Yuan Xue

Haomiao Ni, Yuan Xue, Kelvin Wong et al.

Accurate infarct segmentation in non-contrast CT (NCCT) images is a crucial step toward computer-aided acute ischemic stroke (AIS) assessment. In clinical practice, bilateral symmetric comparison of brain hemispheres is usually used to locate pathological abnormalities. Recent research has explored asymmetries to assist with AIS segmentation. However, most previous symmetry-based work mixed different types of asymmetries when evaluating their contribution to AIS. In this paper, we propose a novel Asymmetry Disentanglement Network (ADN) to automatically separate pathological asymmetries and intrinsic anatomical asymmetries in NCCTs for more effective and interpretable AIS segmentation. ADN first performs asymmetry disentanglement based on input NCCTs, which produces different types of 3D asymmetry maps. Then a synthetic, intrinsic-asymmetry-compensated and pathology-asymmetry-salient NCCT volume is generated and later used as input to a segmentation network. The training of ADN incorporates domain knowledge and adopts a tissue-type aware regularization loss function to encourage clinically-meaningful pathological asymmetry extraction. Coupled with an unsupervised 3D transformation network, ADN achieves state-of-the-art AIS segmentation performance on a public NCCT dataset. In addition to the superior performance, we believe the learned clinically-interpretable asymmetry maps can also provide insights towards a better understanding of AIS assessment. Our code is available at https://github.com/nihaomiao/MICCAI22_ADN.

Jian Jin, Yuan Xue, Xingxing Zhang et al.

Significant improvement has been made on just noticeable difference (JND) modelling due to the development of deep neural networks, especially for the recently developed unsupervised-JND generation models. However, they have a major drawback that the generated JND is assessed in the real-world signal domain instead of in the perceptual domain in the human brain. There is an obvious difference when JND is assessed in such two domains since the visual signal in the real world is encoded before it is delivered into the brain with the human visual system (HVS). Hence, we propose an HVS-inspired signal degradation network for JND estimation. To achieve this, we carefully analyze the HVS perceptual process in JND subjective viewing to obtain relevant insights, and then design an HVS-inspired signal degradation (HVS-SD) network to represent the signal degradation in the HVS. On the one hand, the well learnt HVS-SD enables us to assess the JND in the perceptual domain. On the other hand, it provides more accurate prior information for better guiding JND generation. Additionally, considering the requirement that reasonable JND should not lead to visual attention shifting, a visual attention loss is proposed to control JND generation. Experimental results demonstrate that the proposed method achieves the SOTA performance for accurately estimating the redundancy of the HVS. Source code will be available at https://github.com/jianjin008/HVS-SD-JND.

Lianrui Zuo, Yihao Liu, Yuan Xue et al.

The lack of standardization is a prominent issue in magnetic resonance (MR) imaging. This often causes undesired contrast variations in the acquired images due to differences in hardware and acquisition parameters. In recent years, image synthesis-based MR harmonization with disentanglement has been proposed to compensate for the undesired contrast variations. Despite the success of existing methods, we argue that three major improvements can be made. First, most existing methods are built upon the assumption that multi-contrast MR images of the same subject share the same anatomy. This assumption is questionable, since different MR contrasts are specialized to highlight different anatomical features. Second, these methods often require a fixed set of MR contrasts for training (e.g., both T1-weighted and T2-weighted images), limiting their applicability. Lastly, existing methods are generally sensitive to imaging artifacts. In this paper, we present Harmonization with Attention-based Contrast, Anatomy, and Artifact Awareness (HACA3), a novel approach to address these three issues. HACA3 incorporates an anatomy fusion module that accounts for the inherent anatomical differences between MR contrasts. Furthermore, HACA3 is also robust to imaging artifacts and can be trained and applied to any set of MR contrasts. HACA3 is developed and evaluated on diverse MR datasets acquired from 21 sites with varying field strengths, scanner platforms, and acquisition protocols. Experiments show that HACA3 achieves state-of-the-art performance under multiple image quality metrics. We also demonstrate the applicability and versatility of HACA3 on downstream tasks including white matter lesion segmentation and longitudinal volumetric analyses.

