Benchmarking Pretrained Attention-based Models for Real-Time Recognition in Robot-Assisted Esophagectomy

Esophageal cancer is among the most common types of cancer worldwide. It is traditionally treated using open esophagectomy, but in recent years, robot-assisted minimally invasive esophagectomy (RAMIE) has emerged as a promising alternative. However, robot-assisted surgery can be challenging for novice surgeons, as they often suffer from a loss of spatial orientation. Computer-aided anatomy recognition holds promise for improving surgical navigation, but research in this area remains limited. In this study, we developed a comprehensive dataset for semantic segmentation in RAMIE, featuring the largest collection of vital anatomical structures and surgical instruments to date. Handling this diverse set of classes presents challenges, including class imbalance and the recognition of complex structures such as nerves. This study aims to understand the challenges and limitations of current state-of-the-art algorithms on this novel dataset and problem. Therefore, we benchmarked eight real-time deep learning models using two pretraining datasets. We assessed both traditional and attention-based networks, hypothesizing that attention-based networks better capture global patterns and address challenges such as occlusion caused by blood or other tissues. The benchmark includes our RAMIE dataset and the publicly available CholecSeg8k dataset, enabling a thorough assessment of surgical segmentation tasks. Our findings indicate that pretraining on ADE20k, a dataset for semantic segmentation, is more effective than pretraining on ImageNet. Furthermore, attention-based models outperform traditional convolutional neural networks, with SegNeXt and Mask2Former achieving higher Dice scores, and Mask2Former additionally excelling in average symmetric surface distance.

Can Your Generative Model Detect Out-of-Distribution Covariate Shift?

Detecting Out-of-Distribution~(OOD) sensory data and covariate distribution shift aims to identify new test examples with different high-level image statistics to the captured, normal and In-Distribution (ID) set. Existing OOD detection literature largely focuses on semantic shift with little-to-no consensus over covariate shift. Generative models capture the ID data in an unsupervised manner, enabling them to effectively identify samples that deviate significantly from this learned distribution, irrespective of the downstream task. In this work, we elucidate the ability of generative models to detect and quantify domain-specific covariate shift through extensive analyses that involves a variety of models. To this end, we conjecture that it is sufficient to detect most occurring sensory faults (anomalies and deviations in global signals statistics) by solely modeling high-frequency signal-dependent and independent details. We propose a novel method, CovariateFlow, for OOD detection, specifically tailored to covariate heteroscedastic high-frequency image-components using conditional Normalizing Flows (cNFs). Our results on CIFAR10 vs. CIFAR10-C and ImageNet200 vs. ImageNet200-C demonstrate the effectiveness of the method by accurately detecting OOD covariate shift. This work contributes to enhancing the fidelity of imaging systems and aiding machine learning models in OOD detection in the presence of covariate shift.

Find the Assembly Mistakes: Error Segmentation for Industrial Applications

Recognizing errors in assembly and maintenance procedures is valuable for industrial applications, since it can increase worker efficiency and prevent unplanned down-time. Although assembly state recognition is gaining attention, none of the current works investigate assembly error localization. Therefore, we propose StateDiffNet, which localizes assembly errors based on detecting the differences between a (correct) intended assembly state and a test image from a similar viewpoint. StateDiffNet is trained on synthetically generated image pairs, providing full control over the type of meaningful change that should be detected. The proposed approach is the first to correctly localize assembly errors taken from real ego-centric video data for both states and error types that are never presented during training. Furthermore, the deployment of change detection to this industrial application provides valuable insights and considerations into the mechanisms of state-of-the-art change detection algorithms. The code and data generation pipeline are publicly available at: https://timschoonbeek.github.io/error_seg.

Supervised Representation Learning towards Generalizable Assembly State Recognition

Assembly state recognition facilitates the execution of assembly procedures, offering feedback to enhance efficiency and minimize errors. However, recognizing assembly states poses challenges in scalability, since parts are frequently updated, and the robustness to execution errors remains underexplored. To address these challenges, this paper proposes an approach based on representation learning and the novel intermediate-state informed loss function modification (ISIL). ISIL leverages unlabeled transitions between states and demonstrates significant improvements in clustering and classification performance for all tested architectures and losses. Despite being trained exclusively on images without execution errors, thorough analysis on error states demonstrates that our approach accurately distinguishes between correct states and states with various types of execution errors. The integration of the proposed algorithm can offer meaningful assistance to workers and mitigate unexpected losses due to procedural mishaps in industrial settings. The code is available at: https://timschoonbeek.github.io/state_rec

Exploring the Effect of Dataset Diversity in Self-Supervised Learning for Surgical Computer Vision

Over the past decade, computer vision applications in minimally invasive surgery have rapidly increased. Despite this growth, the impact of surgical computer vision remains limited compared to other medical fields like pathology and radiology, primarily due to the scarcity of representative annotated data. Whereas transfer learning from large annotated datasets such as ImageNet has been conventionally the norm to achieve high-performing models, recent advancements in self-supervised learning (SSL) have demonstrated superior performance. In medical image analysis, in-domain SSL pretraining has already been shown to outperform ImageNet-based initialization. Although unlabeled data in the field of surgical computer vision is abundant, the diversity within this data is limited. This study investigates the role of dataset diversity in SSL for surgical computer vision, comparing procedure-specific datasets against a more heterogeneous general surgical dataset across three different downstream surgical applications. The obtained results show that using solely procedure-specific data can lead to substantial improvements of 13.8%, 9.5%, and 36.8% compared to ImageNet pretraining. However, extending this data with more heterogeneous surgical data further increases performance by an additional 5.0%, 5.2%, and 2.5%, suggesting that increasing diversity within SSL data is beneficial for model performance. The code and pretrained model weights are made publicly available at https://github.com/TimJaspers0801/SurgeNet.

