Adapting SAM for Surgical Instrument Tracking and Segmentation in Endoscopic Submucosal Dissection Videos

The precise tracking and segmentation of surgical instruments have led to a remarkable enhancement in the efficiency of surgical procedures. However, the challenge lies in achieving accurate segmentation of surgical instruments while minimizing the need for manual annotation and reducing the time required for the segmentation process. To tackle this, we propose a novel framework for surgical instrument segmentation and tracking. Specifically, with a tiny subset of frames for segmentation, we ensure accurate segmentation across the entire surgical video. Our method adopts a two-stage approach to efficiently segment videos. Initially, we utilize the Segment-Anything (SAM) model, which has been fine-tuned using the Low-Rank Adaptation (LoRA) on the EndoVis17 Dataset. The fine-tuned SAM model is applied to segment the initial frames of the video accurately. Subsequently, we deploy the XMem++ tracking algorithm to follow the annotated frames, thereby facilitating the segmentation of the entire video sequence. This workflow enables us to precisely segment and track objects within the video. Through extensive evaluation of the in-distribution dataset (EndoVis17) and the out-of-distribution datasets (EndoVis18 \& the endoscopic submucosal dissection surgery (ESD) dataset), our framework demonstrates exceptional accuracy and robustness, thus showcasing its potential to advance the automated robotic-assisted surgery.

Class-Incremental Few-Shot Event Detection

Event detection is one of the fundamental tasks in information extraction and knowledge graph. However, a realistic event detection system often needs to deal with new event classes constantly. These new classes usually have only a few labeled instances as it is time-consuming and labor-intensive to annotate a large number of unlabeled instances. Therefore, this paper proposes a new task, called class-incremental few-shot event detection. Nevertheless, this task faces two problems, i.e., old knowledge forgetting and new class overfitting. To solve these problems, this paper further presents a novel knowledge distillation and prompt learning based method, called Prompt-KD. Specifically, to handle the forgetting problem about old knowledge, Prompt-KD develops an attention based multi-teacher knowledge distillation framework, where the ancestor teacher model pre-trained on base classes is reused in all learning sessions, and the father teacher model derives the current student model via adaptation. On the other hand, in order to cope with the few-shot learning scenario and alleviate the corresponding new class overfitting problem, Prompt-KD is also equipped with a prompt learning mechanism. Extensive experiments on two benchmark datasets, i.e., FewEvent and MAVEN, demonstrate the superior performance of Prompt-KD.

Selective Temporal Knowledge Graph Reasoning

Temporal Knowledge Graph (TKG), which characterizes temporally evolving facts in the form of (subject, relation, object, timestamp), has attracted much attention recently. TKG reasoning aims to predict future facts based on given historical ones. However, existing TKG reasoning models are unable to abstain from predictions they are uncertain, which will inevitably bring risks in real-world applications. Thus, in this paper, we propose an abstention mechanism for TKG reasoning, which helps the existing models make selective, instead of indiscriminate, predictions. Specifically, we develop a confidence estimator, called Confidence Estimator with History (CEHis), to enable the existing TKG reasoning models to first estimate their confidence in making predictions, and then abstain from those with low confidence. To do so, CEHis takes two kinds of information into consideration, namely, the certainty of the current prediction and the accuracy of historical predictions. Experiments with representative TKG reasoning models on two benchmark datasets demonstrate the effectiveness of the proposed CEHis.

KnowCoder: Coding Structured Knowledge into LLMs for Universal Information Extraction

In this paper, we propose KnowCoder, a Large Language Model (LLM) to conduct Universal Information Extraction (UIE) via code generation. KnowCoder aims to develop a kind of unified schema representation that LLMs can easily understand and an effective learning framework that encourages LLMs to follow schemas and extract structured knowledge accurately. To achieve these, KnowCoder introduces a code-style schema representation method to uniformly transform different schemas into Python classes, with which complex schema information, such as constraints among tasks in UIE, can be captured in an LLM-friendly manner. We further construct a code-style schema library covering over $\textbf{30,000}$ types of knowledge, which is the largest one for UIE, to the best of our knowledge. To ease the learning process of LLMs, KnowCoder contains a two-phase learning framework that enhances its schema understanding ability via code pretraining and its schema following ability via instruction tuning. After code pretraining on around $1.5$B automatically constructed data, KnowCoder already attains remarkable generalization ability and achieves relative improvements by $\textbf{49.8%}$ F1, compared to LLaMA2, under the few-shot setting. After instruction tuning, KnowCoder further exhibits strong generalization ability on unseen schemas and achieves up to $\textbf{12.5%}$ and $\textbf{21.9%}$, compared to sota baselines, under the zero-shot setting and the low resource setting, respectively. Additionally, based on our unified schema representations, various human-annotated datasets can simultaneously be utilized to refine KnowCoder, which achieves significant improvements up to $\textbf{7.5%}$ under the supervised setting.

