Is Self-Pretraining really useful to improve diagnosis in medical Time Series?

Amos et al. (2024) showed that the accuracy of Transformer models in sequence classification can be significantly improved by first pretraining with a masked token prediction objective without external data or augmentation, a procedure referred to as self-pretraining (SPT). While the primary objective of Amos et al. (2024) was to showcase that Transformers can achieve strong performance on the Long-Range Arena (LRA), their pipeline raises more fundamental questions: How does SPT drive optimization to better solutions? Why can standard supervised training fail in Transformers? To better understand this, we replicate and systematically ablate the findings of Amos et al. (2024). Our ablations suggest that a central bottleneck in the studied settings is not depth or generalization alone, but the ability of label supervision to learn useful query-key Attention patterns from random initialization. With a minimal setup, we identify learning proximity interactions - turning absolute positional encodings into proximity-biased Attention scores - as a key source of the improvements brought by SPT. Finally, in a simplified theoretical setup, we show that label supervision can be locally blind to certain Attention-score directions that are instead detectable through masked reconstruction.

Medical time series, such as electrocardiograms (ECG) and electroencephalograms (EEG), exhibit complex temporal dynamics and structured cross-channel dependencies, posing fundamental challenges for automated analysis. Conventional convolutional and recurrent models struggle to capture long-range dependencies, while Transformer-based approaches incur quadratic complexity and often introduce redundant interactions that are misaligned with the intrinsic structure of physiological signals. To address these limitations, we propose MedMamba, a principle-driven multi-scale bidirectional state space architecture tailored for medical time series classification. Our design is guided by three key inductive biases of physiological signals: spatial centralization, multi-timescale temporal composition, and non-causal contextual dependency. These principles are instantiated through a lightweight channel-mixing module for cross-channel reparameterization, multi-scale convolutional tokenization for temporal decomposition, and bidirectional Mamba blocks for efficient global context modeling with linear complexity. Extensive experiments on six benchmark datasets spanning EEG, ECG, and human activity signals demonstrate that MedMamba consistently outperforms state-of-the-art methods across diverse modalities. Notably, it achieves 85.97% accuracy on PTB and establishes new state-of-the-art performance on the challenging ADFTD dataset (54.72% accuracy and 52.01% F1-score). Strong results on long-sequence benchmarks, such as SleepEDF, further validate its capability in modeling long-range dependencies. Moreover, MedMamba achieves a speedup of 4.6x in inference, highlighting its practicality for real-time clinical deployment. These results suggest that principle-guided state space modeling offers an effective and scalable alternative to Transformer-based approaches for medical time series analysis.

Deep learning techniques have revolutionised medical imaging, improving diagnostic accuracy and enabling both more accurate and earlier disease detection. However, the relationship between pre-training strategies and downstream performance in medical imaging models requires further exploration. Here, we systematically compare convolutional neural networks and transformers, examining various pre-training approaches, including supervised and self-supervised learning, as well as different initialisations and data modalities. Models are evaluated on natural images, chest X-rays, chest CT and retina OCT images, considering the effects of matching pre-training data with target modalities. Our findings indicate that only pre-training on data closely matching the target modality significantly improves downstream performance. While self-supervised learning can outperform supervised methods, its effectiveness varies with context. The study underscores the importance of pre-training strategies to enhance the reliability and effectiveness of deep learning models in medical imaging. By addressing these key factors, our research aims to contribute to the development of more accurate and dependable diagnostic tools, ultimately improving patient outcomes in clinical settings.