Chaojing Duan

William Han, Tony Chen, Chaojing Duan et al. · cmu

ECG-Language Models (ELMs) extend recent progress in Multimodal Large Language Models (MLLMs) to automated ECG interpretation. However, most ELMs follow Vision-Language Model (VLM) designs and depend on pretrained ECG encoders, adding architectural and training complexity. Inspired by encoder-free VLMs, we introduce ELF, an encoder-free ELM that replaces the ECG encoder with a single projection layer trained jointly with the LLM. Across five datasets, ELF matches or exceeds state-of-the-art ELMs that use far more complex encoders and training pipelines. We also test whether adding architectural biases to ELF improves performance and find that the single linear projection remains competitive. Finally, we show that ELF, and potentially other ELMs, often rely more on benchmark artifacts and language priors than ECG-derived information, highlighting limitations in current evaluation practices and ELM design. All data and code is available at https://github.com/willxxy/ECG-Bench.

Jielin Qiu, Jiacheng Zhu, Shiqi Liu et al. · cmu

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.

Xiaoyu Song, William Han, Tony Chen et al. · cmu

Interest in generative Electrocardiogram-Language Models (ELMs) is growing, as they can produce textual responses conditioned on ECG signals and textual queries. Unlike traditional classifiers that output label probabilities, ELMs are more versatile, supporting domain-specific tasks (e.g., waveform analysis, diagnosis, prognosis) as well as general tasks (e.g., open-ended questions, dialogue). Retrieval-Augmented Generation (RAG), widely used in Large Language Models (LLMs) to ground LLM outputs in retrieved knowledge, helps reduce hallucinations and improve natural language generation (NLG). However, despite its promise, no open-source implementation or systematic study of RAG pipeline design for ELMs currently exists. To address this gap, we present the first open-source RAG pipeline for ELMs, along with baselines and ablation studies for NLG. Experiments on three public datasets show that ELMs with RAG consistently improves performance over non-RAG baselines and highlights key ELM design considerations. Our code is available at: https://github.com/willxxy/ECG-Bench.

William Han, Chaojing Duan, Michael A. Rosenberg et al. · cmu

Large Language Models (LLMs) have demonstrated exceptional versatility across domains, including applications to electrocardiograms (ECGs). A growing body of work focuses on generating text from multi-channeled ECG signals and corresponding textual prompts. Existing approaches often involve a two-stage process: pretraining an ECG-specific encoder with a self-supervised learning (SSL) objective, followed by finetuning an LLM for natural language generation (NLG) using encoder-derived features. However, these methods face two key limitations: inefficiency due to multi-stage training and challenges in interpreting encoder-generated features. To overcome these issues, we propose ECG-Byte, an adapted byte pair encoding (BPE) tokenizer pipeline for autoregressive language modeling of ECGs. ECG-Byte compresses and encodes ECG signals into tokens, enabling direct end-to-end LLM training by combining ECG and text tokens. This approach enhances interpretability, as ECG tokens can be directly mapped back to the original signals. Leveraging ECG-Byte, we achieve competitive NLG performance while training 3 times faster and using just 48\% of the data required by traditional two-stage methods.

William Jongwon Han, Diana Gomez, Avi Alok et al. · cmu

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.

William Han, Chaojing Duan, Zhepeng Cen et al. · cmu

Recent advances have increasingly applied large language models (LLMs) to electrocardiogram (ECG) interpretation, giving rise to Electrocardiogram-Language Models (ELMs). Conditioned on an ECG and a textual query, an ELM autoregressively generates a free-form textual response. Unlike traditional classification-based systems, ELMs emulate expert cardiac electrophysiologists by issuing diagnoses, analyzing waveform morphology, identifying contributing factors, and proposing patient-specific action plans. To realize this potential, researchers are curating instruction-tuning datasets that pair ECGs with textual dialogues and are training ELMs on these resources. Yet before scaling ELMs further, there is a fundamental question yet to be explored: What is the most effective ECG input representation? In recent works, three candidate representations have emerged-raw time-series signals, rendered images, and discretized symbolic sequences. We present the first comprehensive benchmark of these modalities across 6 public datasets and 5 evaluation metrics. We find symbolic representations achieve the greatest number of statistically significant wins over both signal and image inputs. We further ablate the LLM backbone, ECG duration, and token budget, and we evaluate robustness to signal perturbations. We hope that our findings offer clear guidance for selecting input representations when developing the next generation of ELMs.

Siheng Chen, Chaojing Duan, Yaoqing Yang et al.

We propose a deep autoencoder with graph topology inference and filtering to achieve compact representations of unorganized 3D point clouds in an unsupervised manner. Many previous works discretize 3D points to voxels and then use lattice-based methods to process and learn 3D spatial information; however, this leads to inevitable discretization errors. In this work, we handle raw 3D points without such compromise. The proposed networks follow the autoencoder framework with a focus on designing the decoder. The encoder adopts similar architectures as in PointNet. The decoder involves three novel modules. The folding module folds a canonical 2D lattice to the underlying surface of a 3D point cloud, achieving coarse reconstruction; the graph-topology-inference module learns a graph topology to represent pairwise relationships between 3D points, pushing the latent code to preserve both coordinates and pairwise relationships of points in 3D point clouds; and the graph-filtering module couples the above two modules, refining the coarse reconstruction through a learnt graph topology to obtain the final reconstruction. The proposed decoder leverages a learnable graph topology to push the codeword to preserve representative features and further improve the unsupervised-learning performance. We further provide theoretical analyses of the proposed architecture. In the experiments, we validate the proposed networks in three tasks, including 3D point cloud reconstruction, visualization, and transfer classification. The experimental results show that (1) the proposed networks outperform the state-of-the-art methods in various tasks; (2) a graph topology can be inferred as auxiliary information without specific supervision on graph topology inference; and (3) graph filtering refines the reconstruction, leading to better performances.

Chaojing Duan, Siheng Chen, Jelena Kovacevic

We present a neural-network-based architecture for 3D point cloud denoising called neural projection denoising (NPD). In our previous work, we proposed a two-stage denoising algorithm, which first estimates reference planes and follows by projecting noisy points to estimated reference planes. Since the estimated reference planes are inevitably noisy, multi-projection is applied to stabilize the denoising performance. NPD algorithm uses a neural network to estimate reference planes for points in noisy point clouds. With more accurate estimations of reference planes, we are able to achieve better denoising performances with only one-time projection. To the best of our knowledge, NPD is the first work to denoise 3D point clouds with deep learning techniques. To conduct the experiments, we sample 40000 point clouds from the 3D data in ShapeNet to train a network and sample 350 point clouds from the 3D data in ModelNet10 to test. Experimental results show that our algorithm can estimate normal vectors of points in noisy point clouds. Comparing to five competitive methods, the proposed algorithm achieves better denoising performance and produces much smaller variances.