Decodable but Not Accessible: Auditing Distance-Based Reliability Estimation on Disentangled Skin-Lesion Representations

Pretrained molecular encoders are commonly evaluated through downstream prediction, but predictive accuracy alone does not establish that a learned representation captures reproducible scientific structure, adds information beyond strong conventional baselines, or transfers out of distribution. We present a reliability-aware audit of generic molecular representations for human olfaction across four distinct claims: global perceptual geometry, incremental predictive value beyond chemistry, cross-dataset replication, and mixture transfer to unseen components. Using the Keller-Vosshall and Bierling single-molecule rating datasets and the Ma binary-mixture dataset, we compare MoLFormer and ChemBERTa against RDKit descriptors and Morgan fingerprints under identity-controlled and matched evaluations. Human three-attribute rating geometry, based on intensity, pleasantness, and familiarity, is reproducible across participant splits (median RSA 0.743 and 0.855), whereas model-human alignment is substantially weaker (RSA 0.019-0.158). Learned embeddings do not consistently outperform conventional representations in global alignment, and MoLFormer provides no clear incremental predictive value beyond a combined RDKit-Morgan baseline in either single-molecule dataset. Human geometry shows positive but incomplete agreement across 63 shared molecules (RSA 0.331; 95% bootstrap interval [0.204, 0.507]). Under one strict unseen-component mixture split, incremental effects are outcome- and representation-dependent, with all intervals crossing zero. These results establish empirical boundaries for the evaluated generic molecular encoders and motivate a broader evaluation principle: representation quality in scientific domains should be assessed separately for target reliability, structural alignment, incremental information, replication, and out-of-distribution transfer.

Class disentanglement (the separation of a representation's class-conditional point clouds along depth and over training) is usually read off descriptive curves. We measure it as certified topological interaction between labeled point clouds, using the recently introduced Intersection Euler Characteristic Profile: the Euler characteristic of the overlap of the clouds' ball unions as a function of scale, computed by one Alpha-complex sweep with no boundary-matrix reduction. Every number carries a test: exact permutation tests in both directions, a guarded separation certificate, and a paired test for the comparative claims applications make. Across 111 trained networks and 52,650 certified measurements, disentanglement is depth-graded and concentrated in the first epochs, and interaction quotients rank class pairs by confusability (Spearman rho=0.83), on par with cheap separability statistics. In a 96-model factorial population, augmentation is the one training choice that separates classes relative to chance; weight decay compresses the overlap without separating, and depth and width do nothing. The structural finding is one only a k-fold statistic can pose: the joint entanglement of a class triple sits below that of its strongest pair in 97% of triple-layer cells and 99.5% of deep cells, far below a measured null floor, in vision encoders and frozen language models alike. This pairwise dominance is a regularity, not a law: expected from the nesting of overlaps but not forced by geometry, present at initialization and in raw pixels, and manufactured in the last stage alone when a network memorizes random labels. The unnormalized profile mass predicts test accuracy (R^2=0.94), the quotient does not, and neither beats a linear probe. One lesson is reported in full: the paired test must use a scale-free statistic, or it certifies feature-norm dynamics as disentanglement.

Out-of-distribution (OOD) robustness is difficult to diagnose when target-domain labels are unavailable. We consider a more restrictive source-only variant of unsupervised accuracy estimation: selecting robust checkpoints using only source-domain representations, with no target samples or target labels. We propose \textbf{TopoGeoScore}, a source-only geometric scorer for label-free OOD checkpoint selection. Given a trained checkpoint, we construct class-conditional mutual $k$-nearest-neighbour graphs from source embeddings and extract three interpretable signals: a torsion-inspired reduced Laplacian log-determinant for global class-manifold complexity, Ollivier--Ricci curvature for local neighbourhood regularity, and higher-order topological summaries for fragmented connectivity, loops, and global--local inconsistency. Instead of fixing their weights by hand, TopoGeoScore learns a non-negative linear score through a self-supervised objective that enforces invariance under approximately geometry-preserving embedding views and separation from structure-breaking views. The score remains interpretable and uses no target-domain samples or labels. Results across CIFAR-based corruption and distribution-shift benchmarks, ImageNet-C, MNLI$\to$HANS transfer, and OGBN-Arxiv suggest that source representations contain measurable global--local--topological evidence of robustness, supporting practical checkpoint selection before deployment under distribution shift.