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.

Blaz Škrlj, Jan Kralj, Nada Lavrač

Relational data mining is becoming ubiquitous in many fields of study. It offers insights into behaviour of complex, real-world systems which cannot be modeled directly using propositional learning. We propose Symbolic Graph Embedding (SGE), an algorithm aimed to learn symbolic node representations. Built on the ideas from the field of inductive logic programming, SGE first samples a given node's neighborhood and interprets it as a transaction database, which is used for frequent pattern mining to identify logical conjuncts of items that co-occur frequently in a given context. Such patterns are in this work used as features to represent individual nodes, yielding interpretable, symbolic node embeddings. The proposed SGE approach on a venue classification task outperforms shallow node embedding methods such as DeepWalk, and performs similarly to metapath2vec, a black-box representation learner that can exploit node and edge types in a given graph. The proposed SGE approach performs especially well when small amounts of data are used for learning, scales to graphs with millions of nodes and edges, and can be run on an of-the-shelf laptop.

Blaž Škrlj, Jan Kralj, Nada Lavrač

Mining complex data in the form of networks is of increasing interest in many scientific disciplines. Network communities correspond to densely connected subnetworks, and often represent key functional parts of real-world systems. In this work, we propose Silhouette Community Detection (SCD), an approach for detecting communities, based on clustering of network node embeddings, i.e. real valued representations of nodes derived from their neighborhoods. We investigate the performance of the proposed SCD approach on 234 synthetic networks, as well as on a real-life social network. Even though SCD is not based on any form of modularity optimization, it performs comparably or better than state-of-the-art community detection algorithms, such as the InfoMap and Louvain algorithms. Further, we demonstrate how SCD's outputs can be used along with domain ontologies in semantic subgroup discovery, yielding human-understandable explanations of communities detected in a real-life protein interaction network. Being embedding-based, SCD is widely applicable and can be tested out-of-the-box as part of many existing network learning and exploration pipelines.

Blaž Škrlj, Jan Kralj, Janez Konc et al.

Network node embedding is an active research subfield of complex network analysis. This paper contributes a novel approach to learning network node embeddings and direct node classification using a node ranking scheme coupled with an autoencoder-based neural network architecture. The main advantages of the proposed Deep Node Ranking (DNR) algorithm are competitive or better classification performance, significantly higher learning speed and lower space requirements when compared to state-of-the-art approaches on 15 real-life node classification benchmarks. Furthermore, it enables exploration of the relationship between symbolic and the derived sub-symbolic node representations, offering insights into the learned node space structure. To avoid the space complexity bottleneck in a direct node classification setting, DNR computes stationary distributions of personalized random walks from given nodes in mini-batches, scaling seamlessly to larger networks. The scaling laws associated with DNR were also investigated on 1488 synthetic Erdős-Rényi networks, demonstrating its scalability to tens of millions of links.

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.