EndoOOD: Uncertainty-aware Out-of-distribution Detection in Capsule Endoscopy Diagnosis

Wireless capsule endoscopy (WCE) is a non-invasive diagnostic procedure that enables visualization of the gastrointestinal (GI) tract. Deep learning-based methods have shown effectiveness in disease screening using WCE data, alleviating the burden on healthcare professionals. However, existing capsule endoscopy classification methods mostly rely on pre-defined categories, making it challenging to identify and classify out-of-distribution (OOD) data, such as undefined categories or anatomical landmarks. To address this issue, we propose the Endoscopy Out-of-Distribution (EndoOOD) framework, which aims to effectively handle the OOD detection challenge in WCE diagnosis. The proposed framework focuses on improving the robustness and reliability of WCE diagnostic capabilities by incorporating uncertainty-aware mixup training and long-tailed in-distribution (ID) data calibration techniques. Additionally, virtual-logit matching is employed to accurately distinguish between OOD and ID data while minimizing information loss. To assess the performance of our proposed solution, we conduct evaluations and comparisons with 12 state-of-the-art (SOTA) methods using two publicly available datasets. The results demonstrate the effectiveness of the proposed framework in enhancing diagnostic accuracy and supporting clinical decision-making.

OSSAR: Towards Open-Set Surgical Activity Recognition in Robot-assisted Surgery

In the realm of automated robotic surgery and computer-assisted interventions, understanding robotic surgical activities stands paramount. Existing algorithms dedicated to surgical activity recognition predominantly cater to pre-defined closed-set paradigms, ignoring the challenges of real-world open-set scenarios. Such algorithms often falter in the presence of test samples originating from classes unseen during training phases. To tackle this problem, we introduce an innovative Open-Set Surgical Activity Recognition (OSSAR) framework. Our solution leverages the hyperspherical reciprocal point strategy to enhance the distinction between known and unknown classes in the feature space. Additionally, we address the issue of over-confidence in the closed set by refining model calibration, avoiding misclassification of unknown classes as known ones. To support our assertions, we establish an open-set surgical activity benchmark utilizing the public JIGSAWS dataset. Besides, we also collect a novel dataset on endoscopic submucosal dissection for surgical activity tasks. Extensive comparisons and ablation experiments on these datasets demonstrate the significant outperformance of our method over existing state-of-the-art approaches. Our proposed solution can effectively address the challenges of real-world surgical scenarios. Our code is publicly accessible at https://github.com/longbai1006/OSSAR.

Privacy-Preserving Synthetic Continual Semantic Segmentation for Robotic Surgery

Deep Neural Networks (DNNs) based semantic segmentation of the robotic instruments and tissues can enhance the precision of surgical activities in robot-assisted surgery. However, in biological learning, DNNs cannot learn incremental tasks over time and exhibit catastrophic forgetting, which refers to the sharp decline in performance on previously learned tasks after learning a new one. Specifically, when data scarcity is the issue, the model shows a rapid drop in performance on previously learned instruments after learning new data with new instruments. The problem becomes worse when it limits releasing the dataset of the old instruments for the old model due to privacy concerns and the unavailability of the data for the new or updated version of the instruments for the continual learning model. For this purpose, we develop a privacy-preserving synthetic continual semantic segmentation framework by blending and harmonizing (i) open-source old instruments foreground to the synthesized background without revealing real patient data in public and (ii) new instruments foreground to extensively augmented real background. To boost the balanced logit distillation from the old model to the continual learning model, we design overlapping class-aware temperature normalization (CAT) by controlling model learning utility. We also introduce multi-scale shifted-feature distillation (SD) to maintain long and short-range spatial relationships among the semantic objects where conventional short-range spatial features with limited information reduce the power of feature distillation. We demonstrate the effectiveness of our framework on the EndoVis 2017 and 2018 instrument segmentation dataset with a generalized continual learning setting. Code is available at~\url{https://github.com/XuMengyaAmy/Synthetic_CAT_SD}.

