Jan Kralj

Jan Kralj, Blaž Škrlj, Živa Ramšak et al.

Biological systems can be studied at multiple levels of information, including gene, protein, RNA and different interaction networks levels. The goal of this work is to explore how the fusion of systems' level information with temporal dynamics of gene expression can be used in combination with non-linear approximation power of deep neural networks to predict novel gene functions in a non-model organism potato \emph{Solanum tuberosum}. We propose DDeMON (Dynamic Deep learning from temporal Multiplex Ontology-annotated Networks), an approach for scalable, systems-level inference of function annotation using time-dependent multiscale biological information. The proposed method, which is capable of considering billions of potential links between the genes of interest, was applied on experimental gene expression data and the background knowledge network to reliably classify genes with unknown function into five different functional ontology categories, linked to the experimental data set. Predicted novel functions of genes were validated using extensive protein domain search approach.

Blaž Škrlj, Matej Martinc, Jan Kralj et al.

The use of background knowledge is largely unexploited in text classification tasks. This paper explores word taxonomies as means for constructing new semantic features, which may improve the performance and robustness of the learned classifiers. We propose tax2vec, a parallel algorithm for constructing taxonomy-based features, and demonstrate its use on six short text classification problems: prediction of gender, personality type, age, news topics, drug side effects and drug effectiveness. The constructed semantic features, in combination with fast linear classifiers, tested against strong baselines such as hierarchical attention neural networks, achieves comparable classification results on short text documents. The algorithm's performance is also tested in a few-shot learning setting, indicating that the inclusion of semantic features can improve the performance in data-scarce situations. The tax2vec capability to extract corpus-specific semantic keywords is also demonstrated. Finally, we investigate the semantic space of potential features, where we observe a similarity with the well known Zipf's law.