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

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. Here we analyzed both productivity and impact measures for a large set of researchers publishing in high-impact journals, accounting for censoring biases in the publication data by using distinct researcher cohorts defined over non-overlapping time periods. 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 producing research findings in the highest citation-impact echelon, as well as the role played by finite career and knowledge life-cycles, and the intriguing possibility that confirmation bias plays a role in the evaluation of scientific careers

Commentary: 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+\Delta t), a scientist's h-index \Delta t 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+\Delta t) 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.Comment: 2 pages, 1 figur

The evolution of networks of innovators within and across borders: Evidence from patent data

Recent studies on the geography of knowledge networks have documented a negative impact of physical distance and institutional borders upon research and development (R&D) collaborations. Though it is widely recognized that geographic constraints and national borders impede the diffusion of knowledge, less attention has been devoted to the temporal evolution of these constraints. In this study we use data on patents filed with the European Patent Office (EPO) for OECD countries to analyze the impact of physical distance and country borders on inter-regional links in four different networks over the period 1988-2009: (1) co-inventorship, (2) patent citations, (3) inventor mobility and (4) the location of R&D laboratories. We find the constraint imposed by country borders and distance decreased until mid-1990s then started to grow, particularly for distance. We further investigate the role of large innovation "hubs" as attractors of new collaboration opportunities and the impact of region size and locality on the evolution of cross-border patenting activities. The intensity of European cross-country inventor collaborations increased at a higher pace than their non-European counterparts until 2004, with no significant relative progress thereafter. Moreover, when analyzing networks of geographical mobility, multinational R&D activities and patent citations we cannot detect any substantial progress in European research integration above and beyond the common global trend

Networks of innovators within and across borders. Evidence from patent data

Recent studies on the geography of knowledge networks have documented a negative impact of physical distance and institutional borders upon research and development (R&D) collaborations. Though it is widely recognized that geographic constraints hamper the diffusion of knowledge, less attention has been devoted to the temporal evolution of these constraints. In this study we use data on patents filed with the European Patent Office (EPO) for 50 countries to analyze the impact of physical distance and country borders on inter-regional links in four different networks over the period 1988-2009: (1) co-inventorship, (2) patent citations, (3) inventor mobility and (4) the location of R&D laboratories. We find the constraint imposed by country borders and distance decreased until mid-1990s then started to grow, particularly for distance. The intensity of European cross-country inventor collaborations increased at a higher pace than their non-European counterparts until 2004, with no significant relative progress afterwards. Moreover, when analyzing networks of geographical mobility, multinational R&D activities and patent citations we do not depict any substantial progress in European research integration aside from the influence of common global trends

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.Comment: 14 pages, 5 figure

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 $\Delta c$ 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.Comment: Final published version of the main manuscript including additional analysis: 9 pages, 4 figures, 1 table, and full reference list, including those in the Supplementary Information. For the SI Appendix, see http://physics.bu.edu/~amp17/webpage_files/MyPapers/Reputation_SI.pd

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.Comment: 10 pages, 5 figures. Edited for typos, clarity, figures improved for readabilit

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.Comment: 19 pages + 16 pages of supplementary materia