Automated segmentation of the blood vessels in 3D volumes is an essential step for the quantitative diagnosis and treatment of many vascular diseases. 3D vessel segmentation is being actively investigated in existing works, mostly in deep learning approaches. However, training 3D deep networks requires large amounts of manual 3D annotations from experts, which are laborious to obtain. This is especially the case for 3D vessel segmentation, as vessels are sparse yet spread out over many slices and disconnected when visualized in 2D slices. In this work, we propose a novel method to segment the 3D peripancreatic arteries solely from one annotated 2D projection per training image with depth supervision. We perform extensive experiments on the segmentation of peripancreatic arteries on 3D contrast-enhanced CT images and demonstrate how well we capture the rich depth information from 2D projections. We demonstrate that by annotating a single, randomly chosen projection for each training sample, we obtain comparable performance to annotating multiple 2D projections, thereby reducing the annotation effort. Furthermore, by mapping the 2D labels to the 3D space using depth information and incorporating this into training, we almost close the performance gap between 3D supervision and 2D supervision. Our code is available at: //github.com/alinafdima/3Dseg-mip-depth.
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Pathological captioning of Whole Slide Images (WSIs), though is essential in computer-aided pathological diagnosis, has rarely been studied due to the limitations in datasets and model training efficacy. In this paper, we propose a new paradigm Subtype-guided Masked Transformer (SGMT) for pathological captioning based on Transformers, which treats a WSI as a sequence of sparse patches and generates an overall caption sentence from the sequence. An accompanying subtype prediction is introduced into SGMT to guide the training process and enhance the captioning accuracy. We also present an Asymmetric Masked Mechansim approach to tackle the large size constraint of pathological image captioning, where the numbers of sequencing patches in SGMT are sampled differently in the training and inferring phases, respectively. Experiments on the PatchGastricADC22 dataset demonstrate that our approach effectively adapts to the task with a transformer-based model and achieves superior performance than traditional RNN-based methods. Our codes are to be made available for further research and development.
In the era of the Internet of Things (IoT), the retrieval of relevant medical information has become essential for efficient clinical decision-making. This paper introduces MedFusionRank, a novel approach to zero-shot medical information retrieval (MIR) that combines the strengths of pre-trained language models and statistical methods while addressing their limitations. The proposed approach leverages a pre-trained BERT-style model to extract compact yet informative keywords. These keywords are then enriched with domain knowledge by linking them to conceptual entities within a medical knowledge graph. Experimental evaluations on medical datasets demonstrate MedFusion Rank's superior performance over existing methods, with promising results with a variety of evaluation metrics. MedFusionRank demonstrates efficacy in retrieving relevant information, even from short or single-term queries.
Procedural activity understanding requires perceiving human actions in terms of a broader task, where multiple keysteps are performed in sequence across a long video to reach a final goal state -- such as the steps of a recipe or a DIY fix-it task. Prior work largely treats keystep recognition in isolation of this broader structure, or else rigidly confines keysteps to align with a predefined sequential script. We propose discovering a task graph automatically from how-to videos to represent probabilistically how people tend to execute keysteps, and then leverage this graph to regularize keystep recognition in novel videos. On multiple datasets of real-world instructional videos, we show the impact: more reliable zero-shot keystep localization and improved video representation learning, exceeding the state of the art.
Assessing the condition and visibility of veins is a crucial step before obtaining intravenous access in the antecubital fossa, which is a common procedure to draw blood or administer intravenous therapies (IV therapies). Even though medical practitioners are highly skilled at intravenous cannulation, they usually struggle to perform the procedure in patients with low visible veins due to fluid retention, age, overweight, dark skin tone, or diabetes. Recently, several investigations proposed combining Near Infrared (NIR) imaging and deep learning (DL) techniques for forearm vein segmentation. Although they have demonstrated compelling results, their use has been rather limited owing to the portability and precision requirements to perform venipuncture. In this paper, we aim to contribute to bridging this gap using three strategies. First, we introduce a new NIR-based forearm vein segmentation dataset of 2,016 labelled images collected from 1,008 subjects with low visible veins. Second, we propose a modified U-Net architecture that locates veins specifically in the antecubital fossa region of the examined patient. Finally, a compressed version of the proposed architecture was deployed inside a bespoke, portable vein finder device after testing four common embedded microcomputers and four common quantization modalities. Experimental results showed that the model compressed with Dynamic Range Quantization and deployed on a Raspberry Pi 4B card produced the best execution time and precision balance, with 5.14 FPS and 0.957 of latency and Intersection over Union (IoU), respectively. These results show promising performance inside a resource-restricted low-cost device.
