Deepak Alapatt

Sanat Ramesh, Vinkle Srivastav, Deepak Alapatt et al.

The field of surgical computer vision has undergone considerable breakthroughs in recent years with the rising popularity of deep neural network-based methods. However, standard fully-supervised approaches for training such models require vast amounts of annotated data, imposing a prohibitively high cost; especially in the clinical domain. Self-Supervised Learning (SSL) methods, which have begun to gain traction in the general computer vision community, represent a potential solution to these annotation costs, allowing to learn useful representations from only unlabeled data. Still, the effectiveness of SSL methods in more complex and impactful domains, such as medicine and surgery, remains limited and unexplored. In this work, we address this critical need by investigating four state-of-the-art SSL methods (MoCo v2, SimCLR, DINO, SwAV) in the context of surgical computer vision. We present an extensive analysis of the performance of these methods on the Cholec80 dataset for two fundamental and popular tasks in surgical context understanding, phase recognition and tool presence detection. We examine their parameterization, then their behavior with respect to training data quantities in semi-supervised settings. Correct transfer of these methods to surgery, as described and conducted in this work, leads to substantial performance gains over generic uses of SSL - up to 7.4% on phase recognition and 20% on tool presence detection - as well as state-of-the-art semi-supervised phase recognition approaches by up to 14%. Further results obtained on a highly diverse selection of surgical datasets exhibit strong generalization properties. The code is available at https://github.com/CAMMA-public/SelfSupSurg.

Matthias Eisenmann, Annika Reinke, Vivienn Weru et al. · utoronto

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.

Chinedu Innocent Nwoye, Deepak Alapatt, Tong Yu et al.

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of <instrument, verb, target> combination delivers comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. The challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. A total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms by competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery.

Chinedu Innocent Nwoye, Tong Yu, Saurav Sharma et al.

Formalizing surgical activities as triplets of the used instruments, actions performed, and target anatomies is becoming a gold standard approach for surgical activity modeling. The benefit is that this formalization helps to obtain a more detailed understanding of tool-tissue interaction which can be used to develop better Artificial Intelligence assistance for image-guided surgery. Earlier efforts and the CholecTriplet challenge introduced in 2021 have put together techniques aimed at recognizing these triplets from surgical footage. Estimating also the spatial locations of the triplets would offer a more precise intraoperative context-aware decision support for computer-assisted intervention. This paper presents the CholecTriplet2022 challenge, which extends surgical action triplet modeling from recognition to detection. It includes weakly-supervised bounding box localization of every visible surgical instrument (or tool), as the key actors, and the modeling of each tool-activity in the form of <instrument, verb, target> triplet. The paper describes a baseline method and 10 new deep learning algorithms presented at the challenge to solve the task. It also provides thorough methodological comparisons of the methods, an in-depth analysis of the obtained results across multiple metrics, visual and procedural challenges; their significance, and useful insights for future research directions and applications in surgery.

Aditya Murali, Deepak Alapatt, Pietro Mascagni et al.

Assessing the critical view of safety in laparoscopic cholecystectomy requires accurate identification and localization of key anatomical structures, reasoning about their geometric relationships to one another, and determining the quality of their exposure. Prior works have approached this task by including semantic segmentation as an intermediate step, using predicted segmentation masks to then predict the CVS. While these methods are effective, they rely on extremely expensive ground-truth segmentation annotations and tend to fail when the predicted segmentation is incorrect, limiting generalization. In this work, we propose a method for CVS prediction wherein we first represent a surgical image using a disentangled latent scene graph, then process this representation using a graph neural network. Our graph representations explicitly encode semantic information - object location, class information, geometric relations - to improve anatomy-driven reasoning, as well as visual features to retain differentiability and thereby provide robustness to semantic errors. Finally, to address annotation cost, we propose to train our method using only bounding box annotations, incorporating an auxiliary image reconstruction objective to learn fine-grained object boundaries. We show that our method not only outperforms several baseline methods when trained with bounding box annotations, but also scales effectively when trained with segmentation masks, maintaining state-of-the-art performance.

Hasan Kassem, Deepak Alapatt, Pietro Mascagni et al.

Recent advancements in deep learning methods bring computer-assistance a step closer to fulfilling promises of safer surgical procedures. However, the generalizability of such methods is often dependent on training on diverse datasets from multiple medical institutions, which is a restrictive requirement considering the sensitive nature of medical data. Recently proposed collaborative learning methods such as Federated Learning (FL) allow for training on remote datasets without the need to explicitly share data. Even so, data annotation still represents a bottleneck, particularly in medicine and surgery where clinical expertise is often required. With these constraints in mind, we propose FedCy, a federated semi-supervised learning (FSSL) method that combines FL and self-supervised learning to exploit a decentralized dataset of both labeled and unlabeled videos, thereby improving performance on the task of surgical phase recognition. By leveraging temporal patterns in the labeled data, FedCy helps guide unsupervised training on unlabeled data towards learning task-specific features for phase recognition. We demonstrate significant performance gains over state-of-the-art FSSL methods on the task of automatic recognition of surgical phases using a newly collected multi-institutional dataset of laparoscopic cholecystectomy videos. Furthermore, we demonstrate that our approach also learns more generalizable features when tested on data from an unseen domain.

