Evidence-aware multi-modal data fusion and its application to total knee replacement prediction

Deep neural networks have been widely studied for predicting a medical condition, such as total knee replacement (TKR). It has shown that data of different modalities, such as imaging data, clinical variables and demographic information, provide complementary information and thus can improve the prediction accuracy together. However, the data sources of various modalities may not always be of high quality, and each modality may have only partial information of medical condition. Thus, predictions from different modalities can be opposite, and the final prediction may fail in the presence of such a conflict. Therefore, it is important to consider the reliability of each source data and the prediction output when making a final decision. In this paper, we propose an evidence-aware multi-modal data fusion framework based on the Dempster-Shafer theory (DST). The backbone models contain an image branch, a non-image branch and a fusion branch. For each branch, there is an evidence network that takes the extracted features as input and outputs an evidence score, which is designed to represent the reliability of the output from the current branch. The output probabilities along with the evidence scores from multiple branches are combined with the Dempster's combination rule to make a final prediction. Experimental results on the public OA initiative (OAI) dataset for the TKR prediction task show the superiority of the proposed fusion strategy on various backbone models.

DuDoRNeXt: A hybrid model for dual-domain undersampled MRI reconstruction

Undersampled MRI reconstruction is crucial for accelerating clinical scanning procedures. Recent deep learning methods for MRI reconstruction adopt CNN or ViT as backbone, which lack in utilizing the complementary properties of CNN and ViT. In this paper, we propose DuDoRNeXt, whose backbone hybridizes CNN and ViT in an domain-specific, intra-stage way. Besides our hybrid vertical layout design, we introduce domain-specific modules for dual-domain reconstruction, namely image-domain parallel local detail enhancement and k-space global initialization. We evaluate different conventions of MRI reconstruction including image-domain, k-space-domain, and dual-domain reconstruction with a reference protocol on the IXI dataset and an in-house multi-contrast dataset. DuDoRNeXt achieves significant improvements over competing deep learning methods.

GDDS: Pulmonary Bronchioles Segmentation with Group Deep Dense Supervision

Airway segmentation, especially bronchioles segmentation, is an important but challenging task because distal bronchus are sparsely distributed and of a fine scale. Existing neural networks usually exploit sparse topology to learn the connectivity of bronchioles and inefficient shallow features to capture such high-frequency information, leading to the breakage or missed detection of individual thin branches. To address these problems, we contribute a new bronchial segmentation method based on Group Deep Dense Supervision (GDDS) that emphasizes fine-scale bronchioles segmentation in a simple-but-effective manner. First, Deep Dense Supervision (DDS) is proposed by constructing local dense topology skillfully and implementing dense topological learning on a specific shallow feature layer. GDDS further empowers the shallow features with better perception ability to detect bronchioles, even the ones that are not easily discernible to the naked eye. Extensive experiments on the BAS benchmark dataset have shown that our method promotes the network to have a high sensitivity in capturing fine-scale branches and outperforms state-of-the-art methods by a large margin (+12.8 % in BD and +8.8 % in TD) while only introducing a small number of extra parameters.

FairAdaBN: Mitigating unfairness with adaptive batch normalization and its application to dermatological disease classification

Deep learning is becoming increasingly ubiquitous in medical research and applications while involving sensitive information and even critical diagnosis decisions. Researchers observe a significant performance disparity among subgroups with different demographic attributes, which is called model unfairness, and put lots of effort into carefully designing elegant architectures to address unfairness, which poses heavy training burden, brings poor generalization, and reveals the trade-off between model performance and fairness. To tackle these issues, we propose FairAdaBN by making batch normalization adaptive to sensitive attribute. This simple but effective design can be adopted to several classification backbones that are originally unaware of fairness. Additionally, we derive a novel loss function that restrains statistical parity between subgroups on mini-batches, encouraging the model to converge with considerable fairness. In order to evaluate the trade-off between model performance and fairness, we propose a new metric, named Fairness-Accuracy Trade-off Efficiency (FATE), to compute normalized fairness improvement over accuracy drop. Experiments on two dermatological datasets show that our proposed method outperforms other methods on fairness criteria and FATE.

O2CTA: Introducing Annotations from OCT to CCTA in Coronary Plaque Analysis

Targeted diagnosis and treatment plans for patients with coronary artery disease vary according to atherosclerotic plaque component. Coronary CT angiography (CCTA) is widely used for artery imaging and determining the stenosis degree. However, the limited spatial resolution and susceptibility to artifacts fail CCTA in obtaining lumen morphological characteristics and plaque composition. It can be settled by invasive optical coherence tomography (OCT) without much trouble for physicians, but bringing higher costs and potential risks to patients. Therefore, it is clinically critical to introduce annotations of plaque tissue and lumen characteristics from OCT to paired CCTA scans, denoted as \textbf{the O2CTA problem} in this paper. We propose a method to handle the O2CTA problem. CCTA scans are first reconstructed into multi-planar reformatted (MPR) images, which agree with OCT images in term of semantic contents. The artery segment in OCT, which is manually labelled, is then spatially aligned with the entire artery in MPR images via the proposed alignment strategy. Finally, a classification model involving a 3D CNN and a Transformer, is learned to extract local features and capture dependence along arteries. Experiments on 55 paired OCT and CCTA we curate demonstrate that it is feasible to classify the CCTA based on the OCT labels, with an accuracy of 86.2%, while the manual readings of OCT and CCTA vary significantly, with a Kappa coefficient of 0.113. We will make our source codes, models, data, and results publicly available to benefit the research community.

