Liangyu Wu, Qibin Liu, Alexander Yue +1cs.LG hep-ph
We present a lightweight approach to foundation modeling (\textbf{NEXUS}) that leverages pre-trained learning from collider physics data towards out-of-domain tasks in other scientific datasets, using a fully connected autoencoder model with approximately 3 million parameters. The model pre-trains with no supervision over a large-scale collision dataset from the Large Hadron Collider modeled by charged particle track features. Downstream tasks for collider analyses, such as kinematic regression and event classification, are developed on pre-trained model weights and achieve improved accuracy with only small labeled datasets when compared to equivalent architectures trained from scratch. The benefits of pre-training are additionally investigated through latent space interpretation and application to other domains, including gravitational waves, flood forecasting, and neural activity. Furthermore, the relative computational simplicity of NEXUS is demonstrated compared to transformer approaches at comparable scale, opening the door to power-efficient inference and real-time or edge applications of foundation models in scientific experiments.
Post-hoc explanation methods are routinely used to interpret scientific machine learning models, with the deliverable understood to be insight into the phenomenon the model has been trained on. The transition may be taken to be secured once the model is reliable enough and the explanation faithful enough. We argue it is not. Reliability checks that the model's predictions match the phenomenon's outcomes, and faithfulness checks that the explanation matches the model, but neither checks whether the model works as the phenomenon works, which is what a claim about structure requires. The chain can support candidate hypotheses under external corroboration, but it cannot, on its own, support claims about how the phenomenon is in fact structured.
Scientific machine-learning (SciML) surrogates approximate expensive simulations, but exact expected outputs for arbitrary inputs are unavailable (the oracle problem). Metamorphic testing checks relations across executions, yet a candidate relation is not automatically valid: its preconditions, output mapping, and the numerical floor of the scoring operator determine whether a violation is meaningful. We study how candidate metamorphic relations (MRs) can be screened for domain validity and turned into executable, oracle-free test assets for SciML surrogates. We propose (i) a domain-validity rubric that admits a candidate only when its tolerance dominates the operator's numerical floor and its preconditions hold; (ii) an MR-card executable-asset format recording source cases, transformations, metrics, tolerances, and typed relation-level verdicts; and (iii) a case-study protocol on MeshGraphNets cylinder-flow surrogates, with a claim ledger binding every result to a tracked artifact. On a MeshGraphNets checkpoint, node permutation holds to machine precision, mirror-y is a bounded out-of-distribution stress finding rather than an exact symmetry, and absolute conservation stays deferred while a reference-relative guard passes. The same readings hold across held-out trajectories, a checkpoint roster, three further architectures, and PhysicsNeMo. On a second CFD task (compressible airfoil) the predicate instead rejects incompressible continuity on physical grounds, showing it reasons about domain validity rather than running a fixed checklist. On a second PDE family, FNO Burgers and heat surrogates run full admit/reject/execute verdicts. The evidence spans two CFD tasks and a second PDE family, supporting a validity-aware bridge from candidate MRs to auditable SciML test assets that separates model-level violations from out-of-domain applications.
Small-to-medium scientific datasets place machine learning pipelines under two compounding pressures. Single-run feature selection produces feature sets that change substantially under small perturbations of the training data, and any procedure that uses the same data for selection, tuning, and evaluation produces optimistically biased performance estimates. The two failure modes are routinely treated as separable, but in the regimes where scientific data live, they interact: an unstable selection inflates the variance of an already-optimistic score, and standard remedies for one rarely address the other. RobustModelMaker is a Python framework that couples bootstrap stability selection with strict nested cross-validation, performs all preprocessing and selection inside each fold, and produces a stability-tested feature subset together with a leakage-safe performance estimate. The framework supports nine algorithms across binary classification, multiclass classification, and regression. Behaviour is verified by a deterministic test suite spanning unit, performance, and reproducibility checks on three real scientific datasets comparing to three alternative selectors (ANOVA F-test, recursive feature elimination with cross-validation, and Boruta) on both predictive score and a Jaccard measure of selection stability. RobustModelMaker is competitive in score with the best alternative selector on each dataset, and occupies a position on the joint score-stability frontier that none of the alternatives match across all three task types. Two example applications, ovarian cancer biomarker discovery from the PLCO Trial and critical-temperature regression on the UCI Superconductivity Data, illustrate how the framework is used in practice and what trade-offs become visible when stability is treated as a first-class deliverable rather than an emergent property.