Carl T. Bergstrom's research while affiliated with University of Washington Seattle and other places

Publications (167)

Article
Authors of biomedical research should provide clear and accurate information to society, whilst working to combat misinformation and disinformation.
Preprint
Natural selection enriches genotypes that are well-adapted to their environment. Over successive generations, these changes to the frequencies of types accumulate information about the selective conditions. Thus, we can think of selection as an algorithm by which populations acquire information about their environment. Kimura (1961) pointed out tha...
Preprint
Replication surveys are becoming a common tool for assessing the knowledge production of scientific disciplines. In psychology, economics, and preclinical cancer biology, replication rates near 50% have been argued as evidence the disciplines are not reliably producing knowledge, are rife with questionable research practices, and warrant reform. Co...
Article
Significance Science operates within social structures that govern and shape scientific activity. One such institution is peer review, which focuses attention on promising and interesting science while encouraging scientists to pursue some questions instead of others. Here, we show that ex ante review of proposals for future work and ex post review...
Article
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Significance As the COVID-19 pandemic drags on, we need strategies for reopening those schools that have remained closed. We developed stochastic network models to study the risks associated with returning to in-person learning during the COVID-19 pandemic, and to explore the value of mitigation measures in reducing these risks. Our models indicate...
Preprint
During the initial stages of the COVID-19 pandemic, many workplaces and universities implemented institution-wide proactive testing programs of all individuals, ir-respective of symptoms. These measures have proven effective in mitigating outbreaks. As a greater fraction of the population becomes vaccinated, we need to understand what continued ben...
Article
Bergstrom, Carl T. and Jevin D. West. 2020. Calling Bullshit: The Art of Skepticism in a Data-Driven World. (New York: Random House) 336 pp. ISBN 978-0525509202. While statistical methods receive greater attention, the art of critically evaluating information in everyday life more commonly depends on thinking outside the black box of the algorithm....
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We explore the commonalities between methods for assuring the security of computer systems (cybersecurity) and the mechanisms that have evolved through natural selection to protect vertebrates against pathogens, and how insights derived from studying the evolution of natural defenses can inform the design of more effective cybersecurity systems. Mo...
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Collective behavior provides a framework for understanding how the actions and properties of groups emerge from the way individuals generate and share information. In humans, information flows were initially shaped by natural selection yet are increasingly structured by emerging communication technologies. Our larger, more complex social networks n...
Preprint
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Peer review is an integral component of contemporary science. While peer review focuses attention on promising and interesting science, it also encourages scientists to pursue some questions at the expense of others. Here, we use ideas from forecasting assessment to examine how two modes of peer review -- ex ante review of proposals for future work...
Article
BACKGROUND . The increasing availability of digital data on scholarly inputs and outputs – from research funding, productivity, and collaboration to paper citations and scientist mobility – offers unprecedented opportunities to explore the structure and evolution of science. The science of science (SciSci) offers a quantitative understanding of the...
Article
Humans learn about the world by collectively acquiring information, filtering it, and sharing what we know. Misinformation undermines this process. The repercussions are extensive. Without reliable and accurate sources of information, we cannot hope to halt climate change, make reasoned democratic decisions, or control a global pandemic. Most analy...
Preprint
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Reopening schools is an urgent priority as the COVID-19 pandemic drags on throughout much of the world. To explore the risks associated with returning to in-person learning and the value of mitigation measures in a school setting, we use the stochastic, network-based SEIRS+ epidemiological modeling platform to simulate SARS-CoV-2 transmission in sc...
Preprint
The SARS-CoV-2 coronavirus has proven difficult to control not only because of its high transmissibility, but because those who are infected readily spread the virus before symptoms appear, and because some infected individuals, though contagious, never exhibit symptoms. Proactive testing of asymptomatic individuals is therefore a powerful, and pro...
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"Signals" are a conceptual apparatus in many scientific disciplines. Biologists inquire about the evolution of signals, economists talk about the signaling function of purchases and prices, and philosophers discuss the conditions under which signals acquire meaning. However, little attention has been paid to what is a signal. This paper is an attem...
Preprint
Using the corpus of JSTOR articles, we investigate the role of gender in collaboration patterns across the scholarly landscape by analyzing gender-based homophily--the tendency for researchers to co-author with individuals of the same gender. For a nuanced analysis of gender homophily, we develop methodology necessitated by the fact that the data c...
Article
An analysis shows that information flow between individuals in a social network can be ‘gerrymandered’ to skew perceptions of how others in the community will vote — which can alter the outcomes of elections. Network rewiring can alter perception of others’ voting intentions.
Data
Parallel results to Fig 2, except with the second alternative parameter set. See S1 Text for parameter values in this alternative parameter set. (EPS)
Data
Random samples from copula distributions used to model error in assessment of grant proposals. A: Clayton copula with θ = 10. B: Clayton copula with θ = 5. Blue dashed lines give the median of the assessed quantile as a function of the actual quantile. (TIF)
Data
Parallel results to Fig 3, except with the first alternative parameter set. Note that the vertical axis in panel A does not extend to 0. (EPS)
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Mathematical details. (PDF)
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Parallel results to Fig 2, except with perfect assessment of proposal strength. All other parameter values are the same as in Fig 2. (EPS)
Data
Parallel results to Fig 3, except with perfect assessment of proposal strength. All other parameter values are the same as in Fig 3. Note that the vertical axis in panel A does not extend to 0. (EPS)
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The success rate of grant proposals for NIH R01 and equivalents has declined substantially over the past 50 years. Data from FY 1962–2008 include R01, R23, R29, and R37 proposals, as reported by NIH's Office of Extramural Research [34]. Data from 1962–1969 are NIH estimates. Data for FY 2009–2016 include R01 and R37 proposals, as reported by [2] (R...
