Chao Li

Zhijian Hou, Lei Ji, Difei Gao et al.

In this report, we present our champion solution for Ego4D Natural Language Queries (NLQ) Challenge in CVPR 2023. Essentially, to accurately ground in a video, an effective egocentric feature extractor and a powerful grounding model are required. Motivated by this, we leverage a two-stage pre-training strategy to train egocentric feature extractors and the grounding model on video narrations, and further fine-tune the model on annotated data. In addition, we introduce a novel grounding model GroundNLQ, which employs a multi-modal multi-scale grounding module for effective video and text fusion and various temporal intervals, especially for long videos. On the blind test set, GroundNLQ achieves 25.67 and 18.18 for R1@IoU=0.3 and R1@IoU=0.5, respectively, and surpasses all other teams by a noticeable margin. Our code will be released at\url{https://github.com/houzhijian/GroundNLQ}.

Yiran Wei, Xi Chen, Lei Zhu et al.

The isocitrate dehydrogenase (IDH) gene mutation is an essential biomarker for the diagnosis and prognosis of glioma. It is promising to better predict glioma genotype by integrating focal tumor image and geometric features with brain network features derived from MRI. Convolutions neural networks show reasonable performance in predicting IDH mutation, which, however, cannot learn from non-Euclidean data, e.g., geometric and network data. In this study, we propose a multi-modal learning framework using three separate encoders to extract features of focal tumor image, tumor geometrics and global brain networks. To mitigate the limited availability of diffusion MRI, we develop a self-supervised approach to generate brain networks from anatomical multi-sequence MRI. Moreover, to extract tumor-related features from the brain network, we design a hierarchical attention module for the brain network encoder. Further, we design a bi-level multi-modal contrastive loss to align the multi-modal features and tackle the domain gap at the focal tumor and global brain. Finally, we propose a weighted population graph to integrate the multi-modal features for genotype prediction. Experimental results on the testing set show that the proposed model outperforms the baseline deep learning models. The ablation experiments validate the performance of different components of the framework. The visualized interpretation corresponds to clinical knowledge with further validation. In conclusion, the proposed learning framework provides a novel approach for predicting the genotype of glioma.

Yiran Wei, Stephen J. Price, Carola-Bibiane Schönlieb et al.

Alzheimer's disease (AD) is the most common age-related dementia. Mild cognitive impairment (MCI) is the early stage of cognitive decline before AD. It is crucial to predict the MCI-to-AD conversion for precise management, which remains challenging due to the diversity of patients. Previous evidence shows that the brain network generated from diffusion MRI promises to classify dementia using deep learning. However, the limited availability of diffusion MRI challenges the model training. In this study, we develop a self-supervised contrastive learning approach to generate structural brain networks from routine anatomical MRI under the guidance of diffusion MRI. The generated brain networks are applied to train a learning framework for predicting the MCI-to-AD conversion. Instead of directly modelling the AD brain networks, we train a graph encoder and a variational autoencoder to model the healthy ageing trajectories from brain networks of healthy controls. To predict the MCI-to-AD conversion, we further design a recurrent neural networks based approach to model the longitudinal deviation of patients' brain networks from the healthy ageing trajectory. Numerical results show that the proposed methods outperform the benchmarks in the prediction task. We also visualize the model interpretation to explain the prediction and identify abnormal changes of white matter tracts.

Chaoyu Liu, Zhonghua Qiao, Chao Li et al.

Traditional image processing methods employing partial differential equations (PDEs) offer a multitude of meaningful regularizers, along with valuable theoretical foundations for a wide range of image-related tasks. This makes their integration into neural networks a promising avenue. In this paper, we introduce a novel regularization approach inspired by the reverse process of PDE-based evolution models. Specifically, we propose inverse evolution layers (IELs), which serve as bad property amplifiers to penalize neural networks of which outputs have undesired characteristics. Using IELs, one can achieve specific regularization objectives and endow neural networks' outputs with corresponding properties of the PDE models. Our experiments, focusing on semantic segmentation tasks using heat-diffusion IELs, demonstrate their effectiveness in mitigating noisy label effects. Additionally, we develop curve-motion IELs to enforce convex shape regularization in neural network-based segmentation models for preventing the generation of concave outputs. Theoretical analysis confirms the efficacy of IELs as an effective regularization mechanism, particularly in handling training with label issues.