Lianrui Zuo, Yihao Liu, Yuan Xue et al.

Disentangling anatomical and contrast information from medical images has gained attention recently, demonstrating benefits for various image analysis tasks. Current methods learn disentangled representations using either paired multi-modal images with the same underlying anatomy or auxiliary labels (e.g., manual delineations) to provide inductive bias for disentanglement. However, these requirements could significantly increase the time and cost in data collection and limit the applicability of these methods when such data are not available. Moreover, these methods generally do not guarantee disentanglement. In this paper, we present a novel framework that learns theoretically and practically superior disentanglement from single modality magnetic resonance images. Moreover, we propose a new information-based metric to quantitatively evaluate disentanglement. Comparisons over existing disentangling methods demonstrate that the proposed method achieves superior performance in both disentanglement and cross-domain image-to-image translation tasks.

Chang Yan, Muhan Shao, Zhangxing Bian et al.

The thalamus is a subcortical gray matter structure that plays a key role in relaying sensory and motor signals within the brain. Its nuclei can atrophy or otherwise be affected by neurological disease and injuries including mild traumatic brain injury. Segmenting both the thalamus and its nuclei is challenging because of the relatively low contrast within and around the thalamus in conventional magnetic resonance (MR) images. This paper explores imaging features to determine key tissue signatures that naturally cluster, from which we can parcellate thalamic nuclei. Tissue contrasts include T1-weighted and T2-weighted images, MR diffusion measurements including FA, mean diffusivity, Knutsson coefficients that represent fiber orientation, and synthetic multi-TI images derived from FGATIR and T1-weighted images. After registration of these contrasts and isolation of the thalamus, we use the uniform manifold approximation and projection (UMAP) method for dimensionality reduction to produce a low-dimensional representation of the data within the thalamus. Manual labeling of the thalamus provides labels for our UMAP embedding from which k nearest neighbors can be used to label new unseen voxels in that same UMAP embedding. N -fold cross-validation of the method reveals comparable performance to state-of-the-art methods for thalamic parcellation.

Lianrui Zuo, Yuan Xue, Blake E. Dewey et al.

Image quality control (IQC) can be used in automated magnetic resonance (MR) image analysis to exclude erroneous results caused by poorly acquired or artifact-laden images. Existing IQC methods for MR imaging generally require human effort to craft meaningful features or label large datasets for supervised training. The involvement of human labor can be burdensome and biased, as labeling MR images based on their quality is a subjective task. In this paper, we propose an automatic IQC method that evaluates the extent of artifacts in MR images without supervision. In particular, we design an artifact encoding network that learns representations of artifacts based on contrastive learning. We then use a normalizing flow to estimate the density of learned representations for unsupervised classification. Our experiments on large-scale multi-cohort MR datasets show that the proposed method accurately detects images with high levels of artifacts, which can inform downstream analysis tasks about potentially flawed data.

Samuel W. Remedios, Shuo Han, Yuan Xue et al.

In 2D multi-slice magnetic resonance (MR) acquisition, the through-plane signals are typically of lower resolution than the in-plane signals. While contemporary super-resolution (SR) methods aim to recover the underlying high-resolution volume, the estimated high-frequency information is implicit via end-to-end data-driven training rather than being explicitly stated and sought. To address this, we reframe the SR problem statement in terms of perfect reconstruction filter banks, enabling us to identify and directly estimate the missing information. In this work, we propose a two-stage approach to approximate the completion of a perfect reconstruction filter bank corresponding to the anisotropic acquisition of a particular scan. In stage 1, we estimate the missing filters using gradient descent and in stage 2, we use deep networks to learn the mapping from coarse coefficients to detail coefficients. In addition, the proposed formulation does not rely on external training data, circumventing the need for domain shift correction. Under our approach, SR performance is improved particularly in "slice gap" scenarios, likely due to the constrained solution space imposed by the framework.

Yonglong Jiang, Liangliang Li, Yuan Xue et al.

