arXiv subjects

Orion Penner

Publications and source records attributed to Orion Penner.

12 recordsLinked to original sources

arXiv2020

Renormalizing individual performance metrics for cultural heritage management of sports records

Individual performance metrics are commonly used to compare players from different eras. However, such cross-era comparison is often biased due to significant changes in success factors underlying player achievement rates (e.g. performance enhancing drugs and modern training regimens). Such historical comparison is more than fodder for casual discussion among sports fans, as it is also an issue of critical importance to the multi-billion dollar professional sport industry and the institutions (e.g. Hall of Fame) charged with preserving sports history and the legacy of outstanding players and achievements. To address this cultural heritage management issue, we report an objective statistical method for renormalizing career achievement metrics, one that is particularly tailored for common seasonal performance metrics, which are often aggregated into summary career metrics -- despite the fact that many player careers span different eras. Remarkably, we find that the method applied to comprehensive Major League Baseball and National Basketball Association player data preserves the overall functional form of the distribution of career achievement, both at the season and career level. As such, subsequent re-ranking of the top-50 all-time records in MLB and the NBA using renormalized metrics indicates reordering at the local rank level, as opposed to bulk reordering by era. This local order refinement signals time-independent mechanisms underlying annual and career achievement in professional sports, meaning that appropriately renormalized achievement metrics can be used to compare players from eras with different season lengths, team strategies, rules -- and possibly even different sports.

physics.soc-ph↗

arXiv2015

Identifying Geographic Clusters: A Network Analytic Approach

In recent years there has been a growing interest in the role of networks and clusters in the global economy. Despite being a popular research topic in economics, sociology and urban studies, geographical clustering of human activity has often studied been by means of predetermined geographical units such as administrative divisions and metropolitan areas. This approach is intrinsically time invariant and it does not allow one to differentiate between different activities. Our goal in this paper is to present a new methodology for identifying clusters, that can be applied to different empirical settings. We use a graph approach based on k-shell decomposition to analyze world biomedical research clusters based on PubMed scientific publications. We identify research institutions and locate their activities in geographical clusters. Leading areas of scientific production and their top performing research institutions are consistently identified at different geographic scales.

physics.soc-ph↗

arXiv2014

Exploiting citation networks for large-scale author name disambiguation

We present a novel algorithm and validation method for disambiguating author names in very large bibliographic data sets and apply it to the full Web of Science (WoS) citation index. Our algorithm relies only upon the author and citation graphs available for the whole period covered by the WoS. A pair-wise publication similarity metric, which is based on common co-authors, self-citations, shared references and citations, is established to perform a two-step agglomerative clustering that first connects individual papers and then merges similar clusters. This parameterized model is optimized using an h-index based recall measure, favoring the correct assignment of well-cited publications, and a name-initials-based precision using WoS metadata and cross-referenced Google Scholar profiles. Despite the use of limited metadata, we reach a recall of 87% and a precision of 88% with a preference for researchers with high h-index values. 47 million articles of WoS can be disambiguated on a single machine in less than a day. We develop an h-index distribution model, confirming that the prediction is in excellent agreement with the empirical data, and yielding insight into the utility of the h-index in real academic ranking scenarios.

cs.DL↗

arXiv2014

Inequality and cumulative advantage in science careers: a case study of high-impact journals

Analyzing a large data set of publications drawn from the most competitive journals in the natural and social sciences we show that research careers exhibit the broad distributions of individual achievement characteristic of systems in which cumulative advantage plays a key role. While most researchers are personally aware of the competition implicit in the publication process, little is known about the levels of inequality at the level of individual researchers. We analyzed both productivity and impact measures for a large set of researchers publishing in high-impact journals. For each researcher cohort we calculated Gini inequality coefficients, with average Gini values around 0.48 for total publications and 0.73 for total citations. For perspective, these observed values are well in excess of the inequality levels observed for personal income in developing countries. Investigating possible sources of this inequality, we identify two potential mechanisms that act at the level of the individual that may play defining roles in the emergence of the broad productivity and impact distributions found in science. First, we show that the average time interval between a researcher's successive publications in top journals decreases with each subsequent publication. Second, after controlling for the time dependent features of citation distributions, we compare the citation impact of subsequent publications within a researcher's publication record. We find that as researchers continue to publish in top journals, there is more likely to be a decreasing trend in the relative citation impact with each subsequent publication. This pattern highlights the difficulty of repeatedly publishing high-impact research and the intriguing possibility that confirmation bias plays a role in the evaluation of scientific careers.

