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Add to EdgePrompt-driven Universal Model for View-Agnostic Echocardiography Analysis
Apr 09, 2024
Echocardiography segmentation for cardiac analysis is time-consuming and resource-intensive due to the variability in image quality and the necessity to process scans from various standard views. While current automated segmentation methods in echocardiography show promising performance, they are trained on specific scan views to analyze corresponding data. However, this solution has a limitation as the number of required models increases with the number of standard views. To address this, in this paper, we present a prompt-driven universal method for view-agnostic echocardiography analysis. Considering the domain shift between standard views, we first introduce a method called prompt matching, aimed at learning prompts specific to different views by matching prompts and querying input embeddings using a pre-trained vision model. Then, we utilized a pre-trained medical language model to align textual information with pixel data for accurate segmentation. Extensive experiments on three standard views showed that our approach significantly outperforms the state-of-the-art universal methods and achieves comparable or even better performances over the segmentation model trained and tested on same views.
SP$^2$OT: Semantic-Regularized Progressive Partial Optimal Transport for Imbalanced Clustering
Apr 04, 2024Deep clustering, which learns representation and semantic clustering without labels information, poses a great challenge for deep learning-based approaches. Despite significant progress in recent years, most existing methods focus on uniformly distributed datasets, significantly limiting the practical applicability of their methods. In this paper, we propose a more practical problem setting named deep imbalanced clustering, where the underlying classes exhibit an imbalance distribution. To address this challenge, we introduce a novel optimal transport-based pseudo-label learning framework. Our framework formulates pseudo-label generation as a Semantic-regularized Progressive Partial Optimal Transport (SP$^2$OT) problem, which progressively transports each sample to imbalanced clusters under several prior distribution and semantic relation constraints, thus generating high-quality and imbalance-aware pseudo-labels. To solve SP$^2$OT, we develop a Majorization-Minimization-based optimization algorithm. To be more precise, we employ the strategy of majorization to reformulate the SP$^2$OT problem into a Progressive Partial Optimal Transport problem, which can be transformed into an unbalanced optimal transport problem with augmented constraints and can be solved efficiently by a fast matrix scaling algorithm. Experiments on various datasets, including a human-curated long-tailed CIFAR100, challenging ImageNet-R, and large-scale subsets of fine-grained iNaturalist2018 datasets, demonstrate the superiority of our method.
Cardiac Magnetic Resonance 2D+T Short- and Long-axis Segmentation via Spatio-temporal SAM Adaptation
Mar 15, 2024
Accurate 2D+T myocardium segmentation in cine cardiac magnetic resonance (CMR) scans is essential to analyze LV motion throughout the cardiac cycle comprehensively. The Segment Anything Model (SAM), known for its accurate segmentation and zero-shot generalization, has not yet been tailored for CMR 2D+T segmentation. We therefore introduce CMR2D+T-SAM, a novel approach to adapt SAM for CMR 2D+T segmentation using spatio-temporal adaption. This approach also incorporates a U-Net framework for multi-scale feature extraction, as well as text prompts for accurate segmentation on both short-axis (SAX) and long-axis (LAX) views using a single model. CMR2D+T-SAM outperforms existing deep learning methods on the STACOM2011 dataset, achieving a myocardium Dice score of 0.885 and a Hausdorff distance (HD) of 2.900 pixels. It also demonstrates superior zero-shot generalization on the ACDC dataset with a Dice score of 0.840 and a HD of 4.076 pixels.
Medical Image Synthesis via Fine-Grained Image-Text Alignment and Anatomy-Pathology Prompting
Mar 11, 2024
Data scarcity and privacy concerns limit the availability of high-quality medical images for public use, which can be mitigated through medical image synthesis. However, current medical image synthesis methods often struggle to accurately capture the complexity of detailed anatomical structures and pathological conditions. To address these challenges, we propose a novel medical image synthesis model that leverages fine-grained image-text alignment and anatomy-pathology prompts to generate highly detailed and accurate synthetic medical images. Our method integrates advanced natural language processing techniques with image generative modeling, enabling precise alignment between descriptive text prompts and the synthesized images' anatomical and pathological details. The proposed approach consists of two key components: an anatomy-pathology prompting module and a fine-grained alignment-based synthesis module. The anatomy-pathology prompting module automatically generates descriptive prompts for high-quality medical images. To further synthesize high-quality medical images from the generated prompts, the fine-grained alignment-based synthesis module pre-defines a visual codebook for the radiology dataset and performs fine-grained alignment between the codebook and generated prompts to obtain key patches as visual clues, facilitating accurate image synthesis. We validate the superiority of our method through experiments on public chest X-ray datasets and demonstrate that our synthetic images preserve accurate semantic information, making them valuable for various medical applications.
