arXiv subjects

Yueming Jin

Publications and source records attributed to Yueming Jin.

At least 73 records · Page 4Linked to original sources

arXiv2025

Instrument-Splatting: Controllable Photorealistic Reconstruction of Surgical Instruments Using Gaussian Splatting

Real2Sim is becoming increasingly important with the rapid development of surgical artificial intelligence (AI) and autonomy. In this work, we propose a novel Real2Sim methodology, Instrument-Splatting, that leverages 3D Gaussian Splatting to provide fully controllable 3D reconstruction of surgical instruments from monocular surgical videos. To maintain both high visual fidelity and manipulability, we introduce a geometry pre-training to bind Gaussian point clouds on part mesh with accurate geometric priors and define a forward kinematics to control the Gaussians as flexible as real instruments. Afterward, to handle unposed videos, we design a novel instrument pose tracking method leveraging semantics-embedded Gaussians to robustly refine per-frame instrument poses and joint states in a render-and-compare manner, which allows our instrument Gaussian to accurately learn textures and reach photorealistic rendering. We validated our method on 2 publicly released surgical videos and 4 videos collected on ex vivo tissues and green screens. Quantitative and qualitative evaluations demonstrate the effectiveness and superiority of the proposed method.

cs.CV↗

arXiv2025

Surgical SAM 2: Real-time Segment Anything in Surgical Video by Efficient Frame Pruning

Surgical video segmentation is a critical task in computer-assisted surgery and is vital for enhancing surgical quality and patient outcomes. Recently, the Segment Anything Model 2 (SAM2) framework has shown superior advancements in image and video segmentation. However, SAM2 struggles with efficiency due to the high computational demands of processing high-resolution images and complex and long-range temporal dynamics in surgical videos. To address these challenges, we introduce Surgical SAM 2 (SurgSAM2), an advanced model to utilize SAM2 with an Efficient Frame Pruning (EFP) mechanism, to facilitate real-time surgical video segmentation. The EFP mechanism dynamically manages the memory bank by selectively retaining only the most informative frames, reducing memory usage and computational cost while maintaining high segmentation accuracy. Our extensive experiments demonstrate that SurgSAM2 significantly improves both efficiency and segmentation accuracy compared to the vanilla SAM2. Remarkably, SurgSAM2 achieves a 3$\times$ FPS compared with SAM2, while also delivering state-of-the-art performance after fine-tuning with lower-resolution data. These advancements establish SurgSAM2 as a leading model for surgical video analysis, making real-time surgical video segmentation in resource-constrained environments a reality. Our source code is available at https://github.com/jinlab-imvr/Surgical-SAM-2.

cs.CV↗

arXiv2025

Epicardium Prompt-guided Real-time Cardiac Ultrasound Frame-to-volume Registration

A comprehensive guidance view for cardiac interventional surgery can be provided by the real-time fusion of the intraoperative 2D images and preoperative 3D volume based on the ultrasound frame-to-volume registration. However, cardiac ultrasound images are characterized by a low signal-to-noise ratio and small differences between adjacent frames, coupled with significant dimension variations between 2D frames and 3D volumes to be registered, resulting in real-time and accurate cardiac ultrasound frame-to-volume registration being a very challenging task. This paper introduces a lightweight end-to-end Cardiac Ultrasound frame-to-volume Registration network, termed CU-Reg. Specifically, the proposed model leverages epicardium prompt-guided anatomical clues to reinforce the interaction of 2D sparse and 3D dense features, followed by a voxel-wise local-global aggregation of enhanced features, thereby boosting the cross-dimensional matching effectiveness of low-quality ultrasound modalities. We further embed an inter-frame discriminative regularization term within the hybrid supervised learning to increase the distinction between adjacent slices in the same ultrasound volume to ensure registration stability. Experimental results on the reprocessed CAMUS dataset demonstrate that our CU-Reg surpasses existing methods in terms of registration accuracy and efficiency, meeting the guidance requirements of clinical cardiac interventional surgery.