Lan Jiang, Ye Mao, Xi Chen et al.

MRI synthesis promises to mitigate the challenge of missing MRI modality in clinical practice. Diffusion model has emerged as an effective technique for image synthesis by modelling complex and variable data distributions. However, most diffusion-based MRI synthesis models are using a single modality. As they operate in the original image domain, they are memory-intensive and less feasible for multi-modal synthesis. Moreover, they often fail to preserve the anatomical structure in MRI. Further, balancing the multiple conditions from multi-modal MRI inputs is crucial for multi-modal synthesis. Here, we propose the first diffusion-based multi-modality MRI synthesis model, namely Conditioned Latent Diffusion Model (CoLa-Diff). To reduce memory consumption, we design CoLa-Diff to operate in the latent space. We propose a novel network architecture, e.g., similar cooperative filtering, to solve the possible compression and noise in latent space. To better maintain the anatomical structure, brain region masks are introduced as the priors of density distributions to guide diffusion process. We further present auto-weight adaptation to employ multi-modal information effectively. Our experiments demonstrate that CoLa-Diff outperforms other state-of-the-art MRI synthesis methods, promising to serve as an effective tool for multi-modal MRI synthesis.

Ye Mao, Lan Jiang, Xi Chen et al.

Multi-contrast magnetic resonance imaging (MRI) is the most common management tool used to characterize neurological disorders based on brain tissue contrasts. However, acquiring high-resolution MRI scans is time-consuming and infeasible under specific conditions. Hence, multi-contrast super-resolution methods have been developed to improve the quality of low-resolution contrasts by leveraging complementary information from multi-contrast MRI. Current deep learning-based super-resolution methods have limitations in estimating restoration uncertainty and avoiding mode collapse. Although the diffusion model has emerged as a promising approach for image enhancement, capturing complex interactions between multiple conditions introduced by multi-contrast MRI super-resolution remains a challenge for clinical applications. In this paper, we propose a disentangled conditional diffusion model, DisC-Diff, for multi-contrast brain MRI super-resolution. It utilizes the sampling-based generation and simple objective function of diffusion models to estimate uncertainty in restorations effectively and ensure a stable optimization process. Moreover, DisC-Diff leverages a disentangled multi-stream network to fully exploit complementary information from multi-contrast MRI, improving model interpretation under multiple conditions of multi-contrast inputs. We validated the effectiveness of DisC-Diff on two datasets: the IXI dataset, which contains 578 normal brains, and a clinical dataset with 316 pathological brains. Our experimental results demonstrate that DisC-Diff outperforms other state-of-the-art methods both quantitatively and visually.

Hang Zhang, Rongguang Wang, Jinwei Zhang et al.

Compared to natural images, medical images usually show stronger visual patterns and therefore this adds flexibility and elasticity to resource-limited clinical applications by injecting proper priors into neural networks. In this paper, we propose spatially covariant pixel-aligned classifier (SCP) to improve the computational efficiency and meantime maintain or increase accuracy for lesion segmentation. SCP relaxes the spatial invariance constraint imposed by convolutional operations and optimizes an underlying implicit function that maps image coordinates to network weights, the parameters of which are obtained along with the backbone network training and later used for generating network weights to capture spatially covariant contextual information. We demonstrate the effectiveness and efficiency of the proposed SCP using two lesion segmentation tasks from different imaging modalities: white matter hyperintensity segmentation in magnetic resonance imaging and liver tumor segmentation in contrast-enhanced abdominal computerized tomography. The network using SCP has achieved 23.8%, 64.9% and 74.7% reduction in GPU memory usage, FLOPs, and network size with similar or better accuracy for lesion segmentation.

Feihong Shen, Chao Li, Yifeng Geng et al.

