More than Segmentation: Benchmarking SAM 3 for Segmentation, 3D Perception, and Reconstruction in Robotic Surgery

The recent SAM 3 and SAM 3D have introduced significant advancements over the predecessor, SAM 2, particularly with the integration of language-based segmentation and enhanced 3D perception capabilities. SAM 3 supports zero-shot segmentation across a wide range of prompts, including point, bounding box, and language-based prompts, allowing for more flexible and intuitive interactions with the model. In this empirical evaluation, we assess the performance of SAM 3 in robot-assisted surgery, benchmarking its zero-shot segmentation with point and bounding box prompts and exploring its effectiveness in dynamic video tracking, alongside its newly introduced language prompt segmentation. While language prompts show potential, their performance in the surgical domain is currently suboptimal, highlighting the need for further domain-specific training. Additionally, we investigate SAM 3D's depth reconstruction abilities, demonstrating its capacity to process surgical scene data and reconstruct 3D anatomical structures from 2D images. Through comprehensive testing on the MICCAI EndoVis 2017 and EndoVis 2018 benchmarks, SAM 3 shows clear improvements over SAM and SAM 2 in both image and video segmentation under spatial prompts, while the zero-shot evaluations of SAM 3D on SCARED, StereoMIS, and EndoNeRF indicate strong monocular depth estimation and realistic 3D instrument reconstruction, yet also reveal remaining limitations in complex, highly dynamic surgical scenes.

EndoIR: Degradation-Agnostic All-in-One Endoscopic Image Restoration via Noise-Aware Routing Diffusion

Endoscopic images often suffer from diverse and co-occurring degradations such as low lighting, smoke, and bleeding, which obscure critical clinical details. Existing restoration methods are typically task-specific and often require prior knowledge of the degradation type, limiting their robustness in real-world clinical use. We propose EndoIR, an all-in-one, degradation-agnostic diffusion-based framework that restores multiple degradation types using a single model. EndoIR introduces a Dual-Domain Prompter that extracts joint spatial-frequency features, coupled with an adaptive embedding that encodes both shared and task-specific cues as conditioning for denoising. To mitigate feature confusion in conventional concatenation-based conditioning, we design a Dual-Stream Diffusion architecture that processes clean and degraded inputs separately, with a Rectified Fusion Block integrating them in a structured, degradation-aware manner. Furthermore, Noise-Aware Routing Block improves efficiency by dynamically selecting only noise-relevant features during denoising. Experiments on SegSTRONG-C and CEC datasets demonstrate that EndoIR achieves state-of-the-art performance across multiple degradation scenarios while using fewer parameters than strong baselines, and downstream segmentation experiments confirm its clinical utility.

Comparative validation of surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation in endoscopy: Results of the PhaKIR 2024 challenge

Reliable recognition and localization of surgical instruments in endoscopic video recordings are foundational for a wide range of applications in computer- and robot-assisted minimally invasive surgery (RAMIS), including surgical training, skill assessment, and autonomous assistance. However, robust performance under real-world conditions remains a significant challenge. Incorporating surgical context - such as the current procedural phase - has emerged as a promising strategy to improve robustness and interpretability. To address these challenges, we organized the Surgical Procedure Phase, Keypoint, and Instrument Recognition (PhaKIR) sub-challenge as part of the Endoscopic Vision (EndoVis) challenge at MICCAI 2024. We introduced a novel, multi-center dataset comprising thirteen full-length laparoscopic cholecystectomy videos collected from three distinct medical institutions, with unified annotations for three interrelated tasks: surgical phase recognition, instrument keypoint estimation, and instrument instance segmentation. Unlike existing datasets, ours enables joint investigation of instrument localization and procedural context within the same data while supporting the integration of temporal information across entire procedures. We report results and findings in accordance with the BIAS guidelines for biomedical image analysis challenges. The PhaKIR sub-challenge advances the field by providing a unique benchmark for developing temporally aware, context-driven methods in RAMIS and offers a high-quality resource to support future research in surgical scene understanding.