eess.IV↗

arXiv2024

Medical SAM 2: Segment medical images as video via Segment Anything Model 2

Medical image segmentation plays a pivotal role in clinical diagnostics and treatment planning, yet existing models often face challenges in generalization and in handling both 2D and 3D data uniformly. In this paper, we introduce Medical SAM 2 (MedSAM-2), a generalized auto-tracking model for universal 2D and 3D medical image segmentation. The core concept is to leverage the Segment Anything Model 2 (SAM2) pipeline to treat all 2D and 3D medical segmentation tasks as a video object tracking problem. To put it into practice, we propose a novel \emph{self-sorting memory bank} mechanism that dynamically selects informative embeddings based on confidence and dissimilarity, regardless of temporal order. This mechanism not only significantly improves performance in 3D medical image segmentation but also unlocks a \emph{One-Prompt Segmentation} capability for 2D images, allowing segmentation across multiple images from a single prompt without temporal relationships. We evaluated MedSAM-2 on five 2D tasks and nine 3D tasks, including white blood cells, optic cups, retinal vessels, mandibles, coronary arteries, kidney tumors, liver tumors, breast cancer, nasopharynx cancer, vestibular schwannoma, mediastinal lymph nodules, cerebral artery, inferior alveolar nerve, and abdominal organs, comparing it against state-of-the-art (SOTA) models in task-tailored, general and interactive segmentation settings. Our findings demonstrate that MedSAM-2 surpasses a wide range of existing models and updates new SOTA on several benchmarks. The code is released on the project page: https://supermedintel.github.io/Medical-SAM2/.

cs.CV↗

arXiv2024

HC$^3$L-Diff: Hybrid conditional latent diffusion with high frequency enhancement for CBCT-to-CT synthesis

Background: Cone-beam computed tomography (CBCT) plays a crucial role in image-guided radiotherapy, but artifacts and noise make them unsuitable for accurate dose calculation. Artificial intelligence methods have shown promise in enhancing CBCT quality to produce synthetic CT (sCT) images. However, existing methods either produce images of suboptimal quality or incur excessive time costs, failing to satisfy clinical practice standards. Methods and materials: We propose a novel hybrid conditional latent diffusion model for efficient and accurate CBCT-to-CT synthesis, named HC$^3$L-Diff. We employ the Unified Feature Encoder (UFE) to compress images into a low-dimensional latent space, thereby optimizing computational efficiency. Beyond the use of CBCT images, we propose integrating its high-frequency knowledge as a hybrid condition to guide the diffusion model in generating sCT images with preserved structural details. This high-frequency information is captured using our designed High-Frequency Extractor (HFE). During inference, we utilize denoising diffusion implicit model to facilitate rapid sampling. We construct a new in-house prostate dataset with paired CBCT and CT to validate the effectiveness of our method. Result: Extensive experimental results demonstrate that our approach outperforms state-of-the-art methods in terms of sCT quality and generation efficiency. Moreover, our medical physicist conducts the dosimetric evaluations to validate the benefit of our method in practical dose calculation, achieving a remarkable 93.8% gamma passing rate with a 2%/2mm criterion, superior to other methods. Conclusion: The proposed HC$^3$L-Diff can efficiently achieve high-quality CBCT-to-CT synthesis in only over 2 mins per patient. Its promising performance in dose calculation shows great potential for enhancing real-world adaptive radiotherapy.

eess.IV↗

arXiv2024

LLM-Assisted Multi-Teacher Continual Learning for Visual Question Answering in Robotic Surgery

