REVIEW 4 major objections 6 minor 34 references
Robustness of transferability estimation metrics for medical imaging
T0 review · 4 major / 6 minor · reviewed 2026-08-12 · deepseek-v4-flash
Pith's one-line read Transferability estimation metric rankings in medical imaging are unstable to target resampling and to the evaluation metric used for the reference ranking.
desk verdict A careful, well-scoped negative result on transferability estimation in medical imaging; the seed-instability findings are solid, while the low-agreement claim needs reference-noise quantification. read the letter →
The pith
A machine-rendered reading of the paper's core claim, the machinery that carries it, and where it could break.
The reading
Extended reading notes
Core claim
The paper states: "we observe a low agreement between rankings from TE metrics and reference" (Abstract) and shows that rankings from TE metrics change across random seeds and that the evaluation metric changes the reference rankings (Sections 4.1 and 4.2, Figures 3, 7, and 8). If correct, this means TE metric evaluations in medical imaging are not reliable when based on a single random seed or a single evaluation metric.
Load-bearing premise
The reference ranking from fine-tuning is treated as ground truth for transferability. Section 3.3 assumes that fine-tuning with Optuna and test-set evaluation produces a valid ranking, while Section 4.2 admits that on Blood all source models exceed 0.99 AUROC, so ranks rest on negligible differences. If the reference itself is noisy, the low TE/reference agreement could partly reflect reference noise rather than TE metric failure. In addition, only ResNet-18 and MedMNIST v2 are tested, so the generality of the instability finding is assumed rather than demonstrated.
Editorial analysis
A structured set of objections, weighed in public.
Referee Report
Summary. The paper studies the robustness of seven transferability estimation (TE) metrics for medical imaging classification, focusing on two factors: variations in the target dataset representation (subset size and random seed) and the choice of evaluation metric used to construct the reference ranking. The authors use eight MedMNIST v2 targets and thirteen source models, compute TE rankings on nested stratified subsets with five seeds, and fine-tune ResNet-18 models with Optuna to obtain reference rankings under accuracy and AUROC. They report that TE rankings vary across seeds and subset sizes, that reference rankings depend on the evaluation metric, and that agreement between TE rankings and the fine-tuning reference is generally low. The paper also releases code and model checkpoints.
Significance. If the claims are established, this is a useful and cautionary empirical study for the transferability estimation community, particularly for medical imaging where data scarcity makes TE metrics attractive. The paper has notable strengths: it covers seven TE metrics, uses three correlation coefficients, constructs nested stratified subsets with multiple seeds, and provides open code, checkpoints, and data splits. The evidence that TE rankings are seed-sensitive and that reference rankings depend on the evaluation metric is compelling in its qualitative patterns. However, the headline claim of low TE-reference agreement is weakened by the absence of any quantification of reference-ranking noise and by ambiguities in how the reference seeds are handled in the analysis. As written, the central conclusion is not fully separated from measurement error.
major comments (4)
- [Section 3.3, Section 4.2, Figure 8] The reference ranking is treated as ground truth, but its noise is not quantified. Section 3.3 states that the reference is built from a single Optuna run per source-target-metric combination on the full train set, and Section 4.2 concedes that on Blood all source models exceed 0.99 AUROC and that reference rankings change across subset sizes and seeds. Since rank-correlation measures are attenuated by noise in one of the two rankings being compared, the low TE-reference agreement in Figure 8 and the abstract could partly reflect reference noise rather than genuine failure of the TE metrics. The authors should quantify reference noise, for example by repeating fine-tuning runs (even for a subset of conditions) or by comparing the observed TE-reference correlations to the reference-reference stability across the two 5% seeds already available in Appendix F. Without such a comparison, the central 'low agreement' conclusion is not established.
- [Section 3.3, Figures 3, 4, 6, 8] All stability values are reported as averages over seeds with no measure of dispersion, confidence interval, or significance test. For example, Figure 3 averages pairwise Kendall's Tau over five seeds, but no standard deviation, per-seed values, or confidence intervals are shown. This makes it impossible to judge whether the differences between TE metrics or subset sizes are meaningful, and whether the 'low agreement' values in Figure 8 are statistically distinguishable from zero or from each other. Please provide error bars or bootstrap confidence intervals, and include per-seed results in an appendix.
- [Section 3.3 (Ex2), Figure 8 caption] The number of seeds used for the reference ranking in Ex2 is ambiguous. The text says that fine-tuning on 5% subsets is repeated for only two random seeds (Section 3.3), yet Figure 8's caption says that the stability is averaged over five random seeds for subsets smaller than 100%. If only two reference rankings exist for the 5% condition, the five-seed average cannot be computed unless TE rankings on seeds without a corresponding reference are compared against one of the two available references, which would conflate seed variation with TE-reference agreement. Clarify the exact pairing of TE and reference rankings, and if necessary compute the average only over the two seeds for which both TE and reference rankings are available.
