arXiv subjects

Qi Dou

Publications and source records attributed to Qi Dou.

At least 163 records · Page 9Linked to original sources

arXiv2021

Source-Free Domain Adaptive Fundus Image Segmentation with Denoised Pseudo-Labeling

Domain adaptation typically requires to access source domain data to utilize their distribution information for domain alignment with the target data. However, in many real-world scenarios, the source data may not be accessible during the model adaptation in the target domain due to privacy issue. This paper studies the practical yet challenging source-free unsupervised domain adaptation problem, in which only an existing source model and the unlabeled target data are available for model adaptation. We present a novel denoised pseudo-labeling method for this problem, which effectively makes use of the source model and unlabeled target data to promote model self-adaptation from pseudo labels. Importantly, considering that the pseudo labels generated from source model are inevitably noisy due to domain shift, we further introduce two complementary pixel-level and class-level denoising schemes with uncertainty estimation and prototype estimation to reduce noisy pseudo labels and select reliable ones to enhance the pseudo-labeling efficacy. Experimental results on cross-domain fundus image segmentation show that without using any source images or altering source training, our approach achieves comparable or even higher performance than state-of-the-art source-dependent unsupervised domain adaptation methods.

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arXiv2021

SurRoL: An Open-source Reinforcement Learning Centered and dVRK Compatible Platform for Surgical Robot Learning

Autonomous surgical execution relieves tedious routines and surgeon's fatigue. Recent learning-based methods, especially reinforcement learning (RL) based methods, achieve promising performance for dexterous manipulation, which usually requires the simulation to collect data efficiently and reduce the hardware cost. The existing learning-based simulation platforms for medical robots suffer from limited scenarios and simplified physical interactions, which degrades the real-world performance of learned policies. In this work, we designed SurRoL, an RL-centered simulation platform for surgical robot learning compatible with the da Vinci Research Kit (dVRK). The designed SurRoL integrates a user-friendly RL library for algorithm development and a real-time physics engine, which is able to support more PSM/ECM scenarios and more realistic physical interactions. Ten learning-based surgical tasks are built in the platform, which are common in the real autonomous surgical execution. We evaluate SurRoL using RL algorithms in simulation, provide in-depth analysis, deploy the trained policies on the real dVRK, and show that our SurRoL achieves better transferability in the real world.

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arXiv2021

Category-Level 6D Object Pose Estimation via Cascaded Relation and Recurrent Reconstruction Networks

Category-level 6D pose estimation, aiming to predict the location and orientation of unseen object instances, is fundamental to many scenarios such as robotic manipulation and augmented reality, yet still remains unsolved. Precisely recovering instance 3D model in the canonical space and accurately matching it with the observation is an essential point when estimating 6D pose for unseen objects. In this paper, we achieve accurate category-level 6D pose estimation via cascaded relation and recurrent reconstruction networks. Specifically, a novel cascaded relation network is dedicated for advanced representation learning to explore the complex and informative relations among instance RGB image, instance point cloud and category shape prior. Furthermore, we design a recurrent reconstruction network for iterative residual refinement to progressively improve the reconstruction and correspondence estimations from coarse to fine. Finally, the instance 6D pose is obtained leveraging the estimated dense correspondences between the instance point cloud and the reconstructed 3D model in the canonical space. We have conducted extensive experiments on two well-acknowledged benchmarks of category-level 6D pose estimation, with significant performance improvement over existing approaches. On the representatively strict evaluation metrics of $3D_{75}$ and $5^{\circ}2 cm$, our method exceeds the latest state-of-the-art SPD by $4.9\%$ and $17.7\%$ on the CAMERA25 dataset, and by $2.7\%$ and $8.5\%$ on the REAL275 dataset. Codes are available at https://wangjiaze.cn/projects/6DPoseEstimation.html.

