Daily Papers

Electrocardiogram (ECG) delineation, the segmentation of meaningful waveform features, is critical for clinical diagnosis. Despite recent advances using deep learning, progress has been limited by the scarcity of publicly available annotated datasets. Semi-supervised learning presents a promising solution by leveraging abundant unlabeled ECG data. In this study, we present SemiSegECG, the first systematic benchmark for semi-supervised semantic segmentation (SemiSeg) in ECG delineation. We curated and unified multiple public datasets, including previously underused sources, to support robust and diverse evaluation. We adopted five representative SemiSeg algorithms from computer vision, implemented them on two different architectures: the convolutional network and the transformer, and evaluated them in two different settings: in-domain and cross-domain. Additionally, we propose ECG-specific training configurations and augmentation strategies and introduce a standardized evaluation framework. Our results show that the transformer outperforms the convolutional network in semi-supervised ECG delineation. We anticipate that SemiSegECG will serve as a foundation for advancing semi-supervised ECG delineation methods and will facilitate further research in this domain.

An arrhythmia, also known as a dysrhythmia, refers to an irregular heartbeat. There are various types of arrhythmias that can originate from different areas of the heart, resulting in either a rapid, slow, or irregular heartbeat. An electrocardiogram (ECG) is a vital diagnostic tool used to detect heart irregularities and abnormalities, allowing experts to analyze the heart's electrical signals to identify intricate patterns and deviations from the norm. Over the past few decades, numerous studies have been conducted to develop automated methods for classifying heartbeats based on ECG data. In recent years, deep learning has demonstrated exceptional capabilities in tackling various medical challenges, particularly with transformers as a model architecture for sequence processing. By leveraging the transformers, we developed the ECGformer model for the classification of various arrhythmias present in electrocardiogram data. We assessed the suggested approach using the MIT-BIH and PTB datasets. ECG heartbeat arrhythmia classification results show that the proposed method is highly effective.

The electrocardiogram (ECG) is an essential non-invasive diagnostic tool for assessing cardiac conditions. Existing automatic interpretation methods suffer from limited generalizability, focusing on a narrow range of cardiac conditions, and typically depend on raw physiological signals, which may not be readily available in resource-limited settings where only printed or digital ECG images are accessible. Recent advancements in multimodal large language models (MLLMs) present promising opportunities for addressing these challenges. However, the application of MLLMs to ECG image interpretation remains challenging due to the lack of instruction tuning datasets and well-established ECG image benchmarks for quantitative evaluation. To address these challenges, we introduce ECGInstruct, a comprehensive ECG image instruction tuning dataset of over one million samples, covering a wide range of ECG-related tasks from diverse data sources. Using ECGInstruct, we develop PULSE, an MLLM tailored for ECG image comprehension. In addition, we curate ECGBench, a new evaluation benchmark covering four key ECG image interpretation tasks across nine different datasets. Our experiments show that PULSE sets a new state-of-the-art, outperforming general MLLMs with an average accuracy improvement of 15% to 30%. This work highlights the potential of PULSE to enhance ECG interpretation in clinical practice.

The electrocardiogram (ECG) remains a fundamental tool in cardiac diagnostics, yet its interpretation traditionally reliant on the expertise of cardiologists. The emergence of deep learning has heralded a revolutionary era in medical data analysis, particularly in the domain of ECG diagnostics. However, inter-patient variability prohibit the generalibility of ECG-AI model trained on a population dataset, hence degrade the performance of ECG-AI on specific patient or patient group. Many studies have address this challenge using different deep learning technologies. This comprehensive review systematically synthesizes research from a wide range of studies to provide an in-depth examination of cutting-edge deep-learning techniques in personalized ECG diagnosis. The review outlines a rigorous methodology for the selection of pertinent scholarly articles and offers a comprehensive overview of deep learning approaches applied to personalized ECG diagnostics. Moreover, the challenges these methods encounter are investigated, along with future research directions, culminating in insights into how the integration of deep learning can transform personalized ECG diagnosis and enhance cardiac care. By emphasizing both the strengths and limitations of current methodologies, this review underscores the immense potential of deep learning to refine and redefine ECG analysis in clinical practice, paving the way for more accurate, efficient, and personalized cardiac diagnostics.

Electrocardiogram (ECG) serves as the primary non-invasive diagnostic tool for cardiac conditions monitoring, are crucial in assisting clinicians. Recent studies have concentrated on classifying cardiac conditions using ECG data but have overlooked ECG report generation, which is not only time-consuming but also requires clinical expertise. To automate ECG report generation and ensure its versatility, we propose the Multimodal ECG Instruction Tuning (MEIT) framework, the first attempt to tackle ECG report generation with LLMs and multimodal instructions. To facilitate future research, we establish a benchmark to evaluate MEIT with various LLMs backbones across two large-scale ECG datasets. Our approach uniquely aligns the representations of the ECG signal and the report, and we conduct extensive experiments to benchmark MEIT with nine open source LLMs, using more than 800,000 ECG reports. MEIT's results underscore the superior performance of instruction-tuned LLMs, showcasing their proficiency in quality report generation, zero-shot capabilities, and resilience to signal perturbation. These findings emphasize the efficacy of our MEIT framework and its potential for real-world clinical application.

Electrocardiogram (ECG) is essential for the clinical diagnosis of arrhythmias and other heart diseases, but deep learning methods based on ECG often face limitations due to the need for high-quality annotations. Although previous ECG self-supervised learning (eSSL) methods have made significant progress in representation learning from unannotated ECG data, they typically treat ECG signals as ordinary time-series data, segmenting the signals using fixed-size and fixed-step time windows, which often ignore the form and rhythm characteristics and latent semantic relationships in ECG signals. In this work, we introduce a novel perspective on ECG signals, treating heartbeats as words and rhythms as sentences. Based on this perspective, we first designed the QRS-Tokenizer, which generates semantically meaningful ECG sentences from the raw ECG signals. Building on these, we then propose HeartLang, a novel self-supervised learning framework for ECG language processing, learning general representations at form and rhythm levels. Additionally, we construct the largest heartbeat-based ECG vocabulary to date, which will further advance the development of ECG language processing. We evaluated HeartLang across six public ECG datasets, where it demonstrated robust competitiveness against other eSSL methods. Our data and code are publicly available at https://github.com/PKUDigitalHealth/HeartLang.

The electrocardiogram (ECG) is a dependable instrument for assessing the function of the cardiovascular system. There has recently been much emphasis on precisely classifying ECGs. While ECG situations have numerous similarities, little attention has been paid to categorizing ECGs using graph neural networks. In this study, we offer three distinct techniques for classifying heartbeats using deep graph neural networks to classify the ECG signals accurately. We suggest using different methods to extract topological features from the ECG signal and then using a branch of the graph neural network named graph isomorphism network for classifying the ECGs. On the PTB Diagnostics data set, we tested the three proposed techniques. According to the findings, the three proposed techniques are capable of making arrhythmia classification predictions with the accuracy of 99.38, 98.76, and 91.93 percent, respectively.

Twelve-lead electrocardiograms (ECGs) are the clinical gold standard for cardiac diagnosis, providing comprehensive spatial coverage of the heart necessary to detect conditions such as myocardial infarction (MI). However, their lack of portability limits continuous and large-scale use. Three-lead ECG systems are widely used in wearable devices due to their simplicity and mobility, but they often fail to capture pathologies in unmeasured regions. To address this, we propose WearECG, a Variational Autoencoder (VAE) method that reconstructs twelve-lead ECGs from three leads: II, V1, and V5. Our model includes architectural improvements to better capture temporal and spatial dependencies in ECG signals. We evaluate generation quality using MSE, MAE, and Frechet Inception Distance (FID), and assess clinical validity via a Turing test with expert cardiologists. To further validate diagnostic utility, we fine-tune ECGFounder, a large-scale pretrained ECG model, on a multi-label classification task involving over 40 cardiac conditions, including six different myocardial infarction locations, using both real and generated signals. Experiments on the MIMIC dataset show that our method produces physiologically realistic and diagnostically informative signals, with robust performance in downstream tasks. This work demonstrates the potential of generative modeling for ECG reconstruction and its implications for scalable, low-cost cardiac screening.

Heart disease remains a significant threat to human health. As a non-invasive diagnostic tool, the electrocardiogram (ECG) is one of the most widely used methods for cardiac screening. However, the scarcity of high-quality ECG data, driven by privacy concerns and limited medical resources, creates a pressing need for effective ECG signal generation. Existing approaches for generating ECG signals typically rely on small training datasets, lack comprehensive evaluation frameworks, and overlook potential applications beyond data augmentation. To address these challenges, we propose DiffuSETS, a novel framework capable of generating ECG signals with high semantic alignment and fidelity. DiffuSETS accepts various modalities of clinical text reports and patient-specific information as inputs, enabling the creation of clinically meaningful ECG signals. Additionally, to address the lack of standardized evaluation in ECG generation, we introduce a comprehensive benchmarking methodology to assess the effectiveness of generative models in this domain. Our model achieve excellent results in tests, proving its superiority in the task of ECG generation. Furthermore, we showcase its potential to mitigate data scarcity while exploring novel applications in cardiology education and medical knowledge discovery, highlighting the broader impact of our work.

Electrocardiogram (ECG) plays a foundational role in modern cardiovascular care, enabling non-invasive diagnosis of arrhythmias, myocardial ischemia, and conduction disorders. While machine learning has achieved expert-level performance in ECG interpretation, the development of clinically deployable multimodal AI systems remains constrained, primarily due to the lack of publicly available datasets that simultaneously incorporate raw signals, diagnostic images, and interpretation text. Most existing ECG datasets provide only single-modality data or, at most, dual modalities, making it difficult to build models that can understand and integrate diverse ECG information in real-world settings. To address this gap, we introduce MEETI (MIMIC-IV-Ext ECG-Text-Image), the first large-scale ECG dataset that synchronizes raw waveform data, high-resolution plotted images, and detailed textual interpretations generated by large language models. In addition, MEETI includes beat-level quantitative ECG parameters extracted from each lead, offering structured parameters that support fine-grained analysis and model interpretability. Each MEETI record is aligned across four components: (1) the raw ECG waveform, (2) the corresponding plotted image, (3) extracted feature parameters, and (4) detailed interpretation text. This alignment is achieved using consistent, unique identifiers. This unified structure supports transformer-based multimodal learning and supports fine-grained, interpretable reasoning about cardiac health. By bridging the gap between traditional signal analysis, image-based interpretation, and language-driven understanding, MEETI established a robust foundation for the next generation of explainable, multimodal cardiovascular AI. It offers the research community a comprehensive benchmark for developing and evaluating ECG-based AI systems.

Electrocardiogram (ECG) interpretation is a cornerstone of cardiac diagnostics. This paper explores a practical approach to enhance ECG image interpretation using the multimodal LLaMA 3.2 model. We used a parameter-efficient fine-tuning strategy, Low-Rank Adaptation (LoRA), specifically designed to boost the model's ability to understand ECG images and achieve better outcomes across a wide range of cardiac conditions. Our method is tailored for ECG analysis and leverages ECGInstruct, a large-scale instruction dataset with 1 Million samples. This dataset is a rich collection of synthesized ECG images, generated from raw ECG data from trusted open-source repositories like MIMIC-IV ECG and PTB-XL. Each ECG image in ECGInstruct comes with expert-written questions and detailed answers, covering diverse ECG interpretation scenarios, including complex cardiac conditions like Myocardial Infarction and Conduction Disturbances. Our fine-tuning approach efficiently adapts the LLaMA 3.2 model (built upon LLaMA 3) by integrating low-rank adaptation techniques, focusing on efficiency by updating only a small set of parameters, specifically ignoring the `lm_head` and `embed_tokens` layers. This paper details the model setup, our efficient fine-tuning method, and implementation specifics. We provide a thorough evaluation through extensive experiments, demonstrating the effectiveness of our method across various ECG interpretation tasks. The results convincingly show that our parameter-efficient LoRA fine-tuning achieves excellent performance in ECG image interpretation, significantly outperforming baseline models and reaching accuracy comparable to or exceeding traditional CNN-based methods in identifying a wide range of cardiac abnormalities, including over 70 conditions from the PTB-XL dataset.

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

Electrocardiograms (ECGs) play a vital role in monitoring cardiac health and diagnosing heart diseases. However, traditional deep learning approaches for ECG analysis rely heavily on large-scale manual annotations, which are both time-consuming and resource-intensive to obtain. To overcome this limitation, self-supervised learning (SSL) has emerged as a promising alternative, enabling the extraction of robust ECG representations that can be efficiently transferred to various downstream tasks. While previous studies have explored SSL for ECG pretraining and multi-modal ECG-language alignment, they often fail to capture the multi-scale nature of ECG signals. As a result, these methods struggle to learn generalized representations due to their inability to model the hierarchical structure of ECG data. To address this gap, we introduce MELP, a novel Multi-scale ECG-Language Pretraining (MELP) model that fully leverages hierarchical supervision from ECG-text pairs. MELP first pretrains a cardiology-specific language model to enhance its understanding of clinical text. It then applies three levels of cross-modal supervision-at the token, beat, and rhythm levels-to align ECG signals with textual reports, capturing structured information across different time scales. We evaluate MELP on three public ECG datasets across multiple tasks, including zero-shot ECG classification, linear probing, and transfer learning. Experimental results demonstrate that MELP outperforms existing SSL methods, underscoring its effectiveness and adaptability across diverse clinical applications. Our code is available at https://github.com/HKU-MedAI/MELP.