- [Section 4.2, Appendix A] The reference rankings are based on test-set scores rounded to three decimal places (Appendix A), and for some targets the ranking differences are extremely small (e.g., Blood AUROC values from 0.997 to 0.999). Rank correlations computed on such near-ties are dominated by measurement noise, yet no sensitivity analysis is provided on how the ranking would change under small perturbations of the scores. A tie-aware or confidence-interval-aware reference would help establish whether the reference itself is meaningful, especially for the 100% condition in Figure 8 where a single reference run is used.
minor comments (6)
- [Equation (2)] There is a typo in the text: 'both from a the same TE metric' should read 'both from the same TE metric'.
- [Section 4.1] Several missing spaces appear, for example 'NLEEPandSFDA', 'ForNLEEPthis', and 'SFDA, this is due'.
- [Section 2.2] The related work describes the LPFU metric from Juodelyte et al. [13], but LPFU is not included in the seven evaluated metrics; the authors should clarify why it is omitted from the experiments.
- [Section 3.3, Equation (1)] The summation indices in Equation (1) are written as 'u-1 X i=1 u X j=i+1', which is hard to parse; consider using a clearer notation such as summing over all pairs i < j.
- [Appendix C] The NLEEP adjustment in Appendix C is presented post hoc, changing the PCA energy and number of Gaussian components to improve stability. Please state explicitly whether these modified settings are used in any of the main results, or clearly label the appendix as a supplementary diagnostic.
- [References] Several reference entries have awkward line breaks in the DOI or URL fields (e.g., references 20 and 25); please ensure the bibliographic formatting is clean.
Circularity Check
No significant circularity: TE rankings are compared against an external fine-tuning reference, and no claimed prediction is constructed from its own inputs.
full rationale
The central comparison in this paper is not circular. TE metric rankings are measured against a reference ranking produced by actual fine-tuning and test-set evaluation, which is independent of the TE scores. The paper does not fit TE metrics to the reference, nor does it define transferability in terms of the TE scores. The instability results across random seeds (Fig. 3, Eq. 1) are self-contained and do not depend on the reference at all. The low-agreement result in Fig. 8 uses the fine-tuning reference as an external benchmark; even though the reference may be noisy, that is a measurement-validity concern, not a circularity. The only overlapping self-citations are to Juodelyte et al. [13], used for grouping TE metrics, for the known SFDA degeneracy, and for LPFU; these are contextual and not load-bearing for the paper's new findings. The NLEEP adjustment in Appendix C is a post-hoc hyperparameter change presented as a robustness check, not as a validated prediction, and it does not drive the central conclusion. Overall, the derivation chain is self-contained against an external benchmark, so no part of the claimed result is equivalent to its inputs by construction.
Assumptions & free parameters
free parameters (6)
- subset_fractions =
5%, 10%, 25%, 50%, 75%
- n_random_seeds =
5
- architecture =
ResNet-18
- NLEEP_pca_energy =
0.9 (Appendix C; default 0.8)
- NLEEP_gaussian_components =
1 per class
- hyperparameter_search_ranges =
lr 1e-5 to 1e-2; weight decay 1e-6 to 1e-2; batch 128
assumptions (4)
- domain assumption MedMNIST v2 2D datasets and ImageNet are representative of medical transfer learning settings.
- domain assumption Fine-tuned test accuracy and AUROC, after hyperparameter optimization, are valid reference rankings of transferability.
- domain assumption The seven TE metric implementations from original papers are correct and comparable in their default forms.
- standard math Spearman, Kendall, and weighted Kendall correlations are appropriate agreement measures for rankings.
Cite this review
Pith. "Pith review of Robustness of transferability estimation metrics for medical imaging." pith.science (2026). https://pith.science/paper/GE5TE4W6
@misc{pith2026260809999,
author = {Pith},
title = {Pith review of: Robustness of transferability estimation metrics for medical imaging},
year = {2026},
howpublished = {\url{https://pith.science/paper/GE5TE4W6}},
note = {Machine review of arXiv:2608.09999}
}
read the original abstract
In transfer learning, the choice of source model largely influences the performance on a target dataset. Still, selecting a fitting source remains a challenging task, especially in medical imaging where one has to decide between models pre-trained on off-the-shelf options, such as ImageNet, and domain specific datasets. Transferability estimation (TE) metrics address this problem by aiming to predict the best performing source model in a computationally cost effective way. However, previous work has reported conflicting TE metric performances due to differences in experimental setups. Moreover, most TE metrics are designed for and evaluated on natural images, while being optimized for accuracy, whereas in medical imaging metrics that are more robust to class imbalance are typically used. We study the impact of varying the target dataset as an isolated factor, by constructing miniature populations of different sample sizes and random seeds. In addition, we investigate the influence of the evaluation metric used to obtain the reference ranking. We find that small modifications to the target dataset change the rankings. Furthermore, we show that the choice of evaluation metric affects the reference rankings and therefore the evaluation of TE metrics. Overall, we observe a low agreement between rankings from TE metrics and reference. The code, model checkpoints and data splits used in this work are available through https://github.com/niclasclassen/robustness-of-transferability-estimation-metrics-for-medical-imaging.
Figures
Figures from the paper (5 more)
Reference graph
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