TR2M: Transferring Monocular Relative Depth to Metric Depth with Language Descriptions and Scale-Oriented Contrast

This work presents a generalizable framework to transfer relative depth to metric depth. Current monocular depth estimation methods are mainly divided into metric depth estimation (MMDE) and relative depth estimation (MRDE). MMDEs estimate depth in metric scale but are often limited to a specific domain. MRDEs generalize well across different domains, but with uncertain scales which hinders downstream applications. To this end, we aim to build up a framework to solve scale uncertainty and transfer relative depth to metric depth. Previous methods used language as input and estimated two factors for conducting rescaling. Our approach, TR2M, utilizes both text description and image as inputs and estimates two rescale maps to transfer relative depth to metric depth at pixel level. Features from two modalities are fused with a cross-modality attention module to better capture scale information. A strategy is designed to construct and filter confident pseudo metric depth for more comprehensive supervision. We also develop scale-oriented contrastive learning to utilize depth distribution as guidance to enforce the model learning about intrinsic knowledge aligning with the scale distribution. TR2M only exploits a small number of trainable parameters to train on datasets in various domains and experiments not only demonstrate TR2M's great performance in seen datasets but also reveal superior zero-shot capabilities on five unseen datasets. We show the huge potential in pixel-wise transferring relative depth to metric depth with language assistance. (Code is available at: https://github.com/BeileiCui/TR2M)

KnowCoder-V2: Deep Knowledge Analysis

Deep knowledge analysis tasks always involve the systematic extraction and association of knowledge from large volumes of data, followed by logical reasoning to discover insights. However, to solve such complex tasks, existing deep research frameworks face three major challenges: 1) They lack systematic organization and management of knowledge; 2) They operate purely online, making it inefficient for tasks that rely on shared and large-scale knowledge; 3) They cannot perform complex knowledge computation, limiting their abilities to produce insightful analytical results. Motivated by these, in this paper, we propose a \textbf{K}nowledgeable \textbf{D}eep \textbf{R}esearch (\textbf{KDR}) framework that empowers deep research with deep knowledge analysis capability. Specifically, it introduces an independent knowledge organization phase to preprocess large-scale, domain-relevant data into systematic knowledge offline. Based on this knowledge, it extends deep research with an additional kind of reasoning steps that perform complex knowledge computation in an online manner. To enhance the abilities of LLMs to solve knowledge analysis tasks in the above framework, we further introduce \textbf{\KCII}, an LLM that bridges knowledge organization and reasoning via unified code generation. For knowledge organization, it generates instantiation code for predefined classes, transforming data into knowledge objects. For knowledge computation, it generates analysis code and executes on the above knowledge objects to obtain deep analysis results. Experimental results on more than thirty datasets across six knowledge analysis tasks demonstrate the effectiveness of \KCII. Moreover, when integrated into the KDR framework, \KCII can generate high-quality reports with insightful analytical results compared to the mainstream deep research framework.

EndoARSS: Adapting Spatially-Aware Foundation Model for Efficient Activity Recognition and Semantic Segmentation in Endoscopic Surgery

Endoscopic surgery is the gold standard for robotic-assisted minimally invasive surgery, offering significant advantages in early disease detection and precise interventions. However, the complexity of surgical scenes, characterized by high variability in different surgical activity scenarios and confused image features between targets and the background, presents challenges for surgical environment understanding. Traditional deep learning models often struggle with cross-activity interference, leading to suboptimal performance in each downstream task. To address this limitation, we explore multi-task learning, which utilizes the interrelated features between tasks to enhance overall task performance. In this paper, we propose EndoARSS, a novel multi-task learning framework specifically designed for endoscopy surgery activity recognition and semantic segmentation. Built upon the DINOv2 foundation model, our approach integrates Low-Rank Adaptation to facilitate efficient fine-tuning while incorporating Task Efficient Shared Low-Rank Adapters to mitigate gradient conflicts across diverse tasks. Additionally, we introduce the Spatially-Aware Multi-Scale Attention that enhances feature representation discrimination by enabling cross-spatial learning of global information. In order to evaluate the effectiveness of our framework, we present three novel datasets, MTLESD, MTLEndovis and MTLEndovis-Gen, tailored for endoscopic surgery scenarios with detailed annotations for both activity recognition and semantic segmentation tasks. Extensive experiments demonstrate that EndoARSS achieves remarkable performance across multiple benchmarks, significantly improving both accuracy and robustness in comparison to existing models. These results underscore the potential of EndoARSS to advance AI-driven endoscopic surgical systems, offering valuable insights for enhancing surgical safety and efficiency.

