Lennart Purucker

Lennart Purucker, Lennart Schneider, Marie Anastacio et al.

Automated machine learning (AutoML) systems commonly ensemble models post hoc to improve predictive performance, typically via greedy ensemble selection (GES). However, we believe that GES may not always be optimal, as it performs a simple deterministic greedy search. In this work, we introduce two novel population-based ensemble selection methods, QO-ES and QDO-ES, and compare them to GES. While QO-ES optimises solely for predictive performance, QDO-ES also considers the diversity of ensembles within the population, maintaining a diverse set of well-performing ensembles during optimisation based on ideas of quality diversity optimisation. The methods are evaluated using 71 classification datasets from the AutoML benchmark, demonstrating that QO-ES and QDO-ES often outrank GES, albeit only statistically significant on validation data. Our results further suggest that diversity can be beneficial for post hoc ensembling but also increases the risk of overfitting.

Alexander Pfefferle, Johannes Hog, Lennart Purucker et al.

Tabular foundation models such as TabPFN have revolutionized predictive machine learning for tabular data. At the same time, the driving factors of this revolution are hard to understand. Existing open-source tabular foundation models are implemented in complicated pipelines boasting over 10,000 lines of code, lack architecture documentation or code quality. In short, the implementations are hard to understand, not beginner-friendly, and complicated to adapt for new experiments. We introduce nanoTabPFN, a simplified and lightweight implementation of the TabPFN v2 architecture and a corresponding training loop that uses pre-generated training data. nanoTabPFN makes tabular foundation models more accessible to students and researchers alike. For example, restricted to a small data setting it achieves a performance comparable to traditional machine learning baselines within one minute of pre-training on a single GPU (160,000x faster than TabPFN v2 pretraining). This eliminated requirement of large computational resources makes pre-training tabular foundation models accessible for educational purposes. Our code is available at https://github.com/automl/nanoTabPFN.

Lennart Purucker, Joeran Beel

Many state-of-the-art automated machine learning (AutoML) systems use greedy ensemble selection (GES) by Caruana et al. (2004) to ensemble models found during model selection post hoc. Thereby, boosting predictive performance and likely following Auto-Sklearn 1's insight that alternatives, like stacking or gradient-free numerical optimization, overfit. Overfitting in Auto-Sklearn 1 is much more likely than in other AutoML systems because it uses only low-quality validation data for post hoc ensembling. Therefore, we were motivated to analyze whether Auto-Sklearn 1's insight holds true for systems with higher-quality validation data. Consequently, we compared the performance of covariance matrix adaptation evolution strategy (CMA-ES), state-of-the-art gradient-free numerical optimization, to GES on the 71 classification datasets from the AutoML benchmark for AutoGluon. We found that Auto-Sklearn's insight depends on the chosen metric. For the metric ROC AUC, CMA-ES overfits drastically and is outperformed by GES -- statistically significantly for multi-class classification. For the metric balanced accuracy, CMA-ES does not overfit and outperforms GES significantly. Motivated by the successful application of CMA-ES for balanced accuracy, we explored methods to stop CMA-ES from overfitting for ROC AUC. We propose a method to normalize the weights produced by CMA-ES, inspired by GES, that avoids overfitting for CMA-ES and makes CMA-ES perform better than or similar to GES for ROC AUC.

Lennart Purucker, Joeran Beel

Automated Machine Learning (AutoML) frameworks regularly use ensembles. Developers need to compare different ensemble techniques to select appropriate techniques for an AutoML framework from the many potential techniques. So far, the comparison of ensemble techniques is often computationally expensive, because many base models must be trained and evaluated one or multiple times. Therefore, we present Assembled-OpenML. Assembled-OpenML is a Python tool, which builds meta-datasets for ensembles using OpenML. A meta-dataset, called Metatask, consists of the data of an OpenML task, the task's dataset, and prediction data from model evaluations for the task. We can make the comparison of ensemble techniques computationally cheaper by using the predictions stored in a metatask instead of training and evaluating base models. To introduce Assembled-OpenML, we describe the first version of our tool. Moreover, we present an example of using Assembled-OpenML to compare a set of ensemble techniques. For this example comparison, we built a benchmark using Assembled-OpenML and implemented ensemble techniques expecting predictions instead of base models as input. In our example comparison, we gathered the prediction data of $1523$ base models for $31$ datasets. Obtaining the prediction data for all base models using Assembled-OpenML took ${\sim} 1$ hour in total. In comparison, obtaining the prediction data by training and evaluating just one base model on the most computationally expensive dataset took ${\sim} 37$ minutes.

Léo Grinsztajn, Klemens Flöge, Oscar Key et al.

