Berk Atil

Rıza Özçelik, Alperen Bağ, Berk Atıl et al.

Computational models that accurately predict the binding affinity of an input protein-chemical pair can accelerate drug discovery studies. These models are trained on available protein-chemical interaction datasets, which may contain dataset biases that may lead the model to learn dataset-specific patterns, instead of generalizable relationships. As a result, the prediction performance of models drops for previously unseen biomolecules, $\textit{i.e.}$ the prediction models cannot generalize to biomolecules outside of the dataset. The latest approaches that aim to improve model generalizability either have limited applicability or introduce the risk of degrading prediction performance. Here, we present DebiasedDTA, a novel drug-target affinity (DTA) prediction model training framework that addresses dataset biases to improve the generalizability of affinity prediction models. DebiasedDTA reweights the training samples to mitigate the effect of dataset biases and is applicable to most DTA prediction models. The results suggest that models trained in the DebiasedDTA framework can achieve improved generalizability in predicting the interactions of the previously unseen biomolecules, as well as performance improvements on those previously seen. Extensive experiments with different biomolecule representations, model architectures, and datasets demonstrate that DebiasedDTA can upgrade DTA prediction models irrespective of the biomolecule representation, model architecture, and training dataset. Last but not least, we release DebiasedDTA as an open-source python library to enable other researchers to debias their own predictors and/or develop their own debiasing methods. We believe that this python library will corroborate and foster research to develop more generalizable DTA prediction models.

Thi Kim Nhung Dang, Doina Bucur, Berk Atil et al.

Small and medium enterprises rely on detailed Web analytics to be informed about their market and competition. Focused crawlers meet this demand by crawling and indexing specific parts of the Web. Critically, a focused crawler must quickly find new pages that have not yet been indexed. Since a new page can be discovered only by following a new outlink, predicting new outlinks is very relevant in practice. In the literature, many feature designs have been proposed for predicting changes in the Web. In this work we provide a structured analysis of this problem, using new outlinks as our running prediction target. Specifically, we unify earlier feature designs in a taxonomic arrangement of features along two dimensions: static versus dynamic features, and features of a page versus features of the network around it. Within this taxonomy, complemented by our new (mainly, dynamic network) features, we identify best predictors for new outlinks. Our main conclusion is that most informative features are the recent history of new outlinks on a page itself, and of its content-related pages. Hence, we propose a new 'look back, look around' (LBLA) model, that uses only these features. With the obtained predictions, we design a number of scoring functions to guide a focused crawler to pages with most new outlinks, and compare their performance. The LBLA approach proved extremely effective, outperforming other models including those that use a most complete set of features. One of the learners we use, is the recent NGBoost method that assumes a Poisson distribution for the number of new outlinks on a page, and learns its parameters. This connects the two so far unrelated avenues in the literature: predictions based on features of a page, and those based on probabilistic modelling. All experiments were carried out on an original dataset, made available by a commercial focused crawler.