training of deep neural networks.