cs.CV↗

arXiv2021

Accurate Grid Keypoint Learning for Efficient Video Prediction

Video prediction methods generally consume substantial computing resources in training and deployment, among which keypoint-based approaches show promising improvement in efficiency by simplifying dense image prediction to light keypoint prediction. However, keypoint locations are often modeled only as continuous coordinates, so noise from semantically insignificant deviations in videos easily disrupt learning stability, leading to inaccurate keypoint modeling. In this paper, we design a new grid keypoint learning framework, aiming at a robust and explainable intermediate keypoint representation for long-term efficient video prediction. We have two major technical contributions. First, we detect keypoints by jumping among candidate locations in our raised grid space and formulate a condensation loss to encourage meaningful keypoints with strong representative capability. Second, we introduce a 2D binary map to represent the detected grid keypoints and then suggest propagating keypoint locations with stochasticity by selecting entries in the discrete grid space, thus preserving the spatial structure of keypoints in the longterm horizon for better future frame generation. Extensive experiments verify that our method outperforms the state-ofthe-art stochastic video prediction methods while saves more than 98% of computing resources. We also demonstrate our method on a robotic-assisted surgery dataset with promising results. Our code is available at https://github.com/xjgaocs/Grid-Keypoint-Learning.

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arXiv2021

Domain Adaptive Robotic Gesture Recognition with Unsupervised Kinematic-Visual Data Alignment

Automated surgical gesture recognition is of great importance in robot-assisted minimally invasive surgery. However, existing methods assume that training and testing data are from the same domain, which suffers from severe performance degradation when a domain gap exists, such as the simulator and real robot. In this paper, we propose a novel unsupervised domain adaptation framework which can simultaneously transfer multi-modality knowledge, i.e., both kinematic and visual data, from simulator to real robot. It remedies the domain gap with enhanced transferable features by using temporal cues in videos, and inherent correlations in multi-modal towards recognizing gesture. Specifically, we first propose an MDO-K to align kinematics, which exploits temporal continuity to transfer motion directions with smaller gap rather than position values, relieving the adaptation burden. Moreover, we propose a KV-Relation-ATT to transfer the co-occurrence signals of kinematics and vision. Such features attended by correlation similarity are more informative for enhancing domain-invariance of the model. Two feature alignment strategies benefit the model mutually during the end-to-end learning process. We extensively evaluate our method for gesture recognition using DESK dataset with peg transfer procedure. Results show that our approach recovers the performance with great improvement gains, up to 12.91% in ACC and 20.16% in F1score without using any annotations in real robot.

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arXiv2021

Trans-SVNet: Accurate Phase Recognition from Surgical Videos via Hybrid Embedding Aggregation Transformer

Real-time surgical phase recognition is a fundamental task in modern operating rooms. Previous works tackle this task relying on architectures arranged in spatio-temporal order, however, the supportive benefits of intermediate spatial features are not considered. In this paper, we introduce, for the first time in surgical workflow analysis, Transformer to reconsider the ignored complementary effects of spatial and temporal features for accurate surgical phase recognition. Our hybrid embedding aggregation Transformer fuses cleverly designed spatial and temporal embeddings by allowing for active queries based on spatial information from temporal embedding sequences. More importantly, our framework processes the hybrid embeddings in parallel to achieve a high inference speed. Our method is thoroughly validated on two large surgical video datasets, i.e., Cholec80 and M2CAI16 Challenge datasets, and outperforms the state-of-the-art approaches at a processing speed of 91 fps.

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arXiv2021

E-DSSR: Efficient Dynamic Surgical Scene Reconstruction with Transformer-based Stereoscopic Depth Perception

Reconstructing the scene of robotic surgery from the stereo endoscopic video is an important and promising topic in surgical data science, which potentially supports many applications such as surgical visual perception, robotic surgery education and intra-operative context awareness. However, current methods are mostly restricted to reconstructing static anatomy assuming no tissue deformation, tool occlusion and de-occlusion, and camera movement. However, these assumptions are not always satisfied in minimal invasive robotic surgeries. In this work, we present an efficient reconstruction pipeline for highly dynamic surgical scenes that runs at 28 fps. Specifically, we design a transformer-based stereoscopic depth perception for efficient depth estimation and a light-weight tool segmentor to handle tool occlusion. After that, a dynamic reconstruction algorithm which can estimate the tissue deformation and camera movement, and aggregate the information over time is proposed for surgical scene reconstruction. We evaluate the proposed pipeline on two datasets, the public Hamlyn Centre Endoscopic Video Dataset and our in-house DaVinci robotic surgery dataset. The results demonstrate that our method can recover the scene obstructed by the surgical tool and handle the movement of camera in realistic surgical scenarios effectively at real-time speed.

