Uncertainty-Aware Deep Learning for Genomics Applications: Insights from an Empirical Study

The deployment of deep neural networks in safety-critical domains demands reliable estimates of predictive confidence, yet conventional architectures lack principled uncertainty quantification. This survey provides a structured, critical review of methods for Uncertainty Quantification (UQ) in deep learning, scoped to ensemble-based and approximate Bayesian approaches and the measures used to summarize their outputs. Relative to existing UQ surveys, our contribution is depth on efficient ensemble approximations and single-pass methods, and a unified treatment that separates the method producing a predictive distribution from the measure that summarizes its uncertainty. We organize methods into five families: Bayesian neural networks, Monte Carlo Dropout, deep ensembles, efficient ensemble approximations, and last-layer or single-pass approaches. We situate adjacent work on evidential and prior networks, conformal prediction, and post-hoc calibration, together with the decision-time tasks of out-of-distribution detection and selective prediction. For each, we examine theoretical motivation, implementation, empirical performance, and limitations. We then review ensemble diversity theory and uncertainty measures and their decompositions, contrasting the entropy decomposition with pairwise divergence measures, and consolidate evaluation methodology so that our qualitative comparisons share a common basis. We close with a brief treatment of uncertainty in large language models and open research directions, including efficient epistemic measures for classification, last-layer diversity, diversity and calibration under shift, and hybrid architectures.

Epistemic uncertainty quantification (UQ) for deep neural networks (DNNs) is a requirement for safe adoption of AI in mission-critical settings. Several leading methods for UQ linearize DNNs to form Bayesian Generalized Linear Models (GLMs), where epistemic uncertainty is modeled via the predictive posterior distribution. Linearizing around the parameters of the final connected layer of a DNN is a commonly used approximation for reducing the computational burden of such GLMs, though it is often believed to come at the cost of degraded performance. In this work, we compare GLMs arising from full-network and last-layer linearization using both theoretical and empirical approaches. We first employ tools from random matrix theory to conduct a theoretical comparison; this analysis reveals no meaningful improvement in the UQ capabilities of full linearization. Coupled with a large-scale empirical evaluation across a range of modern machine learning tasks, we arrive at the following conclusion: a last-layer approximation yields comparable UQ performance while offering substantially improved computational efficiency.

Progress in genomic foundation models is difficult to assess due to fragmented benchmarks, incompatible evaluation protocols, and task-specific reporting. As a result, claims of superiority or generality across models are often not directly comparable. We introduce GENEB, a large-scale diagnostic benchmark that evaluates frozen representations from 40 genomic foundation models across 100 tasks spanning 13 functional categories under a unified probing-based protocol, including few-shot regimes. GENEB enables controlled comparison across model scale, architecture, tokenization, and pretraining data while explicitly exposing task-level trade-offs. Our analysis shows that aggregate leaderboards are unstable: model rankings vary sharply across task categories, scale provides only modest and inconsistent gains, and architectural and pretraining alignment frequently outweigh parameter count. These results highlight limitations of current evaluation practices and position GENEB as a reference framework for principled comparison and category-aware model selection in genomic machine learning.