Pulse-PPG: An Open-Source Field-Trained PPG Foundation Model for Wearable Applications Across Lab and Field Settings

Photoplethysmography (PPG)-based foundation models are gaining traction due to the widespread use of PPG in biosignal monitoring and their potential to generalize across diverse health applications. In this paper, we introduce Pulse-PPG, the first open-source PPG foundation model trained exclusively on raw PPG data collected over a 100-day field study with 120 participants. Existing PPG foundation models are either open-source but trained on clinical data or closed-source, limiting their applicability in real-world settings. We evaluate Pulse-PPG across multiple datasets and downstream tasks, comparing its performance against a state-of-the-art foundation model trained on clinical data. Our results demonstrate that Pulse-PPG, trained on uncurated field data, exhibits superior generalization across clinical and mobile health applications in both lab and field settings. This suggests that exposure to real-world variability enables the model to learn fine-grained representations, making it more adaptable across tasks. Furthermore, pre-training on field data surprisingly outperforms its pre-training on clinical data in many tasks, reinforcing the importance of training on real-world, diverse datasets. To encourage further advancements in robust foundation models leveraging field data, we plan to release Pulse-PPG, providing researchers with a powerful resource for developing more generalizable PPG-based models.

PyPulse: A Python Library for Biosignal Imputation

We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data transmission loss. PyPulse's framework provides a modular and extendable framework with high ease-of-use for a broad userbase, including non-machine-learning bioresearchers. Specifically, its new capabilities include using pre-trained imputation methods out-of-the-box on custom datasets, running the full workflow of training or testing a baseline method with a single line of code, and comparing baseline methods in an interactive visualization tool. We released PyPulse under the MIT License on Github and PyPI. The source code can be found at: https://github.com/rehg-lab/pulseimpute.

RelCon: Relative Contrastive Learning for a Motion Foundation Model for Wearable Data

We present RelCon, a novel self-supervised \textit{Rel}ative \textit{Con}trastive learning approach that uses a learnable distance measure in combination with a softened contrastive loss for training an motion foundation model from wearable sensors. The learnable distance measure captures motif similarity and domain-specific semantic information such as rotation invariance. The learned distance provides a measurement of semantic similarity between a pair of accelerometer time-series segments, which is used to measure the distance between an anchor and various other sampled candidate segments. The self-supervised model is trained on 1 billion segments from 87,376 participants from a large wearables dataset. The model achieves strong performance across multiple downstream tasks, encompassing both classification and regression. To our knowledge, we are the first to show the generalizability of a self-supervised learning model with motion data from wearables across distinct evaluation tasks.

Towards Time Series Reasoning with LLMs

Multi-modal large language models (MLLMs) have enabled numerous advances in understanding and reasoning in domains like vision, but we have not yet seen this broad success for time-series. Although prior works on time-series MLLMs have shown promising performance in time-series forecasting, very few works show how an LLM could be used for time-series reasoning in natural language. We propose a novel multi-modal time-series LLM approach that learns generalizable information across various domains with powerful zero-shot performance. First, we train a lightweight time-series encoder on top of an LLM to directly extract time-series information. Then, we fine-tune our model with chain-of-thought augmented time-series tasks to encourage the model to generate reasoning paths. We show that our model learns a latent representation that reflects specific time-series features (e.g. slope, frequency), as well as outperforming GPT-4o on a set of zero-shot reasoning tasks on a variety of domains.

Temporally Multi-Scale Sparse Self-Attention for Physical Activity Data Imputation

Wearable sensors enable health researchers to continuously collect data pertaining to the physiological state of individuals in real-world settings. However, such data can be subject to extensive missingness due to a complex combination of factors. In this work, we study the problem of imputation of missing step count data, one of the most ubiquitous forms of wearable sensor data. We construct a novel and large scale data set consisting of a training set with over 3 million hourly step count observations and a test set with over 2.5 million hourly step count observations. We propose a domain knowledge-informed sparse self-attention model for this task that captures the temporal multi-scale nature of step-count data. We assess the performance of the model relative to baselines and conduct ablation studies to verify our specific model designs.

Retrieval-Based Reconstruction For Time-series Contrastive Learning

The success of self-supervised contrastive learning hinges on identifying positive data pairs that, when pushed together in embedding space, encode useful information for subsequent downstream tasks. However, in time-series, this is challenging because creating positive pairs via augmentations may break the original semantic meaning. We hypothesize that if we can retrieve information from one subsequence to successfully reconstruct another subsequence, then they should form a positive pair. Harnessing this intuition, we introduce our novel approach: REtrieval-BAsed Reconstruction (REBAR) contrastive learning. First, we utilize a convolutional cross-attention architecture to calculate the REBAR error between two different time-series. Then, through validation experiments, we show that the REBAR error is a predictor of mutual class membership, justifying its usage as a positive/negative labeler. Finally, once integrated into a contrastive learning framework, our REBAR method can learn an embedding that achieves state-of-the-art performance on downstream tasks across various modalities.

PulseImpute: A Novel Benchmark Task for Pulsative Physiological Signal Imputation

The promise of Mobile Health (mHealth) is the ability to use wearable sensors to monitor participant physiology at high frequencies during daily life to enable temporally-precise health interventions. However, a major challenge is frequent missing data. Despite a rich imputation literature, existing techniques are ineffective for the pulsative signals which comprise many mHealth applications, and a lack of available datasets has stymied progress. We address this gap with PulseImpute, the first large-scale pulsative signal imputation challenge which includes realistic mHealth missingness models, an extensive set of baselines, and clinically-relevant downstream tasks. Our baseline models include a novel transformer-based architecture designed to exploit the structure of pulsative signals. We hope that PulseImpute will enable the ML community to tackle this significant and challenging task.

Efficient Learning and Decoding of the Continuous-Time Hidden Markov Model for Disease Progression Modeling

The Continuous-Time Hidden Markov Model (CT-HMM) is an attractive approach to modeling disease progression due to its ability to describe noisy observations arriving irregularly in time. However, the lack of an efficient parameter learning algorithm for CT-HMM restricts its use to very small models or requires unrealistic constraints on the state transitions. In this paper, we present the first complete characterization of efficient EM-based learning methods for CT-HMM models, as well as the first solution to decoding the optimal state transition sequence and the corresponding state dwelling time. We show that EM-based learning consists of two challenges: the estimation of posterior state probabilities and the computation of end-state conditioned statistics. We solve the first challenge by reformulating the estimation problem as an equivalent discrete time-inhomogeneous hidden Markov model. The second challenge is addressed by adapting three distinct approaches from the continuous time Markov chain (CTMC) literature to the CT-HMM domain. Additionally, we further improve the efficiency of the most efficient method by a factor of the number of states. Then, for decoding, we incorporate a state-of-the-art method from the (CTMC) literature, and extend the end-state conditioned optimal state sequence decoding to the CT-HMM case with the computation of the expected state dwelling time. We demonstrate the use of CT-HMMs with more than 100 states to visualize and predict disease progression using a glaucoma dataset and an Alzheimer's disease dataset, and to decode and visualize the most probable state transition trajectory for individuals on the glaucoma dataset, which helps to identify progressing phenotypes in a comprehensive way. Finally, we apply the CT-HMM modeling and decoding strategy to investigate the progression of language acquisition and development.