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.

To address this, we propose Cross-environment Intra-class Alignment (CIA), which explicitly eliminates spurious features by aligning cross-environment representations conditioned on the same class, bypassing the need for explicit knowledge of the causal pattern structure.

Tropical Cyclone (TC) estimation aims to accurately estimate various TC attributes in real time. However, distribution shifts arising from the complex and dynamic nature of TC environmental fields, such as varying geographical conditions and seasonal changes, present significant challenges to reliable estimation. Most existing methods rely on multi-modal fusion for feature extraction but overlook the intrinsic distribution of feature representations, leading to poor generalization under out-of-distribution (OOD) scenarios. To address this, we propose an effective Identity Distribution-Oriented Physical Invariant Learning framework (IDOL), which imposes identity-oriented constraints to regulate the feature space under the guidance of prior physical knowledge, thereby dealing distribution variability with physical invariance. Specifically, the proposed IDOL employs the wind field model and dark correlation knowledge of TC to model task-shared and task-specific identity tokens. These tokens capture task dependencies and intrinsic physical invariances of TC, enabling robust estimation of TC wind speed, pressure, inner-core, and outer-core size under distribution shifts. Extensive experiments conducted on multiple datasets and tasks demonstrate the outperformance of the proposed IDOL, verifying that imposing identity-oriented constraints based on prior physical knowledge can effectively mitigates diverse distribution shifts in TC estimation.Code is available at https://github.com/Zjut-MultimediaPlus/IDOL.

Federated Learning (FL) enables decentralized, privacy-preserving model training but struggles to balance global generalization and local personalization due to non-identical data distributions across clients. Personalized Fine-Tuning (PFT), a popular post-hoc solution, fine-tunes the final global model locally but often overfits to skewed client distributions or fails under domain shifts. We propose adapting Linear Probing followed by full Fine-Tuning (LP-FT), a principled centralized strategy for alleviating feature distortion (Kumar et al., 2022), to the FL setting. Through systematic evaluation across seven datasets and six PFT variants, we demonstrate LP-FT's superiority in balancing personalization and generalization. Our analysis uncovers federated feature distortion, a phenomenon where local fine-tuning destabilizes globally learned features, and theoretically characterizes how LP-FT mitigates this via phased parameter updates. We further establish conditions (e.g., partial feature overlap, covariate-concept shift) under which LP-FT outperforms standard fine-tuning, offering actionable guidelines for deploying robust personalization in FL.

One of the most common assumptions for machine learning models is that the training and test data are independently and identically sampled (IID) from the same distribution. In practice, this assumption does not hold in many practical scenarios (Bengio et al., 2020).

GOOD provides 11 datasets with 17 domain selections. For covariate shift splits, given a domain selection, we sort the graphs/nodes by their domains and divide the data into a certain number of domains by specifying the split ratio. Consequently, to build a specific concept, each graph has a domain-label probability to be included in this concept. Therefore, we build each concept by scanning the whole dataset and selecting graphs to be included according to their probabilities. Similarly, in node classification tasks, we apply the screening process to nodes instead of graphs.

Out-of-distribution (OOD) learning deals with scenarios in which training and test data follow different distributions.

To address this, we propose Cross-environment Intra-class Alignment (CIA), which explicitly eliminates spurious features by aligning cross-environment representations conditioned on the same class, bypassing the need for explicit knowledge of the causal pattern structure.

One of the most common assumptions for machine learning models is that the training and test data are independently and identically sampled (IID) from the same distribution. In practice, this assumption does not hold in many practical scenarios (Bengio et al., 2020).