Conditional Score-Based Diffusion Model for Cortical Thickness Trajectory Prediction
Mar 11, 2024
Alzheimer's Disease (AD) is a neurodegenerative condition characterized by diverse progression rates among individuals, with changes in cortical thickness (CTh) closely linked to its progression. Accurately forecasting CTh trajectories can significantly enhance early diagnosis and intervention strategies, providing timely care. However, the longitudinal data essential for these studies often suffer from temporal sparsity and incompleteness, presenting substantial challenges in modeling the disease's progression accurately. Existing methods are limited, focusing primarily on datasets without missing entries or requiring predefined assumptions about CTh progression. To overcome these obstacles, we propose a conditional score-based diffusion model specifically designed to generate CTh trajectories with the given baseline information, such as age, sex, and initial diagnosis. Our conditional diffusion model utilizes all available data during the training phase to make predictions based solely on baseline information during inference without needing prior history about CTh progression. The prediction accuracy of the proposed CTh prediction pipeline using a conditional score-based model was compared for sub-groups consisting of cognitively normal, mild cognitive impairment, and AD subjects. The Bland-Altman analysis shows our diffusion-based prediction model has a near-zero bias with narrow 95% confidential interval compared to the ground-truth CTh in 6-36 months. In addition, our conditional diffusion model has a stochastic generative nature, therefore, we demonstrated an uncertainty analysis of patient-specific CTh prediction through multiple realizations.
P$^2$OT: Progressive Partial Optimal Transport for Deep Imbalanced Clustering
Jan 17, 2024
Deep clustering, which learns representation and semantic clustering without labels information, poses a great challenge for deep learning-based approaches. Despite significant progress in recent years, most existing methods focus on uniformly distributed datasets, significantly limiting the practical applicability of their methods. In this paper, we first introduce a more practical problem setting named deep imbalanced clustering, where the underlying classes exhibit an imbalance distribution. To tackle this problem, we propose a novel pseudo-labeling-based learning framework. Our framework formulates pseudo-label generation as a progressive partial optimal transport problem, which progressively transports each sample to imbalanced clusters under prior distribution constraints, thus generating imbalance-aware pseudo-labels and learning from high-confident samples. In addition, we transform the initial formulation into an unbalanced optimal transport problem with augmented constraints, which can be solved efficiently by a fast matrix scaling algorithm. Experiments on various datasets, including a human-curated long-tailed CIFAR100, challenging ImageNet-R, and large-scale subsets of fine-grained iNaturalist2018 datasets, demonstrate the superiority of our method.
CohortGPT: An Enhanced GPT for Participant Recruitment in Clinical Study
Jul 21, 2023
Participant recruitment based on unstructured medical texts such as clinical notes and radiology reports has been a challenging yet important task for the cohort establishment in clinical research. Recently, Large Language Models (LLMs) such as ChatGPT have achieved tremendous success in various downstream tasks thanks to their promising performance in language understanding, inference, and generation. It is then natural to test their feasibility in solving the cohort recruitment task, which involves the classification of a given paragraph of medical text into disease label(s). However, when applied to knowledge-intensive problem settings such as medical text classification, where the LLMs are expected to understand the decision made by human experts and accurately identify the implied disease labels, the LLMs show a mediocre performance. A possible explanation is that, by only using the medical text, the LLMs neglect to use the rich context of additional information that languages afford. To this end, we propose to use a knowledge graph as auxiliary information to guide the LLMs in making predictions. Moreover, to further boost the LLMs adapt to the problem setting, we apply a chain-of-thought (CoT) sample selection strategy enhanced by reinforcement learning, which selects a set of CoT samples given each individual medical report. Experimental results and various ablation studies show that our few-shot learning method achieves satisfactory performance compared with fine-tuning strategies and gains superb advantages when the available data is limited. The code and sample dataset of the proposed CohortGPT model is available at: https://anonymous.4open.science/r/CohortGPT-4872/
Exploring Multimodal Approaches for Alzheimer's Disease Detection Using Patient Speech Transcript and Audio Data
Jul 05, 2023
Alzheimer's disease (AD) is a common form of dementia that severely impacts patient health. As AD impairs the patient's language understanding and expression ability, the speech of AD patients can serve as an indicator of this disease. This study investigates various methods for detecting AD using patients' speech and transcripts data from the DementiaBank Pitt database. The proposed approach involves pre-trained language models and Graph Neural Network (GNN) that constructs a graph from the speech transcript, and extracts features using GNN for AD detection. Data augmentation techniques, including synonym replacement, GPT-based augmenter, and so on, were used to address the small dataset size. Audio data was also introduced, and WavLM model was used to extract audio features. These features were then fused with text features using various methods. Finally, a contrastive learning approach was attempted by converting speech transcripts back to audio and using it for contrastive learning with the original audio. We conducted intensive experiments and analysis on the above methods. Our findings shed light on the challenges and potential solutions in AD detection using speech and audio data.