Image retargeting is the task of adjusting the aspect ratio of images to suit different display devices or presentation environments. However, existing retargeting methods often struggle to balance the preservation of key semantics and image quality, resulting in either deformation or loss of important objects, or the introduction of local artifacts such as discontinuous pixels and inconsistent regenerated content. To address these issues, we propose a content-aware retargeting method called PruneRepaint. It incorporates semantic importance for each pixel to guide the identification of regions that need to be pruned or preserved in order to maintain key semantics. Additionally, we introduce an adaptive repainting module that selects image regions for repainting based on the distribution of pruned pixels and the proportion between foreground size and target aspect ratio, thus achieving local smoothness after pruning. By focusing on the content and structure of the foreground, our PruneRepaint approach adaptively avoids key content loss and deformation, while effectively mitigating artifacts with local repainting. We conduct experiments on the public RetargetMe benchmark and demonstrate through objective experimental results and subjective user studies that our method outperforms previous approaches in terms of preserving semantics and aesthetics, as well as better generalization across diverse aspect ratios. Codes will be available at https://github.com/fhshen2022/PruneRepaint.

Hao Tang, Hanyu Liu, Alessandro Perelli et al.

Diffusion MRI (dMRI) is a critical non-invasive technique to estimate fiber orientation distribution (FOD) for characterizing white matter integrity. Estimating FOD from single-shell low angular resolution dMRI (LAR-FOD) is limited by accuracy, whereas estimating FOD from multi-shell high angular resolution dMRI (HAR-FOD) requires a long scanning time, which limits its applicability. Diffusion models have shown promise in estimating HAR-FOD based on LAR-FOD. However, using diffusion models to efficiently generate HAR-FOD is challenging due to the large number of spherical harmonic (SH) coefficients in FOD. Here, we propose a 3D multi-channel patch diffusion model to predict HAR-FOD from LAR-FOD. We design the FOD-patch adapter by introducing the prior brain anatomy for more efficient patch-based learning. Furthermore, we introduce a voxel-level conditional coordinating module to enhance the global understanding of the model. We design the SH attention module to effectively learn the complex correlations of the SH coefficients. Our experimental results show that our method achieves the best performance in HAR-FOD prediction and outperforms other state-of-the-art methods.

Ruodan Yan, Carola-Bibiane Schönlieb, Chao Li

Perfusion MRI (pMRI) offers valuable insights into tumor vascularity and promises to predict tumor genotypes, thus benefiting prognosis for glioma patients, yet effective models tailored to 4D pMRI are still lacking. This study presents the first attempt to model 4D pMRI using a GNN-based spatiotemporal model PerfGAT, integrating spatial information and temporal kinetics to predict Isocitrate DeHydrogenase (IDH) mutation status in glioma patients. Specifically, we propose a graph structure learning approach based on edge attention and negative graphs to optimize temporal correlations modeling. Moreover, we design a dual-attention feature fusion module to integrate spatiotemporal features while addressing tumor-related brain regions. Further, we develop a class-balanced augmentation methods tailored to spatiotemporal data, which could mitigate the common label imbalance issue in clinical datasets. Our experimental results demonstrate that the proposed method outperforms other state-of-the-art approaches, promising to model pMRI effectively for patient characterization.

Juanhua Zhang, Ruodan Yan, Alessandro Perelli et al.

Diffusion MRI (dMRI) is an important neuroimaging technique with high acquisition costs. Deep learning approaches have been used to enhance dMRI and predict diffusion biomarkers through undersampled dMRI. To generate more comprehensive raw dMRI, generative adversarial network based methods are proposed to include b-values and b-vectors as conditions, but they are limited by unstable training and less desirable diversity. The emerging diffusion model (DM) promises to improve generative performance. However, it remains challenging to include essential information in conditioning DM for more relevant generation, i.e., the physical principles of dMRI and white matter tract structures. In this study, we propose a physics-guided diffusion model to generate high-quality dMRI. Our model introduces the physical principles of dMRI in the noise evolution in the diffusion process and introduce a query-based conditional mapping within the difussion model. In addition, to enhance the anatomical fine detials of the generation, we introduce the XTRACT atlas as prior of white matter tracts by adopting an adapter technique. Our experiment results show that our method outperforms other state-of-the-art methods and has the potential to advance dMRI enhancement.

Yiran Wei, Chao Li, Xi Chen et al.

