Data repositories have accumulated a large number of tabular datasets from various domains. Machine Learning researchers are actively using these datasets to evaluate novel approaches. Consequently, data repositories have an important standing in tabular data research. They not only host datasets but also provide information on how to use them in supervised learning tasks. In this paper, we argue that, despite great achievements in usability, the unreflected usage of datasets from data repositories may have led to reduced research quality and scientific rigor. We present examples from prominent recent studies that illustrate the problematic use of datasets from OpenML, a large data repository for tabular data. Our illustrations help users of data repositories avoid falling into the traps of (1) using suboptimal model selection strategies, (2) overlooking strong baselines, and (3) inappropriate preprocessing. In response, we discuss possible solutions for how data repositories can prevent the inappropriate use of datasets and become the cornerstones for improved overall quality of empirical research studies. In tabular data research, the OpenML repository is used extensively (Gijsbers et al., 2019; Salinas & Erickson, 2024; Liu et al., 2024; Hollmann et al., 2025). A driving factor for tabular data repository usage is the recent increase in efforts to transfer the success of deep learning to the tabular domain. The development of novel neural network models (Arik & Pfister, 2021; Chang et al., 2021; Gorishniy et al., 2021; 2023; 2024), and more recently tabular foundation models (Gardner et al., 2024; Hollmann et al., 2025) dominates the tabular machine learning community. In response, recent comparative studies try to gather as many datasets as possible to facilitate a rigorous and comprehensive evaluation of novel approaches (Grinsztajn et al., 2022; McElfresh et al., 2023; Ye et al., 2024a). While McElfresh et al. (2023) used 196 datasets, a recent study scales up to 300 datasets from OpenML (Ye et al., 2024a). Similarly, studies evaluating foundation models seem to include as many datasets from these benchmarks as possible, apparently taking their quality and appropriateness for granted (Yan et al., 2024; Gardner et al., 2024). Different authors have recently criticized the intense focus on model development and the limited attention to data quality. Existing benchmarks often use outdated data (Kohli et al., 2024), ignore task-specific preprocessing (Tschalzev et al., 2024), or use inappropriate data splits (Rubachev et al., 2024).

In this technical report, we investigate the predictive performance differences of a rule-based approach and the GNN architectures NBFNet and A*Net with respect to knowledge graph completion. For the two most common benchmarks, we find that a substantial fraction of the performance difference can be explained by one unique negative pattern on each dataset that is hidden from the rule-based approach. Our findings add a unique perspective on the performance difference of different model classes for knowledge graph completion: Models can achieve a predictive performance advantage by penalizing scores of incorrect facts opposed to providing high scores for correct facts.

Within this paper, we show that the evaluation protocol currently used for inductive link prediction is heavily flawed as it relies on ranking the true entity in a small set of randomly sampled negative entities. Due to the limited size of the set of negatives, a simple rule-based baseline can achieve state-of-the-art results, which simply ranks entities higher based on the validity of their type. As a consequence of these insights, we reevaluate current approaches for inductive link prediction on several benchmarks using the link prediction protocol usually applied to the transductive setting. As some inductive methods suffer from scalability issues when evaluated in this setting, we propose and apply additionally an improved sampling protocol, which does not suffer from the problem mentioned above. The results of our evaluation differ drastically from the results reported in so far.

Tabular data is prevalent in real-world machine learning applications, and new models for supervised learning of tabular data are frequently proposed. Comparative studies assessing the performance of models typically consist of model-centric evaluation setups with overly standardized data preprocessing. This paper demonstrates that such model-centric evaluations are biased, as real-world modeling pipelines often require dataset-specific preprocessing and feature engineering. Therefore, we propose a data-centric evaluation framework. We select 10 relevant datasets from Kaggle competitions and implement expert-level preprocessing pipelines for each dataset. We conduct experiments with different preprocessing pipelines and hyperparameter optimization (HPO) regimes to quantify the impact of model selection, HPO, feature engineering, and test-time adaptation. Our main findings are: 1. After dataset-specific feature engineering, model rankings change considerably, performance differences decrease, and the importance of model selection reduces. 2. Recent models, despite their measurable progress, still significantly benefit from manual feature engineering. This holds true for both tree-based models and neural networks. 3. While tabular data is typically considered static, samples are often collected over time, and adapting to distribution shifts can be important even in supposedly static data. These insights suggest that research efforts should be directed toward a data-centric perspective, acknowledging that tabular data requires feature engineering and often exhibits temporal characteristics.

