arXiv subjects

Matus Medo

Publications and source records attributed to Matus Medo.

At least 19 recordsLinked to original sources

arXiv2022

Phase transitions in growing groups: How cohesion can persist

The cohesion of a social group is the group's tendency to remain united. It has important implications for the stability and survival of social organizations, such as political parties, research teams, or online groups. Empirical studies suggest that cohesion is affected by both the admission process of new members and the group size. Yet, a theoretical understanding of their interplay is still lacking. To this end, we propose a model where a group grows by a noisy admission process of new members who can be of two different types. Cohesion is defined in this framework as the fraction of members of the same type and the noise in the admission process represents the level of randomness in the evaluation of new candidates. The model can reproduce the empirically reported decrease of cohesion with the group size. When the admission of new candidates involves the decision of only one group member, the group growth causes a loss of cohesion even for infinitesimal levels of noise. However, when admissions require a consensus of several group members, there is a critical noise level below which the growing group remains cohesive. The nature of the transition between the cohesive and non-cohesive phases depends on the model parameters and forms a rich structure reminiscent of critical phenomena in ferromagnetic materials.

physics.soc-ph↗

arXiv2021

Technical comment on The impact of population-wide rapid antigen testing on SARS-CoV-2 prevalence in Slovakia

Pavelka et al. (Science, Reports, 7 May 2021) claim that a single round of population-wide antigen testing in Slovakia reduced the observed COVID-19 prevalence by 58%, and that it played a substantial role in curbing the pandemic. We argue that this estimate, which is based on incorrect assumptions, is exaggerated, and that the relief was short-lived with little effect on mitigating the pandemic.

q-bio.PE↗

arXiv2019

ProtRank: Bypassing the imputation of missing values in differential expression analysis of proteomic data

Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values with random numbers, a process known as "imputation", avoids apparent infinite fold-change values. However, the procedure comes at a cost: Imputing a large number of missing values has the potential to significantly impact the results of the subsequent differential expression analysis. We propose a method that identifies differentially expressed proteins by ranking their observed changes with respect to the changes observed for other proteins. Missing values are taken into account by this method directly, without the need to impute them. We illustrate the performance of the new method on two distinct datasets and show that it is robust to missing values and, at the same time, provides results that are otherwise similar to those obtained with edgeR which is a state-of-art differential expression analysis method. The new method for the differential expression analysis of proteomic data is available as an easy to use Python package.

q-bio.QM↗

arXiv2019

Optimal timescale for community detection in growing networks

Time-stamped data are increasingly available for many social, economic, and information systems that can be represented as networks growing with time. The World Wide Web, social contact networks, and citation networks of scientific papers and online news articles, for example, are of this kind. Static methods can be inadequate for the analysis of growing networks as they miss essential information on the system's dynamics. At the same time, time-aware methods require the choice of an observation timescale, yet we lack principled ways to determine it. We focus on the popular community detection problem which aims to partition a network's nodes into meaningful groups. We use a multi-layer quality function to show, on both synthetic and real datasets, that the observation timescale that leads to optimal communities is tightly related to the system's intrinsic aging timescale that can be inferred from the time-stamped network data. The use of temporal information leads to drastically different conclusions on the community structure of real information networks, which challenges the current understanding of the large-scale organization of growing networks. Our findings indicate that before attempting to assess structural patterns of evolving networks, it is vital to uncover the timescales of the dynamical processes that generated them.

physics.soc-ph↗

arXiv2017

Randomizing growing networks with a time-respecting null model

Complex networks are often used to represent systems that are not static but grow with time: people make new friendships, new papers are published and refer to the existing ones, and so forth. To assess the statistical significance of measurements made on such networks, we propose a randomization methodology---a time-respecting null model---that preserves both the network's degree sequence and the time evolution of individual nodes' degree values. By preserving the temporal linking patterns of the analyzed system, the proposed model is able to factor out the effect of the system's temporal patterns on its structure. We apply the model to the citation network of Physical Review scholarly papers and the citation network of US movies. The model reveals that the two datasets are strikingly different with respect to their degree-degree correlations, and we discuss the important implications of this finding on the information provided by paradigmatic node centrality metrics such as indegree and Google's PageRank. The randomization methodology proposed here can be used to assess the significance of any structural property in growing networks, which could bring new insights into the problems where null models play a critical role, such as the detection of communities and network motifs.

physics.soc-ph↗

arXiv2017

Early identification of important patents through network centrality

One of the most challenging problems in technological forecasting is to identify as early as possible those technologies that have the potential to lead to radical changes in our society. In this paper, we use the US patent citation network (1926-2010) to test our ability to early identify a list of historically significant patents through citation network analysis. We show that in order to effectively uncover these patents shortly after they are issued, we need to go beyond raw citation counts and take into account both the citation network topology and temporal information. In particular, an age-normalized measure of patent centrality, called rescaled PageRank, allows us to identify the significant patents earlier than citation count and PageRank score. In addition, we find that while high-impact patents tend to rely on other high-impact patents in a similar way as scientific papers, the patents' citation dynamics is significantly slower than that of papers, which makes the early identification of significant patents more challenging than that of significant papers.