Visual question answering (VQA) is crucial for promoting surgical education. In practice, the needs of trainees are constantly evolving, such as learning more surgical types, adapting to different robots, and learning new surgical instruments and techniques for various surgeries. However, patient data privacy often restricts the availability of old data when updating the model, necessitating an exemplar-free continual learning (CL) setup. Prior CL studies overlooked two vital problems in the surgical domain: 1) large domain shifts from diverse surgical operations collected from multiple sources, and 2) severe data imbalance arising from the uneven presence of surgical instruments or activities. This paper proposes addressing these problems with a multimodal large language model (LLM) and an adaptive weight assignment methodology. We first develop a new multi-teacher CL framework that leverages a multimodal LLM as the additional teacher. The strong generalization ability of the LLM can bridge the knowledge gap when domain shifts and data imbalances occur. We then put forth a novel data processing method that transforms complex LLM embeddings into logits compatible with our CL framework. We further design an adaptive weight assignment approach that balances the generalization ability of the LLM and the domain expertise of the old CL model. Finally, to comprehensively test the effectiveness of our proposed method, we have also constructed two new surgical VQA datasets that are largely different from existing ones and could be valuable resources for future research. Extensive experimental results on the tested datasets demonstrate the superiority of our method to other advanced CL schemes.

cs.IR↗

arXiv2024

Prompt Your Brain: Scaffold Prompt Tuning for Efficient Adaptation of fMRI Pre-trained Model

We introduce Scaffold Prompt Tuning (ScaPT), a novel prompt-based framework for adapting large-scale functional magnetic resonance imaging (fMRI) pre-trained models to downstream tasks, with high parameter efficiency and improved performance compared to fine-tuning and baselines for prompt tuning. The full fine-tuning updates all pre-trained parameters, which may distort the learned feature space and lead to overfitting with limited training data which is common in fMRI fields. In contrast, we design a hierarchical prompt structure that transfers the knowledge learned from high-resource tasks to low-resource ones. This structure, equipped with a Deeply-conditioned Input-Prompt (DIP) mapping module, allows for efficient adaptation by updating only 2% of the trainable parameters. The framework enhances semantic interpretability through attention mechanisms between inputs and prompts, and it clusters prompts in the latent space in alignment with prior knowledge. Experiments on public resting state fMRI datasets reveal ScaPT outperforms fine-tuning and multitask-based prompt tuning in neurodegenerative diseases diagnosis/prognosis and personality trait prediction, even with fewer than 20 participants. It highlights ScaPT's efficiency in adapting pre-trained fMRI models to low-resource tasks.

q-bio.NC↗

arXiv2024

Personalizing Federated Instrument Segmentation with Visual Trait Priors in Robotic Surgery

Personalized federated learning (PFL) for surgical instrument segmentation (SIS) is a promising approach. It enables multiple clinical sites to collaboratively train a series of models in privacy, with each model tailored to the individual distribution of each site. Existing PFL methods rarely consider the personalization of multi-headed self-attention, and do not account for appearance diversity and instrument shape similarity, both inherent in surgical scenes. We thus propose PFedSIS, a novel PFL method with visual trait priors for SIS, incorporating global-personalized disentanglement (GPD), appearance-regulation personalized enhancement (APE), and shape-similarity global enhancement (SGE), to boost SIS performance in each site. GPD represents the first attempt at head-wise assignment for multi-headed self-attention personalization. To preserve the unique appearance representation of each site and gradually leverage the inter-site difference, APE introduces appearance regulation and provides customized layer-wise aggregation solutions via hypernetworks for each site's personalized parameters. The mutual shape information of instruments is maintained and shared via SGE, which enhances the cross-style shape consistency on the image level and computes the shape-similarity contribution of each site on the prediction level for updating the global parameters. PFedSIS outperforms state-of-the-art methods with +1.51% Dice, +2.11% IoU, -2.79 ASSD, -15.55 HD95 performance gains. The corresponding code and models will be released at https://github.com/wzjialang/PFedSIS.

