MIRCID: Inferred Hub-miRNAs Drive Cross-Task Improvements in Drug Mechanistic Modeling

Abstract:Drug mechanism-of-action (MoA) modeling commonly relies on perturbational transcriptomes, but matched microRNA (miRNA) measurements are often unavailable. Inferred regulatory features offer a scalable way to reuse these data. Here, we present MIRCID, a framework comparing gene expression with inferred transcription factor (TF) activity and miRNA expression across pathway classification and similarity-based MoA retrieval. HubmiRNet infers 414 pan-cancer hub miRNAs (HubmiRs) from 977 L1000 landmark genes, achieving a Pearson correlation coefficient of 87.72\%; its 1,298-output variant also outperformed SiCmiR on the full-miRNA task (71.21\% versus 67.30\%). In the evaluated comparisons, miRNA augmentation provided more consistent gains than TF activity. Generic embedding controls showed model-dependent utility, while complementarity analyses identified a distinct, partially linearly recoverable representation that retained gene-derived structure. Illustrative rescue cases linked improved classification to biologically plausible miRNA patterns in samples with weak transcriptional signatures. These findings support inferred HubmiRs as a biologically informed recoding of transcriptomic data for perturbational drug modeling, while leaving recovery of measured perturbational miRNA responses to further validation.

Machine Learning (cs.LG)

arXiv:2609.21280 [cs.LG]

(or arXiv:2609.21280v1 [cs.LG] for this version)

https://doi.org/10.48550/arXiv.2609.21280 Focus to learn more arXiv-issued DOI via DataCite (pending registration)

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