cs.SI↗

arXiv2017

Ranking in evolving complex networks

Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Well-established ranking algorithms (such as the popular Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. The recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of real network traffic, prediction of future links, and identification of highly-significant nodes.

physics.soc-ph↗

arXiv2017

Quantifying and suppressing ranking bias in a large citation network

It is widely recognized that citation counts for papers from different fields cannot be directly compared because different scientific fields adopt different citation practices. Citation counts are also strongly biased by paper age since older papers had more time to attract citations. Various procedures aim at suppressing these biases and give rise to new normalized indicators, such as the relative citation count. We use a large citation dataset from Microsoft Academic Graph and a new statistical framework based on the Mahalanobis distance to show that the rankings by well known indicators, including the relative citation count and Google's PageRank score, are significantly biased by paper field and age. We propose a general normalization procedure motivated by the $z$-score which produces much less biased rankings when applied to citation count and PageRank score.

physics.soc-ph↗

arXiv2016

Identification of milestone papers through time-balanced network centrality

Citations between scientific papers and related bibliometric indices, such as the $h$-index for authors and the impact factor for journals, are being increasingly used - often in controversial ways - as quantitative tools for research evaluation. Yet, a fundamental research question remains still open: to which extent do quantitative metrics capture the significance of scientific works? We analyze the network of citations among the $449,935$ papers published by the American Physical Society (APS) journals between 1893 and 2009, and focus on the comparison of metrics built on the citation count with network-based metrics. We contrast five article-level metrics with respect to the rankings that they assign to a set of fundamental papers, called Milestone Letters, carefully selected by the APS editors for "making long-lived contributions to physics, either by announcing significant discoveries, or by initiating new areas of research". A new metric, which combines PageRank centrality with the explicit requirement that paper score is not biased by paper age, is the best-performing metric overall in identifying the Milestone Letters. The lack of time bias in the new metric makes it also possible to use it to compare papers of different age on the same scale. We find that network-based metrics identify the Milestone Letters better than metrics based on the citation count, which suggests that the structure of the citation network contains information that can be used to improve the ranking of scientific publications. The methods and results presented here are relevant for all evolving systems where network centrality metrics are applied, for example the World Wide Web and online social networks. An interactive Web platform where it is possible to view the ranking of the APS papers by rescaled PageRank is available at the address \url{http://www.sciencenow.info}.

physics.soc-ph↗

arXiv2016

Spatial firm competition in two dimensions with linear transportation costs: simulations and analytical results

Models of spatial firm competition assume that customers are distributed in space and transportation costs are associated with their purchases of products from a small number of firms that are also placed at definite locations. It has been long known that the competition equilibrium is not guaranteed to exist if the most straightforward linear transportation costs are assumed. We show by simulations and also analytically that if periodic boundary conditions in two dimensions are assumed, the equilibrium exists for a pair of firms at any distance. When a larger number of firms is considered, we find that their total equilibrium profit is inversely proportional to the square root of the number of firms. We end with a numerical investigation of the system's behavior for a general transportation cost exponent.

q-fin.TR↗

arXiv2016

The essential role of time in network-based recommendation

Random walks on bipartite networks have been used extensively to design personalized recommendation methods. While aging has been identified as a key component in the growth of information networks, most research has focused on the networks' structural properties and neglected the often available time information. Time has been largely ignored both by the investigated recommendation methods as well as by the methodology used to evaluate them. We show that this time-unaware approach overestimates the methods' recommendation performance. Motivated by microscopic rules of network growth, we propose a time-aware modification of an existing recommendation method and show that by combining the temporal and structural aspects, it outperforms the existing methods. The performance improvements are particularly striking in systems with fast aging.

cs.IR↗

arXiv2016

Model-based evaluation of scientific impact indicators

Using bibliometric data artificially generated through a model of citation dynamics calibrated on empirical data, we compare several indicators for the scientific impact of individual researchers. The use of such a controlled setup has the advantage of avoiding the biases present in real databases, and allows us to assess which aspects of the model dynamics and which traits of individual researchers a particular indicator actually reflects. We find that the simple citation average performs well in capturing the intrinsic scientific ability of researchers, whatever the length of their career. On the other hand, when productivity complements ability in the evaluation process, the notorious $h$ and $g$ indices reveal their potential, yet their normalized variants do not always yield a fair comparison between researchers at different career stages. Notably, the use of logarithmic units for citation counts allows us to build simple indicators with performance equal to that of $h$ and $g$. Our analysis may provide useful hints for a proper use of bibliometric indicators. Additionally, our framework can be extended by including other aspects of the scientific production process and citation dynamics, with the potential to become a standard tool for the assessment of impact metrics.

