Lan Ma

Tsai Hor Chan, Fernando Julio Cendra, Lan Ma et al.

Graph-based methods have been extensively applied to whole-slide histopathology image (WSI) analysis due to the advantage of modeling the spatial relationships among different entities. However, most of the existing methods focus on modeling WSIs with homogeneous graphs (e.g., with homogeneous node type). Despite their successes, these works are incapable of mining the complex structural relations between biological entities (e.g., the diverse interaction among different cell types) in the WSI. We propose a novel heterogeneous graph-based framework to leverage the inter-relationships among different types of nuclei for WSI analysis. Specifically, we formulate the WSI as a heterogeneous graph with "nucleus-type" attribute to each node and a semantic similarity attribute to each edge. We then present a new heterogeneous-graph edge attribute transformer (HEAT) to take advantage of the edge and node heterogeneity during massage aggregating. Further, we design a new pseudo-label-based semantic-consistent pooling mechanism to obtain graph-level features, which can mitigate the over-parameterization issue of conventional cluster-based pooling. Additionally, observing the limitations of existing association-based localization methods, we propose a causal-driven approach attributing the contribution of each node to improve the interpretability of our framework. Extensive experiments on three public TCGA benchmark datasets demonstrate that our framework outperforms the state-of-the-art methods with considerable margins on various tasks. Our codes are available at https://github.com/HKU-MedAI/WSI-HGNN.

Fernando Julio Cendra, Lan Ma, Jiajun Shen et al.

Deep learning has attained remarkable success in many 3D visual recognition tasks, including shape classification, object detection, and semantic segmentation. However, many of these results rely on manually collecting densely annotated real-world 3D data, which is highly time-consuming and expensive to obtain, limiting the scalability of 3D recognition tasks. Thus, we study unsupervised 3D recognition and propose a Self-supervised-Self-Labeled 3D Recognition (SL3D) framework. SL3D simultaneously solves two coupled objectives, i.e., clustering and learning feature representation to generate pseudo-labeled data for unsupervised 3D recognition. SL3D is a generic framework and can be applied to solve different 3D recognition tasks, including classification, object detection, and semantic segmentation. Extensive experiments demonstrate its effectiveness. Code is available at https://github.com/fcendra/sl3d.

Ruitao Zhang, Xueying Han, Ijaz Gul et al.

Acute leukemia is a type of blood cancer with a high mortality rate. Current therapeutic methods include bone marrow transplantation, supportive therapy, and chemotherapy. Although a satisfactory remission of the disease can be achieved, the risk of recurrence is still high. Therefore, novel treatments are demanding. Chimeric antigen receptor-T (CAR-T) therapy has emerged as a promising approach to treat and cure acute leukemia. To harness the therapeutic potential of CAR-T cell therapy for blood diseases, reliable cell morphological identification is crucial. Nevertheless, the identification of CAR-T cells is a big challenge posed by their phenotypic similarity with other blood cells. To address this substantial clinical challenge, herein we first construct a CAR-T dataset with 500 original microscopy images after staining. Following that, we create a novel integrated model called RCMNet (ResNet18 with CBAM and MHSA) that combines the convolutional neural network (CNN) and Transformer. The model shows 99.63% top-1 accuracy on the public dataset. Compared with previous reports, our model obtains satisfactory results for image classification. Although testing on the CAR-T cells dataset, a decent performance is observed, which is attributed to the limited size of the dataset. Transfer learning is adapted for RCMNet and a maximum of 83.36% accuracy has been achieved, which is higher than other SOTA models. The study evaluates the effectiveness of RCMNet on a big public dataset and translates it to a clinical dataset for diagnostic applications.

Kin Wai Lau, Yasar Abbas Ur Rehman, Yuyang Xie et al.

This report presents the technical details of our submission to the 2023 Epic-Kitchen EPIC-SOUNDS Audio-Based Interaction Recognition Challenge. The task is to learn the mapping from audio samples to their corresponding action labels. To achieve this goal, we propose a simple yet effective single-stream CNN-based architecture called AudioInceptionNeXt that operates on the time-frequency log-mel-spectrogram of the audio samples. Motivated by the design of the InceptionNeXt, we propose parallel multi-scale depthwise separable convolutional kernels in the AudioInceptionNeXt block, which enable the model to learn the time and frequency information more effectively. The large-scale separable kernels capture the long duration of activities and the global frequency semantic information, while the small-scale separable kernels capture the short duration of activities and local details of frequency information. Our approach achieved 55.43% of top-1 accuracy on the challenge test set, ranked as 1st on the public leaderboard. Codes are available anonymously at https://github.com/StevenLauHKHK/AudioInceptionNeXt.git.

