arXiv subjects

Long Bai

Publications and source records attributed to Long Bai.

At least 91 records · Page 5Linked to original sources

arXiv2024

Registering Neural 4D Gaussians for Endoscopic Surgery

The recent advance in neural rendering has enabled the ability to reconstruct high-quality 4D scenes using neural networks. Although 4D neural reconstruction is popular, registration for such representations remains a challenging task, especially for dynamic scene registration in surgical planning and simulation. In this paper, we propose a novel strategy for dynamic surgical neural scene registration. We first utilize 4D Gaussian Splatting to represent the surgical scene and capture both static and dynamic scenes effectively. Then, a spatial aware feature aggregation method, Spatially Weight Cluttering (SWC) is proposed to accurately align the feature between surgical scenes, enabling precise and realistic surgical simulations. Lastly, we present a novel strategy of deformable scene registration to register two dynamic scenes. By incorporating both spatial and temporal information for correspondence matching, our approach achieves superior performance compared to existing registration methods for implicit neural representation. The proposed method has the potential to improve surgical planning and training, ultimately leading to better patient outcomes.

cs.RO↗

arXiv2024

ASI-Seg: Audio-Driven Surgical Instrument Segmentation with Surgeon Intention Understanding

Surgical instrument segmentation is crucial in surgical scene understanding, thereby facilitating surgical safety. Existing algorithms directly detected all instruments of pre-defined categories in the input image, lacking the capability to segment specific instruments according to the surgeon's intention. During different stages of surgery, surgeons exhibit varying preferences and focus toward different surgical instruments. Therefore, an instrument segmentation algorithm that adheres to the surgeon's intention can minimize distractions from irrelevant instruments and assist surgeons to a great extent. The recent Segment Anything Model (SAM) reveals the capability to segment objects following prompts, but the manual annotations for prompts are impractical during the surgery. To address these limitations in operating rooms, we propose an audio-driven surgical instrument segmentation framework, named ASI-Seg, to accurately segment the required surgical instruments by parsing the audio commands of surgeons. Specifically, we propose an intention-oriented multimodal fusion to interpret the segmentation intention from audio commands and retrieve relevant instrument details to facilitate segmentation. Moreover, to guide our ASI-Seg segment of the required surgical instruments, we devise a contrastive learning prompt encoder to effectively distinguish the required instruments from the irrelevant ones. Therefore, our ASI-Seg promotes the workflow in the operating rooms, thereby providing targeted support and reducing the cognitive load on surgeons. Extensive experiments are performed to validate the ASI-Seg framework, which reveals remarkable advantages over classical state-of-the-art and medical SAMs in both semantic segmentation and intention-oriented segmentation. The source code is available at https://github.com/Zonmgin-Zhang/ASI-Seg.

cs.CV↗

arXiv2024

EndoUIC: Promptable Diffusion Transformer for Unified Illumination Correction in Capsule Endoscopy

Wireless Capsule Endoscopy (WCE) is highly valued for its non-invasive and painless approach, though its effectiveness is compromised by uneven illumination from hardware constraints and complex internal dynamics, leading to overexposed or underexposed images. While researchers have discussed the challenges of low-light enhancement in WCE, the issue of correcting for different exposure levels remains underexplored. To tackle this, we introduce EndoUIC, a WCE unified illumination correction solution using an end-to-end promptable diffusion transformer (DiT) model. In our work, the illumination prompt module shall navigate the model to adapt to different exposure levels and perform targeted image enhancement, in which the Adaptive Prompt Integration (API) and Global Prompt Scanner (GPS) modules shall further boost the concurrent representation learning between the prompt parameters and features. Besides, the U-shaped restoration DiT model shall capture the long-range dependencies and contextual information for unified illumination restoration. Moreover, we present a novel Capsule-endoscopy Exposure Correction (CEC) dataset, including ground-truth and corrupted image pairs annotated by expert photographers. Extensive experiments against a variety of state-of-the-art (SOTA) methods on four datasets showcase the effectiveness of our proposed method and components in WCE illumination restoration, and the additional downstream experiments further demonstrate its utility for clinical diagnosis and surgical assistance.

