Effective Lymph Nodes Detection in CT Scans Using Location Debiased Query Selection and Contrastive Query Representation in Transformer

Lymph node (LN) assessment is a critical, indispensable yet very challenging task in the routine clinical workflow of radiology and oncology. Accurate LN analysis is essential for cancer diagnosis, staging, and treatment planning. Finding scatteredly distributed, low-contrast clinically relevant LNs in 3D CT is difficult even for experienced physicians under high inter-observer variations. Previous automatic LN detection works typically yield limited recall and high false positives (FPs) due to adjacent anatomies with similar image intensities, shapes, or textures (vessels, muscles, esophagus, etc). In this work, we propose a new LN DEtection TRansformer, named LN-DETR, to achieve more accurate performance. By enhancing the 2D backbone with a multi-scale 2.5D feature fusion to incorporate 3D context explicitly, more importantly, we make two main contributions to improve the representation quality of LN queries. 1) Considering that LN boundaries are often unclear, an IoU prediction head and a location debiased query selection are proposed to select LN queries of higher localization accuracy as the decoder query's initialization. 2) To reduce FPs, query contrastive learning is employed to explicitly reinforce LN queries towards their best-matched ground-truth queries over unmatched query predictions. Trained and tested on 3D CT scans of 1067 patients (with 10,000+ labeled LNs) via combining seven LN datasets from different body parts (neck, chest, and abdomen) and pathologies/cancers, our method significantly improves the performance of previous leading methods by > 4-5% average recall at the same FP rates in both internal and external testing. We further evaluate on the universal lesion detection task using NIH DeepLesion benchmark, and our method achieves the top performance of 88.46% averaged recall across 0.5 to 4 FPs per image, compared with other leading reported results.

ReSynthDetect: A Fundus Anomaly Detection Network with Reconstruction and Synthetic Features

Detecting anomalies in fundus images through unsupervised methods is a challenging task due to the similarity between normal and abnormal tissues, as well as their indistinct boundaries. The current methods have limitations in accurately detecting subtle anomalies while avoiding false positives. To address these challenges, we propose the ReSynthDetect network which utilizes a reconstruction network for modeling normal images, and an anomaly generator that produces synthetic anomalies consistent with the appearance of fundus images. By combining the features of consistent anomaly generation and image reconstruction, our method is suited for detecting fundus abnormalities. The proposed approach has been extensively tested on benchmark datasets such as EyeQ and IDRiD, demonstrating state-of-the-art performance in both image-level and pixel-level anomaly detection. Our experiments indicate a substantial 9% improvement in AUROC on EyeQ and a significant 17.1% improvement in AUPR on IDRiD.

Learning Anatomically Consistent Embedding for Chest Radiography

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Source-Free Domain Adaptation for Medical Image Segmentation via Prototype-Anchored Feature Alignment and Contrastive Learning

Unsupervised domain adaptation (UDA) has increasingly gained interests for its capacity to transfer the knowledge learned from a labeled source domain to an unlabeled target domain. However, typical UDA methods require concurrent access to both the source and target domain data, which largely limits its application in medical scenarios where source data is often unavailable due to privacy concern. To tackle the source data-absent problem, we present a novel two-stage source-free domain adaptation (SFDA) framework for medical image segmentation, where only a well-trained source segmentation model and unlabeled target data are available during domain adaptation. Specifically, in the prototype-anchored feature alignment stage, we first utilize the weights of the pre-trained pixel-wise classifier as source prototypes, which preserve the information of source features. Then, we introduce the bi-directional transport to align the target features with class prototypes by minimizing its expected cost. On top of that, a contrastive learning stage is further devised to utilize those pixels with unreliable predictions for a more compact target feature distribution. Extensive experiments on a cross-modality medical segmentation task demonstrate the superiority of our method in large domain discrepancy settings compared with the state-of-the-art SFDA approaches and even some UDA methods. Code is available at https://github.com/CSCYQJ/MICCAI23-ProtoContra-SFDA.

Region and Spatial Aware Anomaly Detection for Fundus Images

Recently anomaly detection has drawn much attention in diagnosing ocular diseases. Most existing anomaly detection research in fundus images has relatively large anomaly scores in the salient retinal structures, such as blood vessels, optical cups and discs. In this paper, we propose a Region and Spatial Aware Anomaly Detection (ReSAD) method for fundus images, which obtains local region and long-range spatial information to reduce the false positives in the normal structure. ReSAD transfers a pre-trained model to extract the features of normal fundus images and applies the Region-and-Spatial-Aware feature Combination module (ReSC) for pixel-level features to build a memory bank. In the testing phase, ReSAD uses the memory bank to determine out-of-distribution samples as abnormalities. Our method significantly outperforms the existing anomaly detection methods for fundus images on two publicly benchmark datasets.