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arXiv2021

Relational Graph Learning on Visual and Kinematics Embeddings for Accurate Gesture Recognition in Robotic Surgery

Automatic surgical gesture recognition is fundamentally important to enable intelligent cognitive assistance in robotic surgery. With recent advancement in robot-assisted minimally invasive surgery, rich information including surgical videos and robotic kinematics can be recorded, which provide complementary knowledge for understanding surgical gestures. However, existing methods either solely adopt uni-modal data or directly concatenate multi-modal representations, which can not sufficiently exploit the informative correlations inherent in visual and kinematics data to boost gesture recognition accuracies. In this regard, we propose a novel online approach of multi-modal relational graph network (i.e., MRG-Net) to dynamically integrate visual and kinematics information through interactive message propagation in the latent feature space. In specific, we first extract embeddings from video and kinematics sequences with temporal convolutional networks and LSTM units. Next, we identify multi-relations in these multi-modal embeddings and leverage them through a hierarchical relational graph learning module. The effectiveness of our method is demonstrated with state-of-the-art results on the public JIGSAWS dataset, outperforming current uni-modal and multi-modal methods on both suturing and knot typing tasks. Furthermore, we validated our method on in-house visual-kinematics datasets collected with da Vinci Research Kit (dVRK) platforms in two centers, with consistent promising performance achieved.

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arXiv2021

Federated Semi-supervised Medical Image Classification via Inter-client Relation Matching

Federated learning (FL) has emerged with increasing popularity to collaborate distributed medical institutions for training deep networks. However, despite existing FL algorithms only allow the supervised training setting, most hospitals in realistic usually cannot afford the intricate data labeling due to absence of budget or expertise. This paper studies a practical yet challenging FL problem, named \textit{Federated Semi-supervised Learning} (FSSL), which aims to learn a federated model by jointly utilizing the data from both labeled and unlabeled clients (i.e., hospitals). We present a novel approach for this problem, which improves over traditional consistency regularization mechanism with a new inter-client relation matching scheme. The proposed learning scheme explicitly connects the learning across labeled and unlabeled clients by aligning their extracted disease relationships, thereby mitigating the deficiency of task knowledge at unlabeled clients and promoting discriminative information from unlabeled samples. We validate our method on two large-scale medical image classification datasets. The effectiveness of our method has been demonstrated with the clear improvements over state-of-the-arts as well as the thorough ablation analysis on both tasks\footnote{Code will be made available at \url{https://github.com/liuquande/FedIRM}}.

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arXiv2021

FedBN: Federated Learning on Non-IID Features via Local Batch Normalization

The emerging paradigm of federated learning (FL) strives to enable collaborative training of deep models on the network edge without centrally aggregating raw data and hence improving data privacy. In most cases, the assumption of independent and identically distributed samples across local clients does not hold for federated learning setups. Under this setting, neural network training performance may vary significantly according to the data distribution and even hurt training convergence. Most of the previous work has focused on a difference in the distribution of labels or client shifts. Unlike those settings, we address an important problem of FL, e.g., different scanners/sensors in medical imaging, different scenery distribution in autonomous driving (highway vs. city), where local clients store examples with different distributions compared to other clients, which we denote as feature shift non-iid. In this work, we propose an effective method that uses local batch normalization to alleviate the feature shift before averaging models. The resulting scheme, called FedBN, outperforms both classical FedAvg, as well as the state-of-the-art for non-iid data (FedProx) on our extensive experiments. These empirical results are supported by a convergence analysis that shows in a simplified setting that FedBN has a faster convergence rate than FedAvg. Code is available at https://github.com/med-air/FedBN.

cs.LG↗

arXiv2021

Cascaded Robust Learning at Imperfect Labels for Chest X-ray Segmentation

The superior performance of CNN on medical image analysis heavily depends on the annotation quality, such as the number of labeled image, the source of image, and the expert experience. The annotation requires great expertise and labour. To deal with the high inter-rater variability, the study of imperfect label has great significance in medical image segmentation tasks. In this paper, we present a novel cascaded robust learning framework for chest X-ray segmentation with imperfect annotation. Our model consists of three independent network, which can effectively learn useful information from the peer networks. The framework includes two stages. In the first stage, we select the clean annotated samples via a model committee setting, the networks are trained by minimizing a segmentation loss using the selected clean samples. In the second stage, we design a joint optimization framework with label correction to gradually correct the wrong annotation and improve the network performance. We conduct experiments on the public chest X-ray image datasets collected by Shenzhen Hospital. The results show that our methods could achieve a significant improvement on the accuracy in segmentation tasks compared to the previous methods.