eess.IV↗

arXiv2024

Learning to Adapt Foundation Model DINOv2 for Capsule Endoscopy Diagnosis

Foundation models have become prominent in computer vision, achieving notable success in various tasks. However, their effectiveness largely depends on pre-training with extensive datasets. Applying foundation models directly to small datasets of capsule endoscopy images from scratch is challenging. Pre-training on broad, general vision datasets is crucial for successfully fine-tuning our model for specific tasks. In this work, we introduce a simplified approach called Adapt foundation models with a low-rank adaptation (LoRA) technique for easier customization. Our method, inspired by the DINOv2 foundation model, applies low-rank adaptation learning to tailor foundation models for capsule endoscopy diagnosis effectively. Unlike traditional fine-tuning methods, our strategy includes LoRA layers designed to absorb specific surgical domain knowledge. During the training process, we keep the main model (the backbone encoder) fixed and focus on optimizing the LoRA layers and the disease classification component. We tested our method on two publicly available datasets for capsule endoscopy disease classification. The results were impressive, with our model achieving 97.75% accuracy on the Kvasir-Capsule dataset and 98.81% on the Kvasirv2 dataset. Our solution demonstrates that foundation models can be adeptly adapted for capsule endoscopy diagnosis, highlighting that mere reliance on straightforward fine-tuning or pre-trained models from general computer vision tasks is inadequate for such specific applications.

cs.CV↗

arXiv2024

LighTDiff: Surgical Endoscopic Image Low-Light Enhancement with T-Diffusion

Advances in endoscopy use in surgeries face challenges like inadequate lighting. Deep learning, notably the Denoising Diffusion Probabilistic Model (DDPM), holds promise for low-light image enhancement in the medical field. However, DDPMs are computationally demanding and slow, limiting their practical medical applications. To bridge this gap, we propose a lightweight DDPM, dubbed LighTDiff. It adopts a T-shape model architecture to capture global structural information using low-resolution images and gradually recover the details in subsequent denoising steps. We further prone the model to significantly reduce the model size while retaining performance. While discarding certain downsampling operations to save parameters leads to instability and low efficiency in convergence during the training, we introduce a Temporal Light Unit (TLU), a plug-and-play module, for more stable training and better performance. TLU associates time steps with denoised image features, establishing temporal dependencies of the denoising steps and improving denoising outcomes. Moreover, while recovering images using the diffusion model, potential spectral shifts were noted. We further introduce a Chroma Balancer (CB) to mitigate this issue. Our LighTDiff outperforms many competitive LLIE methods with exceptional computational efficiency.

eess.IV↗

arXiv2024

EndoDAC: Efficient Adapting Foundation Model for Self-Supervised Depth Estimation from Any Endoscopic Camera

Depth estimation plays a crucial role in various tasks within endoscopic surgery, including navigation, surface reconstruction, and augmented reality visualization. Despite the significant achievements of foundation models in vision tasks, including depth estimation, their direct application to the medical domain often results in suboptimal performance. This highlights the need for efficient adaptation methods to adapt these models to endoscopic depth estimation. We propose Endoscopic Depth Any Camera (EndoDAC) which is an efficient self-supervised depth estimation framework that adapts foundation models to endoscopic scenes. Specifically, we develop the Dynamic Vector-Based Low-Rank Adaptation (DV-LoRA) and employ Convolutional Neck blocks to tailor the foundational model to the surgical domain, utilizing remarkably few trainable parameters. Given that camera information is not always accessible, we also introduce a self-supervised adaptation strategy that estimates camera intrinsics using the pose encoder. Our framework is capable of being trained solely on monocular surgical videos from any camera, ensuring minimal training costs. Experiments demonstrate that our approach obtains superior performance even with fewer training epochs and unaware of the ground truth camera intrinsics. Code is available at https://github.com/BeileiCui/EndoDAC.

eess.IV↗

arXiv2024

Nested Event Extraction upon Pivot Element Recogniton

Nested Event Extraction (NEE) aims to extract complex event structures where an event contains other events as its arguments recursively. Nested events involve a kind of Pivot Elements (PEs) that simultaneously act as arguments of outer-nest events and as triggers of inner-nest events, and thus connect them into nested structures. This special characteristic of PEs brings challenges to existing NEE methods, as they cannot well cope with the dual identities of PEs. Therefore, this paper proposes a new model, called PerNee, which extracts nested events mainly based on recognizing PEs. Specifically, PerNee first recognizes the triggers of both inner-nest and outer-nest events and further recognizes the PEs via classifying the relation type between trigger pairs. The model uses prompt learning to incorporate information from both event types and argument roles for better trigger and argument representations to improve NEE performance. Since existing NEE datasets (e.g., Genia11) are limited to specific domains and contain a narrow range of event types with nested structures, we systematically categorize nested events in the generic domain and construct a new NEE dataset, called ACE2005-Nest. Experimental results demonstrate that PerNee consistently achieves state-of-the-art performance on ACE2005-Nest, Genia11, and Genia13. The ACE2005-Nest dataset and the code of the PerNee model are available at https://github.com/waysonren/PerNee.