cs.CV↗

arXiv2024

S^2Former-OR: Single-Stage Bi-Modal Transformer for Scene Graph Generation in OR

Scene graph generation (SGG) of surgical procedures is crucial in enhancing holistically cognitive intelligence in the operating room (OR). However, previous works have primarily relied on multi-stage learning, where the generated semantic scene graphs depend on intermediate processes with pose estimation and object detection. This pipeline may potentially compromise the flexibility of learning multimodal representations, consequently constraining the overall effectiveness. In this study, we introduce a novel single-stage bi-modal transformer framework for SGG in the OR, termed S^2Former-OR, aimed to complementally leverage multi-view 2D scenes and 3D point clouds for SGG in an end-to-end manner. Concretely, our model embraces a View-Sync Transfusion scheme to encourage multi-view visual information interaction. Concurrently, a Geometry-Visual Cohesion operation is designed to integrate the synergic 2D semantic features into 3D point cloud features. Moreover, based on the augmented feature, we propose a novel relation-sensitive transformer decoder that embeds dynamic entity-pair queries and relational trait priors, which enables the direct prediction of entity-pair relations for graph generation without intermediate steps. Extensive experiments have validated the superior SGG performance and lower computational cost of S^2Former-OR on 4D-OR benchmark, compared with current OR-SGG methods, e.g., 3 percentage points Precision increase and 24.2M reduction in model parameters. We further compared our method with generic single-stage SGG methods with broader metrics for a comprehensive evaluation, with consistently better performance achieved.

cs.CV↗

arXiv2024

SimCol3D -- 3D Reconstruction during Colonoscopy Challenge

Colorectal cancer is one of the most common cancers in the world. While colonoscopy is an effective screening technique, navigating an endoscope through the colon to detect polyps is challenging. A 3D map of the observed surfaces could enhance the identification of unscreened colon tissue and serve as a training platform. However, reconstructing the colon from video footage remains difficult. Learning-based approaches hold promise as robust alternatives, but necessitate extensive datasets. Establishing a benchmark dataset, the 2022 EndoVis sub-challenge SimCol3D aimed to facilitate data-driven depth and pose prediction during colonoscopy. The challenge was hosted as part of MICCAI 2022 in Singapore. Six teams from around the world and representatives from academia and industry participated in the three sub-challenges: synthetic depth prediction, synthetic pose prediction, and real pose prediction. This paper describes the challenge, the submitted methods, and their results. We show that depth prediction from synthetic colonoscopy images is robustly solvable, while pose estimation remains an open research question.

cs.CV↗

arXiv2024

Think Step by Step: Chain-of-Gesture Prompting for Error Detection in Robotic Surgical Videos

Despite significant advancements in robotic systems and surgical data science, ensuring safe and optimal execution in robot-assisted minimally invasive surgery (RMIS) remains a complex challenge. Current surgical error detection methods involve two parts: identifying surgical gestures and then detecting errors within each gesture clip. These methods seldom consider the rich contextual and semantic information inherent in surgical videos, limiting their performance due to reliance on accurate gesture identification. Motivated by the chain-of-thought prompting in natural language processing, this letter presents a novel and real-time end-to-end error detection framework, Chain-of-Thought (COG) prompting, leveraging contextual information from surgical videos. This encompasses two reasoning modules designed to mimic the decision-making processes of expert surgeons. Concretely, we first design a Gestural-Visual Reasoning module, which utilizes transformer and attention architectures for gesture prompting, while the second, a Multi-Scale Temporal Reasoning module, employs a multi-stage temporal convolutional network with both slow and fast paths for temporal information extraction. We extensively validate our method on the public benchmark RMIS dataset JIGSAWS. Our method encapsulates the reasoning processes inherent to surgical activities enabling it to outperform the state-of-the-art by 4.6% in F1 score, 4.6% in Accuracy, and 5.9% in Jaccard index while processing each frame in 6.69 milliseconds on average, demonstrating the great potential of our approach in enhancing the safety and efficacy of RMIS procedures and surgical education. The code will be available.

cs.CV↗

arXiv2024

CalibNet: Dual-branch Cross-modal Calibration for RGB-D Salient Instance Segmentation