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arXiv2021

Temporal Memory Relation Network for Workflow Recognition from Surgical Video

Automatic surgical workflow recognition is a key component for developing context-aware computer-assisted systems in the operating theatre. Previous works either jointly modeled the spatial features with short fixed-range temporal information, or separately learned visual and long temporal cues. In this paper, we propose a novel end-to-end temporal memory relation network (TMRNet) for relating long-range and multi-scale temporal patterns to augment the present features. We establish a long-range memory bank to serve as a memory cell storing the rich supportive information. Through our designed temporal variation layer, the supportive cues are further enhanced by multi-scale temporal-only convolutions. To effectively incorporate the two types of cues without disturbing the joint learning of spatio-temporal features, we introduce a non-local bank operator to attentively relate the past to the present. In this regard, our TMRNet enables the current feature to view the long-range temporal dependency, as well as tolerate complex temporal extents. We have extensively validated our approach on two benchmark surgical video datasets, M2CAI challenge dataset and Cholec80 dataset. Experimental results demonstrate the outstanding performance of our method, consistently exceeding the state-of-the-art methods by a large margin (e.g., 67.0% v.s. 78.9% Jaccard on Cholec80 dataset).

cs.CV↗

arXiv2021

One to Many: Adaptive Instrument Segmentation via Meta Learning and Dynamic Online Adaptation in Robotic Surgical Video

Surgical instrument segmentation in robot-assisted surgery (RAS) - especially that using learning-based models - relies on the assumption that training and testing videos are sampled from the same domain. However, it is impractical and expensive to collect and annotate sufficient data from every new domain. To greatly increase the label efficiency, we explore a new problem, i.e., adaptive instrument segmentation, which is to effectively adapt one source model to new robotic surgical videos from multiple target domains, only given the annotated instruments in the first frame. We propose MDAL, a meta-learning based dynamic online adaptive learning scheme with a two-stage framework to fast adapt the model parameters on the first frame and partial subsequent frames while predicting the results. MDAL learns the general knowledge of instruments and the fast adaptation ability through the video-specific meta-learning paradigm. The added gradient gate excludes the noisy supervision from pseudo masks for dynamic online adaptation on target videos. We demonstrate empirically that MDAL outperforms other state-of-the-art methods on two datasets (including a real-world RAS dataset). The promising performance on ex-vivo scenes also benefits the downstream tasks such as robot-assisted suturing and camera control.

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arXiv2021

MIcro-Surgical Anastomose Workflow recognition challenge report

The "MIcro-Surgical Anastomose Workflow recognition on training sessions" (MISAW) challenge provided a data set of 27 sequences of micro-surgical anastomosis on artificial blood vessels. This data set was composed of videos, kinematics, and workflow annotations described at three different granularity levels: phase, step, and activity. The participants were given the option to use kinematic data and videos to develop workflow recognition models. Four tasks were proposed to the participants: three of them were related to the recognition of surgical workflow at three different granularity levels, while the last one addressed the recognition of all granularity levels in the same model. One ranking was made for each task. We used the average application-dependent balanced accuracy (AD-Accuracy) as the evaluation metric. This takes unbalanced classes into account and it is more clinically relevant than a frame-by-frame score. Six teams, including a non-competing team, participated in at least one task. All models employed deep learning models, such as CNN or RNN. The best models achieved more than 95% AD-Accuracy for phase recognition, 80% for step recognition, 60% for activity recognition, and 75% for all granularity levels. For high levels of granularity (i.e., phases and steps), the best models had a recognition rate that may be sufficient for applications such as prediction of remaining surgical time or resource management. However, for activities, the recognition rate was still low for applications that can be employed clinically. The MISAW data set is publicly available to encourage further research in surgical workflow recognition. It can be found at www.synapse.org/MISAW

cs.LG↗

arXiv2021

Future Frame Prediction for Robot-assisted Surgery

Predicting future frames for robotic surgical video is an interesting, important yet extremely challenging problem, given that the operative tasks may have complex dynamics. Existing approaches on future prediction of natural videos were based on either deterministic models or stochastic models, including deep recurrent neural networks, optical flow, and latent space modeling. However, the potential in predicting meaningful movements of robots with dual arms in surgical scenarios has not been tapped so far, which is typically more challenging than forecasting independent motions of one arm robots in natural scenarios. In this paper, we propose a ternary prior guided variational autoencoder (TPG-VAE) model for future frame prediction in robotic surgical video sequences. Besides content distribution, our model learns motion distribution, which is novel to handle the small movements of surgical tools. Furthermore, we add the invariant prior information from the gesture class into the generation process to constrain the latent space of our model. To our best knowledge, this is the first time that the future frames of dual arm robots are predicted considering their unique characteristics relative to general robotic videos. Experiments demonstrate that our model gains more stable and realistic future frame prediction scenes with the suturing task on the public JIGSAWS dataset.

