Beyond Predictive Uncertainty: Reliable Representation Learning with Structural Constraints

Uncertainty estimation in machine learning has traditionally focused on the prediction stage, aiming to quantify confidence in model outputs while treating learned representations as deterministic and reliable by default. In this work, we challenge this implicit assumption and argue that reliability should be regarded as a first-class property of learned representations themselves. We propose a principled framework for reliable representation learning that explicitly models representation-level uncertainty and leverages structural constraints as inductive biases to regularize the space of feasible representations. Our approach introduces uncertainty-aware regularization directly in the representation space, encouraging representations that are not only predictive but also stable, well-calibrated, and robust to noise and structural perturbations. Structural constraints, such as sparsity, relational structure, or feature-group dependencies, are incorporated to define meaningful geometry and reduce spurious variability in learned representations, without assuming fully correct or noise-free structure. Importantly, the proposed framework is independent of specific model architectures and can be integrated with a wide range of representation learning methods.

Robust Machine Learning for Regulatory Sequence Modeling under Biological and Technical Distribution Shifts

Robust machine learning for regulatory genomics is studied under biologically and technically induced distribution shifts. Deep convolutional and attention based models achieve strong in distribution performance on DNA regulatory sequence prediction tasks but are usually evaluated under i.i.d. assumptions, even though real applications involve cell type specific programs, evolutionary turnover, assay protocol changes, and sequencing artifacts. We introduce a robustness framework that combines a mechanistic simulation benchmark with real data analysis on a massively parallel reporter assay (MPRA) dataset to quantify performance degradation, calibration failures, and uncertainty based reliability. In simulation, motif driven regulatory outputs are generated with cell type specific programs, PWM perturbations, GC bias, depth variation, batch effects, and heteroscedastic noise, and CNN, BiLSTM, and transformer models are evaluated. Models remain accurate and reasonably calibrated under mild GC content shifts but show higher error, severe variance miscalibration, and coverage collapse under motif effect rewiring and noise dominated regimes, revealing robustness gaps invisible to standard i.i.d. evaluation. Adding simple biological structural priors motif derived features in simulation and global GC content in MPRA improves in distribution error and yields consistent robustness gains under biologically meaningful genomic shifts, while providing only limited protection against strong assay noise. Uncertainty-aware selective prediction offers an additional safety layer that risk coverage analyses on simulated and MPRA data show that filtering low confidence inputs recovers low risk subsets, including under GC-based out-of-distribution conditions, although reliability gains diminish when noise dominates.