On the Role of Inductive Bias in Time-Series Pretraining: A Case Study in Learning Generalizable Representations for Clinical Time Series
Authors: Sharmita Dey, Diego Paez-Granados
Organizations: ETH Zurich, Zurich, Switzerland · Swiss Paraplegic Research, Nottwil
Abstract
Clinical time-series learning is routinely constrained by small, heterogeneous cohorts and protocol drift, while its downstream use spans both classification (e.g., pathology diagnosis) and regression (e.g., temporal forecasting). These constraints make foundation-model pretraining appealing, but raises an important question of which inductive biases should the pretraining objective impose so that representations transfer across task types and subjects. We study this question in pathological gait analysis for spinal cord injury (SCI) via PathoFM, an encoder-centric transformer pretrained on multivariate gait windows with three complementary objectives: Local Completion (reconstruct contiguous masked spans to enforce local structure), Temporal Continuity (predict a masked mid-horizon continuation from an observed prefix to enforce smoothness and causal consistency), and Unsupervised In-Context Dynamics (support-query reconstruction conditioned on subject exemplar windows via attention). Empirically comparing objective families (grouping/contrastive, dynamics-based, and generative reconstruction), we find that dynamics-centric mixtures produce the most balanced transfer: grouping objectives favor discriminative margins but can degrade magnitude fidelity needed for continuous targets, whereas reconstruction-only objectives preserve waveform structure but may underperform on classification. Overall, combining local reconstruction with temporal continuity, and adding in-context conditioning when exemplar access is realistic, yields robust subject-generalizing representations.
Inspired by recent evidence that transformer architectures benefit from Self-PreTraining (SPT) on long-context benchmarks, we investigate whether similar gains extend to multimodal, multivariate, and even simple univariate medical time series. Our objective is to assess the impact of SPT on the performance and scalability of transformer-based models across diverse medical applications, particularly under limited data conditions. We evaluate transformer architectures on three representative medical time-series tasks: rehabilitation robotics (Camargo dataset), stress detection (Non-EEG Stress), and Parkinson's disease detection (Gait Parkinson's Disease). Models are trained either from scratch or through SPT using four masking-based objectives designed to promote temporal and cross-modal representation learning, and we systematically vary model depth to examine how capacity interacts with pre-training benefits. Across datasets and configurations, SPT consistently improves classification accuracy by 0-6 percentage points depending on masking strategy, dataset and architecture, with gains observed not only in multivariate settings but also when models are restricted to simple univariate inputs. The improvements increase for deeper models that can better exploit the enriched temporal representations learned during pre-training. These findings indicate that SPT is a simple and general strategy that enhances transformer performance on medical time-series tasks without requiring task-specific architectural changes, supporting its potential to improve robustness and accuracy in data-limited clinical settings.
Cross-subject generalization in biomedical time-series refers to training on data from some subjects and testing on unseen subjects.The key challenge is to suppress subject specific variability in BTS representations.Most existing methods implicitly suppress the variability through model building or subject adversarial learning, but rarely model it explicitly.We introduce spectral drift as a new perspective to characterize subject specific variability.Specifically, BTS signals under the same label often share consistent oscillatory structure, yet exhibit subject-dependent magnitude or phase shifts in specific frequency components, which we interpret as subject-specific variability. Building on this insight, we propose BioFormer.At its core is a Frequency-Band Alignment Module(FBAM) that generates band-wise modulation factors from the spectral distribution and adaptively adjusts amplitude and phase to align spectral structure, thereby mitigating variability.We further pair FBAM with Sample Conditional Layer Normalization, which infers normalization parameters from intrinsic signal statistics rather than subject identity, stabilizing cross-subject representations.Extensive experiments on six datasets demonstrate that BioFormer outperforms 12 baselines, yielding absolute F1-score improvements of 6%.
Time series foundation models (TSFMs) have advanced primarily through architectural innovation, while training regimes for large-scale heterogeneous corpora remain under-explored. As a result, pre-training distributions are often poorly controlled with respect to domain imbalance, context requirements, prediction horizons, and missingness. We introduce ORBIT (Omni-Range Bootstrap Incremental Training), a training paradigm that makes this distribution explicit and controllable. ORBIT combines Bootstrap Multi-Level Sampling, which controls dataset exposure and samples records, target variables, context windows, and prediction horizons, with Omni-Range Incremental Training, which varies context lengths and prediction horizons throughout a single training stage. Under ORBIT, we train Falcon-2.0, a simple univariate encoder-only Transformer with missingness-aware triple-channel patch tokenization and parallel patch prediction. We further introduce Rank-Guided Cross-Depth Alignment, a training objective that uses late-layer representations as stop-gradient teachers for shallow layers without additional inference cost. Evaluations on GIFT-Eval and fev-bench demonstrate strong zero-shot forecasting performance across diverse domains and frequencies.