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arXiv2021

FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space

Federated learning allows distributed medical institutions to collaboratively learn a shared prediction model with privacy protection. While at clinical deployment, the models trained in federated learning can still suffer from performance drop when applied to completely unseen hospitals outside the federation. In this paper, we point out and solve a novel problem setting of federated domain generalization (FedDG), which aims to learn a federated model from multiple distributed source domains such that it can directly generalize to unseen target domains. We present a novel approach, named as Episodic Learning in Continuous Frequency Space (ELCFS), for this problem by enabling each client to exploit multi-source data distributions under the challenging constraint of data decentralization. Our approach transmits the distribution information across clients in a privacy-protecting way through an effective continuous frequency space interpolation mechanism. With the transferred multi-source distributions, we further carefully design a boundary-oriented episodic learning paradigm to expose the local learning to domain distribution shifts and particularly meet the challenges of model generalization in medical image segmentation scenario. The effectiveness of our method is demonstrated with superior performance over state-of-the-arts and in-depth ablation experiments on two medical image segmentation tasks. The code is available at "https://github.com/liuquande/FedDG-ELCFS".

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arXiv2020

Contrastive Cross-site Learning with Redesigned Net for COVID-19 CT Classification

The pandemic of coronavirus disease 2019 (COVID-19) has lead to a global public health crisis spreading hundreds of countries. With the continuous growth of new infections, developing automated tools for COVID-19 identification with CT image is highly desired to assist the clinical diagnosis and reduce the tedious workload of image interpretation. To enlarge the datasets for developing machine learning methods, it is essentially helpful to aggregate the cases from different medical systems for learning robust and generalizable models. This paper proposes a novel joint learning framework to perform accurate COVID-19 identification by effectively learning with heterogeneous datasets with distribution discrepancy. We build a powerful backbone by redesigning the recently proposed COVID-Net in aspects of network architecture and learning strategy to improve the prediction accuracy and learning efficiency. On top of our improved backbone, we further explicitly tackle the cross-site domain shift by conducting separate feature normalization in latent space. Moreover, we propose to use a contrastive training objective to enhance the domain invariance of semantic embeddings for boosting the classification performance on each dataset. We develop and evaluate our method with two public large-scale COVID-19 diagnosis datasets made up of CT images. Extensive experiments show that our approach consistently improves the performances on both datasets, outperforming the original COVID-Net trained on each dataset by 12.16% and 14.23% in AUC respectively, also exceeding existing state-of-the-art multi-site learning methods.

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arXiv2020

Multi-Site Infant Brain Segmentation Algorithms: The iSeg-2019 Challenge

To better understand early brain growth patterns in health and disorder, it is critical to accurately segment infant brain magnetic resonance (MR) images into white matter (WM), gray matter (GM), and cerebrospinal fluid (CSF). Deep learning-based methods have achieved state-of-the-art performance; however, one of major limitations is that the learning-based methods may suffer from the multi-site issue, that is, the models trained on a dataset from one site may not be applicable to the datasets acquired from other sites with different imaging protocols/scanners. To promote methodological development in the community, iSeg-2019 challenge (http://iseg2019.web.unc.edu) provides a set of 6-month infant subjects from multiple sites with different protocols/scanners for the participating methods. Training/validation subjects are from UNC (MAP) and testing subjects are from UNC/UMN (BCP), Stanford University, and Emory University. By the time of writing, there are 30 automatic segmentation methods participating in iSeg-2019. We review the 8 top-ranked teams by detailing their pipelines/implementations, presenting experimental results and evaluating performance in terms of the whole brain, regions of interest, and gyral landmark curves. We also discuss their limitations and possible future directions for the multi-site issue. We hope that the multi-site dataset in iSeg-2019 and this review article will attract more researchers on the multi-site issue.

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