The isocitrate dehydrogenase (IDH) gene mutation status is an important biomarker for glioma patients. The gold standard of IDH mutation detection requires tumour tissue obtained via invasive approaches and is usually expensive. Recent advancement in radiogenomics provides a non-invasive approach for predicting IDH mutation based on MRI. Meanwhile, tumor geometrics encompass crucial information for tumour phenotyping. Here we propose a collaborative learning framework that learns both tumor images and tumor geometrics using convolutional neural networks (CNN) and graph neural networks (GNN), respectively. Our results show that the proposed model outperforms the baseline model of 3D-DenseNet121. Further, the collaborative learning model achieves better performance than either the CNN or the GNN alone. The model interpretation shows that the CNN and GNN could identify common and unique regions of interest for IDH mutation prediction. In conclusion, collaborating image and geometric learners provides a novel approach for predicting genotype and characterising glioma.

Yiran Wei, Yonghao Li, Xi Chen et al.

Glioma is a common malignant brain tumor with distinct survival among patients. The isocitrate dehydrogenase (IDH) gene mutation provides critical diagnostic and prognostic value for glioma. It is of crucial significance to non-invasively predict IDH mutation based on pre-treatment MRI. Machine learning/deep learning models show reasonable performance in predicting IDH mutation using MRI. However, most models neglect the systematic brain alterations caused by tumor invasion, where widespread infiltration along white matter tracts is a hallmark of glioma. Structural brain network provides an effective tool to characterize brain organisation, which could be captured by the graph neural networks (GNN) to more accurately predict IDH mutation. Here we propose a method to predict IDH mutation using GNN, based on the structural brain network of patients. Specifically, we firstly construct a network template of healthy subjects, consisting of atlases of edges (white matter tracts) and nodes (cortical/subcortical brain regions) to provide regions of interest (ROIs). Next, we employ autoencoders to extract the latent multi-modal MRI features from the ROIs of edges and nodes in patients, to train a GNN architecture for predicting IDH mutation. The results show that the proposed method outperforms the baseline models using the 3D-CNN and 3D-DenseNet. In addition, model interpretation suggests its ability to identify the tracts infiltrated by tumor, corresponding to clinical prior knowledge. In conclusion, integrating brain networks with GNN offers a new avenue to study brain lesions using computational neuroscience and computer vision approaches.

Yifan Li, Chao Li, Yiran Wei et al.

Glioblastoma is profoundly heterogeneous in regional microstructure and vasculature. Characterizing the spatial heterogeneity of glioblastoma could lead to more precise treatment. With unsupervised learning techniques, glioblastoma MRI-derived radiomic features have been widely utilized for tumor sub-region segmentation and survival prediction. However, the reliability of algorithm outcomes is often challenged by both ambiguous intermediate process and instability introduced by the randomness of clustering algorithms, especially for data from heterogeneous patients. In this paper, we propose an adaptive unsupervised learning approach for efficient MRI intra-tumor partitioning and glioblastoma survival prediction. A novel and problem-specific Feature-enhanced Auto-Encoder (FAE) is developed to enhance the representation of pairwise clinical modalities and therefore improve clustering stability of unsupervised learning algorithms such as K-means. Moreover, the entire process is modelled by the Bayesian optimization (BO) technique with a custom loss function that the hyper-parameters can be adaptively optimized in a reasonably few steps. The results demonstrate that the proposed approach can produce robust and clinically relevant MRI sub-regions and statistically significant survival predictions.

Chao Li, Hang Zhang, Jinwei Zhang et al.

An approach to reduce motion artifacts in Quantitative Susceptibility Mapping using deep learning is proposed. We use an affine motion model with randomly created motion profiles to simulate motion-corrupted QSM images. The simulated QSM image is paired with its motion-free reference to train a neural network using supervised learning. The trained network is tested on unseen simulated motion-corrupted QSM images, in healthy volunteers and in Parkinson's disease patients. The results show that motion artifacts, such as ringing and ghosting, were successfully suppressed.

Chao Li, Yiran Wei, Xi Chen et al.