Bilateral-Fuser: A Novel Multi-cue Fusion Architecture with Anatomical-aware Tokens for Fovea Localization

Accurate localization of fovea is one of the primary steps in analyzing retinal diseases since it helps prevent irreversible vision loss. Although current deep learning-based methods achieve better performance than traditional methods, there still remain challenges such as utilizing anatomical landmarks insufficiently, sensitivity to diseased retinal images and various image conditions. In this paper, we propose a novel transformer-based architecture (Bilateral-Fuser) for multi-cue fusion. This architecture explicitly incorporates long-range connections and global features using retina and vessel distributions for robust fovea localization. We introduce a spatial attention mechanism in the dual-stream encoder for extracting and fusing self-learned anatomical information. This design focuses more on features distributed along blood vessels and significantly decreases computational costs by reducing token numbers. Our comprehensive experiments show that the proposed architecture achieves state-of-the-art performance on two public and one large-scale private datasets. We also present that the Bilateral-Fuser is more robust on both normal and diseased retina images and has better generalization capacity in cross-dataset experiments.

Coarse Retinal Lesion Annotations Refinement via Prototypical Learning

Deep-learning-based approaches for retinal lesion segmentation often require an abundant amount of precise pixel-wise annotated data. However, coarse annotations such as circles or ellipses for outlining the lesion area can be six times more efficient than pixel-level annotation. Therefore, this paper proposes an annotation refinement network to convert a coarse annotation into a pixel-level segmentation mask. Our main novelty is the application of the prototype learning paradigm to enhance the generalization ability across different datasets or types of lesions. We also introduce a prototype weighing module to handle challenging cases where the lesion is overly small. The proposed method was trained on the publicly available IDRiD dataset and then generalized to the public DDR and our real-world private datasets. Experiments show that our approach substantially improved the initial coarse mask and outperformed the non-prototypical baseline by a large margin. Moreover, we demonstrate the usefulness of the prototype weighing module in both cross-dataset and cross-class settings.

Weakly Supervised Online Action Detection for Infant General Movements

To make the earlier medical intervention of infants' cerebral palsy (CP), early diagnosis of brain damage is critical. Although general movements assessment(GMA) has shown promising results in early CP detection, it is laborious. Most existing works take videos as input to make fidgety movements(FMs) classification for the GMA automation. Those methods require a complete observation of videos and can not localize video frames containing normal FMs. Therefore we propose a novel approach named WO-GMA to perform FMs localization in the weakly supervised online setting. Infant body keypoints are first extracted as the inputs to WO-GMA. Then WO-GMA performs local spatio-temporal extraction followed by two network branches to generate pseudo clip labels and model online actions. With the clip-level pseudo labels, the action modeling branch learns to detect FMs in an online fashion. Experimental results on a dataset with 757 videos of different infants show that WO-GMA can get state-of-the-art video-level classification and cliplevel detection results. Moreover, only the first 20% duration of the video is needed to get classification results as good as fully observed, implying a significantly shortened FMs diagnosis time. Code is available at: https://github.com/scofiedluo/WO-GMA.

MDT-Net: Multi-domain Transfer by Perceptual Supervision for Unpaired Images in OCT Scan

Deep learning models tend to underperform in the presence of domain shifts. Domain transfer has recently emerged as a promising approach wherein images exhibiting a domain shift are transformed into other domains for augmentation or adaptation. However, with the absence of paired and annotated images, most domain transfer methods mainly rely on adversarial networks and weak cycle consistency, which could result in incomplete domain transfer or poor adherence to the original image content. In this paper, we introduce MDT-Net to address the limitations above through a multi-domain transfer model based on perceptual supervision. Specifically, our model consists of an encoder-decoder network, which aims to preserve anatomical structures, and multiple domain-specific transfer modules, which guide the domain transition through feature transformation. During the inference, MDT-Net can directly transfer images from the source domain to multiple target domains at one time without any reference image. To demonstrate the performance of MDT-Net, we evaluate it on RETOUCH dataset, comprising OCT scans from three different scanner devices (domains), for multi-domain transfer. We also take the transformed results as additional training images for fluid segmentation in OCT scans in the tasks of domain adaptation and data augmentation. Experimental results show that MDT-Net can outperform other domain transfer models qualitatively and quantitatively. Furthermore, the significant improvement in dice scores over multiple segmentation models also demonstrates the effectiveness and efficiency of our proposed method.

Bilateral-ViT for Robust Fovea Localization

The fovea is an important anatomical landmark of the retina. Detecting the location of the fovea is essential for the analysis of many retinal diseases. However, robust fovea localization remains a challenging problem, as the fovea region often appears fuzzy, and retina diseases may further obscure its appearance. This paper proposes a novel vision transformer (ViT) approach that integrates information both inside and outside the fovea region to achieve robust fovea localization. Our proposed network named Bilateral-Vision-Transformer (Bilateral-ViT) consists of two network branches: a transformer-based main network branch for integrating global context across the entire fundus image and a vessel branch for explicitly incorporating the structure of blood vessels. The encoded features from both network branches are subsequently merged with a customized multi-scale feature fusion (MFF) module. Our comprehensive experiments demonstrate that the proposed approach is significantly more robust for diseased images and establishes the new state of the arts on both Messidor and PALM datasets.