Electrocardiography plays a central role in cardiovascular diagnostics, yet existing automated approaches often struggle to generalize across clinical tasks and offer limited support for open-ended reasoning. We present DiagECG, a novel framework that integrates time-series and language modeling by enabling large language models to process 12-lead ECG signals for clinical text generation tasks. Our approach discretizes continuous ECG embeddings into symbolic tokens using a lead-independent encoder and quantization module. These tokens are then used to extend the vocabulary of LLM, allowing the model to handle both ECG and natural language inputs in a unified manner. To bridge the modality gap, we pretrain the model on an autoregressive ECG forecasting task, enabling the LLM to model temporal dynamics using its native language modeling capabilities. Finally, we perform instruction tuning on both ECG question answering and diagnostic report generation. Without modifying the core model, DiagECG achieves strong performance across tasks while maintaining generalization to out-of-distribution settings. Extensive experiments demonstrate the effectiveness of each component and highlight the potential of integrating symbolic ECG representations into LLMs for medical reasoning.

In clinical practice, electrocardiography (ECG) remains the gold standard for cardiac monitoring, providing crucial insights for diagnosing a wide range of cardiovascular diseases (CVDs). However, its reliance on specialized equipment and trained personnel limits feasibility for continuous routine monitoring. Photoplethysmography (PPG) offers accessible, continuous monitoring but lacks definitive electrophysiological information, preventing conclusive diagnosis. Generative models present a promising approach to translate PPG into clinically valuable ECG signals, yet current methods face substantial challenges, including the misalignment of physiological semantics in generative models and the complexity of modeling in high-dimensional signals. To this end, we propose PPGFlowECG, a two-stage framework that aligns PPG and ECG in a shared latent space via the CardioAlign Encoder and employs latent rectified flow to generate ECGs with high fidelity and interpretability. To the best of our knowledge, this is the first study to experiment on MCMED, a newly released clinical-grade dataset comprising over 10 million paired PPG-ECG samples from more than 118,000 emergency department visits with expert-labeled cardiovascular disease annotations. Results demonstrate the effectiveness of our method for PPG-to-ECG translation and cardiovascular disease detection. Moreover, cardiologist-led evaluations confirm that the synthesized ECGs achieve high fidelity and improve diagnostic reliability, underscoring our method's potential for real-world cardiovascular screening.

Electrocardiography (ECG) signal generation has been heavily explored using generative adversarial networks (GAN) because the implementation of 12-lead ECGs is not always feasible. The GAN models have achieved remarkable results in reproducing ECG signals but are only designed for multiple lead inputs and the features the GAN model preserves have not been identified-limiting the generated signals use in cardiovascular disease (CVD)-predictive models. This paper presents ECGNet which is a procedure that generates a complete set of 12-lead ECG signals from any single lead input using a GAN framework with a bidirectional long short-term memory (LSTM) generator and a convolutional neural network (CNN) discriminator. Cross and auto-correlation analysis performed on the generated signals identifies features conserved during the signal generation-i.e., features that can characterize the unique-nature of each signal and thus likely indicators of CVD. Finally, by using ECG signals annotated with the CVD-indicative features detailed by the correlation analysis as inputs for a CVD-onset-predictive CNN model, we overcome challenges preventing the prediction of multiple-CVD targets. Our models are experimented on 15s 12-lead ECG dataset recorded using MyoVista's wavECG. Functional outcome data for each patient is recorded and used in the CVD-predictive model. Our best GAN model achieves state-of-the-art accuracy with Frechet Distance (FD) scores of 4.73, 4.89, 5.18, 4.77, 4.71, and 5.55 on the V1-V6 pre-cordial leads respectively and shows strength in preserving the P-Q segments and R-peaks in the generated signals. To the best of our knowledge, ECGNet is the first to predict all of the remaining eleven leads from the input of any single lead.

Electrocardiogram (ECG) interpretation requires specialized expertise, often involving synthesizing insights from ECG signals with complex clinical queries posed in natural language. The scarcity of labeled ECG data coupled with the diverse nature of clinical inquiries presents a significant challenge for developing robust and adaptable ECG diagnostic systems. This work introduces a novel multimodal meta-learning method for few-shot ECG question answering, addressing the challenge of limited labeled data while leveraging the rich knowledge encoded within large language models (LLMs). Our LLM-agnostic approach integrates a pre-trained ECG encoder with a frozen LLM (e.g., LLaMA and Gemma) via a trainable fusion module, enabling the language model to reason about ECG data and generate clinically meaningful answers. Extensive experiments demonstrate superior generalization to unseen diagnostic tasks compared to supervised baselines, achieving notable performance even with limited ECG leads. For instance, in a 5-way 5-shot setting, our method using LLaMA-3.1-8B achieves accuracy of 84.6%, 77.3%, and 69.6% on single verify, choose and query question types, respectively. These results highlight the potential of our method to enhance clinical ECG interpretation by combining signal processing with the nuanced language understanding capabilities of LLMs, particularly in data-constrained scenarios.

Automated interpretation of electrocardiograms (ECG) has garnered significant attention with the advancements in machine learning methodologies. Despite the growing interest, most current studies focus solely on classification or regression tasks, which overlook a crucial aspect of clinical cardio-disease diagnosis: the diagnostic report generated by experienced human clinicians. In this paper, we introduce a novel approach to ECG interpretation, leveraging recent breakthroughs in Large Language Models (LLMs) and Vision-Transformer (ViT) models. Rather than treating ECG diagnosis as a classification or regression task, we propose an alternative method of automatically identifying the most similar clinical cases based on the input ECG data. Also, since interpreting ECG as images is more affordable and accessible, we process ECG as encoded images and adopt a vision-language learning paradigm to jointly learn vision-language alignment between encoded ECG images and ECG diagnosis reports. Encoding ECG into images can result in an efficient ECG retrieval system, which will be highly practical and useful in clinical applications. More importantly, our findings could serve as a crucial resource for providing diagnostic services in underdeveloped regions.

Accurate diagnosis of heart arrhythmias requires the interpretation of electrocardiograms (ECG), which capture the electrical activity of the heart. Automating this process through machine learning is challenging due to the need for large annotated datasets, which are difficult and costly to collect. To address this issue, transfer learning is often employed, where models are pre-trained on large datasets and fine-tuned for specific ECG classification tasks with limited labeled data. Self-supervised learning has become a widely adopted pre-training method, enabling models to learn meaningful representations from unlabeled datasets. In this work, we explore the joint-embedding predictive architecture (JEPA) for self-supervised learning from ECG data. Unlike invariance-based methods, JEPA does not rely on hand-crafted data augmentations, and unlike generative methods, it predicts latent features rather than reconstructing input data. We create a large unsupervised pre-training dataset by combining ten public ECG databases, amounting to over one million records. We pre-train Vision Transformers using JEPA on this dataset and fine-tune them on various PTB-XL benchmarks. Our results show that JEPA outperforms existing invariance-based and generative approaches, achieving an AUC of 0.945 on the PTB-XL all statements task. JEPA consistently learns the highest quality representations, as demonstrated in linear evaluations, and proves advantageous for pre-training even in the absence of additional data.

Interpreting electrocardiograms (ECGs) and generating comprehensive reports remain challenging tasks in cardiology, often requiring specialized expertise and significant time investment. To address these critical issues, we propose ECG-ReGen, a retrieval-based approach for ECG-to-text report generation and question answering. Our method leverages a self-supervised learning for the ECG encoder, enabling efficient similarity searches and report retrieval. By combining pre-training with dynamic retrieval and Large Language Model (LLM)-based refinement, ECG-ReGen effectively analyzes ECG data and answers related queries, with the potential of improving patient care. Experiments conducted on the PTB-XL and MIMIC-IV-ECG datasets demonstrate superior performance in both in-domain and cross-domain scenarios for report generation. Furthermore, our approach exhibits competitive performance on ECG-QA dataset compared to fully supervised methods when utilizing off-the-shelf LLMs for zero-shot question answering. This approach, effectively combining self-supervised encoder and LLMs, offers a scalable and efficient solution for accurate ECG interpretation, holding significant potential to enhance clinical decision-making.

Accurate detection of cardiac abnormalities from electrocardiogram recordings is regarded as essential for clinical diagnostics and decision support. Traditional deep learning models such as residual networks and transformer architectures have been applied successfully to this task, but their performance has been limited when long sequential signals are processed. Recently, state space models have been introduced as an efficient alternative. In this study, a hybrid framework named One Dimensional Convolutional Neural Network Electrocardiogram Mamba is introduced, in which convolutional feature extraction is combined with Mamba, a selective state space model designed for effective sequence modeling. The model is built upon Vision Mamba, a bidirectional variant through which the representation of temporal dependencies in electrocardiogram data is enhanced. Comprehensive experiments on the PhysioNet Computing in Cardiology Challenges of 2020 and 2021 were conducted, and superior performance compared with existing methods was achieved. Specifically, the proposed model achieved substantially higher AUPRC and AUROC scores than those reported by the best previously published algorithms on twelve lead electrocardiograms. These results demonstrate the potential of Mamba-based architectures to advance reliable ECG classification. This capability supports early diagnosis and personalized treatment, while enhancing accessibility in telemedicine and resource-constrained healthcare systems.

Electrocardiograms (ECGs), a medical monitoring technology recording cardiac activity, are widely used for diagnosing cardiac arrhythmia. The diagnosis is based on the analysis of the deformation of the signal shapes due to irregular heart rates associated with heart diseases. Due to the infeasibility of manual examination of large volumes of ECG data, this paper aims to propose an automated AI based system for ECG-based arrhythmia classification. To this front, a deep learning based solution has been proposed for ECG-based arrhythmia classification. Twelve lead electrocardiograms (ECG) of length 10 sec from 45, 152 individuals from Shaoxing People's Hospital (SPH) dataset from PhysioNet with four different types of arrhythmias were used. The sampling frequency utilized was 500 Hz. Median filtering was used to preprocess the ECG signals. For every 1 sec of ECG signal, the time-frequency (TF) scalogram was estimated and stacked row wise to obtain a single image from 12 channels, resulting in 10 stacked TF scalograms for each ECG signal. These stacked TF scalograms are fed to the pretrained convolutional neural network (CNN), 1D CNN, and 1D CNN-LSTM (Long short-term memory) models, for arrhythmia classification. The fine-tuned CNN models obtained the best test accuracy of about 98% followed by 95% test accuracy by basic CNN-LSTM in arrhythmia classification.

Electrocardiography (ECG) offers critical cardiovascular insights, such as identifying arrhythmias and myocardial ischemia, but enabling automated systems to answer complex clinical questions directly from ECG signals (ECG-QA) remains a significant challenge. Current approaches often lack robust multimodal reasoning capabilities or rely on generic architectures ill-suited for the nuances of physiological signals. We introduce Q-Heart, a novel multimodal framework designed to bridge this gap. Q-Heart leverages a powerful, adapted ECG encoder and integrates its representations with textual information via a specialized ECG-aware transformer-based mapping layer. Furthermore, Q-Heart leverages dynamic prompting and retrieval of relevant historical clinical reports to guide tuning the language model toward knowledge-aware ECG reasoning. Extensive evaluations on the benchmark ECG-QA dataset show Q-Heart achieves state-of-the-art performance, outperforming existing methods by a 4% improvement in exact match accuracy. Our work demonstrates the effectiveness of combining domain-specific architectural adaptations with knowledge-augmented LLM instruction tuning for complex physiological ECG analysis, paving the way for more capable and potentially interpretable clinical patient care systems.

While recent multimodal large language models (MLLMs) have advanced automated ECG interpretation, they still face two key limitations: (1) insufficient multimodal synergy between time series signals and visual ECG representations, and (2) limited explainability in linking diagnoses to granular waveform evidence. We introduce GEM, the first MLLM unifying ECG time series, 12-lead ECG images and text for grounded and clinician-aligned ECG interpretation. GEM enables feature-grounded analysis, evidence-driven reasoning, and a clinician-like diagnostic process through three core innovations: a dual-encoder framework extracting complementary time series and image features, cross-modal alignment for effective multimodal understanding, and knowledge-guided instruction generation for generating high-granularity grounding data (ECG-Grounding) linking diagnoses to measurable parameters (e.g., QRS/PR Intervals). Additionally, we propose the Grounded ECG Understanding task, a clinically motivated benchmark designed to comprehensively assess the MLLM's capability in grounded ECG understanding. Experimental results on both existing and our proposed benchmarks show GEM significantly improves predictive performance (CSN 7.4% uparrow), explainability (22.7% uparrow), and grounding (24.8% uparrow), making it more suitable for real-world clinical applications. GitHub repository: https://github.com/lanxiang1017/GEM.git

Understanding the irregular electrical activity of atrial fibrillation (AFib) has been a key challenge in electrocardiography. For serious cases of AFib, catheter ablations are performed to collect intracardiac electrograms (EGMs). EGMs offer intricately detailed and localized electrical activity of the heart and are an ideal modality for interpretable cardiac studies. Recent advancements in artificial intelligence (AI) has allowed some works to utilize deep learning frameworks to interpret EGMs during AFib. Additionally, language models (LMs) have shown exceptional performance in being able to generalize to unseen domains, especially in healthcare. In this study, we are the first to leverage pretrained LMs for finetuning of EGM interpolation and AFib classification via masked language modeling. We formulate the EGM as a textual sequence and present competitive performances on AFib classification compared against other representations. Lastly, we provide a comprehensive interpretability study to provide a multi-perspective intuition of the model's behavior, which could greatly benefit the clinical use.

