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A Flexible 2.5D Medical Image Segmentation Approach with In-Slice and Cross-Slice Attention
Apr 30, 2024
Deep learning has become the de facto method for medical image segmentation, with 3D segmentation models excelling in capturing complex 3D structures and 2D models offering high computational efficiency. However, segmenting 2.5D images, which have high in-plane but low through-plane resolution, is a relatively unexplored challenge. While applying 2D models to individual slices of a 2.5D image is feasible, it fails to capture the spatial relationships between slices. On the other hand, 3D models face challenges such as resolution inconsistencies in 2.5D images, along with computational complexity and susceptibility to overfitting when trained with limited data. In this context, 2.5D models, which capture inter-slice correlations using only 2D neural networks, emerge as a promising solution due to their reduced computational demand and simplicity in implementation. In this paper, we introduce CSA-Net, a flexible 2.5D segmentation model capable of processing 2.5D images with an arbitrary number of slices through an innovative Cross-Slice Attention (CSA) module. This module uses the cross-slice attention mechanism to effectively capture 3D spatial information by learning long-range dependencies between the center slice (for segmentation) and its neighboring slices. Moreover, CSA-Net utilizes the self-attention mechanism to understand correlations among pixels within the center slice. We evaluated CSA-Net on three 2.5D segmentation tasks: (1) multi-class brain MRI segmentation, (2) binary prostate MRI segmentation, and (3) multi-class prostate MRI segmentation. CSA-Net outperformed leading 2D and 2.5D segmentation methods across all three tasks, demonstrating its efficacy and superiority. Our code is publicly available at https://github.com/mirthAI/CSA-Net.
RetinaRegNet: A Versatile Approach for Retinal Image Registration
Apr 24, 2024We introduce the RetinaRegNet model, which can achieve state-of-the-art performance across various retinal image registration tasks. RetinaRegNet does not require training on any retinal images. It begins by establishing point correspondences between two retinal images using image features derived from diffusion models. This process involves the selection of feature points from the moving image using the SIFT algorithm alongside random point sampling. For each selected feature point, a 2D correlation map is computed by assessing the similarity between the feature vector at that point and the feature vectors of all pixels in the fixed image. The pixel with the highest similarity score in the correlation map corresponds to the feature point in the moving image. To remove outliers in the estimated point correspondences, we first applied an inverse consistency constraint, followed by a transformation-based outlier detector. This method proved to outperform the widely used random sample consensus (RANSAC) outlier detector by a significant margin. To handle large deformations, we utilized a two-stage image registration framework. A homography transformation was used in the first stage and a more accurate third-order polynomial transformation was used in the second stage. The model's effectiveness was demonstrated across three retinal image datasets: color fundus images, fluorescein angiography images, and laser speckle flowgraphy images. RetinaRegNet outperformed current state-of-the-art methods in all three datasets. It was especially effective for registering image pairs with large displacement and scaling deformations. This innovation holds promise for various applications in retinal image analysis. Our code is publicly available at https://github.com/mirthAI/RetinaRegNet.
Unleashing the Potential of SAM for Medical Adaptation via Hierarchical Decoding
Mar 27, 2024
The Segment Anything Model (SAM) has garnered significant attention for its versatile segmentation abilities and intuitive prompt-based interface. However, its application in medical imaging presents challenges, requiring either substantial training costs and extensive medical datasets for full model fine-tuning or high-quality prompts for optimal performance. This paper introduces H-SAM: a prompt-free adaptation of SAM tailored for efficient fine-tuning of medical images via a two-stage hierarchical decoding procedure. In the initial stage, H-SAM employs SAM's original decoder to generate a prior probabilistic mask, guiding a more intricate decoding process in the second stage. Specifically, we propose two key designs: 1) A class-balanced, mask-guided self-attention mechanism addressing the unbalanced label distribution, enhancing image embedding; 2) A learnable mask cross-attention mechanism spatially modulating the interplay among different image regions based on the prior mask. Moreover, the inclusion of a hierarchical pixel decoder in H-SAM enhances its proficiency in capturing fine-grained and localized details. This approach enables SAM to effectively integrate learned medical priors, facilitating enhanced adaptation for medical image segmentation with limited samples. Our H-SAM demonstrates a 4.78% improvement in average Dice compared to existing prompt-free SAM variants for multi-organ segmentation using only 10% of 2D slices. Notably, without using any unlabeled data, H-SAM even outperforms state-of-the-art semi-supervised models relying on extensive unlabeled training data across various medical datasets. Our code is available at https://github.com/Cccccczh404/H-SAM.
