arXiv subjects

Matúš Medo

Publications and source records attributed to Matúš Medo.

10 recordsLinked to original sources

arXiv2024

A comprehensive comparison of tools for fitting mutational signatures

Mutational signatures connect characteristic mutational patterns in the genome with biological or chemical processes that take place in cancers. Analysis of mutational signatures can help elucidate tumor evolution, prognosis, and therapeutic strategies. Although tools for extracting mutational signatures de novo have been extensively benchmarked, a similar effort is lacking for tools that fit known mutational signatures to a given catalog of mutations. We fill this gap by comprehensively evaluating twelve signature fitting tools on synthetic mutational catalogs with empirically-driven signature weights corresponding to eight cancer types. On average, SigProfilerSingleSample and SigProfilerAssignment/MuSiCal perform best for small and large numbers of mutations per sample, respectively. We further show that ad hoc constraining the list of reference signatures is likely to produce inferior results. Evaluation of real mutational catalogs suggests that the activity of signatures that are absent in the reference catalog poses considerable problems to all evaluated tools.

q-bio.GN↗

arXiv2021

Simple regularities in the dynamics of online news impact

Online news can quickly reach and affect millions of people, yet we do not know yet whether there exist potential dynamical regularities that govern their impact on the public. We use data from two major news outlets, BBC and New York Times, where the number of user comments can be used as a proxy of news impact. We find that the impact dynamics of online news articles does not exhibit popularity patterns found in many other social and information systems. In particular, we find that a simple exponential distribution yields a better fit to the empirical news impact distributions than a power-law distribution. This observation is explained by the lack or limited influence of the otherwise omnipresent rich-get-richer mechanism in the analyzed data. The temporal dynamics of the news impact exhibits a universal exponential decay which allows us to collapse individual news trajectories into an elementary single curve. We also show how daily variations of user activity directly influence the dynamics of the article impact. Our findings challenge the universal applicability of popularity dynamics patterns found in other social contexts.

physics.soc-ph↗

arXiv2020

Limits of PageRank-based ranking methods in sports data

While PageRank has been extensively used to rank sport tournament participants (teams or individuals), its superiority over simpler ranking methods has been never clearly demonstrated. We use sports results from 18 major leagues to calibrate a state-of-art model for synthetic sports results. Model data are then used to assess the ranking performance of PageRank in a controlled setting. We find that PageRank outperforms the benchmark ranking by the number of wins only when a small fraction of all games have been played. Increased randomness in the data, such as intrinsic randomness of outcomes or advantage of home teams, further reduces the range of PageRank's superiority. We propose a new PageRank variant which outperforms PageRank in all evaluated settings, yet shares its sensitivity to increased randomness in the data. Our main findings are confirmed by evaluating the ranking algorithms on real data. Our work demonstrates the danger of using novel metrics and algorithms without considering their limits of applicability.

cs.SI↗

arXiv2020

Contact network models matching the dynamics of the COVID-19 spreading

We study the epidemic spreading on spatial networks where the probability that two nodes are connected decays with their distance as a power law. As the exponent of the distance dependence grows, model networks smoothly transition from the random network limit to the regular lattice limit. We show that despite keeping the average number of contacts constant, the increasing exponent hampers the epidemic spreading by making long-distance connections less frequent. The spreading dynamics is influenced by the distance-dependence exponent as well and changes from exponential growth to power-law growth. The observed power-law growth is compatible with recent analyses of empirical data on the spreading of COVID-19 in numerous countries.

physics.soc-ph↗

arXiv2020

The fragility of opinion formation in a complex world

With vast amounts of high-quality information at our fingertips, how is it possible that many people believe that the Earth is flat and vaccination harmful? Motivated by this question, we quantify the implications of an opinion formation mechanism whereby an uninformed observer gradually forms opinions about a world composed of subjects interrelated by a signed network of mutual trust and distrust. We show numerically and analytically that the observer's resulting opinions are highly inconsistent (they tend to be independent of the observer's initial opinions) and unstable (they exhibit wide stochastic variations). Opinion inconsistency and instability increase with the world complexity represented by the number of subjects, which can be prevented by suitably expanding the observer's initial amount of information. Our findings imply that even an individual who initially trusts credible information sources may end up trusting the deceptive ones if at least a small number of trust relations exist between the credible and deceptive sources.