Pietro Mascagni, Deepak Alapatt, Alfonso Lapergola et al.

Artificial intelligence is set to be deployed in operating rooms to improve surgical care. This early-stage clinical evaluation shows the feasibility of concurrently attaining real-time, high-quality predictions from several deep neural networks for endoscopic video analysis deployed for assistance during three laparoscopic cholecystectomies.

Aditya Murali, Deepak Alapatt, Pietro Mascagni et al.

This technical report provides a detailed overview of Endoscapes, a dataset of laparoscopic cholecystectomy (LC) videos with highly intricate annotations targeted at automated assessment of the Critical View of Safety (CVS). Endoscapes comprises 201 LC videos with frames annotated sparsely but regularly with segmentation masks, bounding boxes, and CVS assessment by three different clinical experts. Altogether, there are 11090 frames annotated with CVS and 1933 frames annotated with tool and anatomy bounding boxes from the 201 videos, as well as an additional 422 frames from 50 of the 201 videos annotated with tool and anatomy segmentation masks. In this report, we provide detailed dataset statistics (size, class distribution, dataset splits, etc.) and a comprehensive performance benchmark for instance segmentation, object detection, and CVS prediction. The dataset and model checkpoints are publically available at https://github.com/CAMMA-public/Endoscapes.

Aditya Murali, Deepak Alapatt, Pietro Mascagni et al.

Recently, spatiotemporal graphs have emerged as a concise and elegant manner of representing video clips in an object-centric fashion, and have shown to be useful for downstream tasks such as action recognition. In this work, we investigate the use of latent spatiotemporal graphs to represent a surgical video in terms of the constituent anatomical structures and tools and their evolving properties over time. To build the graphs, we first predict frame-wise graphs using a pre-trained model, then add temporal edges between nodes based on spatial coherence and visual and semantic similarity. Unlike previous approaches, we incorporate long-term temporal edges in our graphs to better model the evolution of the surgical scene and increase robustness to temporary occlusions. We also introduce a novel graph-editing module that incorporates prior knowledge and temporal coherence to correct errors in the graph, enabling improved downstream task performance. Using our graph representations, we evaluate two downstream tasks, critical view of safety prediction and surgical phase recognition, obtaining strong results that demonstrate the quality and flexibility of the learned representations. Code is available at github.com/CAMMA-public/SurgLatentGraph.

Deepak Alapatt, Pietro Mascagni, Vinkle Srivastav et al.

Deep neural networks power most recent successes of artificial intelligence, spanning from self-driving cars to computer aided diagnosis in radiology and pathology. The high-stake data intensive process of surgery could highly benefit from such computational methods. However, surgeons and computer scientists should partner to develop and assess deep learning applications of value to patients and healthcare systems. This chapter and the accompanying hands-on material were designed for surgeons willing to understand the intuitions behind neural networks, become familiar with deep learning concepts and tasks, grasp what implementing a deep learning model in surgery means, and finally appreciate the specific challenges and limitations of deep neural networks in surgery. For the associated hands-on material, please see https://github.com/CAMMA-public/ai4surgery.

Siddhant Satyanaik, Aditya Murali, Deepak Alapatt et al.

Purpose: Advances in deep learning have resulted in effective models for surgical video analysis; however, these models often fail to generalize across medical centers due to domain shift caused by variations in surgical workflow, camera setups, and patient demographics. Recently, object-centric learning has emerged as a promising approach for improved surgical scene understanding, capturing and disentangling visual and semantic properties of surgical tools and anatomy to improve downstream task performance. In this work, we conduct a multi-centric performance benchmark of object-centric approaches, focusing on Critical View of Safety assessment in laparoscopic cholecystectomy, then propose an improved approach for unseen domain generalization. Methods: We evaluate four object-centric approaches for domain generalization, establishing baseline performance. Next, leveraging the disentangled nature of object-centric representations, we dissect one of these methods through a series of ablations (e.g. ignoring either visual or semantic features for downstream classification). Finally, based on the results of these ablations, we develop an optimized method specifically tailored for domain generalization, LG-DG, that includes a novel disentanglement loss function. Results: Our optimized approach, LG-DG, achieves an improvement of 9.28% over the best baseline approach. More broadly, we show that object-centric approaches are highly effective for domain generalization thanks to their modular approach to representation learning. Conclusion: We investigate the use of object-centric methods for unseen domain generalization, identify method-agnostic factors critical for performance, and present an optimized approach that substantially outperforms existing methods.

Deepak Alapatt, Jennifer Eckhoff, Zhiliang Lyu et al.

