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arXiv · 2510.14419

Interaction Concordance Index: Performance Evaluation for Interaction Prediction Methods

Tapio Pahikkala·Riikka Numminen·Parisa Movahedi·Napsu Karmitsa·Antti Airola
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Abstract

Consider two sets of entities and their members' mutual affinity values, say drug-target affinities (DTA). Drugs and targets are said to interact in their effects on DTAs if drug's effect on it depends on the target. Presence of interaction implies that assigning a drug to a target and another drug to another target does not provide the same aggregate DTA as the reversed assignment would provide. Accordingly, correctly capturing interactions enables better decision-making, for example, in allocation of limited numbers of drug doses to their best matching targets. Learning to predict DTAs is popularly done from either solely from known DTAs or together with side information on the entities, such as chemical structures of drugs and targets. In this paper, we introduce interaction directions' prediction performance estimator we call interaction concordance index (IC-index), for both fixed predictors and machine learning algorithms aimed for inferring them. IC-index complements the popularly used DTA prediction performance estimators by evaluating the ratio of correctly predicted directions of interaction effects in data. First, we show the invariance of IC-index on predictors unable to capture interactions. Secondly, we show that learning algorithm's permutation equivariance regarding drug and target identities implies its inability to capture interactions when either drug, target or both are unseen during training. In practical applications, this equivariance is remedied via incorporation of appropriate side information on drugs and targets. We make a comprehensive empirical evaluation over several biomedical interaction data sets with various state-of-the-art machine learning algorithms. The experiments demonstrate how different types of affinity strength prediction methods perform in terms of IC-index complementing existing prediction performance estimators.

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Tapio Pahikkala, Riikka Numminen, Parisa Movahedi, Napsu Karmitsa, Antti Airola. 2025-10-16. Interaction Concordance Index: Performance Evaluation for Interaction Prediction Methods. https://arxiv.org/abs/2510.14419

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