Biomedical image analysis competitions: The state of current participation practice

The number of international benchmarking competitions is steadily increasing in various fields of machine learning (ML) research and practice. So far, however, little is known about the common practice as well as bottlenecks faced by the community in tackling the research questions posed. To shed light on the status quo of algorithm development in the specific field of biomedical imaging analysis, we designed an international survey that was issued to all participants of challenges conducted in conjunction with the IEEE ISBI 2021 and MICCAI 2021 conferences (80 competitions in total). The survey covered participants' expertise and working environments, their chosen strategies, as well as algorithm characteristics. A median of 72% challenge participants took part in the survey. According to our results, knowledge exchange was the primary incentive (70%) for participation, while the reception of prize money played only a minor role (16%). While a median of 80 working hours was spent on method development, a large portion of participants stated that they did not have enough time for method development (32%). 25% perceived the infrastructure to be a bottleneck. Overall, 94% of all solutions were deep learning-based. Of these, 84% were based on standard architectures. 43% of the respondents reported that the data samples (e.g., images) were too large to be processed at once. This was most commonly addressed by patch-based training (69%), downsampling (37%), and solving 3D analysis tasks as a series of 2D tasks. K-fold cross-validation on the training set was performed by only 37% of the participants and only 50% of the participants performed ensembling based on multiple identical models (61%) or heterogeneous models (39%). 48% of the respondents applied postprocessing steps.

Objective Surgical Skills Assessment and Tool Localization: Results from the MICCAI 2021 SimSurgSkill Challenge

Timely and effective feedback within surgical training plays a critical role in developing the skills required to perform safe and efficient surgery. Feedback from expert surgeons, while especially valuable in this regard, is challenging to acquire due to their typically busy schedules, and may be subject to biases. Formal assessment procedures like OSATS and GEARS attempt to provide objective measures of skill, but remain time-consuming. With advances in machine learning there is an opportunity for fast and objective automated feedback on technical skills. The SimSurgSkill 2021 challenge (hosted as a sub-challenge of EndoVis at MICCAI 2021) aimed to promote and foster work in this endeavor. Using virtual reality (VR) surgical tasks, competitors were tasked with localizing instruments and predicting surgical skill. Here we summarize the winning approaches and how they performed. Using this publicly available dataset and results as a springboard, future work may enable more efficient training of surgeons with advances in surgical data science. The dataset can be accessed from https://console.cloud.google.com/storage/browser/isi-simsurgskill-2021.

Why Deep Surgical Models Fail?: Revisiting Surgical Action Triplet Recognition through the Lens of Robustness

Surgical action triplet recognition provides a better understanding of the surgical scene. This task is of high relevance as it provides to the surgeon with context-aware support and safety. The current go-to strategy for improving performance is the development of new network mechanisms. However, the performance of current state-of-the-art techniques is substantially lower than other surgical tasks. Why is this happening? This is the question that we address in this work. We present the first study to understand the failure of existing deep learning models through the lens of robustness and explainabilty. Firstly, we study current existing models under weak and strong $\delta-$perturbations via adversarial optimisation scheme. We then provide the failure modes via feature based explanations. Our study revels that the key for improving performance and increasing reliability is in the core and spurious attributes. Our work opens the door to more trustworthiness and reliability deep learning models in surgical science.

Pseudo-label Guided Cross-video Pixel Contrast for Robotic Surgical Scene Segmentation with Limited Annotations

Surgical scene segmentation is fundamentally crucial for prompting cognitive assistance in robotic surgery. However, pixel-wise annotating surgical video in a frame-by-frame manner is expensive and time consuming. To greatly reduce the labeling burden, in this work, we study semi-supervised scene segmentation from robotic surgical video, which is practically essential yet rarely explored before. We consider a clinically suitable annotation situation under the equidistant sampling. We then propose PGV-CL, a novel pseudo-label guided cross-video contrast learning method to boost scene segmentation. It effectively leverages unlabeled data for a trusty and global model regularization that produces more discriminative feature representation. Concretely, for trusty representation learning, we propose to incorporate pseudo labels to instruct the pair selection, obtaining more reliable representation pairs for pixel contrast. Moreover, we expand the representation learning space from previous image-level to cross-video, which can capture the global semantics to benefit the learning process. We extensively evaluate our method on a public robotic surgery dataset EndoVis18 and a public cataract dataset CaDIS. Experimental results demonstrate the effectiveness of our method, consistently outperforming the state-of-the-art semi-supervised methods under different labeling ratios, and even surpassing fully supervised training on EndoVis18 with 10.1% labeling.