Electrocardiogram (ECG) is a widely used tool for assessing cardiac function due to its low cost and accessibility. Emergent research shows that ECGs can help make predictions on key outcomes traditionally derived from more complex modalities such as echocardiograms (ECHO), enabling the use of ECGs as a more accessible method to predict broader measurements of cardiac function. ECHO, in particular, are of great importance because they require considerable hospital resources while playing a key role in clinical cardiac assessment. To aid this use case, we introduce EchoingECG, a probabilistic student-teacher model that leverages uncertainty-aware ECG embeddings and ECHO supervision to improve ECG-based cardiac function prediction. Our approach integrates Probabilistic Cross-Modal Embeddings (PCME++), a probabilistic contrastive framework, with ECHO-CLIP, a vision-language pre-trained model trained on ECHO-text pairs, to distill ECHO knowledge into ECG representations. Through experiments and external validation, we showed that EchoingECG outperforms state-of-the-art foundation ECG models in zero-shot, few-shot, and fine-tune settings for ECHO predictions based on ECG. We also highlighted that variance estimation (enabled through our method) enhanced our understanding of model performance by identifying underlying regions of uncertainty within ECGs. The code is available: https://github.com/mcintoshML/EchoingECG.

Objective: To determine if a realistic, but computationally efficient model of the electrocardiogram can be used to pre-train a deep neural network (DNN) with a wide range of morphologies and abnormalities specific to a given condition - T-wave Alternans (TWA) as a result of Post-Traumatic Stress Disorder, or PTSD - and significantly boost performance on a small database of rare individuals. Approach: Using a previously validated artificial ECG model, we generated 180,000 artificial ECGs with or without significant TWA, with varying heart rate, breathing rate, TWA amplitude, and ECG morphology. A DNN, trained on over 70,000 patients to classify 25 different rhythms, was modified the output layer to a binary class (TWA or no-TWA, or equivalently, PTSD or no-PTSD), and transfer learning was performed on the artificial ECG. In a final transfer learning step, the DNN was trained and cross-validated on ECG from 12 PTSD and 24 controls for all combinations of using the three databases. Main results: The best performing approach (AUROC = 0.77, Accuracy = 0.72, F1-score = 0.64) was found by performing both transfer learning steps, using the pre-trained arrhythmia DNN, the artificial data and the real PTSD-related ECG data. Removing the artificial data from training led to the largest drop in performance. Removing the arrhythmia data from training provided a modest, but significant, drop in performance. The final model showed no significant drop in performance on the artificial data, indicating no overfitting. Significance: In healthcare, it is common to only have a small collection of high-quality data and labels, or a larger database with much lower quality (and less relevant) labels. The paradigm presented here, involving model-based performance boosting, provides a solution through transfer learning on a large realistic artificial database, and a partially relevant real database.

Heart disease, also known as cardiovascular disease, is a prevalent and critical medical condition characterized by the impairment of the heart and blood vessels, leading to various complications such as coronary artery disease, heart failure, and myocardial infarction. The timely and accurate detection of heart disease is of paramount importance in clinical practice. Early identification of individuals at risk enables proactive interventions, preventive measures, and personalized treatment strategies to mitigate the progression of the disease and reduce adverse outcomes. In recent years, the field of heart disease detection has witnessed notable advancements due to the integration of sophisticated technologies and computational approaches. These include machine learning algorithms, data mining techniques, and predictive modeling frameworks that leverage vast amounts of clinical and physiological data to improve diagnostic accuracy and risk stratification. In this work, we propose to detect heart disease from ECG images using cutting-edge technologies, namely vision transformer models. These models are Google-Vit, Microsoft-Beit, and Swin-Tiny. To the best of our knowledge, this is the initial endeavor concentrating on the detection of heart diseases through image-based ECG data by employing cuttingedge technologies namely, transformer models. To demonstrate the contribution of the proposed framework, the performance of vision transformer models are compared with state-of-the-art studies. Experiment results show that the proposed framework exhibits remarkable classification results.

Electrocardiograms (ECGs) are inexpensive, widely used, and well-suited to deep learning. Recently, interest has grown in developing foundation models for ECGs - models that generalise across diverse downstream tasks. However, consistent evaluation has been lacking: prior work often uses narrow task selections and inconsistent datasets, hindering fair comparison. Here, we introduce BenchECG, a standardised benchmark comprising a comprehensive suite of publicly available ECG datasets and versatile tasks. We also propose xECG, an xLSTM-based recurrent model trained with SimDINOv2 self-supervised learning, which achieves the best BenchECG score compared to publicly available state-of-the-art models. In particular, xECG is the only publicly available model to perform strongly on all datasets and tasks. By standardising evaluation, BenchECG enables rigorous comparison and aims to accelerate progress in ECG representation learning. xECG achieves superior performance over earlier approaches, defining a new baseline for future ECG foundation models.

Artificial intelligence (AI) has demonstrated significant potential in ECG analysis and cardiovascular disease assessment. Recently, foundation models have played a remarkable role in advancing medical AI. The development of an ECG foundation model holds the promise of elevating AI-ECG research to new heights. However, building such a model faces several challenges, including insufficient database sample sizes and inadequate generalization across multiple domains. Additionally, there is a notable performance gap between single-lead and multi-lead ECG analyses. We introduced an ECG Foundation Model (ECGFounder), a general-purpose model that leverages real-world ECG annotations from cardiology experts to broaden the diagnostic capabilities of ECG analysis. ECGFounder was trained on over 10 million ECGs with 150 label categories from the Harvard-Emory ECG Database, enabling comprehensive cardiovascular disease diagnosis through ECG analysis. The model is designed to be both an effective out-of-the-box solution, and a to be fine-tunable for downstream tasks, maximizing usability. Importantly, we extended its application to lower rank ECGs, and arbitrary single-lead ECGs in particular. ECGFounder is applicable to supporting various downstream tasks in mobile monitoring scenarios. Experimental results demonstrate that ECGFounder achieves expert-level performance on internal validation sets, with AUROC exceeding 0.95 for eighty diagnoses. It also shows strong classification performance and generalization across various diagnoses on external validation sets. When fine-tuned, ECGFounder outperforms baseline models in demographic analysis, clinical event detection, and cross-modality cardiac rhythm diagnosis. The trained model and data will be publicly released upon publication through the bdsp.io. Our code is available at https://github.com/bdsp-core/ECGFounder

Accurate interpretation of Electrocardiogram (ECG) signals is pivotal for diagnosing cardiovascular diseases. Integrating ECG signals with their accompanying textual reports holds immense potential to enhance clinical diagnostics through the combination of physiological data and qualitative insights. However, this integration faces significant challenges due to inherent modality disparities and the scarcity of labeled data for robust cross-modal learning. To address these obstacles, we propose C-MELT, a novel framework that pre-trains ECG and text data using a contrastive masked auto-encoder architecture. C-MELT uniquely combines the strengths of generative with enhanced discriminative capabilities to achieve robust cross-modal representations. This is accomplished through masked modality modeling, specialized loss functions, and an improved negative sampling strategy tailored for cross-modal alignment. Extensive experiments on five public datasets across diverse downstream tasks demonstrate that C-MELT significantly outperforms existing methods, achieving 15% and 2% increases in linear probing and zero-shot performance over state-of-the-art models, respectively. These results highlight the effectiveness of C-MELT, underscoring its potential to advance automated clinical diagnostics through multi-modal representations.

Large Language Models (LLMs) have shown remarkable adaptability across domains beyond text, specifically electrocardiograms (ECGs). More specifically, there is a growing body of work exploring the task of generating text from a multi-channeled ECG and corresponding textual prompt. Current approaches typically involve pretraining an ECG-specific encoder with a self-supervised learning (SSL) objective and using the features output by the pretrained encoder to finetune a LLM for natural language generation (NLG). However, these methods are limited by 1) inefficiency from two-stage training and 2) interpretability challenges with encoder-generated features. To address these limitations, we introduce ECG-Byte, an adapted byte pair encoding (BPE) tokenizer pipeline for autoregressive language modeling of ECGs. This approach compresses and encodes ECG signals into tokens, enabling end-to-end LLM training by combining ECG and text tokens directly, while being much more interpretable since the ECG tokens can be directly mapped back to the original signal. Using ECG-Byte, we achieve competitive performance in NLG tasks in only half the time and ~48% of the data required by two-stage approaches.

Photoplethysmogram (PPG) and electrocardiogram (ECG) are commonly recorded in intesive care unit (ICU) and operating room (OR). However, the high incidence of poor, incomplete, and inconsistent signal quality, can lead to false alarms or diagnostic inaccuracies. The methods explored so far suffer from limited generalizability, reliance on extensive labeled data, and poor cross-task transferability. To overcome these challenges, we introduce QualityFM, a novel multimodal foundation model for these physiological signals, designed to acquire a general-purpose understanding of signal quality. Our model is pre-trained on an large-scale dataset comprising over 21 million 30-second waveforms and 179,757 hours of data. Our approach involves a dual-track architecture that processes paired physiological signals of differing quality, leveraging a self-distillation strategy where an encoder for high-quality signals is used to guide the training of an encoder for low-quality signals. To efficiently handle long sequential signals and capture essential local quasi-periodic patterns, we integrate a windowed sparse attention mechanism within our Transformer-based model. Furthermore, a composite loss function, which combines direct distillation loss on encoder outputs with indirect reconstruction loss based on power and phase spectra, ensures the preservation of frequency-domain characteristics of the signals. We pre-train three models with varying parameter counts (9.6 M to 319 M) and demonstrate their efficacy and practical value through transfer learning on three distinct clinical tasks: false alarm of ventricular tachycardia detection, the identification of atrial fibrillation and the estimation of arterial blood pressure (ABP) from PPG and ECG signals.

Electrocardiograms (ECG) are widely employed as a diagnostic tool for monitoring electrical signals originating from a heart. Recent machine learning research efforts have focused on the application of screening various diseases using ECG signals. However, adapting to the application of screening disease is challenging in that labeled ECG data are limited. Achieving general representation through self-supervised learning (SSL) is a well-known approach to overcome the scarcity of labeled data; however, a naive application of SSL to ECG data, without considering the spatial-temporal relationships inherent in ECG signals, may yield suboptimal results. In this paper, we introduce ST-MEM (Spatio-Temporal Masked Electrocardiogram Modeling), designed to learn spatio-temporal features by reconstructing masked 12-lead ECG data. ST-MEM outperforms other SSL baseline methods in various experimental settings for arrhythmia classification tasks. Moreover, we demonstrate that ST-MEM is adaptable to various lead combinations. Through quantitative and qualitative analysis, we show a spatio-temporal relationship within ECG data. Our code is available at https://github.com/bakqui/ST-MEM.

Question answering (QA) in the field of healthcare has received much attention due to significant advancements in natural language processing. However, existing healthcare QA datasets primarily focus on medical images, clinical notes, or structured electronic health record tables. This leaves the vast potential of combining electrocardiogram (ECG) data with these systems largely untapped. To address this gap, we present ECG-QA, the first QA dataset specifically designed for ECG analysis. The dataset comprises a total of 70 question templates that cover a wide range of clinically relevant ECG topics, each validated by an ECG expert to ensure their clinical utility. As a result, our dataset includes diverse ECG interpretation questions, including those that require a comparative analysis of two different ECGs. In addition, we have conducted numerous experiments to provide valuable insights for future research directions. We believe that ECG-QA will serve as a valuable resource for the development of intelligent QA systems capable of assisting clinicians in ECG interpretations. Dataset URL: https://github.com/Jwoo5/ecg-qa

Anomaly detection in 12-lead electrocardiograms (ECGs) is critical for identifying deviations associated with cardiovascular disease. This work presents a comparative analysis of three autoencoder-based architectures: convolutional autoencoder (CAE), variational autoencoder with bidirectional long short-term memory (VAE-BiLSTM), and VAE-BiLSTM with multi-head attention (VAE-BiLSTM-MHA), for unsupervised anomaly detection in ECGs. To the best of our knowledge, this study reports the first application of a VAE-BiLSTM-MHA architecture to ECG anomaly detection. All models are trained on normal ECG samples to reconstruct non-anomalous cardiac morphology and detect deviations indicative of disease. Using a unified preprocessing and evaluation pipeline on the public China Physiological Signal Challenge (CPSC) dataset, the attention-augmented VAE achieves the best performance, with an AUPRC of 0.81 and a recall of 0.85 on the held-out test set, outperforming the other architectures. To support clinical triage, this model is further integrated into an interactive dashboard that visualizes anomaly localization. In addition, a performance comparison with baseline models from the literature is provided.

Recent advancements in Large Language Models (LLMs) have drawn increasing attention since the learned embeddings pretrained on large-scale datasets have shown powerful ability in various downstream applications. However, whether the learned knowledge by LLMs can be transferred to clinical cardiology remains unknown. In this work, we aim to bridge this gap by transferring the knowledge of LLMs to clinical Electrocardiography (ECG). We propose an approach for cardiovascular disease diagnosis and automatic ECG diagnosis report generation. We also introduce an additional loss function by Optimal Transport (OT) to align the distribution between ECG and language embedding. The learned embeddings are evaluated on two downstream tasks: (1) automatic ECG diagnosis report generation, and (2) zero-shot cardiovascular disease detection. Our approach is able to generate high-quality cardiac diagnosis reports and also achieves competitive zero-shot classification performance even compared with supervised baselines, which proves the feasibility of transferring knowledge from LLMs to the cardiac domain.

Besides entity-centric knowledge, usually organized as Knowledge Graph (KG), events are also an essential kind of knowledge in the world, which trigger the spring up of event-centric knowledge representation form like Event KG (EKG). It plays an increasingly important role in many downstream applications, such as search, question-answering, recommendation, financial quantitative investments, and text generation. This paper provides a comprehensive survey of EKG from history, ontology, instance, and application views. Specifically, to characterize EKG thoroughly, we focus on its history, definition, schema induction, acquisition, related representative graphs/systems, and applications. The development processes and trends are studied therein. We further summarize prospective directions to facilitate future research on EKG.