Images obtained under low-light conditions will seriously affect the quality of the images. Solving the problem of poor low-light image quality can effectively improve the visual quality of images and better improve the usability of computer vision. In addition, it has very important applications in many fields. This paper proposes a DEANet based on Retinex for low-light image enhancement. It combines the frequency information and content information of the image into three sub-networks: decomposition network, enhancement network and adjustment network. These three sub-networks are respectively used for decomposition, denoising, contrast enhancement and detail preservation, adjustment, and image generation. Our model has good robust results for all low-light images. The model is trained on the public data set LOL, and the experimental results show that our method is better than the existing state-of-the-art methods in terms of vision and quality.

Haomiao Ni, Yuan Xue, Liya Ma et al.

General movement assessment (GMA) of infant movement videos (IMVs) is an effective method for early detection of cerebral palsy (CP) in infants. We demonstrate in this paper that end-to-end trainable neural networks for image sequence recognition can be applied to achieve good results in GMA, and more importantly, augmenting raw video with infant body parsing and pose estimation information can significantly improve performance. To solve the problem of efficiently utilizing partially labeled IMVs for body parsing, we propose a semi-supervised model, termed SiamParseNet (SPN), which consists of two branches, one for intra-frame body parts segmentation and another for inter-frame label propagation. During training, the two branches are jointly trained by alternating between using input pairs of only labeled frames and input of both labeled and unlabeled frames. We also investigate training data augmentation by proposing a factorized video generative adversarial network (FVGAN) to synthesize novel labeled frames for training. When testing, we employ a multi-source inference mechanism, where the final result for a test frame is either obtained via the segmentation branch or via propagation from a nearby key frame. We conduct extensive experiments for body parsing using SPN on two infant movement video datasets, where SPN coupled with FVGAN achieves state-of-the-art performance. We further demonstrate that SPN can be easily adapted to the infant pose estimation task with superior performance. Last but not least, we explore the clinical application of our method for GMA. We collected a new clinical IMV dataset with GMA annotations, and our experiments show that SPN models for body parsing and pose estimation trained on the first two datasets generalize well to the new clinical dataset and their results can significantly boost the CRNN-based GMA prediction performance.

Xingxuan Zhang, Haoran Wang, Jiansheng Li et al.

Large language models (LLMs) like GPT-4 and LLaMA-3 utilize the powerful in-context learning (ICL) capability of Transformer architecture to learn on the fly from limited examples. While ICL underpins many LLM applications, its full potential remains hindered by a limited understanding of its generalization boundaries and vulnerabilities. We present a systematic investigation of transformers' generalization capability with ICL relative to training data coverage by defining a task-centric framework along three dimensions: inter-problem, intra-problem, and intra-task generalization. Through extensive simulation and real-world experiments, encompassing tasks such as function fitting, API calling, and translation, we find that transformers lack inter-problem generalization with ICL, but excel in intra-task and intra-problem generalization. When the training data includes a greater variety of mixed tasks, it significantly enhances the generalization ability of ICL on unseen tasks and even on known simple tasks. This guides us in designing training data to maximize the diversity of tasks covered and to combine different tasks whenever possible, rather than solely focusing on the target task for testing.

Yuan Xue, Qi Zhang, Chuanmin Jia et al.

Image Compression for Machines (ICM) aims to compress images for machine vision tasks rather than human viewing. Current works predominantly concentrate on high-level tasks like object detection and semantic segmentation. However, the quality of original images is usually not guaranteed in the real world, leading to even worse perceptual quality or downstream task performance after compression. Low-level (LL) machine vision models, like image restoration models, can help improve such quality, and thereby their compression requirements should also be considered. In this paper, we propose a pioneered ICM framework for LL machine vision tasks, namely LL-ICM. By jointly optimizing compression and LL tasks, the proposed LL-ICM not only enriches its encoding ability in generalizing to versatile LL tasks but also optimizes the processing ability of down-stream LL task models, achieving mutual adaptation for image codecs and LL task models. Furthermore, we integrate large-scale vision-language models into the LL-ICM framework to generate more universal and distortion-robust feature embeddings for LL vision tasks. Therefore, one LL-ICM codec can generalize to multiple tasks. We establish a solid benchmark to evaluate LL-ICM, which includes extensive objective experiments by using both full and no-reference image quality assessments. Experimental results show that LL-ICM can achieve 22.65% BD-rate reductions over the state-of-the-art methods.