Alzheimer's disease (AD) is the most common age-related dementia. It remains a challenge to identify the individuals at risk of dementia for precise management. Brain MRI offers a noninvasive biomarker to detect brain aging. Previous evidence shows that the brain structural change detected by diffusion MRI is associated with dementia. Mounting studies has conceptualised the brain as a complex network, which has shown the utility of this approach in characterising various neurological and psychiatric disorders. Therefore, the structural connectivity shows promise in dementia classification. The proposed BrainNetGAN is a generative adversarial network variant to augment the brain structural connectivity matrices for binary dementia classification tasks. Structural connectivity matrices between separated brain regions are constructed using tractography on diffusion MRI data. The BrainNetGAN model is trained to generate fake brain connectivity matrices, which are expected to reflect latent distribution of the real brain network data. Finally, a convolutional neural network classifier is proposed for binary dementia classification. Numerical results show that the binary classification performance in the testing set was improved using the BrainNetGAN augmented dataset. The proposed methodology allows quick synthesis of an arbitrary number of augmented connectivity matrices and can be easily transferred to similar classification tasks.

Yifan Li, Chao Li, Stephen Price et al.

Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-regions for reliable clinical survival prediction. Hyper-parameters are automatically determined by the global minimum of the trained Gaussian Process (GP) surrogate model through Bayesian optimization(BO) to alleviate the difficulty of tuning parameters for clinical researchers. To enhance the interpretability of the survival prediction model, we incorporated the prior knowledge of intra-tumoral heterogeneity, by segmenting tumor sub-regions and extracting sub-regional features. The results demonstrated that the global minimum of the trained GP surrogate can be used as sub-optimal hyper-parameter solutions for efficient. The sub-regions segmented based on physiological MRI can be applied to predict patient survival, which could enhance the clinical interpretability for the machine learning model.

Zhihui Zhang, Jingwen Leng, Lingxiao Ma et al.

Graph neural networks (GNN) represent an emerging line of deep learning models that operate on graph structures. It is becoming more and more popular due to its high accuracy achieved in many graph-related tasks. However, GNN is not as well understood in the system and architecture community as its counterparts such as multi-layer perceptrons and convolutional neural networks. This work tries to introduce the GNN to our community. In contrast to prior work that only presents characterizations of GCNs, our work covers a large portion of the varieties for GNN workloads based on a general GNN description framework. By constructing the models on top of two widely-used libraries, we characterize the GNN computation at inference stage concerning general-purpose and application-specific architectures and hope our work can foster more system and architecture research for GNNs.

Guanghao Yin, Shouqian Sun, Chao Li et al.

In real-world single image super-resolution (SISR) task, the low-resolution image suffers more complicated degradations, not only downsampled by unknown kernels. However, existing SISR methods are generally studied with the synthetic low-resolution generation such as bicubic interpolation (BI), which greatly limits their performance. Recently, some researchers investigate real-world SISR from the perspective of the camera and smartphone. However, except the acquisition equipment, the display device also involves more complicated degradations. In this paper, we focus on the camera-screen degradation and build a real-world dataset (Cam-ScreenSR), where HR images are original ground truths from the previous DIV2K dataset and corresponding LR images are camera-captured versions of HRs displayed on the screen. We conduct extensive experiments to demonstrate that involving more real degradations is positive to improve the generalization of SISR models. Moreover, we propose a joint two-stage model. Firstly, the downsampling degradation GAN(DD-GAN) is trained to model the degradation and produces more various of LR images, which is validated to be efficient for data augmentation. Then the dual residual channel attention network (DuRCAN) learns to recover the SR image. The weighted combination of L1 loss and proposed Laplacian loss are applied to sharpen the high-frequency edges. Extensive experimental results in both typical synthetic and complicated real-world degradations validate the proposed method outperforms than existing SOTA models with less parameters, faster speed and better visual results. Moreover, in real captured photographs, our model also delivers best visual quality with sharper edge, less artifacts, especially appropriate color enhancement, which has not been accomplished by previous methods.

Dario Fuoli, Zhiwu Huang, Martin Danelljan et al.

This paper reviews the NTIRE 2020 challenge on video quality mapping (VQM), which addresses the issues of quality mapping from source video domain to target video domain. The challenge includes both a supervised track (track 1) and a weakly-supervised track (track 2) for two benchmark datasets. In particular, track 1 offers a new Internet video benchmark, requiring algorithms to learn the map from more compressed videos to less compressed videos in a supervised training manner. In track 2, algorithms are required to learn the quality mapping from one device to another when their quality varies substantially and weakly-aligned video pairs are available. For track 1, in total 7 teams competed in the final test phase, demonstrating novel and effective solutions to the problem. For track 2, some existing methods are evaluated, showing promising solutions to the weakly-supervised video quality mapping problem.