LDTR: Transformer-based Lane Detection with Anchor-chain Representation
Mar 21, 2024
Despite recent advances in lane detection methods, scenarios with limited- or no-visual-clue of lanes due to factors such as lighting conditions and occlusion remain challenging and crucial for automated driving. Moreover, current lane representations require complex post-processing and struggle with specific instances. Inspired by the DETR architecture, we propose LDTR, a transformer-based model to address these issues. Lanes are modeled with a novel anchor-chain, regarding a lane as a whole from the beginning, which enables LDTR to handle special lanes inherently. To enhance lane instance perception, LDTR incorporates a novel multi-referenced deformable attention module to distribute attention around the object. Additionally, LDTR incorporates two line IoU algorithms to improve convergence efficiency and employs a Gaussian heatmap auxiliary branch to enhance model representation capability during training. To evaluate lane detection models, we rely on Frechet distance, parameterized F1-score, and additional synthetic metrics. Experimental results demonstrate that LDTR achieves state-of-the-art performance on well-known datasets.
RSAM-Seg: A SAM-based Approach with Prior Knowledge Integration for Remote Sensing Image Semantic Segmentation
Feb 29, 2024The development of high-resolution remote sensing satellites has provided great convenience for research work related to remote sensing. Segmentation and extraction of specific targets are essential tasks when facing the vast and complex remote sensing images. Recently, the introduction of Segment Anything Model (SAM) provides a universal pre-training model for image segmentation tasks. While the direct application of SAM to remote sensing image segmentation tasks does not yield satisfactory results, we propose RSAM-Seg, which stands for Remote Sensing SAM with Semantic Segmentation, as a tailored modification of SAM for the remote sensing field and eliminates the need for manual intervention to provide prompts. Adapter-Scale, a set of supplementary scaling modules, are proposed in the multi-head attention blocks of the encoder part of SAM. Furthermore, Adapter-Feature are inserted between the Vision Transformer (ViT) blocks. These modules aim to incorporate high-frequency image information and image embedding features to generate image-informed prompts. Experiments are conducted on four distinct remote sensing scenarios, encompassing cloud detection, field monitoring, building detection and road mapping tasks . The experimental results not only showcase the improvement over the original SAM and U-Net across cloud, buildings, fields and roads scenarios, but also highlight the capacity of RSAM-Seg to discern absent areas within the ground truth of certain datasets, affirming its potential as an auxiliary annotation method. In addition, the performance in few-shot scenarios is commendable, underscores its potential in dealing with limited datasets.
Unraveling Attacks in Machine Learning-based IoT Ecosystems: A Survey and the Open Libraries Behind Them
Jan 27, 2024The advent of the Internet of Things (IoT) has brought forth an era of unprecedented connectivity, with an estimated 80 billion smart devices expected to be in operation by the end of 2025. These devices facilitate a multitude of smart applications, enhancing the quality of life and efficiency across various domains. Machine Learning (ML) serves as a crucial technology, not only for analyzing IoT-generated data but also for diverse applications within the IoT ecosystem. For instance, ML finds utility in IoT device recognition, anomaly detection, and even in uncovering malicious activities. This paper embarks on a comprehensive exploration of the security threats arising from ML's integration into various facets of IoT, spanning various attack types including membership inference, adversarial evasion, reconstruction, property inference, model extraction, and poisoning attacks. Unlike previous studies, our work offers a holistic perspective, categorizing threats based on criteria such as adversary models, attack targets, and key security attributes (confidentiality, availability, and integrity). We delve into the underlying techniques of ML attacks in IoT environment, providing a critical evaluation of their mechanisms and impacts. Furthermore, our research thoroughly assesses 65 libraries, both author-contributed and third-party, evaluating their role in safeguarding model and data privacy. We emphasize the availability and usability of these libraries, aiming to arm the community with the necessary tools to bolster their defenses against the evolving threat landscape. Through our comprehensive review and analysis, this paper seeks to contribute to the ongoing discourse on ML-based IoT security, offering valuable insights and practical solutions to secure ML models and data in the rapidly expanding field of artificial intelligence in IoT.
