Query Performance Prediction (QPP) estimates the effectiveness of retrieval systems for a given query, offering valuable insights for search effectiveness and query processing. Despite extensive research, a critical gap remains in understanding how well QPPs generalize across diverse retrieval paradigms and collections, a question of robustness that has significant implications for their practical utility. This article provides the first comprehensive cross-paradigm evaluation of QPP robustness and generalization capabilities, examining state-of-the-art QPPs including NQC, WIG, LETOR-based features, and newly explored dense-based predictors MQPPF and BERT-QPP. We systematically assess their performance across diverse sparse (BM25, DFree with and without query expansion), hybrid (SPLADE), and dense (ColBERT, TCT-ColBERT) rankers on four benchmark collections: TREC Robust, GOV2, WT10G, and MS-MARCO. The results reveal fundamental robustness challenges: predictors exhibit significant variability in accuracy, with collection being the dominant factor, followed by ranker type. Some sparse predictors perform adequately on specific collections such as TREC Robust and GOV2, but critically fail to generalize to other collections like WT10G and MS-MARCO. Dense-based predictors, while showing promise in specific scenarios with dense rankers, similarly lack generalization to sparse contexts. We demonstrate that these generalization failures severely limit practical applications: QPP-driven selective query processing achieves only marginal gains ( \(\approx\) 4% NDCG improvement), with reliability varying dramatically across settings. Our findings underscore that current QPP methods lack the robustness necessary for real-world deployment and highlight the urgent need for predictors that generalize reliably across diverse collections, align with modern dense retrieval architectures, and provide consistent utility for downstream applications. We publicly release our data and code to facilitate future research on robust QPP methods ( https://github.com/adrianchifu/UncoveringTheLimitationsofQPP/ ).

Kernel methods have been proven to be a powerful tool for the integration and analysis of highthroughput technologies generated data. Kernels offer a nonlinear version of any linear algorithm solely based on dot products. The kernelized version of Principal Component Analysis is a valid nonlinear alternative to tackle the nonlinearity of biological sample spaces. This paper proposes a novel methodology to obtain a data-driven feature importance based on the KPCA representation of the data. The proposed method, kernel PCA Interpretable Gradient (KPCA-IG), provides a datadriven feature importance that is computationally fast and based solely on linear algebra calculations. It has been compared with existing methods on three benchmark datasets. The accuracy obtained using KPCA-IG selected features is equal to or greater than the other methods' average. Also, the computational complexity required demonstrates the high efficiency of the method. An exhaustive literature search has been conducted on the selected genes from a publicly available Hepatocellular carcinoma dataset to validate the retained features from a biological point of view. The results once again remark on the appropriateness of the computed ranking. The black-box nature of kernel PCA needs new methods to interpret the original features. Our proposed methodology KPCA-IG proved to be a valid alternative to select influential variables in high-dimensional high-throughput datasets, potentially unravelling new biological and medical biomarkers.

BACKGROUND: The rapid development of omics acquisition techniques has induced the production of a large volume of heterogeneous and multi-level omics datasets, which require specific and sometimes complex analyses to obtain relevant biological information. Here, we present ASTERICS (version 2.5), a publicly available web interface for the analyses of omics datasets. RESULTS: ASTERICS is designed to make both standard and complex exploratory and integration analysis workflows easily available to biologists and to provide high quality interactive plots. Special care has been taken to provide a comprehensive documentation of the implemented analyses and to guide users toward sound analysis choices regarding some specific omics data. Data and analyses are organized in a comprehensive graphical workflow within ASTERICS workspace to facilitate the understanding of successive data editions and analyses leading to a given result. CONCLUSION: ASTERICS provides an easy to use platform for omics data exploration and integration. The modular organization of its open source code makes it easy to incorporate new workflows and analyses by external contributors. ASTERICS is available at https://asterics.miat.inrae.fr and can also be deployed using provided docker images.

High-throughput data generated by new biotechnologies require specific and adapted statistical treatment in order to be efficiently used in biological studies. In this article, we propose a powerful framework to manage and analyse multi-omics heterogeneous data to carry out an integrative analysis. We have illustrated this using the mixOmics package for R software as it specifically addresses data integration issues. Our work also aims at applying the most recent functionalities of mixOmics to real datasets. Although multi-block integrative methodologies exist, we hope to encourage a more widespread use of such approaches in an operational framework by biologists. We have used natural populations of the model plant Arabidopsis thaliana in this work, but the framework proposed is not limited to this plant and can be deployed whatever the organisms of interest and the biological question may be. Four omics datasets (phenomics, metabolomics, cell wall proteomics and transcriptomics) were collected, analysed and integrated to study the cell wall plasticity of plants exposed to sub-optimal temperature growth conditions. The methodologies presented here start from basic univariate statistics leading to multi-block integration analysis. We have also highlighted the fact that each method, either unsupervised or supervised, is associated with one biological issue. Using this powerful framework enabled us to arrive at novel conclusions on the biological system, which would not have been possible using standard statistical approaches.

Feature selection in learning to rank has recently emerged as a crucial issue. Whereas several preprocessing approaches have been proposed, only a few have focused on integrating feature selection into the learning process. In this paper, we propose a general framework for feature selection in learning to rank using support vector machines with a sparse regularization term. We investigate both classical convex regularizations, such as ℓ1or weighted ℓ1, and nonconvex regularization terms, such as log penalty, minimax concave penalty, or ℓppseudo-norm with p1scheme to address nonconvex regularizations. We conduct intensive experiments on nine datasets from Letor 3.0 and Letor 4.0 corpora. Numerical results show that the use of nonconvex regularizations we propose leads to more sparsity in the resulting models while preserving the prediction performance. The number of features is decreased by up to a factor of 6 compared to the ℓ1regularization. In addition, the software is publicly available on the web.

MOTIVATION: With the availability of many 'omics' data, such as transcriptomics, proteomics or metabolomics, the integrative or joint analysis of multiple datasets from different technology platforms is becoming crucial to unravel the relationships between different biological functional levels. However, the development of such an analysis is a major computational and technical challenge as most approaches suffer from high data dimensionality. New methodologies need to be developed and validated. RESULTS: integrOmics efficiently performs integrative analyses of two types of 'omics' variables that are measured on the same samples. It includes a regularized version of canonical correlation analysis to enlighten correlations between two datasets, and a sparse version of partial least squares (PLS) regression that includes simultaneous variable selection in both datasets. The usefulness of both approaches has been demonstrated previously and successfully applied in various integrative studies. AVAILABILITY: integrOmics is freely available from http://CRAN.R-project.org/ or from the web site companion (http://math.univ-toulouse.fr/biostat) that provides full documentation and tutorials. CONTACT: [email protected] SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.