Kai Zhang, Shuhang Gu, Radu Timofte et al.

This paper reviews the NTIRE 2020 challenge on perceptual extreme super-resolution with focus on proposed solutions and results. The challenge task was to super-resolve an input image with a magnification factor 16 based on a set of prior examples of low and corresponding high resolution images. The goal is to obtain a network design capable to produce high resolution results with the best perceptual quality and similar to the ground truth. The track had 280 registered participants, and 19 teams submitted the final results. They gauge the state-of-the-art in single image super-resolution.

Zihao Huang, Chao Li, Feng Duan et al.

It is a challenging task to restore images from their variants with combined distortions. In the existing works, a promising strategy is to apply parallel "operations" to handle different types of distortion. However, in the feature fusion phase, a small number of operations would dominate the restoration result due to the features' heterogeneity by different operations. To this end, we introduce the tensor 1x1 convolutional layer by imposing high-order tensor (outer) product, by which we not only harmonize the heterogeneous features but also take additional non-linearity into account. To avoid the unacceptable kernel size resulted from the tensor product, we construct the kernels with tensor network decomposition, which is able to convert the exponential growth of the dimension to linear growth. Armed with the new layer, we propose High-order OWAN for multi-distorted image restoration. In the numerical experiments, the proposed net outperforms the previous state-of-the-art and shows promising performance even in more difficult tasks.

Chaohao Xie, Shaohui Liu, Chao Li et al.

Most convolutional network (CNN)-based inpainting methods adopt standard convolution to indistinguishably treat valid pixels and holes, making them limited in handling irregular holes and more likely to generate inpainting results with color discrepancy and blurriness. Partial convolution has been suggested to address this issue, but it adopts handcrafted feature re-normalization, and only considers forward mask-updating. In this paper, we present a learnable attention map module for learning feature renormalization and mask-updating in an end-to-end manner, which is effective in adapting to irregular holes and propagation of convolution layers. Furthermore, learnable reverse attention maps are introduced to allow the decoder of U-Net to concentrate on filling in irregular holes instead of reconstructing both holes and known regions, resulting in our learnable bidirectional attention maps. Qualitative and quantitative experiments show that our method performs favorably against state-of-the-arts in generating sharper, more coherent and visually plausible inpainting results. The source code and pre-trained models will be available.

Wei He, Quanming Yao, Chao Li et al.

Non-local low-rank tensor approximation has been developed as a state-of-the-art method for hyperspectral image (HSI) denoising. Unfortunately, with more spectral bands for HSI, while the running time of these methods significantly increases, their denoising performance benefits little. In this paper, we claim that the HSI underlines a global spectral low-rank subspace, and the spectral subspaces of each full band patch groups should underlie this global low-rank subspace. This motivates us to propose a unified spatial-spectral paradigm for HSI denoising. As the new model is hard to optimize, we further propose an efficient algorithm for optimization, which is motivated by alternating minimization. This is done by first learning a low-dimensional projection and the related reduced image from the noisy HSI. Then, the non-local low-rank denoising and iterative regularization are developed to refine the reduced image and projection, respectively. Finally, experiments on synthetic and both real datasets demonstrate the superiority against the other state-of-the-arts HSI denoising methods.

Chao Li, Yi Yang, Min Feng et al.

Leveraging large data sets, deep Convolutional Neural Networks (CNNs) achieve state-of-the-art recognition accuracy. Due to the substantial compute and memory operations, however, they require significant execution time. The massive parallel computing capability of GPUs make them as one of the ideal platforms to accelerate CNNs and a number of GPU-based CNN libraries have been developed. While existing works mainly focus on the computational efficiency of CNNs, the memory efficiency of CNNs have been largely overlooked. Yet CNNs have intricate data structures and their memory behavior can have significant impact on the performance. In this work, we study the memory efficiency of various CNN layers and reveal the performance implication from both data layouts and memory access patterns. Experiments show the universal effect of our proposed optimizations on both single layers and various networks, with up to 27.9x for a single layer and up to 5.6x on the whole networks.