Characterization of Transfer Using Multi-task Learning Curves

Transfer effects manifest themselves both during training using a fixed data set and in inductive inference using accumulating data. We hypothesize that perturbing the data set by including more samples, instead of perturbing the model by gradient updates, provides a complementary and more fundamental characterization of transfer effects. To capture this phenomenon, we quantitatively model transfer effects using multi-task learning curves approximating the inductive performance over varying sample sizes. We describe an efficient method to approximate multi-task learning curves analogous to the Task Affinity Grouping method applied during training. We compare the statistical and computational approaches to transfer, which indicates considerably higher compute costs for the previous but better power and broader applicability. Evaluations are performed using a benchmark drug-target interaction data set. Our results show that learning curves can better capture the effects of multi-task learning and their multi-task extensions can delineate pairwise and contextual transfer effects in foundation models.

DTI-GP: Bayesian operations for drug-target interactions using deep kernel Gaussian processes

Precise probabilistic information about drug-target interaction (DTI) predictions is vital for understanding limitations and boosting predictive performance. Gaussian processes (GP) offer a scalable framework to integrate state-of-the-art DTI representations and Bayesian inference, enabling novel operations, such as Bayesian classification with rejection, top-$K$ selection, and ranking. We propose a deep kernel learning-based GP architecture (DTI-GP), which incorporates a combined neural embedding module for chemical compounds and protein targets, and a GP module. The workflow continues with sampling from the predictive distribution to estimate a Bayesian precedence matrix, which is used in fast and accurate selection and ranking operations. DTI-GP outperforms state-of-the-art solutions, and it allows (1) the construction of a Bayesian accuracy-confidence enrichment score, (2) rejection schemes for improved enrichment, and (3) estimation and search for top-$K$ selections and ranking with high expected utility.