Effects of Training Data Quality on Classifier Performance

High-quality training data is essential for the success of machine learning models. However, real-world datasets often contain mixed types of errors arising from systematic flaws in data preparation pipelines, including label errors, feature errors, and spurious correlations. Effective debugging of training data requires both detecting erroneous samples and identifying their specific error types to enable targeted repair, yet existing data cleaning and attribution methods fail to adequately address this dual requirement. In this paper, we propose DeMix, a novel framework that simultaneously diagnoses erroneous samples and their error types. Our key insight is that different error types produce distinct patterns on model behavior. DeMix captures such error-specific patterns by influence vectors that characterize how each training sample affects model predictions across all validation samples. We formulate training data debugging as a multi-label classification problem where a classifier is developed to predict error types directly from influence vectors. We further introduce an intervention-based learning strategy that guides the classifier to capture invariant rationales specific to each error type, ensuring the learned classifier generalizes effectively. Empirical evaluations on 11 tasks across tabular data prediction, recommendation systems, and LLM alignment demonstrate that DeMix significantly outperforms state-of-the-art approaches, achieving a 22.61% improvement in data debugging F1-score and a 9.32% gain in task model performance after data repair. Code is available at: https://github.com/SJTU-DMTai/DeMix.

Metagenomic taxonomic annotation is essential for interpreting complex microbial communities, yet reliable annotation remains challenging under reference database incompleteness and ambiguous taxonomic boundaries. Existing similarity-based tools are efficient, but they often produce noisy pseudo-labels in complex environments; learning-based post-hoc correction methods can further inherit this noise when trained on hard pseudo-labels generated by upstream classifiers. We propose TaxDistill, a plug-and-play knowledge distillation framework for reliable metagenomic taxonomic recalibration. TaxDistill uses the genomic foundation model GenomeOcean as a semantic teacher and performs one-way online distillation, where the teacher is updated by hierarchical taxonomic supervision while its detached soft probability distributions guide a lightweight student network. This design mitigates the student's overfitting to noisy hard pseudo-labels and supports confidence based rejection of potentially unreliable predictions. Comprehensive experiments on seven diverse CAMI2 datasets with MMseqs2, Metabuli, and Kraken2 show that TaxDistill improves annotation reliability over existing baselines in most scenarios. For example, on the Gastrointestinal dataset, TaxDistill improves the F1 score of MMseqs2 from 0.763 to 0.941, surpassing the Taxometer baseline. Our results suggest that large genomic foundation models can provide semantic supervision for noisy scientific annotations, enabling lightweight post-hoc recalibration of existing metagenomic annotation results.

This paper studies an optimal linear combination of binary classifiers based on a logical structuration of the dataset via truth tables. The given classifiers partition data into equivalence classes, allowing for a rigorous analysis of the convexified empirical risk through a multidimensional generalization of classification calibrated functions. We establish sufficient conditions for the existence and uniqueness of the (global) point of minimum of the convexified empirical risk for any list of classifiers (when the number of classifiers is large, there frequently could be no point of minimum). In the case of three classifiers, our analysis allows to list all the configurations leading to either a unique solution, infima or non-unique points of minimum. Furthermore, we derive explicit analytical formulae for optimal weights using Exponential (Boost) and Logistic (Logit) loss functions, bypassing iterative optimization. The stability of the resulting classifier and the analysis of data quality can be evaluated through the introduction of the notion of $φ$-frontiers.