physics.soc-ph↗

arXiv2014

Reputation and Impact in Academic Careers

Reputation is an important social construct in science, which enables informed quality assessments of both publications and careers of scientists in the absence of complete systemic information. However, the relation between reputation and career growth of an individual remains poorly understood, despite recent proliferation of quantitative research evaluation methods. Here we develop an original framework for measuring how a publication's citation rate $Δc$ depends on the reputation of its central author $i$, in addition to its net citation count $c$. To estimate the strength of the reputation effect, we perform a longitudinal analysis on the careers of 450 highly-cited scientists, using the total citations $C_{i}$ of each scientist as his/her reputation measure. We find a citation crossover $c_{\times}$ which distinguishes the strength of the reputation effect. For publications with $c < c_{\times}$, the author's reputation is found to dominate the annual citation rate. Hence, a new publication may gain a significant early advantage corresponding to roughly a 66% increase in the citation rate for each tenfold increase in $C_{i}$. However, the reputation effect becomes negligible for highly cited publications meaning that for $c\geq c_{\times}$ the citation rate measures scientific impact more transparently. In addition we have developed a stochastic reputation model, which is found to reproduce numerous statistical observations for real careers, thus providing insight into the microscopic mechanisms underlying cumulative advantage in science.

physics.soc-ph↗

arXiv2013

On the Predictability of Future Impact in Science

Correctly assessing a scientist's past research impact and potential for future impact is key in recruitment decisions and other evaluation processes. While a candidate's future impact is the main concern for these decisions, most measures only quantify the impact of previous work. Recently, it has been argued that linear regression models are capable of predicting a scientist's future impact. By applying that future impact model to 762 careers drawn from three disciplines: physics, biology, and mathematics, we identify a number of subtle, but critical, flaws in current models. Specifically, cumulative non-decreasing measures like the h-index contain intrinsic autocorrelation, resulting in significant overestimation of their "predictive power". Moreover, the predictive power of these models depend heavily upon scientists' career age, producing least accurate estimates for young researchers. Our results place in doubt the suitability of such models, and indicate further investigation is required before they can be used in recruiting decisions.

physics.soc-ph↗

arXiv2013

The case for caution in predicting scientists' future impact

We stress-test the career predictability model proposed by Acuna et al. [Nature 489, 201-202 2012] by applying their model to a longitudinal career data set of 100 Assistant professors in physics, two from each of the top 50 physics departments in the US. The Acuna model claims to predict h(t+Δt), a scientist's h-index Δt years into the future, using a linear combination of 5 cumulative career measures taken at career age t. Here we investigate how the "predictability" depends on the aggregation of career data across multiple age cohorts. We confirm that the Acuna model does a respectable job of predicting h(t+Δt) up to roughly 6 years into the future when aggregating all age cohorts together. However, when calculated using subsets of specific age cohorts (e.g. using data for only t=3), we find that the model's predictive power significantly decreases, especially when applied to early career years. For young careers, the model does a much worse job of predicting future impact, and hence, exposes a serious limitation. The limitation is particularly concerning as early career decisions make up a significant portion, if not the majority, of cases where quantitative approaches are likely to be applied.

physics.soc-ph↗

arXiv2013

Is Europe Evolving Toward an Integrated Research Area?

An integrated European Research Area (ERA) is a critical component for a more competitive and open European R&D system. However, the impact of EU-specific integration policies aimed at overcoming innovation barriers associated with national borders is not well understood. Here we analyze 2.4 x 10^6 patent applications filed with the European Patent Office (EPO) over the 25-year period 1986-2010 along with a sample of 2.6 x 10^5 records from the ISI Web of Science to quantitatively measure the role of borders in international R&D collaboration and mobility. From these data we construct five different networks for each year analyzed: (i) the patent co-inventor network, (ii) the publication co-author network, (iii) the co-applicant patent network, (iv) the patent citation network, and (v) the patent mobility network. We use methods from network science and econometrics to perform a comparative analysis across time and between EU and non-EU countries to determine the "treatment effect" resulting from EU integration policies. Using non-EU countries as a control set, we provide quantitative evidence that, despite decades of efforts to build a European Research Area, there has been little integration above global trends in patenting and publication. This analysis provides concrete evidence that Europe remains a collection of national innovation systems.

physics.soc-ph↗

arXiv2011

Detrending career statistics in professional baseball: Accounting for the steroids era and beyond