EndoVLA: Dual-Phase Vision-Language-Action Model for Autonomous Tracking in Endoscopy

In endoscopic procedures, autonomous tracking of abnormal regions and following circumferential cutting markers can significantly reduce the cognitive burden on endoscopists. However, conventional model-based pipelines are fragile for each component (e.g., detection, motion planning) requires manual tuning and struggles to incorporate high-level endoscopic intent, leading to poor generalization across diverse scenes. Vision-Language-Action (VLA) models, which integrate visual perception, language grounding, and motion planning within an end-to-end framework, offer a promising alternative by semantically adapting to surgeon prompts without manual recalibration. Despite their potential, applying VLA models to robotic endoscopy presents unique challenges due to the complex and dynamic anatomical environments of the gastrointestinal (GI) tract. To address this, we introduce EndoVLA, designed specifically for continuum robots in GI interventions. Given endoscopic images and surgeon-issued tracking prompts, EndoVLA performs three core tasks: (1) polyp tracking, (2) delineation and following of abnormal mucosal regions, and (3) adherence to circular markers during circumferential cutting. To tackle data scarcity and domain shifts, we propose a dual-phase strategy comprising supervised fine-tuning on our EndoVLA-Motion dataset and reinforcement fine-tuning with task-aware rewards. Our approach significantly improves tracking performance in endoscopy and enables zero-shot generalization in diverse scenes and complex sequential tasks.

Mixture Policy based Multi-Hop Reasoning over N-tuple Temporal Knowledge Graphs

Temporal Knowledge Graphs (TKGs), which utilize quadruples in the form of (subject, predicate, object, timestamp) to describe temporal facts, have attracted extensive attention. N-tuple TKGs (N-TKGs) further extend traditional TKGs by utilizing n-tuples to incorporate auxiliary elements alongside core elements (i.e., subject, predicate, and object) of facts, so as to represent them in a more fine-grained manner. Reasoning over N-TKGs aims to predict potential future facts based on historical ones. However, existing N-TKG reasoning methods often lack explainability due to their black-box nature. Therefore, we introduce a new Reinforcement Learning-based method, named MT-Path, which leverages the temporal information to traverse historical n-tuples and construct a temporal reasoning path. Specifically, in order to integrate the information encapsulated within n-tuples, i.e., the entity-irrelevant information within the predicate, the information about core elements, and the complete information about the entire n-tuples, MT-Path utilizes a mixture policy-driven action selector, which bases on three low-level policies, namely, the predicate-focused policy, the core-element-focused policy and the whole-fact-focused policy. Further, MT-Path utilizes an auxiliary element-aware GCN to capture the rich semantic dependencies among facts, thereby enabling the agent to gain a deep understanding of each n-tuple. Experimental results demonstrate the effectiveness and the explainability of MT-Path.

PvNeXt: Rethinking Network Design and Temporal Motion for Point Cloud Video Recognition

Point cloud video perception has become an essential task for the realm of 3D vision. Current 4D representation learning techniques typically engage in iterative processing coupled with dense query operations. Although effective in capturing temporal features, this approach leads to substantial computational redundancy. In this work, we propose a framework, named as PvNeXt, for effective yet efficient point cloud video recognition, via personalized one-shot query operation. Specially, PvNeXt consists of two key modules, the Motion Imitator and the Single-Step Motion Encoder. The former module, the Motion Imitator, is designed to capture the temporal dynamics inherent in sequences of point clouds, thus generating the virtual motion corresponding to each frame. The Single-Step Motion Encoder performs a one-step query operation, associating point cloud of each frame with its corresponding virtual motion frame, thereby extracting motion cues from point cloud sequences and capturing temporal dynamics across the entire sequence. Through the integration of these two modules, {PvNeXt} enables personalized one-shot queries for each frame, effectively eliminating the need for frame-specific looping and intensive query processes. Extensive experiments on multiple benchmarks demonstrate the effectiveness of our method.

Can DeepSeek Reason Like a Surgeon? An Empirical Evaluation for Vision-Language Understanding in Robotic-Assisted Surgery

DeepSeek series have demonstrated outstanding performance in general scene understanding, question-answering (QA), and text generation tasks, owing to its efficient training paradigm and strong reasoning capabilities. In this study, we investigate the dialogue capabilities of the DeepSeek model in robotic surgery scenarios, focusing on tasks such as Single Phrase QA, Visual QA, and Detailed Description. The Single Phrase QA tasks further include sub-tasks such as surgical instrument recognition, action understanding, and spatial position analysis. We conduct extensive evaluations using publicly available datasets, including EndoVis18 and CholecT50, along with their corresponding dialogue data. Our comprehensive evaluation results indicate that, when provided with specific prompts, DeepSeek-V3 performs well in surgical instrument and tissue recognition tasks However, DeepSeek-V3 exhibits significant limitations in spatial position analysis and struggles to understand surgical actions accurately. Additionally, our findings reveal that, under general prompts, DeepSeek-V3 lacks the ability to effectively analyze global surgical concepts and fails to provide detailed insights into surgical scenarios. Based on our observations, we argue that the DeepSeek-V3 is not ready for vision-language tasks in surgical contexts without fine-tuning on surgery-specific datasets.