Advances in artificial intelligence (AI) for surgical quality assessment promise to democratize access to expertise, with applications in training, guidance, and accreditation. This study presents the SAGES Critical View of Safety (CVS) Challenge, the first AI competition organized by a surgical society, using the CVS in laparoscopic cholecystectomy, a universally recommended yet inconsistently performed safety step, as an exemplar of surgical quality assessment. A global collaboration across 54 institutions in 24 countries engaged hundreds of clinicians and engineers to curate 1,000 videos annotated by 20 surgical experts according to a consensus-validated protocol. The challenge addressed key barriers to real-world deployment in surgery, including achieving high performance, capturing uncertainty in subjective assessment, and ensuring robustness to clinical variability. To enable this scale of effort, we developed EndoGlacier, a framework for managing large, heterogeneous surgical video and multi-annotator workflows. Thirteen international teams participated, achieving up to a 17\% relative gain in assessment performance, over 80\% reduction in calibration error, and a 17\% relative improvement in robustness over the state-of-the-art. Analysis of results highlighted methodological trends linked to model performance, providing guidance for future research toward robust, clinically deployable AI for surgical quality assessment.

Deepak Alapatt, Aditya Murali, Vinkle Srivastav et al.

Consensus amongst researchers and industry points to a lack of large, representative annotated datasets as the biggest obstacle to progress in the field of surgical data science. Advances in Self-Supervised Learning (SSL) represent a solution, reducing the dependence on large labeled datasets by providing task-agnostic initializations. However, the robustness of current self-supervised learning methods to domain shifts remains unclear, limiting our understanding of its utility for leveraging diverse sources of surgical data. Shifting the focus from methods to data, we demonstrate that the downstream value of SSL-based initializations is intricately intertwined with the composition of pre-training datasets. These results underscore an important gap that needs to be filled as we scale self-supervised approaches toward building general-purpose "foundation models" that enable diverse use-cases within the surgical domain. Through several stages of controlled experimentation, we develop recommendations for pretraining dataset composition evidenced through over 300 experiments spanning 20 pre-training datasets, 9 surgical procedures, 7 centers (hospitals), 3 labeled-data settings, 3 downstream tasks, and multiple runs. Using the approaches here described, we outperform state-of-the-art pre-trainings on two public benchmarks for phase recognition: up to 2.2% on Cholec80 and 5.1% on AutoLaparo.

Deepak Alapatt, Pietro Mascagni, Armine Vardazaryan et al.

A major obstacle to building models for effective semantic segmentation, and particularly video semantic segmentation, is a lack of large and well annotated datasets. This bottleneck is particularly prohibitive in highly specialized and regulated fields such as medicine and surgery, where video semantic segmentation could have important applications but data and expert annotations are scarce. In these settings, temporal clues and anatomical constraints could be leveraged during training to improve performance. Here, we present Temporally Constrained Neural Networks (TCNN), a semi-supervised framework used for video semantic segmentation of surgical videos. In this work, we show that autoencoder networks can be used to efficiently provide both spatial and temporal supervisory signals to train deep learning models. We test our method on a newly introduced video dataset of laparoscopic cholecystectomy procedures, Endoscapes, and an adaptation of a public dataset of cataract surgeries, CaDIS. We demonstrate that lower-dimensional representations of predicted masks can be leveraged to provide a consistent improvement on both sparsely labeled datasets with no additional computational cost at inference time. Further, the TCNN framework is model-agnostic and can be used in conjunction with other model design choices with minimal additional complexity.

Imanol Luengo, Maria Grammatikopoulou, Rahim Mohammadi et al.

Surgical scene segmentation is essential for anatomy and instrument localization which can be further used to assess tissue-instrument interactions during a surgical procedure. In 2017, the Challenge on Automatic Tool Annotation for cataRACT Surgery (CATARACTS) released 50 cataract surgery videos accompanied by instrument usage annotations. These annotations included frame-level instrument presence information. In 2020, we released pixel-wise semantic annotations for anatomy and instruments for 4670 images sampled from 25 videos of the CATARACTS training set. The 2020 CATARACTS Semantic Segmentation Challenge, which was a sub-challenge of the 2020 MICCAI Endoscopic Vision (EndoVis) Challenge, presented three sub-tasks to assess participating solutions on anatomical structure and instrument segmentation. Their performance was assessed on a hidden test set of 531 images from 10 videos of the CATARACTS test set.

Pietro Mascagni, Deepak Alapatt, Alain Garcia et al.

Minimally invasive image-guided surgery heavily relies on vision. Deep learning models for surgical video analysis could therefore support visual tasks such as assessing the critical view of safety (CVS) in laparoscopic cholecystectomy (LC), potentially contributing to surgical safety and efficiency. However, the performance, reliability and reproducibility of such models are deeply dependent on the quality of data and annotations used in their development. Here, we present a protocol, checklists, and visual examples to promote consistent annotation of hepatocystic anatomy and CVS criteria. We believe that sharing annotation guidelines can help build trustworthy multicentric datasets for assessing generalizability of performance, thus accelerating the clinical translation of deep learning models for surgical video analysis.