Reducing cross-sample prediction churn in scientific machine learning
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| Format: | Preprint |
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2026
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| _version_ | 1866913124429332480 |
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| author | Prastalo, Gordan Jablonka, Kevin Maik |
| author_facet | Prastalo, Gordan Jablonka, Kevin Maik |
| contents | Scientific machine learning reports predictive performance. It does not report whether the same prediction would survive a different draw of training data. Across $9$ chemistry benchmarks, two classifiers trained on independent bootstraps of the same training set agree on aggregate accuracy to within $1.3\text{--}4.2$ percentage points but disagree on the class label of $8.0\text{--}21.8\%$ of test molecules. We call this gap \emph{cross-sample prediction churn}. The standard parameter-side techniques (deep ensembles, MC dropout, stochastic weight averaging) do not reduce this gap; two data-side methods do. The first is $K$-bootstrap bagging, which cuts the rate $40\text{--}54\%$ on every dataset at no accuracy cost ($K{\times}$-ERM compute). The second is \emph{twin-bootstrap}, our proposal: two networks trained jointly on independent bootstraps with a sym-KL consistency loss between their predictions, which at matched $2{\times}$-ERM compute reduces churn a further median $45\%$ beyond bagging-$K{=}2$. Cross-sample prediction churn deserves a column alongside predictive performance in scientific-ML benchmark reports, because without it the parameter-side and data-side methods are indistinguishable on the metric they actually differ on. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_2605_13826 |
| institution | arXiv |
| publishDate | 2026 |
| record_format | arxiv |
| spellingShingle | Reducing cross-sample prediction churn in scientific machine learning Prastalo, Gordan Jablonka, Kevin Maik Machine Learning Materials Science Chemical Physics Scientific machine learning reports predictive performance. It does not report whether the same prediction would survive a different draw of training data. Across $9$ chemistry benchmarks, two classifiers trained on independent bootstraps of the same training set agree on aggregate accuracy to within $1.3\text{--}4.2$ percentage points but disagree on the class label of $8.0\text{--}21.8\%$ of test molecules. We call this gap \emph{cross-sample prediction churn}. The standard parameter-side techniques (deep ensembles, MC dropout, stochastic weight averaging) do not reduce this gap; two data-side methods do. The first is $K$-bootstrap bagging, which cuts the rate $40\text{--}54\%$ on every dataset at no accuracy cost ($K{\times}$-ERM compute). The second is \emph{twin-bootstrap}, our proposal: two networks trained jointly on independent bootstraps with a sym-KL consistency loss between their predictions, which at matched $2{\times}$-ERM compute reduces churn a further median $45\%$ beyond bagging-$K{=}2$. Cross-sample prediction churn deserves a column alongside predictive performance in scientific-ML benchmark reports, because without it the parameter-side and data-side methods are indistinguishable on the metric they actually differ on. |
| title | Reducing cross-sample prediction churn in scientific machine learning |
| topic | Machine Learning Materials Science Chemical Physics |
| url | https://arxiv.org/abs/2605.13826 |