The first tabular foundation model, TabPFN, and its successor TabPFNv2 have impacted tabular AI substantially, with dozens of methods building on it and hundreds of applications across different use cases. This report introduces TabPFN-2.5, the next generation of our tabular foundation model, built for datasets with up to 50,000 data points and 2,000 features, a 20x increase in data cells compared to TabPFNv2. TabPFN-2.5 is now the leading method for the industry standard benchmark TabArena (which contains datasets with up to 100,000 training data points), substantially outperforming tuned tree-based models and matching the accuracy of AutoGluon 1.4, a complex four-hour tuned ensemble that even includes the previous TabPFNv2. Remarkably, default TabPFN-2.5 has a 100% win rate against default XGBoost on small to medium-sized classification datasets (<=10,000 data points, 500 features) and a 87% win rate on larger datasets up to 100K samples and 2K features (85% for regression). For production use cases, we introduce a new distillation engine that converts TabPFN-2.5 into a compact MLP or tree ensemble, preserving most of its accuracy while delivering orders-of-magnitude lower latency and plug-and-play deployment. This new release will immediately strengthen the performance of the many applications and methods already built on the TabPFN ecosystem.

Jun Ma, Feifei Li, Sumin Kim et al.

Promptable segmentation foundation models have emerged as a transformative approach to addressing the diverse needs in medical images, but most existing models require expensive computing, posing a big barrier to their adoption in clinical practice. In this work, we organized the first international competition dedicated to promptable medical image segmentation, featuring a large-scale dataset spanning nine common imaging modalities from over 20 different institutions. The top teams developed lightweight segmentation foundation models and implemented an efficient inference pipeline that substantially reduced computational requirements while maintaining state-of-the-art segmentation accuracy. Moreover, the post-challenge phase advanced the algorithms through the design of performance booster and reproducibility tasks, resulting in improved algorithms and validated reproducibility of the winning solution. Furthermore, the best-performing algorithms have been incorporated into the open-source software with a user-friendly interface to facilitate clinical adoption. The data and code are publicly available to foster the further development of medical image segmentation foundation models and pave the way for impactful real-world applications.

Jannis Maier, Felix Möller, Lennart Purucker

Automated Machine Learning (AutoML) significantly simplifies the deployment of machine learning models by automating tasks from data preprocessing to model selection to ensembling. AutoML systems for tabular data often employ post hoc ensembling, where multiple models are combined to improve predictive accuracy. This typically results in longer inference times, a major limitation in practical deployments. Addressing this, we introduce a hardware-aware ensemble selection approach that integrates inference time into post hoc ensembling. By leveraging an existing framework for ensemble selection with quality diversity optimization, our method evaluates ensemble candidates for their predictive accuracy and hardware efficiency. This dual focus allows for a balanced consideration of accuracy and operational efficiency. Thus, our approach enables practitioners to choose from a Pareto front of accurate and efficient ensembles. Our evaluation using 83 classification datasets shows that our approach sustains competitive accuracy and can significantly improve ensembles' operational efficiency. The results of this study provide a foundation for extending these principles to additional hardware constraints, setting the stage for the development of more resource-efficient AutoML systems.

Anurag Garg, Muhammad Ali, Noah Hollmann et al.

Foundation models for tabular data, like TabPFN, achieve strong performance on small datasets when pre-trained solely on synthetic data. We show that this performance can be significantly boosted by a targeted continued pre-training phase. Specifically, we demonstrate that leveraging a small, curated collection of large, real-world datasets for continued pre-training yields superior downstream predictive accuracy compared to using broader, potentially noisier corpora like CommonCrawl or GitTables. Our resulting model, Real-TabPFN, achieves substantial performance gains on 29 datasets from the OpenML AutoML Benchmark.

Martin Mráz, Breenda Das, Anshul Gupta et al.

Foundation models for tabular data are rapidly evolving, with increasing interest in extending them to support additional modalities such as free-text features. However, existing benchmarks for tabular data rarely include textual columns, and identifying real-world tabular datasets with semantically rich text features is non-trivial. We propose a series of simple yet effective ablation-style strategies for incorporating text into conventional tabular pipelines. Moreover, we benchmark how state-of-the-art tabular foundation models can handle textual data by manually curating a collection of real-world tabular datasets with meaningful textual features. Our study is an important step towards improving benchmarking of foundation models for tabular data with text.

Edward Bergman, Lennart Purucker, Frank Hutter

State-of-the-art automated machine learning systems for tabular data often employ cross-validation; ensuring that measured performances generalize to unseen data, or that subsequent ensembling does not overfit. However, using k-fold cross-validation instead of holdout validation drastically increases the computational cost of validating a single configuration. While ensuring better generalization and, by extension, better performance, the additional cost is often prohibitive for effective model selection within a time budget. We aim to make model selection with cross-validation more effective. Therefore, we study early stopping the process of cross-validation during model selection. We investigate the impact of early stopping on random search for two algorithms, MLP and random forest, across 36 classification datasets. We further analyze the impact of the number of folds by considering 3-, 5-, and 10-folds. In addition, we investigate the impact of early stopping with Bayesian optimization instead of random search and also repeated cross-validation. Our exploratory study shows that even a simple-to-understand and easy-to-implement method consistently allows model selection to converge faster; in ~94% of all datasets, on average by ~214%. Moreover, stopping cross-validation enables model selection to explore the search space more exhaustively by considering +167% configurations on average within one hour, while also obtaining better overall performance.