Personalizing Federated Medical Image Segmentation via Local Calibration

Medical image segmentation under federated learning (FL) is a promising direction by allowing multiple clinical sites to collaboratively learn a global model without centralizing datasets. However, using a single model to adapt to various data distributions from different sites is extremely challenging. Personalized FL tackles this issue by only utilizing partial model parameters shared from global server, while keeping the rest to adapt to its own data distribution in the local training of each site. However, most existing methods concentrate on the partial parameter splitting, while do not consider the \textit{inter-site in-consistencies} during the local training, which in fact can facilitate the knowledge communication over sites to benefit the model learning for improving the local accuracy. In this paper, we propose a personalized federated framework with \textbf{L}ocal \textbf{C}alibration (LC-Fed), to leverage the inter-site in-consistencies in both \textit{feature- and prediction- levels} to boost the segmentation. Concretely, as each local site has its alternative attention on the various features, we first design the contrastive site embedding coupled with channel selection operation to calibrate the encoded features. Moreover, we propose to exploit the knowledge of prediction-level in-consistency to guide the personalized modeling on the ambiguous regions, e.g., anatomical boundaries. It is achieved by computing a disagreement-aware map to calibrate the prediction. Effectiveness of our method has been verified on three medical image segmentation tasks with different modalities, where our method consistently shows superior performance to the state-of-the-art personalized FL methods. Code is available at https://github.com/jcwang123/FedLC.

Exploring Intra- and Inter-Video Relation for Surgical Semantic Scene Segmentation

Automatic surgical scene segmentation is fundamental for facilitating cognitive intelligence in the modern operating theatre. Previous works rely on conventional aggregation modules (e.g., dilated convolution, convolutional LSTM), which only make use of the local context. In this paper, we propose a novel framework STswinCL that explores the complementary intra- and inter-video relations to boost segmentation performance, by progressively capturing the global context. We firstly develop a hierarchy Transformer to capture intra-video relation that includes richer spatial and temporal cues from neighbor pixels and previous frames. A joint space-time window shift scheme is proposed to efficiently aggregate these two cues into each pixel embedding. Then, we explore inter-video relation via pixel-to-pixel contrastive learning, which well structures the global embedding space. A multi-source contrast training objective is developed to group the pixel embeddings across videos with the ground-truth guidance, which is crucial for learning the global property of the whole data. We extensively validate our approach on two public surgical video benchmarks, including EndoVis18 Challenge and CaDIS dataset. Experimental results demonstrate the promising performance of our method, which consistently exceeds previous state-of-the-art approaches. Code will be available at https://github.com/YuemingJin/STswinCL.

TraSeTR: Track-to-Segment Transformer with Contrastive Query for Instance-level Instrument Segmentation in Robotic Surgery

Surgical instrument segmentation -- in general a pixel classification task -- is fundamentally crucial for promoting cognitive intelligence in robot-assisted surgery (RAS). However, previous methods are struggling with discriminating instrument types and instances. To address the above issues, we explore a mask classification paradigm that produces per-segment predictions. We propose TraSeTR, a novel Track-to-Segment Transformer that wisely exploits tracking cues to assist surgical instrument segmentation. TraSeTR jointly reasons about the instrument type, location, and identity with instance-level predictions i.e., a set of class-bbox-mask pairs, by decoding query embeddings. Specifically, we introduce the prior query that encoded with previous temporal knowledge, to transfer tracking signals to current instances via identity matching. A contrastive query learning strategy is further applied to reshape the query feature space, which greatly alleviates the tracking difficulty caused by large temporal variations. The effectiveness of our method is demonstrated with state-of-the-art instrument type segmentation results on three public datasets, including two RAS benchmarks from EndoVis Challenges and one cataract surgery dataset CaDIS.