cs.CL↗

arXiv2024

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 but are hampered by slow inference speed, prolonged training, and inconsistent depth estimation. Some previous work utilizes ground truth depth for optimization but is hard to acquire in the surgical domain. To overcome these obstacles, we present Endo-4DGS, a real-time endoscopic dynamic reconstruction approach that utilizes 3D Gaussian Splatting (GS) for 3D representation. Specifically, we propose lightweight MLPs to capture temporal dynamics with Gaussian deformation fields. To obtain a satisfactory Gaussian Initialization, we exploit a powerful depth estimation foundation model, Depth-Anything, to generate pseudo-depth maps as a geometry prior. We additionally propose confidence-guided learning to tackle the ill-pose problems in monocular depth estimation and enhance the depth-guided reconstruction with surface normal constraints and depth regularization. Our approach has been validated on two surgical datasets, where it can effectively render in real-time, compute efficiently, and reconstruct with remarkable accuracy.

cs.CV↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.CL↗

arXiv2024

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.

cs.LG↗

arXiv2024

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.

cs.CV↗

arXiv2024

An In-Context Schema Understanding Method for Knowledge Base Question Answering

The Knowledge Base Question Answering (KBQA) task aims to answer natural language questions based on a given knowledge base. Recently, Large Language Models (LLMs) have shown strong capabilities in language understanding and can be used to solve this task. In doing so, a major challenge for LLMs is to overcome the immensity and heterogeneity of knowledge base schemas.Existing methods bypass this challenge by initially employing LLMs to generate drafts of logic forms without schema-specific details.Then, an extra module is used to inject schema information to these drafts.In contrast, in this paper, we propose a simple In-Context Schema Understanding (ICSU) method that enables LLMs to directly understand schemas by leveraging in-context learning. Specifically, ICSU provides schema information to LLMs using schema-related annotated examples. We investigate three example retrieval strategies based on raw questions, anonymized questions, and generated SPARQL queries. Experimental results show that ICSU demonstrates competitive performance compared to baseline methods on both the KQA Pro and WebQSP datasets.

cs.CL↗

arXiv2024

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.

cs.CV↗

arXiv2024

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}.

cs.CV↗

arXiv2024

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. The complete SAR-RARP50 dataset is available at: https://rdr.ucl.ac.uk/projects/SARRARP50_Segmentation_of_surgical_instrumentation_and_Action_Recognition_on_Robot-Assisted_Radical_Prostatectomy_Challenge/191091

cs.CV↗

arXiv2024

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.

cs.CV↗

arXiv2023

Retrieval-Augmented Code Generation for Universal Information Extraction

Information Extraction (IE) aims to extract structural knowledge (e.g., entities, relations, events) from natural language texts, which brings challenges to existing methods due to task-specific schemas and complex text expressions. Code, as a typical kind of formalized language, is capable of describing structural knowledge under various schemas in a universal way. On the other hand, Large Language Models (LLMs) trained on both codes and texts have demonstrated powerful capabilities of transforming texts into codes, which provides a feasible solution to IE tasks. Therefore, in this paper, we propose a universal retrieval-augmented code generation framework based on LLMs, called Code4UIE, for IE tasks. Specifically, Code4UIE adopts Python classes to define task-specific schemas of various structural knowledge in a universal way. By so doing, extracting knowledge under these schemas can be transformed into generating codes that instantiate the predefined Python classes with the information in texts. To generate these codes more precisely, Code4UIE adopts the in-context learning mechanism to instruct LLMs with examples. In order to obtain appropriate examples for different tasks, Code4UIE explores several example retrieval strategies, which can retrieve examples semantically similar to the given texts. Extensive experiments on five representative IE tasks across nine datasets demonstrate the effectiveness of the Code4UIE framework.

cs.AI↗