The conversational machine reading comprehension (CMRC) task aims to answer questions in conversations, which has been a hot research topic in recent years because of its wide applications. However, existing CMRC benchmarks in which each conversation is assigned a static passage are inconsistent with real scenarios. Thus, model's comprehension ability towards real scenarios are hard to evaluate reasonably. To this end, we propose the first Chinese CMRC benchmark Orca and further provide zero-shot/few-shot settings to evaluate model's generalization ability towards diverse domains. We collect 831 hot-topic driven conversations with 4,742 turns in total. Each turn of a conversation is assigned with a response-related passage, aiming to evaluate model's comprehension ability more reasonably. The topics of conversations are collected from social media platform and cover 33 domains, trying to be consistent with real scenarios. Importantly, answers in Orca are all well-annotated natural responses rather than the specific spans or short phrase in previous datasets. Besides, we implement three strong baselines to tackle the challenge in Orca. The results indicate the great challenge of our CMRC benchmark. Our datatset and checkpoints are available at https://github.com/nuochenpku/Orca.
In this paper, we propose a reduced reference (RR) point cloud quality assessment (PCQA) model named R-PCQA to quantify the distortions introduced by the lossy compression. Specifically, we use the attribute and geometry quantization steps of different compression methods (i.e., V-PCC, G-PCC and AVS) to infer the point cloud quality, assuming that the point clouds have no other distortions before compression. First, we analyze the compression distortion of point clouds under separate attribute compression and geometry compression to avoid their mutual masking, for which we consider 5 point clouds as references to generate a compression dataset (PCCQA) containing independent attribute compression and geometry compression samples. Then, we develop the proposed R-PCQA via fitting the relationship between the quantization steps and the perceptual quality. We evaluate the performance of R-PCQA on both the established dataset and another independent dataset. The results demonstrate that the proposed R-PCQA can exhibit reliable performance and high generalization ability.
Objective: Thigh muscle group segmentation is important for assessment of muscle anatomy, metabolic disease and aging. Many efforts have been put into quantifying muscle tissues with magnetic resonance (MR) imaging including manual annotation of individual muscles. However, leveraging publicly available annotations in MR images to achieve muscle group segmentation on single slice computed tomography (CT) thigh images is challenging. Method: We propose an unsupervised domain adaptation pipeline with self-training to transfer labels from 3D MR to single CT slice. First, we transform the image appearance from MR to CT with CycleGAN and feed the synthesized CT images to a segmenter simultaneously. Single CT slices are divided into hard and easy cohorts based on the entropy of pseudo labels inferenced by the segmenter. After refining easy cohort pseudo labels based on anatomical assumption, self-training with easy and hard splits is applied to fine tune the segmenter. Results: On 152 withheld single CT thigh images, the proposed pipeline achieved a mean Dice of 0.888(0.041) across all muscle groups including sartorius, hamstrings, quadriceps femoris and gracilis. muscles Conclusion: To our best knowledge, this is the first pipeline to achieve thigh imaging domain adaptation from MR to CT. The proposed pipeline is effective and robust in extracting muscle groups on 2D single slice CT thigh images.The container is available for public use at https://github.com/MASILab/DA_CT_muscle_seg
With the rapid development of 3D vision, point cloud has become an increasingly popular 3D visual media content. Due to the irregular structure, point cloud has posed novel challenges to the related research, such as compression, transmission, rendering and quality assessment. In these latest researches, point cloud quality assessment (PCQA) has attracted wide attention due to its significant role in guiding practical applications, especially in many cases where the reference point cloud is unavailable. However, current no-reference metrics which based on prevalent deep neural network have apparent disadvantages. For example, to adapt to the irregular structure of point cloud, they require preprocessing such as voxelization and projection that introduce extra distortions, and the applied grid-kernel networks, such as Convolutional Neural Networks, fail to extract effective distortion-related features. Besides, they rarely consider the various distortion patterns and the philosophy that PCQA should exhibit shifting, scaling, and rotational invariance. In this paper, we propose a novel no-reference PCQA metric named the Graph convolutional PCQA network (GPA-Net). To extract effective features for PCQA, we propose a new graph convolution kernel, i.e., GPAConv, which attentively captures the perturbation of structure and texture. Then, we propose the multi-task framework consisting of one main task (quality regression) and two auxiliary tasks (distortion type and degree predictions). Finally, we propose a coordinate normalization module to stabilize the results of GPAConv under shift, scale and rotation transformations. Experimental results on two independent databases show that GPA-Net achieves the best performance compared to the state-of-the-art no-reference PCQA metrics, even better than some full-reference metrics in some cases.
