3DQ: Compact Quantized Neural Networks for Volumetric Whole Brain Segmentation

Model architectures have been dramatically increasing in size, improving performance at the cost of resource requirements. In this paper we propose 3DQ, a ternary quantization method, applied for the first time to 3D Fully Convolutional Neural Networks (F-CNNs), enabling 16x model compression while maintaining performance on par with full precision models. We extensively evaluate 3DQ on two datasets for the challenging task of whole brain segmentation. Additionally, we showcase our method's ability to generalize on two common 3D architectures, namely 3D U-Net and V-Net. Outperforming a variety of baselines, the proposed method is capable of compressing large 3D models to a few MBytes, alleviating the storage needs in space critical applications.Comment: Accepted to MICCAI 201

Modality-Agnostic Learning for Medical Image Segmentation Using Multi-modality Self-distillation

Medical image segmentation of tumors and organs at risk is a time-consuming yet critical process in the clinic that utilizes multi-modality imaging (e.g, different acquisitions, data types, and sequences) to increase segmentation precision. In this paper, we propose a novel framework, Modality-Agnostic learning through Multi-modality Self-dist-illation (MAG-MS), to investigate the impact of input modalities on medical image segmentation. MAG-MS distills knowledge from the fusion of multiple modalities and applies it to enhance representation learning for individual modalities. Thus, it provides a versatile and efficient approach to handle limited modalities during testing. Our extensive experiments on benchmark datasets demonstrate the high efficiency of MAG-MS and its superior segmentation performance than current state-of-the-art methods. Furthermore, using MAG-MS, we provide valuable insight and guidance on selecting input modalities for medical image segmentation tasks

Continual Learning in Medical Image Analysis: A Comprehensive Review of Recent Advancements and Future Prospects

Medical imaging analysis has witnessed remarkable advancements even surpassing human-level performance in recent years, driven by the rapid development of advanced deep-learning algorithms. However, when the inference dataset slightly differs from what the model has seen during one-time training, the model performance is greatly compromised. The situation requires restarting the training process using both the old and the new data which is computationally costly, does not align with the human learning process, and imposes storage constraints and privacy concerns. Alternatively, continual learning has emerged as a crucial approach for developing unified and sustainable deep models to deal with new classes, tasks, and the drifting nature of data in non-stationary environments for various application areas. Continual learning techniques enable models to adapt and accumulate knowledge over time, which is essential for maintaining performance on evolving datasets and novel tasks. This systematic review paper provides a comprehensive overview of the state-of-the-art in continual learning techniques applied to medical imaging analysis. We present an extensive survey of existing research, covering topics including catastrophic forgetting, data drifts, stability, and plasticity requirements. Further, an in-depth discussion of key components of a continual learning framework such as continual learning scenarios, techniques, evaluation schemes, and metrics is provided. Continual learning techniques encompass various categories, including rehearsal, regularization, architectural, and hybrid strategies. We assess the popularity and applicability of continual learning categories in various medical sub-fields like radiology and histopathology..

Towards Cross-modality Medical Image Segmentation with Online Mutual Knowledge Distillation

The success of deep convolutional neural networks is partially attributed to the massive amount of annotated training data. However, in practice, medical data annotations are usually expensive and time-consuming to be obtained. Considering multi-modality data with the same anatomic structures are widely available in clinic routine, in this paper, we aim to exploit the prior knowledge (e.g., shape priors) learned from one modality (aka., assistant modality) to improve the segmentation performance on another modality (aka., target modality) to make up annotation scarcity. To alleviate the learning difficulties caused by modality-specific appearance discrepancy, we first present an Image Alignment Module (IAM) to narrow the appearance gap between assistant and target modality data.We then propose a novel Mutual Knowledge Distillation (MKD) scheme to thoroughly exploit the modality-shared knowledge to facilitate the target-modality segmentation. To be specific, we formulate our framework as an integration of two individual segmentors. Each segmentor not only explicitly extracts one modality knowledge from corresponding annotations, but also implicitly explores another modality knowledge from its counterpart in mutual-guided manner. The ensemble of two segmentors would further integrate the knowledge from both modalities and generate reliable segmentation results on target modality. Experimental results on the public multi-class cardiac segmentation data, i.e., MMWHS 2017, show that our method achieves large improvements on CT segmentation by utilizing additional MRI data and outperforms other state-of-the-art multi-modality learning methods.Comment: Accepted by AAAI 202