There is a long standing debate over how to objectively compare the career achievements of professional athletes from different historical eras. Developing an objective approach will be of particular importance over the next decade as Major League Baseball (MLB) players from the "steroids era" become eligible for Hall of Fame induction. Here we address this issue, as well as the general problem of comparing statistics from distinct eras, by detrending the seasonal statistics of professional baseball players. We detrend player statistics by normalizing achievements to seasonal averages, which accounts for changes in relative player ability resulting from both exogenous and endogenous factors, such as talent dilution from expansion, equipment and training improvements, as well as performance enhancing drugs (PED). In this paper we compare the probability density function (pdf) of detrended career statistics to the pdf of raw career statistics for five statistical categories -- hits (H), home runs (HR), runs batted in (RBI), wins (W) and strikeouts (K) -- over the 90-year period 1920-2009. We find that the functional form of these pdfs are stationary under detrending. This stationarity implies that the statistical regularity observed in the right-skewed distributions for longevity and success in professional baseball arises from both the wide range of intrinsic talent among athletes and the underlying nature of competition. Using this simple detrending technique, we examine the top 50 all-time careers for H, HR, RBI, W and K. We fit the pdfs for career success by the Gamma distribution in order to calculate objective benchmarks based on extreme statistics which can be used for the identification of extraordinary careers.

physics.soc-ph↗

arXiv2010

Sequence alignment, mutual information, and dissimilarity measures for constructing phylogenies

Existing sequence alignment algorithms use heuristic scoring schemes which cannot be used as objective distance metrics. Therefore one relies on measures like the p- or log-det distances, or makes explicit, and often simplistic, assumptions about sequence evolution. Information theory provides an alternative, in the form of mutual information (MI) which is, in principle, an objective and model independent similarity measure. MI can be estimated by concatenating and zipping sequences, yielding thereby the "normalized compression distance". So far this has produced promising results, but with uncontrolled errors. We describe a simple approach to get robust estimates of MI from global pairwise alignments. Using standard alignment algorithms, this gives for animal mitochondrial DNA estimates that are strikingly close to estimates obtained from the alignment free methods mentioned above. Our main result uses algorithmic (Kolmogorov) information theory, but we show that similar results can also be obtained from Shannon theory. Due to the fact that it is not additive, normalized compression distance is not an optimal metric for phylogenetics, but we propose a simple modification that overcomes the issue of additivity. We test several versions of our MI based distance measures on a large number of randomly chosen quartets and demonstrate that they all perform better than traditional measures like the Kimura or log-det (resp. paralinear) distances. Even a simplified version based on single letter Shannon entropies, which can be easily incorporated in existing software packages, gave superior results throughout the entire animal kingdom. But we see the main virtue of our approach in a more general way. For example, it can also help to judge the relative merits of different alignment algorithms, by estimating the significance of specific alignments.

q-bio.GN↗

arXiv2008

Sequence alignment and mutual information

Background: Alignment of biological sequences such as DNA, RNA or proteins is one of the most widely used tools in computational bioscience. All existing alignment algorithms rely on heuristic scoring schemes based on biological expertise. Therefore, these algorithms do not provide model independent and objective measures for how similar two (or more) sequences actually are. Although information theory provides such a similarity measure -- the mutual information (MI) -- previous attempts to connect sequence alignment and information theory have not produced realistic estimates for the MI from a given alignment. Results: Here we describe a simple and flexible approach to get robust estimates of MI from {\it global} alignments. For mammalian mitochondrial DNA, our approach gives pairwise MI estimates for commonly used global alignment algorithms that are strikingly close to estimates obtained by an entirely unrelated approach -- concatenating and zipping the sequences. Conclusions: This remarkable consistency may help establish MI as a reliable tool for evaluating the quality of global alignments, judging the relative merits of different alignment algorithms, and estimating the significance of specific alignments. We expect that our approach can be extended to establish further connections between information theory and sequence alignment, including applications to local and multiple alignment procedures.

q-bio.GN↗

arXiv2007

Node similarity within subgraphs of protein interaction networks

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess identical neighbours. The graph animal algorithm is used to estimate twinness for each pair of nodes (for subgraph sizes n=4 to n=12) in four different protein interaction networks (PINs). These include an Escherichia coli PIN and three Saccharomyces cerevisiae PINs -- each obtained using state-of-the-art high throughput methods. In almost all cases, the average twinness of node pairs is vastly higher than expected from a null model obtained by switching links. For all n, we observe a difference in the ratio of type A twins (which are unlinked pairs) to type B twins (which are linked pairs) distinguishing the prokaryote E. coli from the eukaryote S. cerevisiae. Interaction similarity is expected due to gene duplication, and whole genome duplication paralogues in S. cerevisiae have been reported to co-cluster into the same complexes. Indeed, we find that these paralogous proteins are over-represented as twins compared to pairs chosen at random. These results indicate that twinness can detect ancestral relationships from currently available PIN data.

q-bio.MN↗