We propose a novel approach for RGB-D salient instance segmentation using a dual-branch cross-modal feature calibration architecture called CalibNet. Our method simultaneously calibrates depth and RGB features in the kernel and mask branches to generate instance-aware kernels and mask features. CalibNet consists of three simple modules, a dynamic interactive kernel (DIK) and a weight-sharing fusion (WSF), which work together to generate effective instance-aware kernels and integrate cross-modal features. To improve the quality of depth features, we incorporate a depth similarity assessment (DSA) module prior to DIK and WSF. In addition, we further contribute a new DSIS dataset, which contains 1,940 images with elaborate instance-level annotations. Extensive experiments on three challenging benchmarks show that CalibNet yields a promising result, i.e., 58.0% AP with 320*480 input size on the COME15K-N test set, which significantly surpasses the alternative frameworks. Our code and dataset are available at: https://github.com/PJLallen/CalibNet.

cs.CV↗

arXiv2024

Dealing with All-stage Missing Modality: Towards A Universal Model with Robust Reconstruction and Personalization

Addressing missing modalities presents a critical challenge in multimodal learning. Current approaches focus on developing models that can handle modality-incomplete inputs during inference, assuming that the full set of modalities are available for all the data during training. This reliance on full-modality data for training limits the use of abundant modality-incomplete samples that are often encountered in practical settings. In this paper, we propose a robust universal model with modality reconstruction and model personalization, which can effectively tackle the missing modality at both training and testing stages. Our method leverages a multimodal masked autoencoder to reconstruct the missing modality and masked patches simultaneously, incorporating an innovative distribution approximation mechanism to fully utilize both modality-complete and modality-incomplete data. The reconstructed modalities then contributes to our designed data-model co-distillation scheme to guide the model learning in the presence of missing modalities. Moreover, we propose a CLIP-driven hyper-network to personalize partial model parameters, enabling the model to adapt to each distinct missing modality scenario. Our method has been extensively validated on two brain tumor segmentation benchmarks. Experimental results demonstrate the promising performance of our method, which consistently exceeds previous state-of-the-art approaches under the all-stage missing modality settings with different missing ratios. Code will be available.

cs.CV↗

arXiv2024

MGI: Multimodal Contrastive pre-training of Genomic and Medical Imaging

Medicine is inherently a multimodal discipline. Medical images can reflect the pathological changes of cancer and tumors, while the expression of specific genes can influence their morphological characteristics. However, most deep learning models employed for these medical tasks are unimodal, making predictions using either image data or genomic data exclusively. In this paper, we propose a multimodal pre-training framework that jointly incorporates genomics and medical images for downstream tasks. To address the issues of high computational complexity and difficulty in capturing long-range dependencies in genes sequence modeling with MLP or Transformer architectures, we utilize Mamba to model these long genomic sequences. We aligns medical images and genes using a self-supervised contrastive learning approach which combines the Mamba as a genetic encoder and the Vision Transformer (ViT) as a medical image encoder. We pre-trained on the TCGA dataset using paired gene expression data and imaging data, and fine-tuned it for downstream tumor segmentation tasks. The results show that our model outperformed a wide range of related methods.

cs.CV↗

arXiv2024

Deform3DGS: Flexible Deformation for Fast Surgical Scene Reconstruction with Gaussian Splatting

Tissue deformation poses a key challenge for accurate surgical scene reconstruction. Despite yielding high reconstruction quality, existing methods suffer from slow rendering speeds and long training times, limiting their intraoperative applicability. Motivated by recent progress in 3D Gaussian Splatting, an emerging technology in real-time 3D rendering, this work presents a novel fast reconstruction framework, termed Deform3DGS, for deformable tissues during endoscopic surgery. Specifically, we introduce 3D GS into surgical scenes by integrating a point cloud initialization to improve reconstruction. Furthermore, we propose a novel flexible deformation modeling scheme (FDM) to learn tissue deformation dynamics at the level of individual Gaussians. Our FDM can model the surface deformation with efficient representations, allowing for real-time rendering performance. More importantly, FDM significantly accelerates surgical scene reconstruction, demonstrating considerable clinical values, particularly in intraoperative settings where time efficiency is crucial. Experiments on DaVinci robotic surgery videos indicate the efficacy of our approach, showcasing superior reconstruction fidelity PSNR: (37.90) and rendering speed (338.8 FPS) while substantially reducing training time to only 1 minute/scene. Our code is available at https://github.com/jinlab-imvr/Deform3DGS.