BMAD: Benchmarks for Medical Anomaly Detection

Anomaly detection (AD) is a fundamental research problem in machine learning and computer vision, with practical applications in industrial inspection, video surveillance, and medical diagnosis. In medical imaging, AD is especially vital for detecting and diagnosing anomalies that may indicate rare diseases or conditions. However, there is a lack of a universal and fair benchmark for evaluating AD methods on medical images, which hinders the development of more generalized and robust AD methods in this specific domain. To bridge this gap, we introduce a comprehensive evaluation benchmark for assessing anomaly detection methods on medical images. This benchmark encompasses six reorganized datasets from five medical domains (i.e. brain MRI, liver CT, retinal OCT, chest X-ray, and digital histopathology) and three key evaluation metrics, and includes a total of fourteen state-of-the-art AD algorithms. This standardized and well-curated medical benchmark with the well-structured codebase enables comprehensive comparisons among recently proposed anomaly detection methods. It will facilitate the community to conduct a fair comparison and advance the field of AD on medical imaging. More information on BMAD is available in our GitHub repository: https://github.com/DorisBao/BMA

Dice Semimetric Losses: Optimizing the Dice Score with Soft Labels

The soft Dice loss (SDL) has taken a pivotal role in many automated segmentation pipelines in the medical imaging community. Over the last years, some reasons behind its superior functioning have been uncovered and further optimizations have been explored. However, there is currently no implementation that supports its direct use in settings with soft labels. Hence, a synergy between the use of SDL and research leveraging the use of soft labels, also in the context of model calibration, is still missing. In this work, we introduce Dice semimetric losses (DMLs), which (i) are by design identical to SDL in a standard setting with hard labels, but (ii) can be used in settings with soft labels. Our experiments on the public QUBIQ, LiTS and KiTS benchmarks confirm the potential synergy of DMLs with soft labels (e.g. averaging, label smoothing, and knowledge distillation) over hard labels (e.g. majority voting and random selection). As a result, we obtain superior Dice scores and model calibration, which supports the wider adoption of DMLs in practice. Code is available at \href{https://github.com/zifuwanggg/JDTLosses}{https://github.com/zifuwanggg/JDTLosses}.Comment: Submitted to MICCAI2023. Code is available at https://github.com/zifuwanggg/JDTLosse

Cross-Modality Deep Feature Learning for Brain Tumor Segmentation

Recent advances in machine learning and prevalence of digital medical images have opened up an opportunity to address the challenging brain tumor segmentation (BTS) task by using deep convolutional neural networks. However, different from the RGB image data that are very widespread, the medical image data used in brain tumor segmentation are relatively scarce in terms of the data scale but contain the richer information in terms of the modality property. To this end, this paper proposes a novel cross-modality deep feature learning framework to segment brain tumors from the multi-modality MRI data. The core idea is to mine rich patterns across the multi-modality data to make up for the insufficient data scale. The proposed cross-modality deep feature learning framework consists of two learning processes: the cross-modality feature transition (CMFT) process and the cross-modality feature fusion (CMFF) process, which aims at learning rich feature representations by transiting knowledge across different modality data and fusing knowledge from different modality data, respectively. Comprehensive experiments are conducted on the BraTS benchmarks, which show that the proposed cross-modality deep feature learning framework can effectively improve the brain tumor segmentation performance when compared with the baseline methods and state-of-the-art methods.Comment: published on Pattern Recognition 202

Continual Learning for Abdominal Multi-Organ and Tumor Segmentation

The ability to dynamically extend a model to new data and classes is critical for multiple organ and tumor segmentation. However, due to privacy regulations, accessing previous data and annotations can be problematic in the medical domain. This poses a significant barrier to preserving the high segmentation accuracy of the old classes when learning from new classes because of the catastrophic forgetting problem. In this paper, we first empirically demonstrate that simply using high-quality pseudo labels can fairly mitigate this problem in the setting of organ segmentation. Furthermore, we put forward an innovative architecture designed specifically for continuous organ and tumor segmentation, which incurs minimal computational overhead. Our proposed design involves replacing the conventional output layer with a suite of lightweight, class-specific heads, thereby offering the flexibility to accommodate newly emerging classes. These heads enable independent predictions for newly introduced and previously learned classes, effectively minimizing the impact of new classes on old ones during the course of continual learning. We further propose incorporating Contrastive Language-Image Pretraining (CLIP) embeddings into the organ-specific heads. These embeddings encapsulate the semantic information of each class, informed by extensive image-text co-training. The proposed method is evaluated on both in-house and public abdominal CT datasets under organ and tumor segmentation tasks. Empirical results suggest that the proposed design improves the segmentation performance of a baseline neural network on newly-introduced and previously-learned classes along the learning trajectory.Comment: MICCAI-202