Deep learning-based electrocardiogram (ECG) classification has shown impressive performance but clinical adoption has been slowed by the lack of transparent and faithful explanations. Post hoc methods such as saliency maps may fail to reflect a model's true decision process. Prototype-based reasoning offers a more transparent alternative by grounding decisions in similarity to learned representations of real ECG segments, enabling faithful, case-based explanations. We introduce ProtoECGNet, a prototype-based deep learning model for interpretable, multi-label ECG classification. ProtoECGNet employs a structured, multi-branch architecture that reflects clinical interpretation workflows: it integrates a 1D CNN with global prototypes for rhythm classification, a 2D CNN with time-localized prototypes for morphology-based reasoning, and a 2D CNN with global prototypes for diffuse abnormalities. Each branch is trained with a prototype loss designed for multi-label learning, combining clustering, separation, diversity, and a novel contrastive loss that encourages appropriate separation between prototypes of unrelated classes while allowing clustering for frequently co-occurring diagnoses. We evaluate ProtoECGNet on all 71 diagnostic labels from the PTB-XL dataset, demonstrating competitive performance relative to state-of-the-art black-box models while providing structured, case-based explanations. To assess prototype quality, we conduct a structured clinician review of the final model's projected prototypes, finding that they are rated as representative and clear. ProtoECGNet shows that prototype learning can be effectively scaled to complex, multi-label time-series classification, offering a practical path toward transparent and trustworthy deep learning models for clinical decision support.

Conventional task-specific electrocardiogram (ECG) analysis models require large annotated datasets to train. Foundation models mitigate this burden by leveraging self-supervised pretraining; however, the scarcity of open-weight ECG foundation models hinders adoption and cross-study comparability. We present ECG-FM, an open foundation model for ECG analysis, and conduct a study using a dataset of 1.5 million ECGs. ECG-FM is a transformer-based model pretrained using a hybrid contrastive and generative self-supervised learning approach. Our downstream tasks include predicting reduced left ventricular ejection fraction (LVEF) and ECG interpretation labels, where we release a benchmark task on the MIMIC-IV-ECG dataset. We affirm that ECG-FM is robust, label-efficient, and functionally discriminative by showcasing data scaling experiments, performing a latent space analysis, and generating saliency maps. ECG-FM markedly outperforms task-specific models in the small-to-medium-scale data regime and demonstrates cross-dataset generalizability, achieving high AUROC on many clinically salient labels such as atrial fibrillation (0.996) and LVEF<=40% (0.929). We release our code, model weights, and benchmark task at https://github.com/bowang-lab/ECG-FM/.

Electrocardiography (ECG) signals are often degraded by noise, which complicates diagnosis in clinical and wearable settings. This study proposes a diffusion-based framework for ECG noise quantification via reconstruction-based anomaly detection, addressing annotation inconsistencies and the limited generalizability of conventional methods. We introduce a distributional evaluation using the Wasserstein-1 distance (W_1), comparing the reconstruction error distributions between clean and noisy ECGs to mitigate inconsistent annotations. Our final model achieved robust noise quantification using only three reverse diffusion steps. The model recorded a macro-average W_1 score of 1.308 across the benchmarks, outperforming the next-best method by over 48%. External validations demonstrated strong generalizability, supporting the exclusion of low-quality segments to enhance diagnostic accuracy and enable timely clinical responses to signal degradation. The proposed method enhances clinical decision-making, diagnostic accuracy, and real-time ECG monitoring capabilities, supporting future advancements in clinical and wearable ECG applications.

This study aims to develop and evaluate an ensemble machine learning-based framework for the automatic detection of Wide QRS Complex Tachycardia (WCT) from ECG signals, emphasizing diagnostic accuracy and interpretability using Explainable AI. The proposed system integrates ensemble learning techniques, i.e., an optimized Random Forest known as CardioForest, and models like XGBoost and LightGBM. The models were trained and tested on ECG data from the publicly available MIMIC-IV dataset. The testing was carried out with the assistance of accuracy, balanced accuracy, precision, recall, F1 score, ROC-AUC, and error rate (RMSE, MAE) measures. In addition, SHAP (SHapley Additive exPlanations) was used to ascertain model explainability and clinical relevance. The CardioForest model performed best on all metrics, achieving a test accuracy of 94.95%, a balanced accuracy of 88.31%, and high precision and recall metrics. SHAP analysis confirmed the model's ability to rank the most relevant ECG features, such as QRS duration, in accordance with clinical intuitions, thereby fostering trust and usability in clinical practice. The findings recognize CardioForest as an extremely dependable and interpretable WCT detection model. Being able to offer accurate predictions and transparency through explainability makes it a valuable tool to help cardiologists make timely and well-informed diagnoses, especially for high-stakes and emergency scenarios.

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

This study introduces OpenECG, a large-scale benchmark of 1.2 million 12-lead ECG recordings from nine centers, to evaluate ECG foundation models (ECG-FMs) trained on public datasets. We investigate three self-supervised learning methods (SimCLR, BYOL, MAE) with ResNet-50 and Vision Transformer architectures, assessing model generalization through leave-one-dataset-out experiments and data scaling analysis. Results show that pre-training on diverse datasets significantly improves generalization, with BYOL and MAE outperforming SimCLR, highlighting the efficacy of feature-consistency and generative learning over contrastive approaches. Data scaling experiments reveal that performance saturates at 60-70% of total data for BYOL and MAE, while SimCLR requires more data. These findings demonstrate that publicly available ECG data can match or surpass proprietary datasets in training robust ECG-FMs, paving the way for scalable, clinically meaningful AI-driven ECG analysis.

Echocardiography (ECHO) is essential for cardiac assessments, but its video quality and interpretation heavily relies on manual expertise, leading to inconsistent results from clinical and portable devices. ECHO video generation offers a solution by improving automated monitoring through synthetic data and generating high-quality videos from routine health data. However, existing models often face high computational costs, slow inference, and rely on complex conditional prompts that require experts' annotations. To address these challenges, we propose ECHOPULSE, an ECG-conditioned ECHO video generation model. ECHOPULSE introduces two key advancements: (1) it accelerates ECHO video generation by leveraging VQ-VAE tokenization and masked visual token modeling for fast decoding, and (2) it conditions on readily accessible ECG signals, which are highly coherent with ECHO videos, bypassing complex conditional prompts. To the best of our knowledge, this is the first work to use time-series prompts like ECG signals for ECHO video generation. ECHOPULSE not only enables controllable synthetic ECHO data generation but also provides updated cardiac function information for disease monitoring and prediction beyond ECG alone. Evaluations on three public and private datasets demonstrate state-of-the-art performance in ECHO video generation across both qualitative and quantitative measures. Additionally, ECHOPULSE can be easily generalized to other modality generation tasks, such as cardiac MRI, fMRI, and 3D CT generation. Demo can seen from https://github.com/levyisthebest/ECHOPulse_Prelease.

The rapid evolution of artificial intelligence (AI), together with the increased availability of social media and news for epidemiological surveillance, are marking a pivotal moment in epidemiology and public health research. Leveraging the power of generative AI, we use an ensemble approach which incorporates multiple Large Language Models (LLMs) to extract valuable actionable epidemiological information from the World Health Organization (WHO) Disease Outbreak News (DONs). DONs is a collection of regular reports on global outbreaks curated by the WHO and the adopted decision-making processes to respond to them. The extracted information is made available in a daily-updated dataset and a knowledge graph, referred to as eKG, derived to provide a nuanced representation of the public health domain knowledge. We provide an overview of this new dataset and describe the structure of eKG, along with the services and tools used to access and utilize the data that we are building on top. These innovative data resources open altogether new opportunities for epidemiological research, and the analysis and surveillance of disease outbreaks.

Cardiac biosignals, such as electrocardiograms (ECG) and photoplethysmograms (PPG), are of paramount importance for the diagnosis, prevention, and management of cardiovascular diseases, and have been extensively used in a variety of clinical tasks. Conventional deep learning approaches for analyzing these signals typically rely on homogeneous datasets and static bespoke models, limiting their robustness and generalizability across diverse clinical settings and acquisition protocols. In this study, we present a cardiac sensing foundation model (CSFM) that leverages advanced transformer architectures and a generative, masked pretraining strategy to learn unified representations from vast, heterogeneous health records. Our model is pretrained on an innovative multi-modal integration of data from multiple large-scale datasets (including MIMIC-III-WDB, MIMIC-IV-ECG, and CODE), comprising cardiac signals and the corresponding clinical or machine-generated text reports from approximately 1.7 million individuals. We demonstrate that the embeddings derived from our CSFM not only serve as effective feature extractors across diverse cardiac sensing scenarios, but also enable seamless transfer learning across varying input configurations and sensor modalities. Extensive evaluations across diagnostic tasks, demographic information recognition, vital sign measurement, clinical outcome prediction, and ECG question answering reveal that CSFM consistently outperforms traditional one-modal-one-task approaches. Notably, CSFM exhibits robust performance across multiple ECG lead configurations from standard 12-lead systems to single-lead setups, and in scenarios where only ECG, only PPG, or a combination thereof is available. These findings highlight the potential of CSFM as a versatile and scalable solution, for comprehensive cardiac monitoring.

Understanding the interaction of neural and cardiac systems during cognitive activity is critical to advancing physiological computing. Although EEG has been the gold standard for assessing mental workload, its limited portability restricts its real-world use. Widely available ECG through wearable devices proposes a pragmatic alternative. This research investigates whether ECG signals can reliably reflect cognitive load and serve as proxies for EEG-based indicators. In this work, we present multimodal data acquired from two different paradigms involving working-memory and passive-listening tasks. For each modality, we extracted ECG time-domain HRV metrics and Catch22 descriptors against EEG spectral and Catch22 features, respectively. We propose a cross-modal XGBoost framework to project the ECG features onto EEG-representative cognitive spaces, thereby allowing workload inferences using only ECG. Our results show that ECG-derived projections expressively capture variation in cognitive states and provide good support for accurate classification. Our findings underpin ECG as an interpretable, real-time, wearable solution for everyday cognitive monitoring.

Databases of electronic health records (EHRs) are increasingly used to inform clinical decisions. Machine learning methods can find patterns in EHRs that are predictive of future adverse outcomes. However, statistical models may be built upon patterns of health-seeking behavior that vary across patient subpopulations, leading to poor predictive performance when training on one patient population and predicting on another. This note proposes two tests to better measure and understand model generalization. We use these tests to compare models derived from two data sources: (i) historical medical records, and (ii) electrocardiogram (EKG) waveforms. In a predictive task, we show that EKG-based models can be more stable than EHR-based models across different patient populations.

Large language models (LLMs) have captured significant interest from both academia and industry due to their impressive performance across various textual tasks. However, the potential of LLMs to analyze physiological time-series data remains an emerging research field. Particularly, there is a notable gap in the utilization of LLMs for analyzing wearable biosignals to achieve cuffless blood pressure (BP) measurement, which is critical for the management of cardiovascular diseases. This paper presents the first work to explore the capacity of LLMs to perform cuffless BP estimation based on wearable biosignals. We extracted physiological features from electrocardiogram (ECG) and photoplethysmogram (PPG) signals and designed context-enhanced prompts by combining these features with BP domain knowledge and user information. Subsequently, we adapted LLMs to BP estimation tasks through fine-tuning. To evaluate the proposed approach, we conducted assessments of ten advanced LLMs using a comprehensive public dataset of wearable biosignals from 1,272 participants. The experimental results demonstrate that the optimally fine-tuned LLM significantly surpasses conventional task-specific baselines, achieving an estimation error of 0.00 pm 9.25 mmHg for systolic BP and 1.29 pm 6.37 mmHg for diastolic BP. Notably, the ablation studies highlight the benefits of our context enhancement strategy, leading to an 8.9% reduction in mean absolute error for systolic BP estimation. This paper pioneers the exploration of LLMs for cuffless BP measurement, providing a potential solution to enhance the accuracy of cuffless BP measurement.

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

The first ACM/IEEE TinyML Design Contest (TDC) held at the 41st International Conference on Computer-Aided Design (ICCAD) in 2022 is a challenging, multi-month, research and development competition. TDC'22 focuses on real-world medical problems that require the innovation and implementation of artificial intelligence/machine learning (AI/ML) algorithms on implantable devices. The challenge problem of TDC'22 is to develop a novel AI/ML-based real-time detection algorithm for life-threatening ventricular arrhythmia over low-power microcontrollers utilized in Implantable Cardioverter-Defibrillators (ICDs). The dataset contains more than 38,000 5-second intracardiac electrograms (IEGMs) segments over 8 different types of rhythm from 90 subjects. The dedicated hardware platform is NUCLEO-L432KC manufactured by STMicroelectronics. TDC'22, which is open to multi-person teams world-wide, attracted more than 150 teams from over 50 organizations. This paper first presents the medical problem, dataset, and evaluation procedure in detail. It further demonstrates and discusses the designs developed by the leading teams as well as representative results. This paper concludes with the direction of improvement for the future TinyML design for health monitoring applications.

Atrial fibrillation (AFib) is the prominent cardiac arrhythmia in the world. It affects mostly the elderly population, with potential consequences such as stroke and heart failure in the absence of necessary treatments as soon as possible. The importance of atrial scarring in the development and progression of AFib has gained recognition, positioning late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) as a crucial technique for the non-invasive evaluation of atrial scar tissue. This review delves into the recent progress in segmenting atrial scars using LGE-MRIs, emphasizing the importance of precise scar measurement in the treatment and management of AFib. Initially, it provides a detailed examination of AFib. Subsequently, it explores the application of deep learning in this domain. The review culminates in a discussion of the latest research advancements in atrial scar segmentation using deep learning methods. By offering a thorough analysis of current technologies and their impact on AFib management strategies, this review highlights the integral role of deep learning in enhancing atrial scar segmentation and its implications for future therapeutic approaches.