Development and Validation of a Deep Learning Model for Prediction of Severe Outcomes in Suspected COVID-19 Infection
Mar 29, 2021
COVID-19 patient triaging with predictive outcome of the patients upon first present to emergency department (ED) is crucial for improving patient prognosis, as well as better hospital resources management and cross-infection control. We trained a deep feature fusion model to predict patient outcomes, where the model inputs were EHR data including demographic information, co-morbidities, vital signs and laboratory measurements, plus patient's CXR images. The model output was patient outcomes defined as the most insensitive oxygen therapy required. For patients without CXR images, we employed Random Forest method for the prediction. Predictive risk scores for COVID-19 severe outcomes ("CO-RISK" score) were derived from model output and evaluated on the testing dataset, as well as compared to human performance. The study's dataset (the "MGB COVID Cohort") was constructed from all patients presenting to the Mass General Brigham (MGB) healthcare system from March 1st to June 1st, 2020. ED visits with incomplete or erroneous data were excluded. Patients with no test order for COVID or confirmed negative test results were excluded. Patients under the age of 15 were also excluded. Finally, electronic health record (EHR) data from a total of 11060 COVID-19 confirmed or suspected patients were used in this study. Chest X-ray (CXR) images were also collected from each patient if available. Results show that CO-RISK score achieved area under the Curve (AUC) of predicting MV/death (i.e. severe outcomes) in 24 hours of 0.95, and 0.92 in 72 hours on the testing dataset. The model shows superior performance to the commonly used risk scores in ED (CURB-65 and MEWS). Comparing with physician's decisions, CO-RISK score has demonstrated superior performance to human in making ICU/floor decisions.
Deep Metric Learning-based Image Retrieval System for Chest Radiograph and its Clinical Applications in COVID-19
Nov 26, 2020
In recent years, deep learning-based image analysis methods have been widely applied in computer-aided detection, diagnosis and prognosis, and has shown its value during the public health crisis of the novel coronavirus disease 2019 (COVID-19) pandemic. Chest radiograph (CXR) has been playing a crucial role in COVID-19 patient triaging, diagnosing and monitoring, particularly in the United States. Considering the mixed and unspecific signals in CXR, an image retrieval model of CXR that provides both similar images and associated clinical information can be more clinically meaningful than a direct image diagnostic model. In this work we develop a novel CXR image retrieval model based on deep metric learning. Unlike traditional diagnostic models which aims at learning the direct mapping from images to labels, the proposed model aims at learning the optimized embedding space of images, where images with the same labels and similar contents are pulled together. It utilizes multi-similarity loss with hard-mining sampling strategy and attention mechanism to learn the optimized embedding space, and provides similar images to the query image. The model is trained and validated on an international multi-site COVID-19 dataset collected from 3 different sources. Experimental results of COVID-19 image retrieval and diagnosis tasks show that the proposed model can serve as a robust solution for CXR analysis and patient management for COVID-19. The model is also tested on its transferability on a different clinical decision support task, where the pre-trained model is applied to extract image features from a new dataset without any further training. These results demonstrate our deep metric learning based image retrieval model is highly efficient in the CXR retrieval, diagnosis and prognosis, and thus has great clinical value for the treatment and management of COVID-19 patients.