Neural networks often assume independence among input data samples, disregarding correlations arising from inherent clustering patterns in real-world datasets (e.g., due to different sites or repeated measurements). Recently, mixed effects neural networks (MENNs) which separate cluster-specific 'random effects' from cluster-invariant 'fixed effects' have been proposed to improve generalization and interpretability for clustered data. However, existing methods only allow for approximate quantification of cluster effects and are limited to regression and binary targets with only one clustering feature. We present MC-GMENN, a novel approach employing Monte Carlo methods to train Generalized Mixed Effects Neural Networks. We empirically demonstrate that MC-GMENN outperforms existing mixed effects deep learning models in terms of generalization performance, time complexity, and quantification of inter-cluster variance. Additionally, MC-GMENN is applicable to a wide range of datasets, including multi-class classification tasks with multiple high-cardinality categorical features. For these datasets, we show that MC-GMENN outperforms conventional encoding and embedding methods, simultaneously offering a principled methodology for interpreting the effects of clustering patterns.

Multi-relational temporal graphs are powerful tools for modeling real-world data, capturing the evolving and interconnected nature of entities over time. Recently, many novel models are proposed for ML on such graphs intensifying the need for robust evaluation and standardized benchmark datasets. However, the availability of such resources remains scarce and evaluation faces added complexity due to reproducibility issues in experimental protocols. To address these challenges, we introduce Temporal Graph Benchmark 2.0 (TGB 2.0), a novel benchmarking framework tailored for evaluating methods for predicting future links on Temporal Knowledge Graphs and Temporal Heterogeneous Graphs with a focus on large-scale datasets, extending the Temporal Graph Benchmark. TGB 2.0 facilitates comprehensive evaluations by presenting eight novel datasets spanning five domains with up to 53 million edges. TGB 2.0 datasets are significantly larger than existing datasets in terms of number of nodes, edges, or timestamps. In addition, TGB 2.0 provides a reproducible and realistic evaluation pipeline for multi-relational temporal graphs. Through extensive experimentation, we observe that 1) leveraging edge-type information is crucial to obtain high performance, 2) simple heuristic baselines are often competitive with more complex methods, 3) most methods fail to run on our largest datasets, highlighting the need for research on more scalable methods.

Temporal Knowledge Graph (TKG) Forecasting aims at predicting links in Knowledge Graphs for future timesteps based on a history of Knowledge Graphs. To this day, standardized evaluation protocols and rigorous comparison across TKG models are available, but the importance of simple baselines is often neglected in the evaluation, which prevents researchers from discerning actual and fictitious progress. We propose to close this gap by designing an intuitive baseline for TKG Forecasting based on predicting recurring facts. Compared to most TKG models, it requires little hyperparameter tuning and no iterative training. Further, it can help to identify failure modes in existing approaches. The empirical findings are quite unexpected: compared to 11 methods on five datasets, our baseline ranks first or third in three of them, painting a radically different picture of the predictive quality of the state of the art.

We present PGTNet, an approach that transforms event logs into graph datasets and leverages graph-oriented data for training Process Graph Transformer Networks to predict the remaining time of business process instances. PGTNet consistently outperforms state-of-the-art deep learning approaches across a diverse range of 20 publicly available real-world event logs. Notably, our approach is most promising for highly complex processes, where existing deep learning approaches encounter difficulties stemming from their limited ability to learn control-flow relationships among process activities and capture long-range dependencies. PGTNet addresses these challenges, while also being able to consider multiple process perspectives during the learning process.

Goal recognition is an important problem in many application domains (e.g., pervasive computing, intrusion detection, computer games, etc.). In many application scenarios, it is important that goal recognition algorithms can recognize goals of an observed agent as fast as possible. However, many early approaches in the area of Plan Recognition As Planning, require quite large amounts of computation time to calculate a solution. Mainly to address this issue, recently, Pereira et al. [11] developed an approach that is based on planning landmarks and is much more computationally efficient than previous approaches. However, the approach, as proposed by Pereira et al., also uses trivial landmarks (i.e., facts that are part of the initial state and goal description are landmarks by definition). In this paper, we show that it does not provide any benefit to use landmarks that are part of the initial state in a planning landmark based goal recognition approach. The empirical results show that omitting initial state landmarks for goal recognition improves goal recognition performance.

Decision Trees (DTs) are commonly used for many machine learning tasks due to their high degree of interpretability. However, learning a DT from data is a difficult optimization problem, as it is non-convex and non-differentiable. Therefore, common approaches learn DTs using a greedy growth algorithm that minimizes the impurity locally at each internal node. Unfortunately, this greedy procedure can lead to inaccurate trees. In this paper, we present a novel approach for learning hard, axis-aligned DTs with gradient descent. The proposed method uses backpropagation with a straight-through operator on a dense DT representation, to jointly optimize all tree parameters. Our approach outperforms existing methods on binary classification benchmarks and achieves competitive results for multi-class tasks. The method is available under: https://github.com/s-marton/GradTree