Medical image segmentation plays a crucial role in clinical diagnosis and treatment planning, where accurate boundary delineation is essential for precise lesion localization, organ identification, and quantitative assessment. In recent years, deep learning-based methods have significantly advanced segmentation accuracy. However, two major challenges remain. First, the performance of these methods heavily relies on large-scale annotated datasets, which are often difficult to obtain in medical scenarios due to privacy concerns and high annotation costs. Second, clinically challenging scenarios, such as low contrast in certain imaging modalities and blurry lesion boundaries caused by malignancy, still pose obstacles to precise segmentation. To address these challenges, we propose MedSAM-CA, an architecture-level fine-tuning approach that mitigates reliance on extensive manual annotations by adapting the pretrained foundation model, Medical Segment Anything (MedSAM). MedSAM-CA introduces two key components: the Convolutional Attention-Enhanced Boundary Refinement Network (CBR-Net) and the Attention-Enhanced Feature Fusion Block (Atte-FFB). CBR-Net operates in parallel with the MedSAM encoder to recover boundary information potentially overlooked by long-range attention mechanisms, leveraging hierarchical convolutional processing. Atte-FFB, embedded in the MedSAM decoder, fuses multi-level fine-grained features from skip connections in CBR-Net with global representations upsampled within the decoder to enhance boundary delineation accuracy. Experiments on publicly available datasets covering dermoscopy, CT, and MRI imaging modalities validate the effectiveness of MedSAM-CA. On dermoscopy dataset, MedSAM-CA achieves 94.43% Dice with only 2% of full training data, reaching 97.25% of full-data training performance, demonstrating strong effectiveness in low-resource clinical settings.

Recent advancements in diffusion probabilistic models (DPMs) have revolutionized image processing, demonstrating significant potential in medical applications. Accurate segmentation of the left ventricle (LV) in echocardiograms is crucial for diagnostic procedures and necessary treatments. However, ultrasound images are notoriously noisy with low contrast and ambiguous LV boundaries, thereby complicating the segmentation process. To address these challenges, this paper introduces Echo-DND, a novel dual-noise diffusion model specifically designed for this task. Echo-DND leverages a unique combination of Gaussian and Bernoulli noises. It also incorporates a multi-scale fusion conditioning module to improve segmentation precision. Furthermore, it utilizes spatial coherence calibration to maintain spatial integrity in segmentation masks. The model's performance was rigorously validated on the CAMUS and EchoNet-Dynamic datasets. Extensive evaluations demonstrate that the proposed framework outperforms existing SOTA models. It achieves high Dice scores of 0.962 and 0.939 on these datasets, respectively. The proposed Echo-DND model establishes a new standard in echocardiogram segmentation, and its architecture holds promise for broader applicability in other medical imaging tasks, potentially improving diagnostic accuracy across various medical domains. Project page: https://abdur75648.github.io/Echo-DND

Tracking biosignals is crucial for monitoring wellness and preempting the development of severe medical conditions. Today, wearable devices can conveniently record various biosignals, creating the opportunity to monitor health status without disruption to one's daily routine. Despite widespread use of wearable devices and existing digital biomarkers, the absence of curated data with annotated medical labels hinders the development of new biomarkers to measure common health conditions. In fact, medical datasets are usually small in comparison to other domains, which is an obstacle for developing neural network models for biosignals. To address this challenge, we have employed self-supervised learning using the unlabeled sensor data collected under informed consent from the large longitudinal Apple Heart and Movement Study (AHMS) to train foundation models for two common biosignals: photoplethysmography (PPG) and electrocardiogram (ECG) recorded on Apple Watch. We curated PPG and ECG datasets from AHMS that include data from ~141K participants spanning ~3 years. Our self-supervised learning framework includes participant level positive pair selection, stochastic augmentation module and a regularized contrastive loss optimized with momentum training, and generalizes well to both PPG and ECG modalities. We show that the pre-trained foundation models readily encode information regarding participants' demographics and health conditions. To the best of our knowledge, this is the first study that builds foundation models using large-scale PPG and ECG data collected via wearable consumer devices x2013 prior works have commonly used smaller-size datasets collected in clinical and experimental settings. We believe PPG and ECG foundation models can enhance future wearable devices by reducing the reliance on labeled data and hold the potential to help the users improve their health.

Accurate delineation of pathological lungs from computed tomography (CT) images remains mostly unsolved because available methods fail to provide a reliable generic solution due to high variability of abnormality appearance. Local descriptor-based classification methods have shown to work well in annotating pathologies; however, these methods are usually computationally intensive which restricts their widespread use in real-time or near-real-time clinical applications. In this paper, we present a novel approach for fast, accurate, reliable segmentation of pathological lungs from CT scans by combining region-based segmentation method with local descriptor classification that is performed on an optimized sampling grid. Our method works in two stages; during stage one, we adapted the fuzzy connectedness (FC) image segmentation algorithm to perform initial lung parenchyma extraction. In the second stage, texture-based local descriptors are utilized to segment abnormal imaging patterns using a near optimal keypoint analysis by employing centroid of supervoxel as grid points. The quantitative results show that our pathological lung segmentation method is fast, robust, and improves on current standards and has potential to enhance the performance of routine clinical tasks.

Heart failure (HF) affects 11.8% of adults aged 65 and older, reducing quality of life and longevity. Preventing HF can reduce morbidity and mortality. We hypothesized that artificial intelligence (AI) applied to 24-hour single-lead electrocardiogram (ECG) data could predict the risk of HF within five years. To research this, the Technion-Leumit Holter ECG (TLHE) dataset, including 69,663 recordings from 47,729 patients, collected over 20 years was used. Our deep learning model, DeepHHF, trained on 24-hour ECG recordings, achieved an area under the receiver operating characteristic curve of 0.80 that outperformed a model using 30-second segments and a clinical score. High-risk individuals identified by DeepHHF had a two-fold chance of hospitalization or death incidents. Explainability analysis showed DeepHHF focused on arrhythmias and heart abnormalities, with key attention between 8 AM and 3 PM. This study highlights the feasibility of deep learning to model 24-hour continuous ECG data, capturing paroxysmal events and circadian variations essential for reliable risk prediction. Artificial intelligence applied to single-lead Holter ECG is non-invasive, inexpensive, and widely accessible, making it a promising tool for HF risk prediction.

Accurate classification of sleep stages from less obtrusive sensor measurements such as the electrocardiogram (ECG) or photoplethysmogram (PPG) could enable important applications in sleep medicine. Existing approaches to this problem have typically used deep learning models designed and trained to operate on one or more specific input signals. However, the datasets used to develop these models often do not contain the same sets of input signals. Some signals, particularly PPG, are much less prevalent than others, and this has previously been addressed with techniques such as transfer learning. Additionally, only training on one or more fixed modalities precludes cross-modal information transfer from other sources, which has proved valuable in other problem domains. To address this, we introduce wav2sleep, a unified model designed to operate on variable sets of input signals during training and inference. After jointly training on over 10,000 overnight recordings from six publicly available polysomnography datasets, including SHHS and MESA, wav2sleep outperforms existing sleep stage classification models across test-time input combinations including ECG, PPG, and respiratory signals.

Human health can be critically affected by cardiovascular diseases, such as hypertension, arrhythmias, and stroke. Heart rate and blood pressure are important biometric information for the monitoring of cardiovascular system and early diagnosis of cardiovascular diseases. Existing methods for estimating the heart rate are based on electrocardiography and photoplethyomography, which require contacting the sensor to the skin surface. Moreover, catheter and cuff-based methods for measuring blood pressure cause inconvenience and have limited applicability. Therefore, in this thesis, we propose a vision-based method for estimating the heart rate and blood pressure. This thesis proposes a 2-stage deep learning framework consisting of a dual remote photoplethysmography network (DRP-Net) and bounded blood pressure network (BBP-Net). In the first stage, DRP-Net infers remote photoplethysmography (rPPG) signals for the acral and facial regions, and these phase-shifted rPPG signals are utilized to estimate the heart rate. In the second stage, BBP-Net integrates temporal features and analyzes phase discrepancy between the acral and facial rPPG signals to estimate SBP and DBP values. To improve the accuracy of estimating the heart rate, we employed a data augmentation method based on a frame interpolation model. Moreover, we designed BBP-Net to infer blood pressure within a predefined range by incorporating a scaled sigmoid function. Our method resulted in estimating the heart rate with the mean absolute error (MAE) of 1.78 BPM, reducing the MAE by 34.31 % compared to the recent method, on the MMSE-HR dataset. The MAE for estimating the systolic blood pressure (SBP) and diastolic blood pressure (DBP) were 10.19 mmHg and 7.09 mmHg. On the V4V dataset, the MAE for the heart rate, SBP, and DBP were 3.83 BPM, 13.64 mmHg, and 9.4 mmHg, respectively.

Most of the existing chest X-ray datasets include labels from a list of findings without specifying their locations on the radiographs. This limits the development of machine learning algorithms for the detection and localization of chest abnormalities. In this work, we describe a dataset of more than 100,000 chest X-ray scans that were retrospectively collected from two major hospitals in Vietnam. Out of this raw data, we release 18,000 images that were manually annotated by a total of 17 experienced radiologists with 22 local labels of rectangles surrounding abnormalities and 6 global labels of suspected diseases. The released dataset is divided into a training set of 15,000 and a test set of 3,000. Each scan in the training set was independently labeled by 3 radiologists, while each scan in the test set was labeled by the consensus of 5 radiologists. We designed and built a labeling platform for DICOM images to facilitate these annotation procedures. All images are made publicly available (https://www.physionet.org/content/vindr-cxr/1.0.0/) in DICOM format along with the labels of both the training set and the test set.

Recent research in medical image analysis with deep learning almost exclusively focuses on grid- or voxel-based data representations. We challenge this common choice by introducing MedFuncta, a modality-agnostic continuous data representation based on neural fields. We demonstrate how to scale neural fields from single instances to large datasets by exploiting redundancy in medical signals and by applying an efficient meta-learning approach with a context reduction scheme. We further address the spectral bias in commonly used SIREN activations, by introducing an omega_0-schedule, improving reconstruction quality and convergence speed. We validate our proposed approach on a large variety of medical signals of different dimensions and modalities (1D: ECG; 2D: Chest X-ray, Retinal OCT, Fundus Camera, Dermatoscope, Colon Histopathology, Cell Microscopy; 3D: Brain MRI, Lung CT) and successfully demonstrate that we can solve relevant downstream tasks on these representations. We additionally release a large-scale dataset of > 550k annotated neural fields to promote research in this direction.

Echocardiogram video segmentation plays an important role in cardiac disease diagnosis. This paper studies the unsupervised domain adaption (UDA) for echocardiogram video segmentation, where the goal is to generalize the model trained on the source domain to other unlabelled target domains. Existing UDA segmentation methods are not suitable for this task because they do not model local information and the cyclical consistency of heartbeat. In this paper, we introduce a newly collected CardiacUDA dataset and a novel GraphEcho method for cardiac structure segmentation. Our GraphEcho comprises two innovative modules, the Spatial-wise Cross-domain Graph Matching (SCGM) and the Temporal Cycle Consistency (TCC) module, which utilize prior knowledge of echocardiogram videos, i.e., consistent cardiac structure across patients and centers and the heartbeat cyclical consistency, respectively. These two modules can better align global and local features from source and target domains, improving UDA segmentation results. Experimental results showed that our GraphEcho outperforms existing state-of-the-art UDA segmentation methods. Our collected dataset and code will be publicly released upon acceptance. This work will lay a new and solid cornerstone for cardiac structure segmentation from echocardiogram videos. Code and dataset are available at: https://github.com/xmed-lab/GraphEcho

Generating clinical reports from raw recordings such as X-rays and electroencephalogram (EEG) is an essential and routine task for doctors. However, it is often time-consuming to write accurate and detailed reports. Most existing methods try to generate the whole reports from the raw input with limited success because 1) generated reports often contain errors that need manual review and correction, 2) it does not save time when doctors want to write additional information into the report, and 3) the generated reports are not customized based on individual doctors' preference. We propose {\it CL}inic{\it A}l {\it R}eport {\it A}uto-completion (CLARA), an interactive method that generates reports in a sentence by sentence fashion based on doctors' anchor words and partially completed sentences. CLARA searches for most relevant sentences from existing reports as the template for the current report. The retrieved sentences are sequentially modified by combining with the input feature representations to create the final report. In our experimental evaluation, CLARA achieved 0.393 CIDEr and 0.248 BLEU-4 on X-ray reports and 0.482 CIDEr and 0.491 BLEU-4 for EEG reports for sentence-level generation, which is up to 35% improvement over the best baseline. Also via our qualitative evaluation, CLARA is shown to produce reports which have a significantly higher level of approval by doctors in a user study (3.74 out of 5 for CLARA vs 2.52 out of 5 for the baseline).

Cardiovascular diseases (CVDs) remain the leading cause of mortality globally, and echocardiography is critical for diagnosis of both common and congenital cardiac conditions. However, echocardiographic data for certain pathologies are scarce, hindering the development of robust automated diagnosis models. In this work, we propose Echo-Path, a novel generative framework to produce echocardiogram videos conditioned on specific cardiac pathologies. Echo-Path can synthesize realistic ultrasound video sequences that exhibit targeted abnormalities, focusing here on atrial septal defect (ASD) and pulmonary arterial hypertension (PAH). Our approach introduces a pathology-conditioning mechanism into a state-of-the-art echo video generator, allowing the model to learn and control disease-specific structural and motion patterns in the heart. Quantitative evaluation demonstrates that the synthetic videos achieve low distribution distances, indicating high visual fidelity. Clinically, the generated echoes exhibit plausible pathology markers. Furthermore, classifiers trained on our synthetic data generalize well to real data and, when used to augment real training sets, it improves downstream diagnosis of ASD and PAH by 7\% and 8\% respectively. Code, weights and dataset are available here https://github.com/Marshall-mk/EchoPathv1

Accurate segmentation is essential for echocardiography-based assessment of cardiovascular diseases (CVDs). However, the variability among sonographers and the inherent challenges of ultrasound images hinder precise segmentation. By leveraging the joint representation of image and text modalities, Vision-Language Segmentation Models (VLSMs) can incorporate rich contextual information, potentially aiding in accurate and explainable segmentation. However, the lack of readily available data in echocardiography hampers the training of VLSMs. In this study, we explore using synthetic datasets from Semantic Diffusion Models (SDMs) to enhance VLSMs for echocardiography segmentation. We evaluate results for two popular VLSMs (CLIPSeg and CRIS) using seven different kinds of language prompts derived from several attributes, automatically extracted from echocardiography images, segmentation masks, and their metadata. Our results show improved metrics and faster convergence when pretraining VLSMs on SDM-generated synthetic images before finetuning on real images. The code, configs, and prompts are available at https://github.com/naamiinepal/synthetic-boost.