physics.soc-ph↗

arXiv2020

History-dependent percolation on multiplex networks

The structure of interconnected systems and its impact on the system dynamics is a much-studied cross-disciplinary topic. Although various critical phenomena have been found in different models, the study on the connections between different percolation transitions is still lacking. Here we propose a unified framework to study the origins of the discontinuous transitions of the percolation process on interacting networks. The model evolves in generations with the result of the present percolation depending on the previous state and thus is history-dependent. Both theoretical analysis and Monte Carlo simulations reveal that the nature of the transition remains the same at finite generations but exhibits an abrupt change for the infinite generation. We use brain functional correlation and morphological similarity data to show that our model also provides a general method to explore the network structure and can contribute to many practical applications, such as detecting the abnormal structures of human brain networks.

cond-mat.stat-mech↗

arXiv2020

Time-invariant degree growth in preferential attachment network models

Preferential attachment drives the evolution of many complex networks. Its analytical studies mostly consider the simplest case of a network that grows uniformly in time despite the accelerating growth of many real networks. Motivated by the observation that the average degree growth of nodes is time-invariant in empirical network data, we study the degree dynamics in the relevant class of network models where preferential attachment is combined with heterogeneous node fitness and aging. We propose a novel analytical framework based on the time-invariance of the studied systems and show that it is self-consistent only for two special network growth forms: the uniform and exponential network growth. Conversely, the breaking of such time-invariance explains the winner-takes-all effect in some model settings, revealing the connection between the Bose-Einstein condensation in the Bianconi-Barabási model and similar gelation in superlinear preferential attachment. Aging is necessary to reproduce realistic node degree growth curves and can prevent the winner-takes-all effect under weak conditions. Our results are verified by extensive numerical simulations.

physics.soc-ph↗

arXiv2020

Unbiased evaluation of ranking metrics reveals consistent performance in science and technology citation data

Despite the increasing use of citation-based metrics for research evaluation purposes, we do not know yet which metrics best deliver on their promise to gauge the significance of a scientific paper or a patent. We assess 17 network-based metrics by their ability to identify milestone papers and patents in three large citation datasets. We find that traditional information-retrieval evaluation metrics are strongly affected by the interplay between the age distribution of the milestone items and age biases of the evaluated metrics. Outcomes of these metrics are therefore not representative of the metrics' ranking ability. We argue in favor of a modified evaluation procedure that explicitly penalizes biased metrics and allows us to reveal metrics' performance patterns that are consistent across the datasets. PageRank and LeaderRank turn out to be the best-performing ranking metrics when their age bias is suppressed by a simple transformation of the scores that they produce, whereas other popular metrics, including citation count, HITS and Collective Influence, produce significantly worse ranking results.

cs.SI↗

arXiv2018

The long-term impact of ranking algorithms in growing networks

When we search online for content, we are constantly exposed to rankings. For example, web search results are presented as a ranking, and online bookstores often show us lists of best-selling books. While popularity-based ranking algorithms (like Google's PageRank) have been extensively studied in previous works, we still lack a clear understanding of their potential systemic consequences. In this work, we fill this gap by introducing a new model of network growth that allows us to compare the properties of the networks generated under the influence of different ranking algorithms. We show that by correcting for the omnipresent age bias of popularity-based ranking algorithms, the resulting networks exhibit a significantly larger agreement between the nodes' inherent quality and their long-term popularity, and a less concentrated popularity distribution. To further promote popularity diversity, we introduce and validate a perturbation of the original rankings where a small number of randomly-selected nodes are promoted to the top of the ranking. Our findings move the first steps toward a model-based understanding of the long-term impact of popularity-based ranking algorithms, and could be used as an informative tool for the design of improved information filtering tools.

physics.soc-ph↗

arXiv2015

Prediction in complex systems: the case of the international trade network

Predicting the future evolution of complex systems is one of the main challenges in complexity science. Based on a current snapshot of a network, link prediction algorithms aim to predict its future evolution. We apply here link prediction algorithms to data on the international trade between countries. This data can be represented as a complex network where links connect countries with the products that they export. Link prediction techniques based on heat and mass diffusion processes are employed to obtain predictions for products exported in the future. These baseline predictions are improved using a recent metric of country fitness and product similarity. The overall best results are achieved with a newly developed metric of product similarity which takes advantage of causality in the network evolution.

physics.soc-ph↗