# SPOTR: Spatio-temporal Pooling One-Token Reconstruction for Universal Physiological Signal Self-supervised Learning

arXiv: https://arxiv.org/abs/2606.21973 · HTML: https://mlsanity.com/paper/2606.21973/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 56 references that are in the map.
- First posted on arXiv 20 Jun 2026.

## Builds on (most cited first, 17 of 17)

- [Masked Autoencoders Are Scalable Vision Learners](https://mlsanity.com/paper/2111.06377/) (2021)
- [MOMENT: A Family of Open Time-series Foundation Models](https://mlsanity.com/paper/2402.03885/) (2024)
- [Large Brain Model for Learning Generic Representations with Tremendous EEG Data in BCI](https://mlsanity.com/paper/2405.18765/) (2024)
- [CBraMod: A Criss-Cross Brain Foundation Model for EEG Decoding](https://mlsanity.com/paper/2412.07236/) (2024)
- [Guiding Masked Representation Learning to Capture Spatio-Temporal Relationship of Electrocardiogram](https://mlsanity.com/paper/2402.09450/) (2024)
- [Diffusion Models as Masked Autoencoders](https://mlsanity.com/paper/2304.03283/) (2023)
- [PaPaGei: Open Foundation Models for Optical Physiological Signals](https://mlsanity.com/paper/2410.20542/) (2024)
- [Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement](https://mlsanity.com/paper/2403.06659/) (2024)
- [CSBrain: A Cross-scale Spatiotemporal Brain Foundation Model for EEG Decoding](https://mlsanity.com/paper/2506.23075/) (2025)
- [SleepFM: Multi-modal Representation Learning for Sleep Across Brain Activity, ECG and Respiratory Signals](https://mlsanity.com/paper/2405.17766/) (2024)
- [Pulse-PPG: An Open-Source Field-Trained PPG Foundation Model for Wearable Applications Across Lab and Field Settings](https://mlsanity.com/paper/2502.01108/) (2025)
- [Reading Your Heart: Learning ECG Words and Sentences via Pre-training ECG Language Model](https://mlsanity.com/paper/2502.10707/) (2025)
- [CL-MAE: Curriculum-Learned Masked Autoencoders](https://mlsanity.com/paper/2308.16572/) (2023)
- [MedGNN: Towards Multi-resolution Spatiotemporal Graph Learning for Medical Time Series Classification](https://mlsanity.com/paper/2502.04515/) (2025)
- [Scaling convolutional neural networks achieves expert-level seizure detection in neonatal EEG](https://mlsanity.com/paper/2405.09911/) (2024)
- [Dynamic Prototype Rehearsal for Continual ECG Arrhythmia Detection](https://mlsanity.com/paper/2501.07555/) (2025)
- [Longitudinal Wrist PPG Analysis for Reliable Hypertension Risk Screening Using Deep Learning](https://mlsanity.com/paper/2411.11863/) (2024)

## Abstract (arXiv)

Physiological signals such as EEG, ECG, and PPG are widely used in clinical monitoring. Recent self-supervised learning (SSL) methods offer an attractive way to leverage unlabeled recordings, yet they still fall short in practice. In particular, current SSL methods struggle across heterogeneous datasets, often distorting clinically meaningful structures or learning shortcuts from temporal and cross-channel redundancy. Consequently, existing SSL methods often deliver limited performance under linear probing, a lightweight adaptation setting that better matches real-world medical scenarios. Moreover, most Transformer-based SSL models encode a flattened spatiotemporal token sequence, incurring high computation and memory cost, and are typically developed within a single modality. To address these limitations, we present SPOTR (Spatio-temporal Pooling One-Token Reconstruction), a compress-reconstruct pretraining framework that introduces a single-token global bottleneck for physiological signals. SPOTR compresses each waveform into a single-token representation and reconstructs the signal conditioned only on this representation. Meanwhile, SPOTR introduces an efficient spatio-temporal compaction module to reduce computation and memory cost. Pretrained on 20 datasets spanning EEG, iEEG, ECG, and PPG, SPOTR consistently outperforms the strongest baseline under linear probing, improving average AUC by 18.49%, 21.71%, 17.86%, and 4.64%, respectively. Compared with a representative general-purpose time-series foundation model, SPOTR achieves around 78% lower latency and 52% lower peak GPU memory on average. The code can be found at https://github.com/5GYYYYY/SPOTR.