arXiv subjects

Blaž Škrlj

Publications and source records attributed to Blaž Škrlj.

49 records · Page 3Linked to original sources

arXiv2020

Ensemble- and Distance-Based Feature Ranking for Unsupervised Learning

In this work, we propose two novel (groups of) methods for unsupervised feature ranking and selection. The first group includes feature ranking scores (Genie3 score, RandomForest score) that are computed from ensembles of predictive clustering trees. The second method is URelief, the unsupervised extension of the Relief family of feature ranking algorithms. Using 26 benchmark data sets and 5 baselines, we show that both the Genie3 score (computed from the ensemble of extra trees) and the URelief method outperform the existing methods and that Genie3 performs best overall, in terms of predictive power of the top-ranked features. Additionally, we analyze the influence of the hyper-parameters of the proposed methods on their performance, and show that for the Genie3 score the highest quality is achieved by the most efficient parameter configuration. Finally, we propose a way of discovering the location of the features in the ranking, which are the most relevant in reality.

cs.LG↗

arXiv2020

SNoRe: Scalable Unsupervised Learning of Symbolic Node Representations

Learning from complex real-life networks is a lively research area, with recent advances in learning information-rich, low-dimensional network node representations. However, state-of-the-art methods are not necessarily interpretable and are therefore not fully applicable to sensitive settings in biomedical or user profiling tasks, where explicit bias detection is highly relevant. The proposed SNoRe (Symbolic Node Representations) algorithm is capable of learning symbolic, human-understandable representations of individual network nodes, based on the similarity of neighborhood hashes which serve as features. SNoRe's interpretable features are suitable for direct explanation of individual predictions, which we demonstrate by coupling it with the widely used instance explanation tool SHAP to obtain nomograms representing the relevance of individual features for a given classification. To our knowledge, this is one of the first such attempts in a structural node embedding setting. In the experimental evaluation on eleven real-life datasets, SNoRe proved to be competitive to strong baselines, such as variational graph autoencoders, node2vec and LINE. The vectorized implementation of SNoRe scales to large networks, making it suitable for contemporary network learning and analysis tasks.

cs.LG↗

arXiv2020

COVID-19 therapy target discovery with context-aware literature mining

The abundance of literature related to the widespread COVID-19 pandemic is beyond manual inspection of a single expert. Development of systems, capable of automatically processing tens of thousands of scientific publications with the aim to enrich existing empirical evidence with literature-based associations is challenging and relevant. We propose a system for contextualization of empirical expression data by approximating relations between entities, for which representations were learned from one of the largest COVID-19-related literature corpora. In order to exploit a larger scientific context by transfer learning, we propose a novel embedding generation technique that leverages SciBERT language model pretrained on a large multi-domain corpus of scientific publications and fine-tuned for domain adaptation on the CORD-19 dataset. The conducted manual evaluation by the medical expert and the quantitative evaluation based on therapy targets identified in the related work suggest that the proposed method can be successfully employed for COVID-19 therapy target discovery and that it outperforms the baseline FastText method by a large margin.

cs.CL↗

arXiv2020

Layer entanglement in multiplex, temporal multiplex, and coupled multilayer networks

Complex networks, such as transportation networks, social networks, or biological networks, capture the complex system they model often by representing only one type of interactions. In real world systems, there may be many different aspects that connect entities together. These can be captured using multilayer networks, which combine different modalities of interactions in a single model. Coupling in multilayer networks may exhibit different properties which can be related to the very nature of the data they model (or to events in time-dependant data). We hypothesise that such properties may be reflected in the way layers are intertwined. In this paper, we investigated these through the prism of layer entanglement in coupled multilayer networks. We test over 30 real-life networks in 6 different disciplines (social, genetic, transport, co-authorship, trade, and neuronal networks). We further propose a random generator, displaying comparable patterns of elementary layer entanglement and transition coupling entanglement across 1,329,696 synthetic coupled multilayer networks. Our experiments demonstrate difference of layer entanglement across disciplines, and even suggest a link between entanglement intensity and homophily. We additionally study entanglement in 3 real world temporal datasets displaying a potential rise in entanglement activity prior to other network activity.

physics.soc-ph↗

arXiv2020

Propositionalization and Embeddings: Two Sides of the Same Coin

Data preprocessing is an important component of machine learning pipelines, which requires ample time and resources. An integral part of preprocessing is data transformation into the format required by a given learning algorithm. This paper outlines some of the modern data processing techniques used in relational learning that enable data fusion from different input data types and formats into a single table data representation, focusing on the propositionalization and embedding data transformation approaches. While both approaches aim at transforming data into tabular data format, they use different terminology and task definitions, are perceived to address different goals, and are used in different contexts. This paper contributes a unifying framework that allows for improved understanding of these two data transformation techniques by presenting their unified definitions, and by explaining the similarities and differences between the two approaches as variants of a unified complex data transformation task. In addition to the unifying framework, the novelty of this paper is a unifying methodology combining propositionalization and embeddings, which benefits from the advantages of both in solving complex data transformation and learning tasks. We present two efficient implementations of the unifying methodology: an instance-based PropDRM approach, and a feature-based PropStar approach to data transformation and learning, together with their empirical evaluation on several relational problems. The results show that the new algorithms can outperform existing relational learners and can solve much larger problems.