Distortion-Disentangled Contrastive Learning

Self-supervised learning is well known for its remarkable performance in representation learning and various downstream computer vision tasks. Recently, Positive-pair-Only Contrastive Learning (POCL) has achieved reliable performance without the need to construct positive-negative training sets. It reduces memory requirements by lessening the dependency on the batch size. The POCL method typically uses a single loss function to extract the distortion invariant representation (DIR) which describes the proximity of positive-pair representations affected by different distortions. This loss function implicitly enables the model to filter out or ignore the distortion variant representation (DVR) affected by different distortions. However, existing POCL methods do not explicitly enforce the disentanglement and exploitation of the actually valuable DVR. In addition, these POCL methods have been observed to be sensitive to augmentation strategies. To address these limitations, we propose a novel POCL framework named Distortion-Disentangled Contrastive Learning (DDCL) and a Distortion-Disentangled Loss (DDL). Our approach is the first to explicitly disentangle and exploit the DVR inside the model and feature stream to improve the overall representation utilization efficiency, robustness and representation ability. Experiments carried out demonstrate the superiority of our framework to Barlow Twins and Simsiam in terms of convergence, representation quality, and robustness on several benchmark datasets.

Mixed-order self-paced curriculum learning for universal lesion detection

Self-paced curriculum learning (SCL) has demonstrated its great potential in computer vision, natural language processing, etc. During training, it implements easy-to-hard sampling based on online estimation of data difficulty. Most SCL methods commonly adopt a loss-based strategy of estimating data difficulty and deweighting the `hard' samples in the early training stage. While achieving success in a variety of applications, SCL stills confront two challenges in a medical image analysis task, such as universal lesion detection, featuring insufficient and highly class-imbalanced data: (i) the loss-based difficulty measurer is inaccurate; ii) the hard samples are under-utilized from a deweighting mechanism. To overcome these challenges, in this paper we propose a novel mixed-order self-paced curriculum learning (Mo-SCL) method. We integrate both uncertainty and loss to better estimate difficulty online and mix both hard and easy samples in the same mini-batch to appropriately alleviate the problem of under-utilization of hard samples. We provide a theoretical investigation of our method in the context of stochastic gradient descent optimization and extensive experiments based on the DeepLesion benchmark dataset for universal lesion detection (ULD). When applied to two state-of-the-art ULD methods, the proposed mixed-order SCL method can provide a free boost to lesion detection accuracy without extra special network designs.

Multi-site Organ Segmentation with Federated Partial Supervision and Site Adaptation

Objective and Impact Statement: Accurate organ segmentation is critical for many clinical applications at different clinical sites, which may have their specific application requirements that concern different organs. Introduction: However, learning high-quality, site-specific organ segmentation models is challenging as it often needs on-site curation of a large number of annotated images. Security concerns further complicate the matter. Methods: The paper aims to tackle these challenges via a two-phase aggregation-then-adaptation approach. The first phase of federated aggregation learns a single multi-organ segmentation model by leveraging the strength of 'bigger data', which are formed by (i) aggregating together datasets from multiple sites that with different organ labels to provide partial supervision, and (ii) conducting partially supervised learning without data breach. The second phase of site adaptation is to transfer the federated multi-organ segmentation model to site-specific organ segmentation models, one model per site, in order to further improve the performance of each site's organ segmentation task. Furthermore, improved marginal loss and exclusion loss functions are used to avoid 'knowledge conflict' problem in a partially supervision mechanism. Results and Conclusion: Extensive experiments on five organ segmentation datasets demonstrate the effectiveness of our multi-site approach, significantly outperforming the site-per-se learned models and achieving the performance comparable to the centrally learned models.

MURPHY: Relations Matter in Surgical Workflow Analysis

Autonomous robotic surgery has advanced significantly based on analysis of visual and temporal cues in surgical workflow, but relational cues from domain knowledge remain under investigation. Complex relations in surgical annotations can be divided into intra- and inter-relations, both valuable to autonomous systems to comprehend surgical workflows. Intra- and inter-relations describe the relevance of various categories within a particular annotation type and the relevance of different annotation types, respectively. This paper aims to systematically investigate the importance of relational cues in surgery. First, we contribute the RLLS12M dataset, a large-scale collection of robotic left lateral sectionectomy (RLLS), by curating 50 videos of 50 patients operated by 5 surgeons and annotating a hierarchical workflow, which consists of 3 inter- and 6 intra-relations, 6 steps, 15 tasks, and 38 activities represented as the triplet of 11 instruments, 8 actions, and 16 objects, totaling 2,113,510 video frames and 12,681,060 annotation entities. Correspondingly, we propose a multi-relation purification hybrid network (MURPHY), which aptly incorporates novel relation modules to augment the feature representation by purifying relational features using the intra- and inter-relations embodied in annotations. The intra-relation module leverages a R-GCN to implant visual features in different graph relations, which are aggregated using a targeted relation purification with affinity information measuring label consistency and feature similarity. The inter-relation module is motivated by attention mechanisms to regularize the influence of relational features based on the hierarchy of annotation types from the domain knowledge. Extensive experimental results on the curated RLLS dataset confirm the effectiveness of our approach, demonstrating that relations matter in surgical workflow analysis.

LE-UDA: Label-efficient unsupervised domain adaptation for medical image segmentation

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift~w.r.t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called ``Label-Efficient Unsupervised Domain Adaptation"~(LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature. Code is available at: https://github.com/jacobzhaoziyuan/LE-UDA.