Assessing the Potential of Masked Autoencoder Foundation Models in Predicting Downhole Metrics from Surface Drilling Data

Downhole drilling telemetry presents a fundamental labeling asymmetry: surface sensor data are generated continuously at 1Hz, while labeled downhole measurements are costly, intermittent, and scarce. Current machine learning approaches for downhole metric prediction universally adopt fully supervised training from scratch, which is poorly suited to this data regime. We present the first empirical evaluation of masked autoencoder (MAE) pretraining for downhole drilling metric prediction. Using two publicly available Utah FORGE geothermal wells comprising approximately 3.5 million timesteps of multivariate drilling telemetry, we conduct a systematic full-factorial design space search across 72 MAE configurations and compare them against supervised LSTM and GRU baselines on the task of predicting Total Mud Volume. Results show that the best MAE configuration reduces test mean absolute error by 19.8% relative to the supervised GRU baseline, while trailing the supervised LSTM baseline by 6.4%. Analysis of design dimensions reveals that latent space width is the dominant architectural choice (Pearson $r = -0.59$ with test MAE), while masking ratio has negligible effect, an unexpected finding attributed to high temporal redundancy in 1Hz drilling data. These results establish MAE pretraining as a viable paradigm for drilling analytics and identify the conditions under which it is most beneficial.

Self-supervised learning (SSL) for time-series representation learning is dominated by two paradigms: contrastive methods, which face challenges in constructing positive or negative pairs, and masking-based methods, which disrupt the temporal continuity of time-series signals. Joint-Embedding Predictive Architecture (JEPA) offers a promising alternative by predicting in representation space rather than reconstructing raw inputs. However, existing time-series JEPA variants still rely on masking and therefore inherit its continuity problem. Crop-based Forward JEPA (CF-JEPA) is proposed as an innovative mask-free framework that replaces masking with multi-horizon forward prediction: random crops serve as context views, and short-, mid-, and long-horizon future representations are predicted in the forward temporal direction, directly leveraging the inherent temporal ordering of time-series data as a learning signal. A strong asymmetry is also identified between the online encoder and the exponential moving average (EMA) target encoder, both produced from a single training run: the online encoder develops higher-rank discriminative features, while the EMA target encoder develops smoother, lower-rank temporal features. Exploiting this asymmetry, classification is routed to the online encoder and forecasting or anomaly detection to the EMA target encoder, achieving a 27% reduction in multivariate forecasting mean squared error (MSE) at no additional training cost. Across 126 University of California, Riverside (UCR) and 26 University of East Anglia (UEA) classification datasets, eight electricity transformer temperature forecasting benchmarks, and Key Performance Indicator /Yahoo anomaly detection, CF-JEPA achieves the highest average accuracy and rank on UCR and UEA among self-supervised baselines and ranks second on univariate forecasting and k-nearest neighbors-scored anomaly detection.

Self-supervised foundation models have shown strong promise in medical imaging. However, existing MRI foundation-model studies have primarily emphasized segmentation and dense prediction tasks, while systematic investigation of self-supervised foundation models for MRI-based disease detection remains limited. In this work, we investigate two major self-supervised pretraining paradigms for MRI-based disease detection: reconstruction-based learning via Masked Autoencoders (MAE) and predictive representation learning via Joint Embedding Predictive Architectures (JEPA). We study the role of auxiliary objectives by introducing a novel spectral-domain reconstruction loss for MAE to enhance sensitivity to fine-grained anatomical structure, and by integrating variance--covariance regularization (VCR) within our JEPA framework to encourage decorrelated latent representations. Our models are pretrained on heterogeneous single-contrast MRI volumes in a contrast-agnostic setting, without modality concatenation. Across five downstream disease detection tasks, our results highlight the importance of self-supervised objective design for medical foundation model pretraining, demonstrating that the downstream benefit of each objective is determined by its relevance to the task's structure. Specifically, spectral regularization yields the largest improvements when the downstream discriminative signal is characterized by strong high-frequency anatomical structures, while covariance regularization is most beneficial when discriminative information spans multiple decorrelated feature dimensions. MAE with spectral-domain supervision consistently achieves superior downstream performance for MRI-based disease detection. These findings suggest that self-supervised objectives in medical imaging encode specific biases, and their downstream benefit is fundamentally conditioned on the task's structure.