Advancing 6-DoF Instrument Pose Estimation in Variable X-Ray Imaging Geometries

Accurate 6-DoF pose estimation of surgical instruments during minimally invasive surgeries can substantially improve treatment strategies and eventual surgical outcome. Existing deep learning methods have achieved accurate results, but they require custom approaches for each object and laborious setup and training environments often stretching to extensive simulations, whilst lacking real-time computation. We propose a general-purpose approach of data acquisition for 6-DoF pose estimation tasks in X-ray systems, a novel and general purpose YOLOv5-6D pose architecture for accurate and fast object pose estimation and a complete method for surgical screw pose estimation under acquisition geometry consideration from a monocular cone-beam X-ray image. The proposed YOLOv5-6D pose model achieves competitive results on public benchmarks whilst being considerably faster at 42 FPS on GPU. In addition, the method generalizes across varying X-ray acquisition geometry and semantic image complexity to enable accurate pose estimation over different domains. Finally, the proposed approach is tested for bone-screw pose estimation for computer-aided guidance during spine surgeries. The model achieves a 92.41% by the 0.1 ADD-S metric, demonstrating a promising approach for enhancing surgical precision and patient outcomes. The code for YOLOv5-6D is publicly available at https://github.com/cviviers/YOLOv5-6D-Pose

IndustReal: A Dataset for Procedure Step Recognition Handling Execution Errors in Egocentric Videos in an Industrial-Like Setting

Although action recognition for procedural tasks has received notable attention, it has a fundamental flaw in that no measure of success for actions is provided. This limits the applicability of such systems especially within the industrial domain, since the outcome of procedural actions is often significantly more important than the mere execution. To address this limitation, we define the novel task of procedure step recognition (PSR), focusing on recognizing the correct completion and order of procedural steps. Alongside the new task, we also present the multi-modal IndustReal dataset. Unlike currently available datasets, IndustReal contains procedural errors (such as omissions) as well as execution errors. A significant part of these errors are exclusively present in the validation and test sets, making IndustReal suitable to evaluate robustness of algorithms to new, unseen mistakes. Additionally, to encourage reproducibility and allow for scalable approaches trained on synthetic data, the 3D models of all parts are publicly available. Annotations and benchmark performance are provided for action recognition and assembly state detection, as well as the new PSR task. IndustReal, along with the code and model weights, is available at: https://github.com/TimSchoonbeek/IndustReal .

Segmentation-based Assessment of Tumor-Vessel Involvement for Surgical Resectability Prediction of Pancreatic Ductal Adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with limited treatment options. This research proposes a workflow and deep learning-based segmentation models to automatically assess tumor-vessel involvement, a key factor in determining tumor resectability. Correct assessment of resectability is vital to determine treatment options. The proposed workflow involves processing CT scans to segment the tumor and vascular structures, analyzing spatial relationships and the extent of vascular involvement, which follows a similar way of working as expert radiologists in PDAC assessment. Three segmentation architectures (nnU-Net, 3D U-Net, and Probabilistic 3D U-Net) achieve a high accuracy in segmenting veins, arteries, and the tumor. The segmentations enable automated detection of tumor involvement with high accuracy (0.88 sensitivity and 0.86 specificity) and automated computation of the degree of tumor-vessel contact. Additionally, due to significant inter-observer variability in these important structures, we present the uncertainty captured by each of the models to further increase insights into the predicted involvement. This result provides clinicians with a clear indication of tumor-vessel involvement and may be used to facilitate more informed decision-making for surgical interventions. The proposed method offers a valuable tool for improving patient outcomes, personalized treatment strategies and survival rates in pancreatic cancer.

Investigating and Improving Latent Density Segmentation Models for Aleatoric Uncertainty Quantification in Medical Imaging

Data uncertainties, such as sensor noise or occlusions, can introduce irreducible ambiguities in images, which result in varying, yet plausible, semantic hypotheses. In Machine Learning, this ambiguity is commonly referred to as aleatoric uncertainty. Latent density models can be utilized to address this problem in image segmentation. The most popular approach is the Probabilistic U-Net (PU-Net), which uses latent Normal densities to optimize the conditional data log-likelihood Evidence Lower Bound. In this work, we demonstrate that the PU- Net latent space is severely inhomogenous. As a result, the effectiveness of gradient descent is inhibited and the model becomes extremely sensitive to the localization of the latent space samples, resulting in defective predictions. To address this, we present the Sinkhorn PU-Net (SPU-Net), which uses the Sinkhorn Divergence to promote homogeneity across all latent dimensions, effectively improving gradient-descent updates and model robustness. Our results show that by applying this on public datasets of various clinical segmentation problems, the SPU-Net receives up to 11% performance gains compared against preceding latent variable models for probabilistic segmentation on the Hungarian-Matched metric. The results indicate that by encouraging a homogeneous latent space, one can significantly improve latent density modeling for medical image segmentation.

A signal processing interpretation of noise-reduction convolutional neural networks

Encoding-decoding CNNs play a central role in data-driven noise reduction and can be found within numerous deep-learning algorithms. However, the development of these CNN architectures is often done in ad-hoc fashion and theoretical underpinnings for important design choices is generally lacking. Up to this moment there are different existing relevant works that strive to explain the internal operation of these CNNs. Still, these ideas are either scattered and/or may require significant expertise to be accessible for a bigger audience. In order to open up this exciting field, this article builds intuition on the theory of deep convolutional framelets and explains diverse ED CNN architectures in a unified theoretical framework. By connecting basic principles from signal processing to the field of deep learning, this self-contained material offers significant guidance for designing robust and efficient novel CNN architectures.