Histology imaging is an important tool in medical diagnosis and research, enabling the examination of tissue structure and composition at the microscopic level. Understanding the underlying molecular mechanisms of tissue architecture is critical in uncovering disease mechanisms and developing effective treatments. Gene expression profiling provides insight into the molecular processes underlying tissue architecture, but the process can be time-consuming and expensive. We present BLEEP (Bi-modaL Embedding for Expression Prediction), a bi-modal embedding framework capable of generating spatially resolved gene expression profiles of whole-slide Hematoxylin and eosin (H&E) stained histology images. BLEEP uses contrastive learning to construct a low-dimensional joint embedding space from a reference dataset using paired image and expression profiles at micrometer resolution. With this approach, the gene expression of any query image patch can be imputed using the expression profiles from the reference dataset. We demonstrate BLEEP's effectiveness in gene expression prediction by benchmarking its performance on a human liver tissue dataset captured using the 10x Visium platform, where it achieves significant improvements over existing methods. Our results demonstrate the potential of BLEEP to provide insights into the molecular mechanisms underlying tissue architecture, with important implications in diagnosis and research of various diseases. The proposed approach can significantly reduce the time and cost associated with gene expression profiling, opening up new avenues for high-throughput analysis of histology images for both research and clinical applications.
The most frequent kind of dementia of the nervous system, Alzheimer's disease, weakens several brain processes (such as memory) and eventually results in death. The clinical study uses magnetic resonance imaging to diagnose AD. Deep learning algorithms are capable of pattern recognition and feature extraction from the inputted raw data. As early diagnosis and stage detection are the most crucial elements in enhancing patient care and treatment outcomes, deep learning algorithms for MRI images have recently allowed for diagnosing a medical condition at the beginning stage and identifying particular symptoms of Alzheimer's disease. As a result, we aimed to analyze five specific studies focused on AD diagnosis using MRI-based deep learning algorithms between 2021 and 2023 in this study. To completely illustrate the differences between these techniques and comprehend how deep learning algorithms function, we attempted to explore selected approaches in depth.
Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.
Medical image segmentation is a fundamental and critical step in many image-guided clinical approaches. Recent success of deep learning-based segmentation methods usually relies on a large amount of labeled data, which is particularly difficult and costly to obtain especially in the medical imaging domain where only experts can provide reliable and accurate annotations. Semi-supervised learning has emerged as an appealing strategy and been widely applied to medical image segmentation tasks to train deep models with limited annotations. In this paper, we present a comprehensive review of recently proposed semi-supervised learning methods for medical image segmentation and summarized both the technical novelties and empirical results. Furthermore, we analyze and discuss the limitations and several unsolved problems of existing approaches. We hope this review could inspire the research community to explore solutions for this challenge and further promote the developments in medical image segmentation field.
Inspired by the human cognitive system, attention is a mechanism that imitates the human cognitive awareness about specific information, amplifying critical details to focus more on the essential aspects of data. Deep learning has employed attention to boost performance for many applications. Interestingly, the same attention design can suit processing different data modalities and can easily be incorporated into large networks. Furthermore, multiple complementary attention mechanisms can be incorporated in one network. Hence, attention techniques have become extremely attractive. However, the literature lacks a comprehensive survey specific to attention techniques to guide researchers in employing attention in their deep models. Note that, besides being demanding in terms of training data and computational resources, transformers only cover a single category in self-attention out of the many categories available. We fill this gap and provide an in-depth survey of 50 attention techniques categorizing them by their most prominent features. We initiate our discussion by introducing the fundamental concepts behind the success of attention mechanism. Next, we furnish some essentials such as the strengths and limitations of each attention category, describe their fundamental building blocks, basic formulations with primary usage, and applications specifically for computer vision. We also discuss the challenges and open questions related to attention mechanism in general. Finally, we recommend possible future research directions for deep attention.
Human doctors with well-structured medical knowledge can diagnose a disease merely via a few conversations with patients about symptoms. In contrast, existing knowledge-grounded dialogue systems often require a large number of dialogue instances to learn as they fail to capture the correlations between different diseases and neglect the diagnostic experience shared among them. To address this issue, we propose a more natural and practical paradigm, i.e., low-resource medical dialogue generation, which can transfer the diagnostic experience from source diseases to target ones with a handful of data for adaptation. It is capitalized on a commonsense knowledge graph to characterize the prior disease-symptom relations. Besides, we develop a Graph-Evolving Meta-Learning (GEML) framework that learns to evolve the commonsense graph for reasoning disease-symptom correlations in a new disease, which effectively alleviates the needs of a large number of dialogues. More importantly, by dynamically evolving disease-symptom graphs, GEML also well addresses the real-world challenges that the disease-symptom correlations of each disease may vary or evolve along with more diagnostic cases. Extensive experiment results on the CMDD dataset and our newly-collected Chunyu dataset testify the superiority of our approach over state-of-the-art approaches. Besides, our GEML can generate an enriched dialogue-sensitive knowledge graph in an online manner, which could benefit other tasks grounded on knowledge graph.
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