Endo-4DGS: Endoscopic Monocular Scene Reconstruction with 4D Gaussian Splatting

In the realm of robot-assisted minimally invasive surgery, dynamic scene reconstruction can significantly enhance downstream tasks and improve surgical outcomes. Neural Radiance Fields (NeRF)-based methods have recently risen to prominence for their exceptional ability to reconstruct scenes. Nonetheless, these methods are hampered by slow inference, prolonged training, and substantial computational demands. Additionally, some rely on stereo depth estimation, which is often infeasible due to the high costs and logistical challenges associated with stereo cameras. Moreover, the monocular reconstruction quality for deformable scenes is currently inadequate. To overcome these obstacles, we present Endo-4DGS, an innovative, real-time endoscopic dynamic reconstruction approach that utilizes 4D Gaussian Splatting (GS) and requires no ground truth depth data. This method extends 3D GS by incorporating a temporal component and leverages a lightweight MLP to capture temporal Gaussian deformations. This effectively facilitates the reconstruction of dynamic surgical scenes with variable conditions. We also integrate Depth-Anything to generate pseudo-depth maps from monocular views, enhancing the depth-guided reconstruction process. Our approach has been validated on two surgical datasets, where it can effectively render in real-time, compute efficiently, and reconstruct with remarkable accuracy. These results underline the vast potential of Endo-4DGS to improve surgical assistance.

Surgical-DINO: Adapter Learning of Foundation Models for Depth Estimation in Endoscopic Surgery

Purpose: Depth estimation in robotic surgery is vital in 3D reconstruction, surgical navigation and augmented reality visualization. Although the foundation model exhibits outstanding performance in many vision tasks, including depth estimation (e.g., DINOv2), recent works observed its limitations in medical and surgical domain-specific applications. This work presents a low-ranked adaptation (LoRA) of the foundation model for surgical depth estimation. Methods: We design a foundation model-based depth estimation method, referred to as Surgical-DINO, a low-rank adaptation of the DINOv2 for depth estimation in endoscopic surgery. We build LoRA layers and integrate them into DINO to adapt with surgery-specific domain knowledge instead of conventional fine-tuning. During training, we freeze the DINO image encoder, which shows excellent visual representation capacity, and only optimize the LoRA layers and depth decoder to integrate features from the surgical scene. Results: Our model is extensively validated on a MICCAI challenge dataset of SCARED, which is collected from da Vinci Xi endoscope surgery. We empirically show that Surgical-DINO significantly outperforms all the state-of-the-art models in endoscopic depth estimation tasks. The analysis with ablation studies has shown evidence of the remarkable effect of our LoRA layers and adaptation. Conclusion: Surgical-DINO shed some light on the successful adaptation of the foundation models into the surgical domain for depth estimation. There is clear evidence in the results that zero-shot prediction on pre-trained weights in computer vision datasets or naive fine-tuning is not sufficient to use the foundation model in the surgical domain directly. Code is available at https://github.com/BeileiCui/SurgicalDINO.

SAR-RARP50: Segmentation of surgical instrumentation and Action Recognition on Robot-Assisted Radical Prostatectomy Challenge

Surgical tool segmentation and action recognition are fundamental building blocks in many computer-assisted intervention applications, ranging from surgical skills assessment to decision support systems. Nowadays, learning-based action recognition and segmentation approaches outperform classical methods, relying, however, on large, annotated datasets. Furthermore, action recognition and tool segmentation algorithms are often trained and make predictions in isolation from each other, without exploiting potential cross-task relationships. With the EndoVis 2022 SAR-RARP50 challenge, we release the first multimodal, publicly available, in-vivo, dataset for surgical action recognition and semantic instrumentation segmentation, containing 50 suturing video segments of Robotic Assisted Radical Prostatectomy (RARP). The aim of the challenge is twofold. First, to enable researchers to leverage the scale of the provided dataset and develop robust and highly accurate single-task action recognition and tool segmentation approaches in the surgical domain. Second, to further explore the potential of multitask-based learning approaches and determine their comparative advantage against their single-task counterparts. A total of 12 teams participated in the challenge, contributing 7 action recognition methods, 9 instrument segmentation techniques, and 4 multitask approaches that integrated both action recognition and instrument segmentation.