Real-time landmark detection for precise endoscopic submucosal dissection via shape-aware relation network

We propose a novel shape-aware relation network for accurate and real-time landmark detection in endoscopic submucosal dissection (ESD) surgery. This task is of great clinical significance but extremely challenging due to bleeding, lighting reflection, and motion blur in the complicated surgical environment. Compared with existing solutions, which either neglect geometric relationships among targeting objects or capture the relationships by using complicated aggregation schemes, the proposed network is capable of achieving satisfactory accuracy while maintaining real-time performance by taking full advantage of the spatial relations among landmarks. We first devise an algorithm to automatically generate relation keypoint heatmaps, which are able to intuitively represent the prior knowledge of spatial relations among landmarks without using any extra manual annotation efforts. We then develop two complementary regularization schemes to progressively incorporate the prior knowledge into the training process. While one scheme introduces pixel-level regularization by multi-task learning, the other integrates global-level regularization by harnessing a newly designed grouped consistency evaluator, which adds relation constraints to the proposed network in an adversarial manner. Both schemes are beneficial to the model in training, and can be readily unloaded in inference to achieve real-time detection. We establish a large in-house dataset of ESD surgery for esophageal cancer to validate the effectiveness of our proposed method. Extensive experimental results demonstrate that our approach outperforms state-of-the-art methods in terms of accuracy and efficiency, achieving better detection results faster. Promising results on two downstream applications further corroborate the great potential of our method in ESD clinical practice.

Comparative Validation of Machine Learning Algorithms for Surgical Workflow and Skill Analysis with the HeiChole Benchmark

PURPOSE: Surgical workflow and skill analysis are key technologies for the next generation of cognitive surgical assistance systems. These systems could increase the safety of the operation through context-sensitive warnings and semi-autonomous robotic assistance or improve training of surgeons via data-driven feedback. In surgical workflow analysis up to 91% average precision has been reported for phase recognition on an open data single-center dataset. In this work we investigated the generalizability of phase recognition algorithms in a multi-center setting including more difficult recognition tasks such as surgical action and surgical skill. METHODS: To achieve this goal, a dataset with 33 laparoscopic cholecystectomy videos from three surgical centers with a total operation time of 22 hours was created. Labels included annotation of seven surgical phases with 250 phase transitions, 5514 occurences of four surgical actions, 6980 occurences of 21 surgical instruments from seven instrument categories and 495 skill classifications in five skill dimensions. The dataset was used in the 2019 Endoscopic Vision challenge, sub-challenge for surgical workflow and skill analysis. Here, 12 teams submitted their machine learning algorithms for recognition of phase, action, instrument and/or skill assessment. RESULTS: F1-scores were achieved for phase recognition between 23.9% and 67.7% (n=9 teams), for instrument presence detection between 38.5% and 63.8% (n=8 teams), but for action recognition only between 21.8% and 23.3% (n=5 teams). The average absolute error for skill assessment was 0.78 (n=1 team). CONCLUSION: Surgical workflow and skill analysis are promising technologies to support the surgical team, but are not solved yet, as shown by our comparison of algorithms. This novel benchmark can be used for comparable evaluation and validation of future work.

Efficient Global-Local Memory for Real-time Instrument Segmentation of Robotic Surgical Video

Performing a real-time and accurate instrument segmentation from videos is of great significance for improving the performance of robotic-assisted surgery. We identify two important clues for surgical instrument perception, including local temporal dependency from adjacent frames and global semantic correlation in long-range duration. However, most existing works perform segmentation purely using visual cues in a single frame. Optical flow is just used to model the motion between only two frames and brings heavy computational cost. We propose a novel dual-memory network (DMNet) to wisely relate both global and local spatio-temporal knowledge to augment the current features, boosting the segmentation performance and retaining the real-time prediction capability. We propose, on the one hand, an efficient local memory by taking the complementary advantages of convolutional LSTM and non-local mechanisms towards the relating reception field. On the other hand, we develop an active global memory to gather the global semantic correlation in long temporal range to current one, in which we gather the most informative frames derived from model uncertainty and frame similarity. We have extensively validated our method on two public benchmark surgical video datasets. Experimental results demonstrate that our method largely outperforms the state-of-the-art works on segmentation accuracy while maintaining a real-time speed.