Recent studies have demonstrated the superior performance of introducing ``scan-wise" contrast labels into contrastive learning for multi-organ segmentation on multi-phase computed tomography (CT). However, such scan-wise labels are limited: (1) a coarse classification, which could not capture the fine-grained ``organ-wise" contrast variations across all organs; (2) the label (i.e., contrast phase) is typically manually provided, which is error-prone and may introduce manual biases of defining phases. In this paper, we propose a novel data-driven contrastive loss function that adapts the similar/dissimilar contrast relationship between samples in each minibatch at organ-level. Specifically, as variable levels of contrast exist between organs, we hypothesis that the contrast differences in the organ-level can bring additional context for defining representations in the latent space. An organ-wise contrast correlation matrix is computed with mean organ intensities under one-hot attention maps. The goal of adapting the organ-driven correlation matrix is to model variable levels of feature separability at different phases. We evaluate our proposed approach on multi-organ segmentation with both non-contrast CT (NCCT) datasets and the MICCAI 2015 BTCV Challenge contrast-enhance CT (CECT) datasets. Compared to the state-of-the-art approaches, our proposed contrastive loss yields a substantial and significant improvement of 1.41% (from 0.923 to 0.936, p-value$<$0.01) and 2.02% (from 0.891 to 0.910, p-value$<$0.01) on mean Dice scores across all organs with respect to NCCT and CECT cohorts. We further assess the trained model performance with the MICCAI 2021 FLARE Challenge CECT datasets and achieve a substantial improvement of mean Dice score from 0.927 to 0.934 (p-value$<$0.01). The code is available at: https://github.com/MASILab/DCC_CL
Full-reference point cloud quality assessment (FR-PCQA) aims to infer the quality of distorted point clouds with available references. Merging the research of cognitive science and intuition of the human visual system (HVS), the difference between the expected perceptual result and the practical perception reproduction in the visual center of the cerebral cortex indicates the subjective quality degradation. Therefore in this paper, we try to derive the point cloud quality by measuring the complexity of transforming the distorted point cloud back to its reference, which in practice can be approximated by the code length of one point cloud when the other is given. For this purpose, we first segment the reference and the distorted point cloud into a series of local patch pairs based on one 3D Voronoi diagram. Next, motivated by the predictive coding theory, we utilize one space-aware vector autoregressive (SA-VAR) model to encode the geometry and color channels of each reference patch in cases with and without the distorted patch, respectively. Specifically, supposing that the residual errors follow the multi-variate Gaussian distributions, we calculate the self-complexity of the reference and the transformational complexity between the reference and the distorted sample via covariance matrices. Besides the complexity terms, the prediction terms generated by SA-VAR are introduced as one auxiliary feature to promote the final quality prediction. Extensive experiments on five public point cloud quality databases demonstrate that the transformational complexity based distortion metric (TCDM) produces state-of-the-art (SOTA) results, and ablation studies have further shown that our metric can be generalized to various scenarios with consistent performance by examining its key modules and parameters.
Point cloud quality assessment (PCQA) has become an appealing research field in recent days. Considering the importance of saliency detection in quality assessment, we propose an effective full-reference PCQA metric which makes the first attempt to utilize the saliency information to facilitate quality prediction, called point cloud quality assessment using 3D saliency maps (PQSM). Specifically, we first propose a projection-based point cloud saliency map generation method, in which depth information is introduced to better reflect the geometric characteristics of point clouds. Then, we construct point cloud local neighborhoods to derive three structural descriptors to indicate the geometry, color and saliency discrepancies. Finally, a saliency-based pooling strategy is proposed to generate the final quality score. Extensive experiments are performed on four independent PCQA databases. The results demonstrate that the proposed PQSM shows competitive performances compared to multiple state-of-the-art PCQA metrics.
2D low-dose single-slice abdominal computed tomography (CT) slice enables direct measurements of body composition, which are critical to quantitatively characterizing health relationships on aging. However, longitudinal analysis of body composition changes using 2D abdominal slices is challenging due to positional variance between longitudinal slices acquired in different years. To reduce the positional variance, we extend the conditional generative models to our C-SliceGen that takes an arbitrary axial slice in the abdominal region as the condition and generates a defined vertebral level slice by estimating the structural changes in the latent space. Experiments on 1170 subjects from an in-house dataset and 50 subjects from BTCV MICCAI Challenge 2015 show that our model can generate high quality images in terms of realism and similarity. External experiments on 20 subjects from the Baltimore Longitudinal Study of Aging (BLSA) dataset that contains longitudinal single abdominal slices validate that our method can harmonize the slice positional variance in terms of muscle and visceral fat area. Our approach provides a promising direction of mapping slices from different vertebral levels to a target slice to reduce positional variance for single slice longitudinal analysis. The source code is available at: https://github.com/MASILab/C-SliceGen.
Transformer-based models, capable of learning better global dependencies, have recently demonstrated exceptional representation learning capabilities in computer vision and medical image analysis. Transformer reformats the image into separate patches and realize global communication via the self-attention mechanism. However, positional information between patches is hard to preserve in such 1D sequences, and loss of it can lead to sub-optimal performance when dealing with large amounts of heterogeneous tissues of various sizes in 3D medical image segmentation. Additionally, current methods are not robust and efficient for heavy-duty medical segmentation tasks such as predicting a large number of tissue classes or modeling globally inter-connected tissues structures. Inspired by the nested hierarchical structures in vision transformer, we proposed a novel 3D medical image segmentation method (UNesT), employing a simplified and faster-converging transformer encoder design that achieves local communication among spatially adjacent patch sequences by aggregating them hierarchically. We extensively validate our method on multiple challenging datasets, consisting anatomies of 133 structures in brain, 14 organs in abdomen, 4 hierarchical components in kidney, and inter-connected kidney tumors). We show that UNesT consistently achieves state-of-the-art performance and evaluate its generalizability and data efficiency. Particularly, the model achieves whole brain segmentation task complete ROI with 133 tissue classes in single network, outperforms prior state-of-the-art method SLANT27 ensembled with 27 network tiles, our model performance increases the mean DSC score of the publicly available Colin and CANDI dataset from 0.7264 to 0.7444 and from 0.6968 to 0.7025, respectively.