A Systematic Evaluation of Imbalance Handling Methods in Biomedical Binary Classification
Authors: Jiandong Chen, Lingjie Su, Le Peng, Yash Travadi, Rui Zhang, Ju Sun
Organizations: Institute for Health Informatics, University of Minnesota, Minneapolis, MN · Department of Computer Science and Engineering, University of Minnesota, Minneapolis, MN · School of Statistics, University of Minnesota, Minneapolis, MN · Division of Computational Health Sciences, Department of Surgery, University of Minnesota, Minneapolis, MN
Objective: The primary goal of this study was to systematically examine the impact of commonly used imbalance handling methods (IHMs) on predictive performance in biomedical binary classification, considering the interplay between model complexity and diverse data modalities. Material and Methods: We evaluated five representative IHMs: random undersampling (RUS), random oversampling (ROS), SMOTE, re-weighting (RW), and direct F1-score optimization (DMO), against a raw training (RAW) baseline. The evaluation encompassed three public biomedical datasets: MIMIC-III (tabular), ADE-Corpus-V2 (text), and MURA (image), spanning three common biomedical data modalities. To assess varying model complexity, we employed a range of architectures, from classical logistic regression and random forest to deep neural networks, including multilayer perceptron (MLP), BiLSTM, BERT, DenseNet, and DINOv2. Results: For simpler models such as logistic regression on tabular data, IHMs yielded no significant advantage over the RAW baseline, aligning with prior findings. However, clear benefits were observed for more complex models and unstructured data: (a) ROS and RW consistently enhanced the performance of powerful models; (b) direct F1-score optimization demonstrated utility primarily for unstructured text and image data; and (c) RUS and SMOTE consistently degraded performance and are therefore not recommended. Conclusion: The effectiveness of IHMs depends on both model complexity and data modality. Performance gains are most pronounced when leveraging appropriate IHMs, such as ROS, RW, and DMO, on high-complexity models.
Imbalanced learning remains a fundamental challenge in tabular data applications. Despite decades of research and numerous proposed algorithms, a systematic empirical understanding of how different imbalanced learning methods behave across diverse data characteristics is still lacking. In particular, it remains unclear how different method families compare in predictive performance, robustness under varying data characteristics, and computational scalability. In this work, we present Tabular Imbalanced Learning Benchmark (TILBench), a large-scale empirical benchmark for tabular imbalanced learning. TILBench evaluates more than 40 representative algorithms across 57 diverse tabular datasets, resulting in over 200000 controlled experiments across a wide range of data characteristics. Our findings show that no single method consistently dominates across all settings; instead, the effectiveness of imbalanced learning methods depends strongly on dataset characteristics and computational constraints. Based on these findings, we provide practical recommendations for selecting appropriate methods in real-world applications.
Class imbalance is a widespread challenge in NLP tasks, significantly hindering robust performance across diverse domains and applications. We introduce Hardness-Aware Meta-Resample (HAMR), a unified framework that adaptively addresses both class imbalance and data difficulty. HAMR employs bi-level optimizations to dynamically estimate instance-level weights that prioritize genuinely challenging samples and minority classes, while a neighborhood-aware resampling mechanism amplifies training focus on hard examples and their semantically similar neighbors. We validate HAMR on six imbalanced datasets covering multiple tasks and spanning biomedical, disaster response, and sentiment domains. Experimental results show that HAMR achieves substantial improvements for minority classes and consistently outperforms strong baselines. Extensive ablation studies demonstrate that our proposed modules synergistically contribute to performance gains and highlight HAMR as a flexible and generalizable approach for class imbalance adaptation. Code is available at https://github.com/trust-nlp/ImbalanceLearning.
Class-level evaluation can conceal substantial performance disparities across subconcepts within the same class, causing models that perform well on average to fail on specific subpopulations. Prior work has shown that common evaluation measures for imbalanced classification are biased toward larger minority subconcepts and that utility-based reweighting using true subconcept labels can mitigate this bias; however, such labels are rarely available at test time. We introduce a practical utility-weighted evaluation that replaces unavailable subconcept labels with predicted posterior probabilities from a multiclass subconcept model. Evaluation weights are defined as the expected utility under this posterior, yielding a soft, uncertainty-aware metric we call predicted-weighted balanced accuracy (pBA). Experiments on tabular benchmarks as well as medical-imaging and text datasets show that unweighted scores can be misleading under within-class heterogeneity, while pBA provides more stable and interpretable assessments when subconcept distributions are uneven but not pathological. Our code is available at: https://anonymous.4open.science/r/correcting-bias-imbalance-9C6C/.