Fully automatic cardiac segmentation can be a fast and reproducible method to extract clinical measurements from an echocardiography examination. The U-Net architecture is the current state-of-the-art deep learning architecture for medical segmentation and can segment cardiac structures in real-time with average errors comparable to inter-observer variability. However, this architecture still generates large outliers that are often anatomically incorrect. This work uses the concept of graph convolutional neural networks that predict the contour points of the structures of interest instead of labeling each pixel. We propose a graph architecture that uses two convolutional rings based on cardiac anatomy and show that this eliminates anatomical incorrect multi-structure segmentations on the publicly available CAMUS dataset. Additionally, this work contributes with an ablation study on the graph convolutional architecture and an evaluation of clinical measurements on the clinical HUNT4 dataset. Finally, we propose to use the inter-model agreement of the U-Net and the graph network as a predictor of both the input and segmentation quality. We show this predictor can detect out-of-distribution and unsuitable input images in real-time. Source code is available online: https://github.com/gillesvntnu/GCN_multistructure

Machine learning models, particularly deep neural networks, have demonstrated strong performance in classifying complex time series data. However, their black-box nature limits trust and adoption, especially in high-stakes domains such as healthcare. To address this challenge, we introduce UniCoMTE, a model-agnostic framework for generating counterfactual explanations for multivariate time series classifiers. The framework identifies temporal features that most heavily influence a model's prediction by modifying the input sample and assessing its impact on the model's prediction. UniCoMTE is compatible with a wide range of model architectures and operates directly on raw time series inputs. In this study, we evaluate UniCoMTE's explanations on a time series ECG classifier. We quantify explanation quality by comparing our explanations' comprehensibility to comprehensibility of established techniques (LIME and SHAP) and assessing their generalizability to similar samples. Furthermore, clinical utility is assessed through a questionnaire completed by medical experts who review counterfactual explanations presented alongside original ECG samples. Results show that our approach produces concise, stable, and human-aligned explanations that outperform existing methods in both clarity and applicability. By linking model predictions to meaningful signal patterns, the framework advances the interpretability of deep learning models for real-world time series applications.

Efficient, reliable and reproducible target volume delineation is a key step in the effective planning of breast radiotherapy. However, post-operative breast target delineation is challenging as the contrast between the tumor bed volume (TBV) and normal breast tissue is relatively low in CT images. In this study, we propose to mimic the marker-guidance procedure in manual target delineation. We developed a saliency-based deep learning segmentation (SDL-Seg) algorithm for accurate TBV segmentation in post-operative breast irradiation. The SDL-Seg algorithm incorporates saliency information in the form of markers' location cues into a U-Net model. The design forces the model to encode the location-related features, which underscores regions with high saliency levels and suppresses low saliency regions. The saliency maps were generated by identifying markers on CT images. Markers' locations were then converted to probability maps using a distance-transformation coupled with a Gaussian filter. Subsequently, the CT images and the corresponding saliency maps formed a multi-channel input for the SDL-Seg network. Our in-house dataset was comprised of 145 prone CT images from 29 post-operative breast cancer patients, who received 5-fraction partial breast irradiation (PBI) regimen on GammaPod. The performance of the proposed method was compared against basic U-Net. Our model achieved mean (standard deviation) of 76.4 %, 6.76 mm, and 1.9 mm for DSC, HD95, and ASD respectively on the test set with computation time of below 11 seconds per one CT volume. SDL-Seg showed superior performance relative to basic U-Net for all the evaluation metrics while preserving low computation cost. The findings demonstrate that SDL-Seg is a promising approach for improving the efficiency and accuracy of the on-line treatment planning procedure of PBI, such as GammaPod based PBI.

Segmentation of the coronary artery is an important task for the quantitative analysis of coronary computed tomography angiography (CCTA) images and is being stimulated by the field of deep learning. However, the complex structures with tiny and narrow branches of the coronary artery bring it a great challenge. Coupled with the medical image limitations of low resolution and poor contrast, fragmentations of segmented vessels frequently occur in the prediction. Therefore, a geometry-based cascaded segmentation method is proposed for the coronary artery, which has the following innovations: 1) Integrating geometric deformation networks, we design a cascaded network for segmenting the coronary artery and vectorizing results. The generated meshes of the coronary artery are continuous and accurate for twisted and sophisticated coronary artery structures, without fragmentations. 2) Different from mesh annotations generated by the traditional marching cube method from voxel-based labels, a finer vectorized mesh of the coronary artery is reconstructed with the regularized morphology. The novel mesh annotation benefits the geometry-based segmentation network, avoiding bifurcation adhesion and point cloud dispersion in intricate branches. 3) A dataset named CCA-200 is collected, consisting of 200 CCTA images with coronary artery disease. The ground truths of 200 cases are coronary internal diameter annotations by professional radiologists. Extensive experiments verify our method on our collected dataset CCA-200 and public ASOCA dataset, with a Dice of 0.778 on CCA-200 and 0.895 on ASOCA, showing superior results. Especially, our geometry-based model generates an accurate, intact and smooth coronary artery, devoid of any fragmentations of segmented vessels.

In this paper, we introduce a novel Multi-Modal Contrastive Pre-training Framework that synergistically combines X-rays, electrocardiograms (ECGs), and radiology/cardiology reports. Our approach leverages transformers to encode these diverse modalities into a unified representation space, aiming to enhance diagnostic accuracy and facilitate comprehensive patient assessments. We utilize LoRA-Peft to significantly reduce trainable parameters in the LLM and incorporate recent linear attention dropping strategy in the Vision Transformer(ViT) for smoother attention. Furthermore, we provide novel multimodal attention explanations and retrieval for our model. To the best of our knowledge, we are the first to propose an integrated model that combines X-ray, ECG, and Radiology/Cardiology Report with this approach. By utilizing contrastive loss, MoRE effectively aligns modality-specific features into a coherent embedding, which supports various downstream tasks such as zero-shot classification and multimodal retrieval. Employing our proposed methodology, we achieve state-of-the-art (SOTA) on the Mimic-IV, CheXpert, Edema Severity, and PtbXl downstream datasets, surpassing existing multimodal approaches. Our proposed framework shows significant improvements in capturing intricate inter-modal relationships and its robustness in medical diagnosis that establishes a framework for future research in multimodal learning in the healthcare sector.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

Medical image segmentation exhibits intra- and inter-annotator variability due to ambiguous object boundaries, annotator preferences, expertise, and tools, among other factors. Lesions with ambiguous boundaries, e.g., spiculated or infiltrative nodules, or irregular borders per the ABCD rule, are particularly prone to disagreement and are often associated with malignancy. In this work, we curate IMA++, the largest multi-annotator skin lesion segmentation dataset, on which we conduct an in-depth study of variability due to annotator, malignancy, tool, and skill factors. We find a statistically significant (p<0.001) association between inter-annotator agreement (IAA), measured using Dice, and the malignancy of skin lesions. We further show that IAA can be accurately predicted directly from dermoscopic images, achieving a mean absolute error of 0.108. Finally, we leverage this association by utilizing IAA as a "soft" clinical feature within a multi-task learning objective, yielding a 4.2% improvement in balanced accuracy averaged across multiple model architectures and across IMA++ and four public dermoscopic datasets. The code is available at https://github.com/sfu-mial/skin-IAV.

Reliable automatic seizure detection from long-term EEG remains a challenge, as current machine learning models often fail to generalize across patients or clinical settings. Manual EEG review remains the clinical standard, underscoring the need for robust models and standardized evaluation. To rigorously assess algorithm performance, we organized a challenge using a private dataset of continuous EEG recordings from 65 subjects (4,360 hours). Expert neurophysiologists annotated the data, providing ground truth for seizure events. Participants were required to detect seizure onset and duration, with evaluation based on event-based metrics, including sensitivity, precision, F1-score, and false positives per day. The SzCORE framework ensured standardized evaluation. The primary ranking criterion was the event-based F1-score, reflecting clinical relevance by balancing sensitivity and false positives. The challenge received 30 submissions from 19 teams, with 28 algorithms evaluated. Results revealed wide variability in performance, with a top F1-score of 43% (sensitivity 37%, precision 45%), highlighting the ongoing difficulty of seizure detection. The challenge also revealed a gap between reported performance and real-world evaluation, emphasizing the importance of rigorous benchmarking. Compared to previous challenges and commercial systems, the best-performing algorithm in this contest showed improved performance. Importantly, the challenge platform now supports continuous benchmarking, enabling reproducible research, integration of new datasets, and clinical evaluation of seizure detection algorithms using a standardized framework.

Brain tumors, particularly gliomas, pose significant chall-enges due to their complex growth patterns, infiltrative nature, and the variability in brain structure across individuals, which makes accurate diagnosis and monitoring difficult. Deep learning models have been developed to accurately delineate these tumors. However, most of these models were trained on relatively homogenous high-resource datasets, limiting their robustness when deployed in underserved regions. In this study, we performed segmentation-aware offline data augmentation on the BraTS-Africa dataset to increase the data sample size and diversity to enhance generalization. We further constructed an ensemble of three distinct architectures, MedNeXt, SegMamba, and Residual-Encoder U-Net, to leverage their complementary strengths. Our best-performing model, MedNeXt, was trained on 1000 epochs and achieved the highest average lesion-wise dice and normalized surface distance scores of 0.86 and 0.81 respectively. However, the ensemble model trained for 500 epochs produced the most balanced segmentation performance across the tumour subregions. This work demonstrates that a combination of advanced augmentation and model ensembling can improve segmentation accuracy and robustness on diverse and underrepresented datasets. Code available at: https://github.com/SPARK-Academy-2025/SPARK-2025/tree/main/SPARK2025_BraTs_MODELS/SPARK_NeuroAshanti

Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural language processing (NLP) techniques, there are still challenges including limited availability of data due to privacy constraints and the high variability of clinical notes caused by different writing habits of medical professionals and various pathological features of patients. In this work, we investigate the semi-structured nature of clinical notes and propose an automatic algorithm to segment them into sections. To address the variability issues in existing ICD coding models with limited data, we introduce a contrastive pre-training approach on sections using a soft multi-label similarity metric based on tree edit distance. Additionally, we design a masked section training strategy to enable ICD coding models to locate sections related to ICD codes. Extensive experimental results demonstrate that our proposed training strategies effectively enhance the performance of existing ICD coding methods.

Image segmentation plays an essential role in medicine for both diagnostic and interventional tasks. Segmentation approaches are either manual, semi-automated or fully-automated. Manual segmentation offers full control over the quality of the results, but is tedious, time consuming and prone to operator bias. Fully automated methods require no human effort, but often deliver sub-optimal results without providing users with the means to make corrections. Semi-automated approaches keep users in control of the results by providing means for interaction, but the main challenge is to offer a good trade-off between precision and required interaction. In this paper we present a deep learning (DL) based semi-automated segmentation approach that aims to be a "smart" interactive tool for region of interest delineation in medical images. We demonstrate its use for segmenting multiple organs on computed tomography (CT) of the abdomen. Our approach solves some of the most pressing clinical challenges: (i) it requires only one to a few user clicks to deliver excellent 2D segmentations in a fast and reliable fashion; (ii) it can generalize to previously unseen structures and "corner cases"; (iii) it delivers results that can be corrected quickly in a smart and intuitive way up to an arbitrary degree of precision chosen by the user and (iv) ensures high accuracy. We present our approach and compare it to other techniques and previous work to show the advantages brought by our method.

Accurate segmentation of cardiac chambers in echocardiography sequences is crucial for the quantitative analysis of cardiac function, aiding in clinical diagnosis and treatment. The imaging noise, artifacts, and the deformation and motion of the heart pose challenges to segmentation algorithms. While existing methods based on convolutional neural networks, Transformers, and space-time memory networks have improved segmentation accuracy, they often struggle with the trade-off between capturing long-range spatiotemporal dependencies and maintaining computational efficiency with fine-grained feature representation. In this paper, we introduce GDKVM, a novel architecture for echocardiography video segmentation. The model employs Linear Key-Value Association (LKVA) to effectively model inter-frame correlations, and introduces Gated Delta Rule (GDR) to efficiently store intermediate memory states. Key-Pixel Feature Fusion (KPFF) module is designed to integrate local and global features at multiple scales, enhancing robustness against boundary blurring and noise interference. We validated GDKVM on two mainstream echocardiography video datasets (CAMUS and EchoNet-Dynamic) and compared it with various state-of-the-art methods. Experimental results show that GDKVM outperforms existing approaches in terms of segmentation accuracy and robustness, while ensuring real-time performance. Code is available at https://github.com/wangrui2025/GDKVM.