cs.LG↗

arXiv2020

AttViz: Online exploration of self-attention for transparent neural language modeling

Neural language models are becoming the prevailing methodology for the tasks of query answering, text classification, disambiguation, completion and translation. Commonly comprised of hundreds of millions of parameters, these neural network models offer state-of-the-art performance at the cost of interpretability; humans are no longer capable of tracing and understanding how decisions are being made. The attention mechanism, introduced initially for the task of translation, has been successfully adopted for other language-related tasks. We propose AttViz, an online toolkit for exploration of self-attention---real values associated with individual text tokens. We show how existing deep learning pipelines can produce outputs suitable for AttViz, offering novel visualizations of the attention heads and their aggregations with minimal effort, online. We show on examples of news segments how the proposed system can be used to inspect and potentially better understand what a model has learned (or emphasized).

cs.LG↗

arXiv2020

tax2vec: Constructing Interpretable Features from Taxonomies for Short Text Classification

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.

cs.CL↗

arXiv2020

Feature Importance Estimation with Self-Attention Networks

Black-box neural network models are widely used in industry and science, yet are hard to understand and interpret. Recently, the attention mechanism was introduced, offering insights into the inner workings of neural language models. This paper explores the use of attention-based neural networks mechanism for estimating feature importance, as means for explaining the models learned from propositional (tabular) data. Feature importance estimates, assessed by the proposed Self-Attention Network (SAN) architecture, are compared with the established ReliefF, Mutual Information and Random Forest-based estimates, which are widely used in practice for model interpretation. For the first time we conduct scale-free comparisons of feature importance estimates across algorithms on ten real and synthetic data sets to study the similarities and differences of the resulting feature importance estimates, showing that SANs identify similar high-ranked features as the other methods. We demonstrate that SANs identify feature interactions which in some cases yield better predictive performance than the baselines, suggesting that attention extends beyond interactions of just a few key features and detects larger feature subsets relevant for the considered learning task.

cs.LG↗

arXiv2019

Language comparison via network topology

Modeling relations between languages can offer understanding of language characteristics and uncover similarities and differences between languages. Automated methods applied to large textual corpora can be seen as opportunities for novel statistical studies of language development over time, as well as for improving cross-lingual natural language processing techniques. In this work, we first propose how to represent textual data as a directed, weighted network by the text2net algorithm. We next explore how various fast, network-topological metrics, such as network community structure, can be used for cross-lingual comparisons. In our experiments, we employ eight different network topology metrics, and empirically showcase on a parallel corpus, how the methods can be used for modeling the relations between nine selected languages. We demonstrate that the proposed method scales to large corpora consisting of hundreds of thousands of aligned sentences on an of-the-shelf laptop. We observe that on the one hand properties such as communities, capture some of the known differences between the languages, while others can be seen as novel opportunities for linguistic studies.

cs.CL↗

arXiv2019

Prediction Uncertainty Estimation for Hate Speech Classification

As a result of social network popularity, in recent years, hate speech phenomenon has significantly increased. Due to its harmful effect on minority groups as well as on large communities, there is a pressing need for hate speech detection and filtering. However, automatic approaches shall not jeopardize free speech, so they shall accompany their decisions with explanations and assessment of uncertainty. Thus, there is a need for predictive machine learning models that not only detect hate speech but also help users understand when texts cross the line and become unacceptable. The reliability of predictions is usually not addressed in text classification. We fill this gap by proposing the adaptation of deep neural networks that can efficiently estimate prediction uncertainty. To reliably detect hate speech, we use Monte Carlo dropout regularization, which mimics Bayesian inference within neural networks. We evaluate our approach using different text embedding methods. We visualize the reliability of results with a novel technique that aids in understanding the classification reliability and errors.

cs.CL↗

arXiv2019

RaKUn: Rank-based Keyword extraction via Unsupervised learning and Meta vertex aggregation

Keyword extraction is used for summarizing the content of a document and supports efficient document retrieval, and is as such an indispensable part of modern text-based systems. We explore how load centrality, a graph-theoretic measure applied to graphs derived from a given text can be used to efficiently identify and rank keywords. Introducing meta vertices (aggregates of existing vertices) and systematic redundancy filters, the proposed method performs on par with state-of-the-art for the keyword extraction task on 14 diverse datasets. The proposed method is unsupervised, interpretable and can also be used for document visualization.

cs.CL↗

arXiv2019

Patterns of Multiplex Layer Entanglement across Real and Synthetic Networks

Real world complex networks often exhibit multiplex structure, connecting entities from different aspects of physical systems such as social, transportation and biological networks. Little is known about general properties of such networks across disciplines. In this work, we first investigate how consistent are connectivity patterns across 35 real world multiplex networks. We demonstrate that entanglement homogeneity and intensity, two measures of layer consistency, indicate apparent differences between social and biological networks. We also investigate trade, co-authorship and transport networks. We show that real networks can be separated in the joint space of homogeneity and intensity, demonstrating the usefulness of the two measures for categorization of real multiplex networks. Finally, we design a multiplex network generator, where similar patterns (as observed in real networks), are emerging over the analysis of 11{,}905 synthetic multiplex networks with various topological properties.

cs.SI↗

arXiv2019

Embedding-based Silhouette Community Detection

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.

cs.SI↗