cs.CV↗

arXiv2024

One-Prompt to Segment All Medical Images

Large foundation models, known for their strong zero-shot generalization, have excelled in visual and language applications. However, applying them to medical image segmentation, a domain with diverse imaging types and target labels, remains an open challenge. Current approaches, such as adapting interactive segmentation models like Segment Anything Model (SAM), require user prompts for each sample during inference. Alternatively, transfer learning methods like few/one-shot models demand labeled samples, leading to high costs. This paper introduces a new paradigm toward the universal medical image segmentation, termed 'One-Prompt Segmentation.' One-Prompt Segmentation combines the strengths of one-shot and interactive methods. In the inference stage, with just \textbf{one prompted sample}, it can adeptly handle the unseen task in a single forward pass. We train One-Prompt Model on 64 open-source medical datasets, accompanied by the collection of over 3,000 clinician-labeled prompts. Tested on 14 previously unseen datasets, the One-Prompt Model showcases superior zero-shot segmentation capabilities, outperforming a wide range of related methods. The code and data is released as https://github.com/KidsWithTokens/one-prompt.

eess.IV↗

arXiv2024

Adaptive Negative Evidential Deep Learning for Open-set Semi-supervised Learning

Semi-supervised learning (SSL) methods assume that labeled data, unlabeled data and test data are from the same distribution. Open-set semi-supervised learning (Open-set SSL) considers a more practical scenario, where unlabeled data and test data contain new categories (outliers) not observed in labeled data (inliers). Most previous works focused on outlier detection via binary classifiers, which suffer from insufficient scalability and inability to distinguish different types of uncertainty. In this paper, we propose a novel framework, Adaptive Negative Evidential Deep Learning (ANEDL) to tackle these limitations. Concretely, we first introduce evidential deep learning (EDL) as an outlier detector to quantify different types of uncertainty, and design different uncertainty metrics for self-training and inference. Furthermore, we propose a novel adaptive negative optimization strategy, making EDL more tailored to the unlabeled dataset containing both inliers and outliers. As demonstrated empirically, our proposed method outperforms existing state-of-the-art methods across four datasets.

cs.LG↗

arXiv2024

Tri-modal Confluence with Temporal Dynamics for Scene Graph Generation in Operating Rooms

A comprehensive understanding of surgical scenes allows for monitoring of the surgical process, reducing the occurrence of accidents and enhancing efficiency for medical professionals. Semantic modeling within operating rooms, as a scene graph generation (SGG) task, is challenging since it involves consecutive recognition of subtle surgical actions over prolonged periods. To address this challenge, we propose a Tri-modal (i.e., images, point clouds, and language) confluence with Temporal dynamics framework, termed TriTemp-OR. Diverging from previous approaches that integrated temporal information via memory graphs, our method embraces two advantages: 1) we directly exploit bi-modal temporal information from the video streaming for hierarchical feature interaction, and 2) the prior knowledge from Large Language Models (LLMs) is embedded to alleviate the class-imbalance problem in the operating theatre. Specifically, our model performs temporal interactions across 2D frames and 3D point clouds, including a scale-adaptive multi-view temporal interaction (ViewTemp) and a geometric-temporal point aggregation (PointTemp). Furthermore, we transfer knowledge from the biomedical LLM, LLaVA-Med, to deepen the comprehension of intraoperative relations. The proposed TriTemp-OR enables the aggregation of tri-modal features through relation-aware unification to predict relations so as to generate scene graphs. Experimental results on the 4D-OR benchmark demonstrate the superior performance of our model for long-term OR streaming.

cs.CV↗