Left ventricular hypertrophy (LVH) results from chronic remodeling caused by a broad range of systemic and cardiovascular disease including hypertension, aortic stenosis, hypertrophic cardiomyopathy, and cardiac amyloidosis. Early detection and characterization of LVH can significantly impact patient care but is limited by under-recognition of hypertrophy, measurement error and variability, and difficulty differentiating etiologies of LVH. To overcome this challenge, we present EchoNet-LVH - a deep learning workflow that automatically quantifies ventricular hypertrophy with precision equal to human experts and predicts etiology of LVH. Trained on 28,201 echocardiogram videos, our model accurately measures intraventricular wall thickness (mean absolute error [MAE] 1.4mm, 95% CI 1.2-1.5mm), left ventricular diameter (MAE 2.4mm, 95% CI 2.2-2.6mm), and posterior wall thickness (MAE 1.2mm, 95% CI 1.1-1.3mm) and classifies cardiac amyloidosis (area under the curve of 0.83) and hypertrophic cardiomyopathy (AUC 0.98) from other etiologies of LVH. In external datasets from independent domestic and international healthcare systems, EchoNet-LVH accurately quantified ventricular parameters (R2 of 0.96 and 0.90 respectively) and detected cardiac amyloidosis (AUC 0.79) and hypertrophic cardiomyopathy (AUC 0.89) on the domestic external validation site. Leveraging measurements across multiple heart beats, our model can more accurately identify subtle changes in LV geometry and its causal etiologies. Compared to human experts, EchoNet-LVH is fully automated, allowing for reproducible, precise measurements, and lays the foundation for precision diagnosis of cardiac hypertrophy. As a resource to promote further innovation, we also make publicly available a large dataset of 23,212 annotated echocardiogram videos.

Neurophysiological recordings such as electroencephalography (EEG) offer accessible and minimally invasive means of estimating physiological activity for applications in healthcare, diagnostic screening, and even immersive entertainment. However, these recordings yield high-dimensional, noisy time-series data that typically require extensive pre-processing and handcrafted feature extraction to reveal meaningful information. Recently, there has been a surge of interest in applying representation learning techniques from large pre-trained (foundation) models to effectively decode and interpret biosignals. We discuss the challenges posed for incorporating such methods and introduce BioCodec, an alternative representation learning framework inspired by neural codecs to capture low-level signal characteristics in the form of discrete tokens. Pre-trained on thousands of EEG hours, BioCodec shows efficacy across multiple downstream tasks, ranging from clinical diagnostic tasks and sleep physiology to decoding speech and motor imagery, particularly in low-resource settings. Additionally, we provide a qualitative analysis of codebook usage and estimate the spatial coherence of codebook embeddings from EEG connectivity. Notably, we also document the suitability of our method to other biosignal data, i.e., electromyographic (EMG) signals. Overall, the proposed approach provides a versatile solution for biosignal tokenization that performs competitively with state-of-the-art models. The source code and model checkpoints are shared.

Colonoscopy is an effective technique for detecting colorectal polyps, which are highly related to colorectal cancer. In clinical practice, segmenting polyps from colonoscopy images is of great importance since it provides valuable information for diagnosis and surgery. However, accurate polyp segmentation is a challenging task, for two major reasons: (i) the same type of polyps has a diversity of size, color and texture; and (ii) the boundary between a polyp and its surrounding mucosa is not sharp. To address these challenges, we propose a parallel reverse attention network (PraNet) for accurate polyp segmentation in colonoscopy images. Specifically, we first aggregate the features in high-level layers using a parallel partial decoder (PPD). Based on the combined feature, we then generate a global map as the initial guidance area for the following components. In addition, we mine the boundary cues using a reverse attention (RA) module, which is able to establish the relationship between areas and boundary cues. Thanks to the recurrent cooperation mechanism between areas and boundaries, our PraNet is capable of calibrating any misaligned predictions, improving the segmentation accuracy. Quantitative and qualitative evaluations on five challenging datasets across six metrics show that our PraNet improves the segmentation accuracy significantly, and presents a number of advantages in terms of generalizability, and real-time segmentation efficiency.

The COVID-19 pandemic has underscored the need for low-cost, scalable approaches to measuring contactless vital signs, either during initial triage at a healthcare facility or virtual telemedicine visits. Remote photoplethysmography (rPPG) can accurately estimate heart rate (HR) when applied to close-up videos of healthy volunteers in well-lit laboratory settings. However, results from such highly optimized laboratory studies may not be readily translated to healthcare settings. One significant barrier to the practical application of rPPG in health care is the accurate localization of the region of interest (ROI). Clinical or telemedicine visits may involve sub-optimal lighting, movement artifacts, variable camera angle, and subject distance. This paper presents an rPPG ROI selection method based on 3D facial landmarks and patient head yaw angle. We then demonstrate the robustness of this ROI selection method when coupled to the Plane-Orthogonal-to-Skin (POS) rPPG method when applied to videos of patients presenting to an Emergency Department for respiratory complaints. Our results demonstrate the effectiveness of our proposed approach in improving the accuracy and robustness of rPPG in a challenging clinical environment.

The label scarcity problem is the main challenge that hinders the wide application of deep learning systems in automatic cardiovascular diseases (CVDs) detection using electrocardiography (ECG). Tuning pre-trained models alleviates this problem by transferring knowledge learned from large datasets to downstream small datasets. However, bottlenecks in computational efficiency and detection performance limit its clinical applications. It is difficult to improve the detection performance without significantly sacrificing the computational efficiency during model training. Here, we propose a computation-efficient semi-supervised learning paradigm (CE-SSL) for robust and computation-efficient CVDs detection using ECG. It enables a robust adaptation of pre-trained models on downstream datasets with limited supervision and high computational efficiency. First, a random-deactivation technique is developed to achieve robust and fast low-rank adaptation of pre-trained weights. Subsequently, we propose a one-shot rank allocation module to determine the optimal ranks for the update matrices of the pre-trained weights. Finally, a lightweight semi-supervised learning pipeline is introduced to enhance model performance by leveraging labeled and unlabeled data with high computational efficiency. Extensive experiments on four downstream datasets demonstrate that CE-SSL not only outperforms the state-of-the-art methods in multi-label CVDs detection but also consumes fewer GPU footprints, training time, and parameter storage space. As such, this paradigm provides an effective solution for achieving high computational efficiency and robust detection performance in the clinical applications of pre-trained models under limited supervision. Code and Supplementary Materials are available at https://github.com/KAZABANA/CE-SSL

Large, labeled datasets have driven deep learning methods to achieve expert-level performance on a variety of medical imaging tasks. We present CheXpert, a large dataset that contains 224,316 chest radiographs of 65,240 patients. We design a labeler to automatically detect the presence of 14 observations in radiology reports, capturing uncertainties inherent in radiograph interpretation. We investigate different approaches to using the uncertainty labels for training convolutional neural networks that output the probability of these observations given the available frontal and lateral radiographs. On a validation set of 200 chest radiographic studies which were manually annotated by 3 board-certified radiologists, we find that different uncertainty approaches are useful for different pathologies. We then evaluate our best model on a test set composed of 500 chest radiographic studies annotated by a consensus of 5 board-certified radiologists, and compare the performance of our model to that of 3 additional radiologists in the detection of 5 selected pathologies. On Cardiomegaly, Edema, and Pleural Effusion, the model ROC and PR curves lie above all 3 radiologist operating points. We release the dataset to the public as a standard benchmark to evaluate performance of chest radiograph interpretation models. The dataset is freely available at https://stanfordmlgroup.github.io/competitions/chexpert .

Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa.nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa.nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10\% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa.nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.

For the immanent challenge of insufficiently annotated samples in the medical field, semi-supervised medical image segmentation (SSMIS) offers a promising solution. Despite achieving impressive results in delineating primary target areas, most current methodologies struggle to precisely capture the subtle details of boundaries. This deficiency often leads to significant diagnostic inaccuracies. To tackle this issue, we introduce C3S3, a novel semi-supervised segmentation model that synergistically integrates complementary competition and contrastive selection. This design significantly sharpens boundary delineation and enhances overall precision. Specifically, we develop an Outcome-Driven Contrastive Learning module dedicated to refining boundary localization. Additionally, we incorporate a Dynamic Complementary Competition module that leverages two high-performing sub-networks to generate pseudo-labels, thereby further improving segmentation quality. The proposed C3S3 undergoes rigorous validation on two publicly accessible datasets, encompassing the practices of both MRI and CT scans. The results demonstrate that our method achieves superior performance compared to previous cutting-edge competitors. Especially, on the 95HD and ASD metrics, our approach achieves a notable improvement of at least 6%, highlighting the significant advancements. The code is available at https://github.com/Y-TARL/C3S3.

Deep learning's growing prevalence has driven its widespread use in healthcare, where AI and sensor advancements enhance diagnosis, treatment, and monitoring. In mobile health, AI-powered tools enable early diagnosis and continuous monitoring of conditions like stress. Wearable technologies and multimodal physiological data have made stress detection increasingly viable, but model efficacy depends on data quality, quantity, and modality. This study develops transformer models for stress detection using the WESAD dataset, training on electrocardiograms (ECG), electrodermal activity (EDA), electromyography (EMG), respiration rate (RESP), temperature (TEMP), and 3-axis accelerometer (ACC) signals. The results demonstrate the effectiveness of single-modality transformers in analyzing physiological signals, achieving state-of-the-art performance with accuracy, precision and recall values in the range of 99.73% to 99.95% for stress detection. Furthermore, this study explores cross-modal performance and also explains the same using 2D visualization of the learned embedding space and quantitative analysis based on data variance. Despite the large body of work on stress detection and monitoring, the robustness and generalization of these models across different modalities has not been explored. This research represents one of the initial efforts to interpret embedding spaces for stress detection, providing valuable information on cross-modal performance.

Tissue segmentation is a routine preprocessing step to reduce the computational cost of whole slide image (WSI) analysis by excluding background regions. Traditional image processing techniques are commonly used for tissue segmentation, but often require manual adjustments to parameter values for atypical cases, fail to exclude all slide and scanning artifacts from the background, and are unable to segment adipose tissue. Pen marking artifacts in particular can be a potential source of bias for subsequent analyses if not removed. In addition, several applications require the separation of individual cross-sections, which can be challenging due to tissue fragmentation and adjacent positioning. To address these problems, we develop a convolutional neural network for tissue and pen marking segmentation using a dataset of 200 H&E stained WSIs. For separating tissue cross-sections, we propose a novel post-processing method based on clustering predicted centroid locations of the cross-sections in a 2D histogram. On an independent test set, the model achieved a mean Dice score of 0.981pm0.033 for tissue segmentation and a mean Dice score of 0.912pm0.090 for pen marking segmentation. The mean absolute difference between the number of annotated and separated cross-sections was 0.075pm0.350. Our results demonstrate that the proposed model can accurately segment H&E stained tissue cross-sections and pen markings in WSIs while being robust to many common slide and scanning artifacts. The model with trained model parameters and post-processing method are made publicly available as a Python package called SlideSegmenter.

Cardiac Magnetic Resonance (CMR) imaging is a critical tool for diagnosing and managing cardiovascular disease, yet its utility is often limited by the sparse acquisition of 2D short-axis slices, resulting in incomplete volumetric information. Accurate 3D reconstruction from these sparse slices is essential for comprehensive cardiac assessment, but existing methods face challenges, including reliance on predefined interpolation schemes (e.g., linear or spherical), computational inefficiency, and dependence on additional semantic inputs such as segmentation labels or motion data. To address these limitations, we propose a novel Cardiac Latent Interpolation Diffusion (CaLID) framework that introduces three key innovations. First, we present a data-driven interpolation scheme based on diffusion models, which can capture complex, non-linear relationships between sparse slices and improves reconstruction accuracy. Second, we design a computationally efficient method that operates in the latent space and speeds up 3D whole-heart upsampling time by a factor of 24, reducing computational overhead compared to previous methods. Third, with only sparse 2D CMR images as input, our method achieves SOTA performance against baseline methods, eliminating the need for auxiliary input such as morphological guidance, thus simplifying workflows. We further extend our method to 2D+T data, enabling the effective modeling of spatiotemporal dynamics and ensuring temporal coherence. Extensive volumetric evaluations and downstream segmentation tasks demonstrate that CaLID achieves superior reconstruction quality and efficiency. By addressing the fundamental limitations of existing approaches, our framework advances the state of the art for spatio and spatiotemporal whole-heart reconstruction, offering a robust and clinically practical solution for cardiovascular imaging.

One of the main challenges in current research on segmentation in cardiac ultrasound is the lack of large and varied labeled datasets and the differences in annotation conventions between datasets. This makes it difficult to design robust segmentation models that generalize well to external datasets. This work utilizes diffusion models to create generative augmentations that can significantly improve diversity of the dataset and thus the generalisability of segmentation models without the need for more annotated data. The augmentations are applied in addition to regular augmentations. A visual test survey showed that experts cannot clearly distinguish between real and fully generated images. Using the proposed generative augmentations, segmentation robustness was increased when training on an internal dataset and testing on an external dataset with an improvement of over 20 millimeters in Hausdorff distance. Additionally, the limits of agreement for automatic ejection fraction estimation improved by up to 20% of absolute ejection fraction value on out of distribution cases. These improvements come exclusively from the increased variation of the training data using the generative augmentations, without modifying the underlying machine learning model. The augmentation tool is available as an open source Python library at https://github.com/GillesVanDeVyver/EchoGAINS.

Optical coherence tomography (OCT) is a non-invasive imaging modality which is widely used in clinical ophthalmology. OCT images are capable of visualizing deep retinal layers which is crucial for early diagnosis of retinal diseases. In this paper, we describe a comprehensive open-access database containing more than 500 highresolution images categorized into different pathological conditions. The image classes include Normal (NO), Macular Hole (MH), Age-related Macular Degeneration (AMD), Central Serous Retinopathy (CSR), and Diabetic Retinopathy (DR). The images were obtained from a raster scan protocol with a 2mm scan length and 512x1024 pixel resolution. We have also included 25 normal OCT images with their corresponding ground truth delineations which can be used for an accurate evaluation of OCT image segmentation. In addition, we have provided a user-friendly GUI which can be used by clinicians for manual (and semi-automated) segmentation.

