Interaction Concordance Index: Performance Evaluation for Interaction Prediction Methods

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.

A Comprehensive Guide to Differential Privacy: From Theory to User Expectations

The increasing availability of personal data has enabled significant advances in fields such as machine learning, healthcare, and cybersecurity. However, this data abundance also raises serious privacy concerns, especially in light of powerful re-identification attacks and growing legal and ethical demands for responsible data use. Differential privacy (DP) has emerged as a principled, mathematically grounded framework for mitigating these risks. This review provides a comprehensive survey of DP, covering its theoretical foundations, practical mechanisms, and real-world applications. It explores key algorithmic tools and domain-specific challenges - particularly in privacy-preserving machine learning and synthetic data generation. The report also highlights usability issues and the need for improved communication and transparency in DP systems. Overall, the goal is to support informed adoption of DP by researchers and practitioners navigating the evolving landscape of data privacy.

Clust-Splitter $-$ an Efficient Nonsmooth Optimization-Based Algorithm for Clustering Large Datasets

Clustering is a fundamental task in data mining and machine learning, particularly for analyzing large-scale data. In this paper, we introduce Clust-Splitter, an efficient algorithm based on nonsmooth optimization, designed to solve the minimum sum-of-squares clustering problem in very large datasets. The clustering task is approached through a sequence of three nonsmooth optimization problems: two auxiliary problems used to generate suitable starting points, followed by a main clustering formulation. To solve these problems effectively, the limited memory bundle method is combined with an incremental approach to develop the Clust-Splitter algorithm. We evaluate Clust-Splitter on real-world datasets characterized by both a large number of attributes and a large number of data points and compare its performance with several state-of-the-art large-scale clustering algorithms. Experimental results demonstrate the efficiency of the proposed method for clustering very large datasets, as well as the high quality of its solutions, which are on par with those of the best existing methods.