physics.soc-ph↗

arXiv2015

Network-based recommendation algorithms: A review

Recommender systems are a vital tool that helps us to overcome the information overload problem. They are being used by most e-commerce web sites and attract the interest of a broad scientific community. A recommender system uses data on users' past preferences to choose new items that might be appreciated by a given individual user. While many approaches to recommendation exist, the approach based on a network representation of the input data has gained considerable attention in the past. We review here a broad range of network-based recommendation algorithms and for the first time compare their performance on three distinct real datasets. We present recommendation topics that go beyond the mere question of which algorithm to use - such as the possible influence of recommendation on the evolution of systems that use it - and finally discuss open research directions and challenges.

cs.IR↗

arXiv2015

Identification and modeling of discoverers in online social systems

The dynamics of individuals is of essential importance for understanding the evolution of social systems. Most existing models assume that individuals in diverse systems, ranging from social networks to e-commerce, all tend to what is already popular. We develop an analytical time-aware framework which shows that when individuals make choices -- which item to buy, for example -- in online social systems, a small fraction of them is consistently successful in discovering popular items long before they actually become popular. We argue that these users, whom we refer to as discoverers, are fundamentally different from the previously known opinion leaders, influentials, and innovators. We use the proposed framework to demonstrate that discoverers are present in a wide range of systems. Once identified, they can be used to predict the future success of items. We propose a network model which reproduces the discovery patterns observed in the real data. Furthermore, data produced by the model pose a fundamental challenge to classical ranking algorithms which neglect the time of link creation and thus fail to discriminate between discoverers and ordinary users in the data. Our results open the door to qualitative and quantitative study of fine temporal patterns in social systems and have far-reaching implications for network modeling and algorithm design.

physics.soc-ph↗

arXiv2015

Measuring economic complexity of countries and products: which metric to use?

Evaluating the economies of countries and their relations with products in the global market is a central problem in economics, with far-reaching implications to our theoretical understanding of the international trade as well as to practical applications, such as policy making and financial investment planning. The recent Economic Complexity approach aims to quantify the competitiveness of countries and the quality of the exported products based on the empirical observation that the most competitive countries have diversified exports, whereas developing countries only export few low quality products -- typically those exported by many other countries. Two different metrics, Fitness-Complexity and the Method of Reflections, have been proposed to measure country and product score in the Economic Complexity framework. We use international trade data and a recent ranking evaluation measure to quantitatively compare the ability of the two metrics to rank countries and products according to their importance in the network. The results show that the Fitness-Complexity metric outperforms the Method of Reflections in both the ranking of products and the ranking of countries. We also investigate a Generalization of the Fitness-Complexity metric and show that it can produce improved rankings provided that the input data are reliable.

econ.GN↗

arXiv2015

Ranking nodes in growing networks: When PageRank fails

PageRank is arguably the most popular ranking algorithm which is being applied in real systems ranging from information to biological and infrastructure networks. Despite its outstanding popularity and broad use in different areas of science, the relation between the algorithm's efficacy and properties of the network on which it acts has not yet been fully understood. We study here PageRank's performance on a network model supported by real data, and show that realistic temporal effects make PageRank fail in individuating the most valuable nodes for a broad range of model parameters. Results on real data are in qualitative agreement with our model-based findings. This failure of PageRank reveals that the static approach to information filtering is inappropriate for a broad class of growing systems, and suggest that time-dependent algorithms that are based on the temporal linking patterns of these systems are needed to better rank the nodes.

physics.soc-ph↗

arXiv2015

Modeling mutual feedback between users and recommender systems

Recommender systems daily influence our decisions on the Internet. While considerable attention has been given to issues such as recommendation accuracy and user privacy, the long-term mutual feedback between a recommender system and the decisions of its users has been neglected so far. We propose here a model of network evolution which allows us to study the complex dynamics induced by this feedback, including the hysteresis effect which is typical for systems with non-linear dynamics. Despite the popular belief that recommendation helps users to discover new things, we find that the long-term use of recommendation can contribute to the rise of extremely popular items and thus ultimately narrow the user choice. These results are supported by measurements of the time evolution of item popularity inequality in real systems. We show that this adverse effect of recommendation can be tamed by sacrificing part of short-term recommendation accuracy.

cs.IR↗

arXiv2014

Ranking users, papers and authors in online scientific communities

The ever-increasing quantity and complexity of scientific production have made it difficult for researchers to keep track of advances in their own fields. This, together with growing popularity of online scientific communities, calls for the development of effective information filtering tools. We propose here a method to simultaneously compute reputation of users and quality of scientific artifacts in an online scientific community. Evaluation on artificially-generated data and real data from the Econophysics Forum is used to determine the method's best-performing variants. We show that when the method is extended by considering author credit, its performance improves on multiple levels. In particular, top papers have higher citation count and top authors have higher $h$-index than top papers and top authors chosen by other algorithms.

cs.SI↗