Despite extensive standardization, diagnostic interviews for mental health disorders encompass substantial subjective judgment. Previous studies have demonstrated that EEG-based neural measures can function as reliable objective correlates of depression, or even predictors of depression and its course. However, their clinical utility has not been fully realized because of 1) the lack of automated ways to deal with the inherent noise associated with EEG data at scale, and 2) the lack of knowledge of which aspects of the EEG signal may be markers of a clinical disorder. Here we adapt an unsupervised pipeline from the recent deep representation learning literature to address these problems by 1) learning a disentangled representation using beta-VAE to denoise the signal, and 2) extracting interpretable features associated with a sparse set of clinical labels using a Symbol-Concept Association Network (SCAN). We demonstrate that our method is able to outperform the canonical hand-engineered baseline classification method on a number of factors, including participant age and depression diagnosis. Furthermore, our method recovers a representation that can be used to automatically extract denoised Event Related Potentials (ERPs) from novel, single EEG trajectories, and supports fast supervised re-mapping to various clinical labels, allowing clinicians to re-use a single EEG representation regardless of updates to the standardized diagnostic system. Finally, single factors of the learned disentangled representations often correspond to meaningful markers of clinical factors, as automatically detected by SCAN, allowing for human interpretability and post-hoc expert analysis of the recommendations made by the model.

Reading and interpreting chest X-ray images is one of the most radiologist's routines. However, it still can be challenging, even for the most experienced ones. Therefore, we proposed a multi-model deep learning-based automated chest X-ray report generator system designed to assist radiologists in their work. The basic idea of the proposed system is by utilizing multi binary-classification models for detecting multi abnormalities, with each model responsible for detecting one abnormality, in a single image. In this study, we limited the radiology abnormalities detection to only cardiomegaly, lung effusion, and consolidation. The system generates a radiology report by performing the following three steps: image pre-processing, utilizing deep learning models to detect abnormalities, and producing a report. The aim of the image pre-processing step is to standardize the input by scaling it to 128x128 pixels and slicing it into three segments, which covers the upper, lower, and middle parts of the lung. After pre-processing, each corresponding model classifies the image, resulting in a 0 (zero) for no abnormality detected and a 1 (one) for the presence of an abnormality. The prediction outputs of each model are then concatenated to form a 'result code'. The 'result code' is used to construct a report by selecting the appropriate pre-determined sentence for each detected abnormality in the report generation step. The proposed system is expected to reduce the workload of radiologists and increase the accuracy of chest X-ray diagnosis.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

Coronary artery disease (CAD) is a leading cause of cardiovascular-related mortality, and accurate stenosis detection is crucial for effective clinical decision-making. Coronary angiography remains the gold standard for diagnosing CAD, but manual analysis of angiograms is prone to errors and subjectivity. This study aims to develop a deep learning-based approach for the automatic segmentation of coronary arteries from angiographic images and the quantitative detection of stenosis, thereby improving the accuracy and efficiency of CAD diagnosis. We propose a novel deep learning-based method for the automatic segmentation of coronary arteries in angiographic images, coupled with a dynamic cohort method for stenosis detection. The segmentation model combines the MedSAM and VM-UNet architectures to achieve high-performance results. After segmentation, the vascular centerline is extracted, vessel diameter is computed, and the degree of stenosis is measured with high precision, enabling accurate identification of arterial stenosis. On the mixed dataset (including the ARCADE, DCA1, and GH datasets), the model achieved an average IoU of 0.6308, with sensitivity and specificity of 0.9772 and 0.9903, respectively. On the ARCADE dataset, the average IoU was 0.6303, with sensitivity of 0.9832 and specificity of 0.9933. Additionally, the stenosis detection algorithm achieved a true positive rate (TPR) of 0.5867 and a positive predictive value (PPV) of 0.5911, demonstrating the effectiveness of our model in analyzing coronary angiography images. SAM-VMNet offers a promising tool for the automated segmentation and detection of coronary artery stenosis. The model's high accuracy and robustness provide significant clinical value for the early diagnosis and treatment planning of CAD. The code and examples are available at https://github.com/qimingfan10/SAM-VMNet.

Automated red blood cell (RBC) classification on blood smear images helps hematologists to analyze RBC lab results in a reduced time and cost. However, overlapping cells can cause incorrect predicted results, and so they have to be separated into multiple single RBCs before classifying. To classify multiple classes with deep learning, imbalance problems are common in medical imaging because normal samples are always higher than rare disease samples. This paper presents a new method to segment and classify RBCs from blood smear images, specifically to tackle cell overlapping and data imbalance problems. Focusing on overlapping cell separation, our segmentation process first estimates ellipses to represent RBCs. The method detects the concave points and then finds the ellipses using directed ellipse fitting. The accuracy from 20 blood smear images was 0.889. Classification requires balanced training datasets. However, some RBC types are rare. The imbalance ratio of this dataset was 34.538 for 12 RBC classes from 20,875 individual RBC samples. The use of machine learning for RBC classification with an imbalanced dataset is hence more challenging than many other applications. We analyzed techniques to deal with this problem. The best accuracy and F1-score were 0.921 and 0.8679, respectively, using EfficientNet-B1 with augmentation. Experimental results showed that the weight balancing technique with augmentation had the potential to deal with imbalance problems by improving the F1-score on minority classes, while data augmentation significantly improved the overall classification performance.

This study aims to explore the implementation of Natural Language Processing (NLP) and machine learning (ML) techniques to automate the coding of medical letters with visualised explainability and light-weighted local computer settings. Currently in clinical settings, coding is a manual process that involves assigning codes to each condition, procedure, and medication in a patient's paperwork (e.g., 56265001 heart disease using SNOMED CT code). There are preliminary research on automatic coding in this field using state-of-the-art ML models; however, due to the complexity and size of the models, the real-world deployment is not achieved. To further facilitate the possibility of automatic coding practice, we explore some solutions in a local computer setting; in addition, we explore the function of explainability for transparency of AI models. We used the publicly available MIMIC-III database and the HAN/HLAN network models for ICD code prediction purposes. We also experimented with the mapping between ICD and SNOMED CT knowledge bases. In our experiments, the models provided useful information for 97.98\% of codes. The result of this investigation can shed some light on implementing automatic clinical coding in practice, such as in hospital settings, on the local computers used by clinicians , project page https://github.com/Glenj01/Medical-Coding.

Photoplethysmography (PPG) signals, which measure changes in blood volume in the skin using light, have recently gained attention in biometric authentication because of their non-invasive acquisition, inherent liveness detection, and suitability for low-cost wearable devices. However, PPG signal quality is challenged by motion artifacts, illumination changes, and inter-subject physiological variability, making robust feature extraction and classification crucial. This study proposes a lightweight and cost-effective biometric authentication framework based on PPG signals extracted from low-frame-rate fingertip videos. The CFIHSR dataset, comprising PPG recordings from 46 subjects at a sampling rate of 14 Hz, is employed for evaluation. The raw PPG signals undergo a standard preprocessing pipeline involving baseline drift removal, motion artifact suppression using Principal Component Analysis (PCA), bandpass filtering, Fourier-based resampling, and amplitude normalization. To generate robust representations, each one-dimensional PPG segment is converted into a two-dimensional time-frequency scalogram via the Continuous Wavelet Transform (CWT), effectively capturing transient cardiovascular dynamics. We developed a hybrid deep learning model, termed CVT-ConvMixer-LSTM, by combining spatial features from the Convolutional Vision Transformer (CVT) and ConvMixer branches with temporal features from a Long Short-Term Memory network (LSTM). The experimental results on 46 subjects demonstrate an authentication accuracy of 98%, validating the robustness of the model to noise and variability between subjects. Due to its efficiency, scalability, and inherent liveness detection capability, the proposed system is well-suited for real-world mobile and embedded biometric security applications.

Medical image segmentation aims to delineate the anatomical or pathological structures of interest, playing a crucial role in clinical diagnosis. A substantial amount of high-quality annotated data is crucial for constructing high-precision deep segmentation models. However, medical annotation is highly cumbersome and time-consuming, especially for medical videos or 3D volumes, due to the huge labeling space and poor inter-frame consistency. Recently, a fundamental task named Moving Object Segmentation (MOS) has made significant advancements in natural images. Its objective is to delineate moving objects from the background within image sequences, requiring only minimal annotations. In this paper, we propose the first foundation model, named iMOS, for MOS in medical images. Extensive experiments on a large multi-modal medical dataset validate the effectiveness of the proposed iMOS. Specifically, with the annotation of only a small number of images in the sequence, iMOS can achieve satisfactory tracking and segmentation performance of moving objects throughout the entire sequence in bi-directions. We hope that the proposed iMOS can help accelerate the annotation speed of experts, and boost the development of medical foundation models.

Automated surgical instrument localization is an important technology to understand the surgical process and in order to analyze them to provide meaningful guidance during surgery or surgical index after surgery to the surgeon. We introduce a new dataset that reflects the kinematic characteristics of surgical instruments for automated surgical instrument localization of surgical videos. The hSDB(hutom Surgery DataBase)-instrument dataset consists of instrument localization information from 24 cases of laparoscopic cholecystecomy and 24 cases of robotic gastrectomy. Localization information for all instruments is provided in the form of a bounding box for object detection. To handle class imbalance problem between instruments, synthesized instruments modeled in Unity for 3D models are included as training data. Besides, for 3D instrument data, a polygon annotation is provided to enable instance segmentation of the tool. To reflect the kinematic characteristics of all instruments, they are annotated with head and body parts for laparoscopic instruments, and with head, wrist, and body parts for robotic instruments separately. Annotation data of assistive tools (specimen bag, needle, etc.) that are frequently used for surgery are also included. Moreover, we provide statistical information on the hSDB-instrument dataset and the baseline localization performances of the object detection networks trained by the MMDetection library and resulting analyses.

Cardiac Magnetic Resonance (CMR) imaging serves as the gold-standard for evaluating cardiac morphology and function. Typically, a multi-view CMR stack, covering short-axis (SA) and 2/3/4-chamber long-axis (LA) views, is acquired for a thorough cardiac assessment. However, efficiently streamlining the complex, high-dimensional 3D+T CMR data and distilling compact, coherent representation remains a challenge. In this work, we introduce a whole-heart self-supervised learning framework that utilizes masked imaging modeling to automatically uncover the correlations between spatial and temporal patches throughout the cardiac stacks. This process facilitates the generation of meaningful and well-clustered heart representations without relying on the traditionally required, and often costly, labeled data. The learned heart representation can be directly used for various downstream tasks. Furthermore, our method demonstrates remarkable robustness, ensuring consistent representations even when certain CMR planes are missing/flawed. We train our model on 14,000 unlabeled CMR data from UK BioBank and evaluate it on 1,000 annotated data. The proposed method demonstrates superior performance to baselines in tasks that demand comprehensive 3D+T cardiac information, e.g. cardiac phenotype (ejection fraction and ventricle volume) prediction and multi-plane/multi-frame CMR segmentation, highlighting its effectiveness in extracting comprehensive cardiac features that are both anatomically and pathologically relevant.

Training convolutional neural networks (CNNs) for segmentation of pulmonary airway, artery, and vein is challenging due to sparse supervisory signals caused by the severe class imbalance between tubular targets and background. We present a CNNs-based method for accurate airway and artery-vein segmentation in non-contrast computed tomography. It enjoys superior sensitivity to tenuous peripheral bronchioles, arterioles, and venules. The method first uses a feature recalibration module to make the best use of features learned from the neural networks. Spatial information of features is properly integrated to retain relative priority of activated regions, which benefits the subsequent channel-wise recalibration. Then, attention distillation module is introduced to reinforce representation learning of tubular objects. Fine-grained details in high-resolution attention maps are passing down from one layer to its previous layer recursively to enrich context. Anatomy prior of lung context map and distance transform map is designed and incorporated for better artery-vein differentiation capacity. Extensive experiments demonstrated considerable performance gains brought by these components. Compared with state-of-the-art methods, our method extracted much more branches while maintaining competitive overall segmentation performance. Codes and models are available at http://www.pami.sjtu.edu.cn/News/56

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Accurate delineation of anatomical structures in volumetric CT scans is crucial for diagnosis and treatment planning. While AI has advanced automated segmentation, current approaches typically target individual structures, creating a fragmented landscape of incompatible models with varying performance and disparate evaluation protocols. Foundational segmentation models address these limitations by providing a holistic anatomical view through a single model. Yet, robust clinical deployment demands comprehensive training data, which is lacking in existing whole-body approaches, both in terms of data heterogeneity and, more importantly, anatomical coverage. In this work, rather than pursuing incremental optimizations in model architecture, we present CADS, an open-source framework that prioritizes the systematic integration, standardization, and labeling of heterogeneous data sources for whole-body CT segmentation. At its core is a large-scale dataset of 22,022 CT volumes with complete annotations for 167 anatomical structures, representing a significant advancement in both scale and coverage, with 18 times more scans than existing collections and 60% more distinct anatomical targets. Building on this diverse dataset, we develop the CADS-model using established architectures for accessible and automated full-body CT segmentation. Through comprehensive evaluation across 18 public datasets and an independent real-world hospital cohort, we demonstrate advantages over SoTA approaches. Notably, thorough testing of the model's performance in segmentation tasks from radiation oncology validates its direct utility for clinical interventions. By making our large-scale dataset, our segmentation models, and our clinical software tool publicly available, we aim to advance robust AI solutions in radiology and make comprehensive anatomical analysis accessible to clinicians and researchers alike.