Data-Centric Evolution in Autonomous Driving: A Comprehensive Survey of Big Data System, Data Mining, and Closed-Loop Technologies
Jan 26, 2024The aspiration of the next generation's autonomous driving (AD) technology relies on the dedicated integration and interaction among intelligent perception, prediction, planning, and low-level control. There has been a huge bottleneck regarding the upper bound of autonomous driving algorithm performance, a consensus from academia and industry believes that the key to surmount the bottleneck lies in data-centric autonomous driving technology. Recent advancement in AD simulation, closed-loop model training, and AD big data engine have gained some valuable experience. However, there is a lack of systematic knowledge and deep understanding regarding how to build efficient data-centric AD technology for AD algorithm self-evolution and better AD big data accumulation. To fill in the identified research gaps, this article will closely focus on reviewing the state-of-the-art data-driven autonomous driving technologies, with an emphasis on the comprehensive taxonomy of autonomous driving datasets characterized by milestone generations, key features, data acquisition settings, etc. Furthermore, we provide a systematic review of the existing benchmark closed-loop AD big data pipelines from the industrial frontier, including the procedure of closed-loop frameworks, key technologies, and empirical studies. Finally, the future directions, potential applications, limitations and concerns are discussed to arouse efforts from both academia and industry for promoting the further development of autonomous driving. The project repository is available at: https://github.com/LincanLi98/Awesome-Data-Centric-Autonomous-Driving.
CIS-UNet: Multi-Class Segmentation of the Aorta in Computed Tomography Angiography via Context-Aware Shifted Window Self-Attention
Jan 23, 2024Advancements in medical imaging and endovascular grafting have facilitated minimally invasive treatments for aortic diseases. Accurate 3D segmentation of the aorta and its branches is crucial for interventions, as inaccurate segmentation can lead to erroneous surgical planning and endograft construction. Previous methods simplified aortic segmentation as a binary image segmentation problem, overlooking the necessity of distinguishing between individual aortic branches. In this paper, we introduce Context Infused Swin-UNet (CIS-UNet), a deep learning model designed for multi-class segmentation of the aorta and thirteen aortic branches. Combining the strengths of Convolutional Neural Networks (CNNs) and Swin transformers, CIS-UNet adopts a hierarchical encoder-decoder structure comprising a CNN encoder, symmetric decoder, skip connections, and a novel Context-aware Shifted Window Self-Attention (CSW-SA) as the bottleneck block. Notably, CSW-SA introduces a unique utilization of the patch merging layer, distinct from conventional Swin transformers. It efficiently condenses the feature map, providing a global spatial context and enhancing performance when applied at the bottleneck layer, offering superior computational efficiency and segmentation accuracy compared to the Swin transformers. We trained our model on computed tomography (CT) scans from 44 patients and tested it on 15 patients. CIS-UNet outperformed the state-of-the-art SwinUNetR segmentation model, which is solely based on Swin transformers, by achieving a superior mean Dice coefficient of 0.713 compared to 0.697, and a mean surface distance of 2.78 mm compared to 3.39 mm. CIS-UNet's superior 3D aortic segmentation offers improved precision and optimization for planning endovascular treatments. Our dataset and code will be publicly available.
CLOMO: Counterfactual Logical Modification with Large Language Models
Nov 30, 2023
In this study, we delve into the realm of counterfactual reasoning capabilities of large language models (LLMs). Our primary objective is to cultivate the counterfactual thought processes within LLMs and rigorously assess these processes for their validity. Specifically, we introduce a novel task, Counterfactual Logical Modification (CLOMO), and a high-quality human-annotated benchmark. In this task, LLMs must adeptly alter a given argumentative text to uphold a predetermined logical relationship. To effectively evaluate a generation model's counterfactual capabilities, we propose an innovative evaluation metric, the LogicAware Counterfactual Score to directly evaluate the natural language output of LLMs instead of modeling the task as a multiple-choice problem. Analysis shows that the proposed automatic metric aligns well with human preference. Our experimental results show that while LLMs demonstrate a notable capacity for logical counterfactual thinking, there remains a discernible gap between their current abilities and human performance.
DistillCSE: Distilled Contrastive Learning for Sentence Embeddings
Oct 30, 2023This paper proposes the DistillCSE framework, which performs contrastive learning under the self-training paradigm with knowledge distillation. The potential advantage of DistillCSE is its self-enhancing feature: using a base model to provide additional supervision signals, a stronger model may be learned through knowledge distillation. However, the vanilla DistillCSE through the standard implementation of knowledge distillation only achieves marginal improvements due to severe overfitting. The further quantitative analyses demonstrate the reason that the standard knowledge distillation exhibits a relatively large variance of the teacher model's logits due to the essence of contrastive learning. To mitigate the issue induced by high variance, this paper accordingly proposed two simple yet effective solutions for knowledge distillation: a Group-P shuffling strategy as an implicit regularization and the averaging logits from multiple teacher components. Experiments on standard benchmarks demonstrate that the proposed DistillCSE outperforms many strong baseline methods and yields a new state-of-the-art performance.