Simon A. Lee

Hao Zhou, Simon A. Lee, Cyrus Tanade et al.

Biosignals acquired from different locations on the body often provide temporally ordered views of the same underlying physiological process. However, most existing self supervised learning methods treat these signals as interchangeable views, overlooking the directional temporal dynamics that link them. A canonical example is the relationship between electrocardiography (ECG), which captures the electrical activation initiating each heartbeat, and photoplethysmography (PPG), which records the resulting peripheral pulse delayed by vascular dynamics. To capture this structured relationship, we introduce xMAE, a biosignal pretraining framework that leverages masked cross modal reconstruction across temporally ordered biosignals as a training time constraint to encourage physiologically meaningful timing structure in the learned representations. We show that pretraining with xMAE yields representations that outperform both unimodal and multimodal baselines on 15 of 19 downstream tasks, including cardiovascular outcome prediction, abnormal laboratory test detection, sleep staging, and demographic inference, while generalizing across devices, body locations, and acquisition settings. Further analysis suggests that the ECG PPG timing structure is reflected in the learned PPG representations. More broadly, xMAE demonstrates the effectiveness of incorporating temporal structure into multimodal pretraining when signals observe different stages of a shared underlying process. Code is available at https://github.com/hzhou3/xMAE.

Zechen Li, Keerthana Natarajan, Weizhi Zhang et al.

Continuous glucose monitoring (CGM) provides a dense view of daily metabolic physiology, yet existing generic time-series and CGM-specific foundation models often encode glucose traces as entangled single-stream sequences, leaving the distinct temporal structure of glycemic dynamics only implicitly modeled. We present GlucoFM, a lightweight CGM foundation model that aligns irregular recordings to a 24-hour chronological grid, preserves observation masks, and decomposes glucose dynamics into slow physiological state and transient event streams, capturing low-frequency glycemic baselines and short-term deviations that may reflect acute physiological responses or sensor artifacts. GlucoFM is pretrained on 109,066 hours of unlabeled CGM recordings from 477 subjects with two complementary objectives: masked contextual latent prediction over fused daily representations and temporal dynamics prediction over state and event streams. Across four diverse cohorts and seven clinical prediction tasks, GlucoFM achieves the strongest subject-disjoint linear-probing performance among evaluated baselines, improving average PR-AUC by 4.1 points over the best CGM-specific foundation model. Its gains are most pronounced on core metabolic outcomes, leading PR-AUC on all diabetes-risk and $β$-cell dysfunction tasks and on 3 of 4 insulin-resistance tasks. GlucoFM also achieves the best overall cross-dataset transfer performance and strong few-shot adaptation among evaluated methods, and consistent gains when aggregating multiple days for subject-level prediction, highlighting physiology-aware decomposition as an effective inductive bias for transferable CGM representation learning.

Simon A. Lee, Sujay Jain, Alex Chen et al.

In this work, we introduce the Multiple Embedding Model for EHR (MEME), an approach that serializes multimodal EHR tabular data into text using pseudo-notes, mimicking clinical text generation. This conversion not only preserves better representations of categorical data and learns contexts but also enables the effective employment of pretrained foundation models for rich feature representation. To address potential issues with context length, our framework encodes embeddings for each EHR modality separately. We demonstrate the effectiveness of MEME by applying it to several decision support tasks within the Emergency Department across multiple hospital systems. Our findings indicate that MEME outperforms traditional machine learning, EHR-specific foundation models, and general LLMs, highlighting its potential as a general and extendible EHR representation strategy.

Simon A. Lee, Timothy Lindsey

Large Language Models (LLMs) have become a pivotal research area, potentially making beneficial contributions in fields like healthcare where they can streamline automated billing and decision support. However, the frequent use of specialized coded languages like ICD-10, which are regularly updated and deviate from natural language formats, presents potential challenges for LLMs in creating accurate and meaningful latent representations. This raises concerns among healthcare professionals about potential inaccuracies or ``hallucinations" that could result in the direct impact of a patient. Therefore, this study evaluates whether large language models (LLMs) are aware of medical code ontologies and can accurately generate names from these codes. We assess the capabilities and limitations of both general and biomedical-specific generative models, such as GPT, LLaMA-2, and Meditron, focusing on their proficiency with domain-specific terminologies. While the results indicate that LLMs struggle with coded language, we offer insights on how to adapt these models to reason more effectively.