Zhuo Deng, Yuanhao Cai, Lu Chen et al.

Ophthalmologists have used fundus images to screen and diagnose eye diseases. However, different equipments and ophthalmologists pose large variations to the quality of fundus images. Low-quality (LQ) degraded fundus images easily lead to uncertainty in clinical screening and generally increase the risk of misdiagnosis. Thus, real fundus image restoration is worth studying. Unfortunately, real clinical benchmark has not been explored for this task so far. In this paper, we investigate the real clinical fundus image restoration problem. Firstly, We establish a clinical dataset, Real Fundus (RF), including 120 low- and high-quality (HQ) image pairs. Then we propose a novel Transformer-based Generative Adversarial Network (RFormer) to restore the real degradation of clinical fundus images. The key component in our network is the Window-based Self-Attention Block (WSAB) which captures non-local self-similarity and long-range dependencies. To produce more visually pleasant results, a Transformer-based discriminator is introduced. Extensive experiments on our clinical benchmark show that the proposed RFormer significantly outperforms the state-of-the-art (SOTA) methods. In addition, experiments of downstream tasks such as vessel segmentation and optic disc/cup detection demonstrate that our proposed RFormer benefits clinical fundus image analysis and applications. The dataset, code, and models are publicly available at https://github.com/dengzhuo-AI/Real-Fundus

Zheng Gong, Zhuo Deng, Run Gan et al.

The retinal fundus images are utilized extensively in the diagnosis, and their quality can directly affect the diagnosis results. However, due to the insufficient dataset and algorithm application, current fundus image quality assessment (FIQA) methods are not powerful enough to meet ophthalmologists` demands. In this paper, we address the limitations of datasets and algorithms in FIQA. First, we establish a new FIQA dataset, Fundus Quality Score(FQS), which includes 2246 fundus images with two labels: a continuous Mean Opinion Score varying from 0 to 100 and a three-level quality label. Then, we propose a FIQA Transformer-based Hypernetwork (FTHNet) to solve these tasks with regression results rather than classification results in conventional FIQA works. The FTHNet is optimized for the FIQA tasks with extensive experiments. Results on our FQS dataset show that the FTHNet can give quality scores for fundus images with PLCC of 0.9423 and SRCC of 0.9488, significantly outperforming other methods with fewer parameters and less computation complexity.We successfully build a dataset and model addressing the problems of current FIQA methods. Furthermore, the model deployment experiments demonstrate its potential in automatic medical image quality control. All experiments are carried out with 10-fold cross-validation to ensure the significance of the results.

Yasar Abbas Ur Rehman, Kin Wai Lau, Yuyang Xie et al.

Recent studies have demonstrated that vision models can effectively learn multimodal audio-image representations when paired. However, the challenge of enabling deep models to learn representations from unpaired modalities remains unresolved. This issue is especially pertinent in scenarios like Federated Learning (FL), where data is often decentralized, heterogeneous, and lacks a reliable guarantee of paired data. Previous attempts tackled this issue through the use of auxiliary pretrained encoders or generative models on local clients, which invariably raise computational cost with increasing number modalities. Unlike these approaches, in this paper, we aim to address the task of unpaired audio and image recognition using \texttt{FSSUAVL}, a single deep model pretrained in FL with self-supervised contrastive learning (SSL). Instead of aligning the audio and image modalities, \texttt{FSSUAVL} jointly discriminates them by projecting them into a common embedding space using contrastive SSL. This extends the utility of \texttt{FSSUAVL} to paired and unpaired audio and image recognition tasks. Our experiments with CNN and ViT demonstrate that \texttt{FSSUAVL} significantly improves performance across various image- and audio-based downstream tasks compared to using separate deep models for each modality. Additionally, \texttt{FSSUAVL}'s capacity to learn multimodal feature representations allows for integrating auxiliary information, if available, to enhance recognition accuracy.