On the Promises and Limits of Multi-omics Integration for Deconvolution: The HADACA3 Benchmark

Abstract

Understanding the cellular composition of complex tissues, such as tumors, is a key challenge in biology and medicine. A common approach, known as deconvolution, aims to estimate the cellular composition from bulk molecular measurements. With the growing availability of multiple types of molecular data, it is often assumed that combining data sources should improve deconvolution performance. Here, we present HADACA3, a community-driven benchmark designed to evaluate this assumption. We conducted a four-day collaborative competition followed by a large-scale computational benchmark, testing more than 250,000 analysis pipelines across nine datasets with matched DNA methylation (DNAm) and RNA profiles, representing a wide range of biological and experimental conditions. Our framework jointly evaluates the impact of preprocessing, feature selection, modeling, and integration strategies. We find that DNAm alone achieves the highest median performance across datasets, making it the most stable and reliable single-modality approach. However, multi-omics integration strategies can regularly achieve higher top performance in specific datasets and pipeline configurations. Among the tested strategies, late integration based on error-weighted averaging provides a strong and reliable baseline, while non-linear early integration methods, such as optimal transport, show promising results on real biological datasets. Overall, our results show that multi-omics integration does not systematically improve average performance over DNAm alone, but can improve best-case performance in specific settings. This highlights a trade-off between robustness and peak performance, and emphasizes the importance of aligning integration strategies with the statistical properties of the data. All data, code, and evaluation tools are publicly available to support reproducible research and future method development.