Simon A. Lee, Anthony Wu, Jeffrey N. Chiang

We introduce Clinical ModernBERT, a transformer based encoder pretrained on large scale biomedical literature, clinical notes, and medical ontologies, incorporating PubMed abstracts, MIMIC IV clinical data, and medical codes with their textual descriptions. Building on ModernBERT the current state of the art natural language text encoder featuring architectural upgrades such as rotary positional embeddings (RoPE), Flash Attention, and extended context length up to 8,192 tokens our model adapts these innovations specifically for biomedical and clinical domains. Clinical ModernBERT excels at producing semantically rich representations tailored for long context tasks. We validate this both by analyzing its pretrained weights and through empirical evaluation on a comprehensive suite of clinical NLP benchmarks.

Simon A. Lee, John Lee, Jeffrey N. Chiang

In this study, we introduce FEET, a standardized protocol designed to guide the development and benchmarking of foundation models. While numerous benchmark datasets exist for evaluating these models, we propose a structured evaluation protocol across three distinct scenarios to gain a comprehensive understanding of their practical performance. We define three primary use cases: frozen embeddings, few-shot embeddings, and fully fine-tuned embeddings. Each scenario is detailed and illustrated through two case studies: one in sentiment analysis and another in the medical domain, demonstrating how these evaluations provide a thorough assessment of foundation models' effectiveness in research applications. We recommend this protocol as a standard for future research aimed at advancing representation learning models.

Ulzee An, Moonseong Jeong, Simon A. Lee et al.

Current challenges in developing foundational models for volumetric imaging data, such as magnetic resonance imaging (MRI), stem from the computational complexity of training state-of-the-art architectures in high dimensions and curating sufficiently large datasets of volumes. To address these challenges, we introduce Raptor (Random Planar Tensor Reduction), a train-free method for generating semantically rich embeddings for volumetric data. Raptor leverages a frozen 2D foundation model, pretrained on natural images, to extract visual tokens from individual cross-sections of medical volumes. These tokens are then spatially compressed using random projections, significantly reducing computational complexity while retaining semantic information. Extensive experiments on ten diverse medical volume tasks verify the superior performance of Raptor over state-of-the-art methods, including those pretrained exclusively on medical volumes (+3% SuPreM, +6% MISFM, +10% Merlin, +13% VoCo, and +14% SLIViT), while entirely bypassing the need for costly training. Our results highlight the effectiveness and versatility of Raptor as a foundation for advancing deep learning-based methods for medical volumes.

Simon A. Lee, Cyrus Tanade, Hao Zhou et al.

Wearable sensors provide abundant physiological time series, yet the principles governing their predictive utility remain unclear. We hypothesize that temporal resolution is a fundamental axis of representation learning, with different clinical and behavioral outcomes relying on structure at distinct scales. To test this resolution hypothesis, we introduce HiMAE (Hierarchical Masked Autoencoder), a self supervised framework that combines masked autoencoding with a hierarchical convolutional encoder decoder. HiMAE produces multi resolution embeddings that enable systematic evaluation of which temporal scales carry predictive signal, transforming resolution from a hyperparameter into a probe for interpretability. Across classification, regression, and generative benchmarks, HiMAE consistently outperforms state of the art foundation models that collapse scale, while being orders of magnitude smaller. HiMAE is an efficient representation learner compact enough to run entirely on watch, achieving sub millisecond inference on smartwatch class CPUs for true edge inference. Together, these contributions position HiMAE as both an efficient self supervised learning method and a discovery tool for scale sensitive structure in wearable health.

Kyoka Ono, Simon A. Lee

Recent research has explored how Language Models (LMs) can be used for feature representation and prediction in tabular machine learning tasks. This involves employing text serialization and supervised fine-tuning (SFT) techniques. Despite the simplicity of these techniques, significant gaps remain in our understanding of the applicability and reliability of LMs in this context. Our study assesses how emerging LM technologies compare with traditional paradigms in tabular machine learning and evaluates the feasibility of adopting similar approaches with these advanced technologies. At the data level, we investigate various methods of data representation and curation of serialized tabular data, exploring their impact on prediction performance. At the classification level, we examine whether text serialization combined with LMs enhances performance on tabular datasets (e.g. class imbalance, distribution shift, biases, and high dimensionality), and assess whether this method represents a state-of-the-art (SOTA) approach for addressing tabular machine learning challenges. Our findings reveal current pre-trained models should not replace conventional approaches.