Data
Parallel results to Fig 3 for a three-tier lottery with equally sized tiers and a 3:2:1 ratio of funding probabilities across the tiers. The horizontal axis gives the proportion of proposals that qualify for any tier of the lottery. Scientific value and scientific waste per funded proposal are independent of the actual payline, as long as the payli...
Data
Parallel results to Fig 3, except with the second alternative parameter set. In this figure, data are shown for paylines ranging from p = 0.001 to p = 0.999. Note that the vertical axis in panel A does not extend to 0. (EPS)
Data
Parallel results to Fig 2, except with the first alternative parameter set. See S1 Text for parameter values in this alternative parameter set. (EPS)
Preprint
Scatter plots carry an implicit if subtle message about causality. Whether we look at functions of one variable in pure mathematics, plots of experimental measurements as a function of the experimental conditions, or scatter plots of predictor and response variables, the value plotted on the vertical axis is by convention assumed to be determined o...
Article
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Scientific research funding is allocated largely through a system of soliciting and ranking competitive grant proposals. Funding agencies use these contests not to extract work form participants, but rather as a screening mechanism intended to reveal the most promising research. At a first approximation, the work invested in writing proposals provi...
Preprint
How common is self-citation in scholarly publication, and does the practice vary by gender? Using novel methods and a data set of 1.5 million research papers in the scholarly database JSTOR published between 1779 and 2011, the authors find that nearly 10 percent of references are self-citations by a paper’s authors. The findings also show that betw...
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The whys and wherefores of SciSci The science of science (SciSci) is based on a transdisciplinary approach that uses large data sets to study the mechanisms underlying the doing of science—from the choice of a research problem to career trajectories and progress within a field. In a Review, Fortunato et al. explain that the underlying rationale is...
Article
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How common is self-citation in scholarly publication, and does the practice vary by gender? Using novel methods and a data set of 1.5 million research papers in the scholarly database JSTOR published between 1779 and 2011, the authors find that nearly 10 percent of references are self-citations by a paper’s authors. The findings also show that betw...
Article
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Science is facing a "replication crisis" in which many experimental findings cannot be replicated and are likely to be false. Does this imply that many scientific facts are false as well? To find out, we explore the process by which a claim becomes fact. We model the community's confidence in a claim as a Markov process with successive published re...
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Depression and anxiety disorders inflict untold harm on an enormous number of people. In the United States in a single year, nearly 10% of the population will suffer from a mood disorder and more than 20% will suffer from an anxiety disorder. Over the course of a lifetime, these numbers increase to 20% for mood disorders and 30% for anxiety disorde...
Article
Microsoft Research hosted the 2016 WSDM Cup Challenge based on the Microsoft Academic Graph. The goal was to provide static rankings for the articles that make up the graph, with the rankings to be evaluated against those of human judges. While the Microsoft Academic Graph provided metadata about many aspects of each scholarly document, we focused...
Article
The scholarly literature is expanding at a rate that necessitates intelligent algorithms for search and navigation.For the most part, the problem of delivering scholarly articles has been solved. If one knows the title of an article, locating it requires little effort and, paywalls permitting, acquiring a digital copy has become trivial. However, t...
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Scientists pursue collective knowledge, but they also seek personal recognition from their peers. When scientists decide whether or not to work on a big new problem, they weigh the potential rewards of a major discovery against the costs of setting aside other projects. These self-interested choices can potentially spread researchers across problem...
Article
To the Editor: For all the understandable uproar over the term "research parasites" - an inflammatory term that gives short shrift to how open data changed our understanding of Tamiflu, Paxil, and other treatments - those of us who support increased data sharing should realize that Drazen and Longo(1),(2) were giving voice to an opinion that many r...
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Theoretical ideas have a rich history in many areas of biology, and new theories and mathematical models have much to offer in the future.
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Modelling of the interactions between antibiotic production and antibiotic degradation reveals that these opposing activities are key to maintaining diversity in microbial communities. See Letter p.516
Article
We use an information-theoretic approach to describe changes in lending relationships between financial institutions around the time of the Lehman Brothers failure. Unlike previous work that conducts maximum likelihood estimation on undirected networks our analysis distinguishes between borrowers and lenders and looks for broader lending relationsh...
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Normal anxiety is considered an adaptive response to the possible presence of danger, but it appears highly susceptible to dysregulation. Anxiety disorders are prevalent at high frequency in contemporary human societies, yet impose substantial disability upon their sufferers. This raises a puzzle: why has evolution left us vulnerable to anxiety dis...
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Background: Although the emergence and spread of antibiotic resistance have been well studied for endemic infections, comparably little is understood for epidemic infections such as influenza. The availability of antimicrobial treatments for epidemic diseases raises the urgent question of how to deploy treatments to achieve maximum benefit despite...
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Two categories of evolutionary challenges result from escalating human impacts on the planet. The first arises from cancers, pathogens, and pests that evolve too quickly and the second, from the inability of many valued species to adapt quickly enough. Applied evolutionary biology provides a suite of strategies to address these global challenges th...
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Divergent interests, expertise, and language form cultural barriers to communication. No formalism has been available to characterize these “cultural holes.” Here we use information theory to measure cultural holes and demonstrate our formalism in the context of scientific communication using papers from JSTOR. We extract scientific fields from the...
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Open access publishing has been proposed as one possible solution to the serials crisis—the rapidly growing subscription prices in scholarly journal publishing. However, open access publishing can present economic pitfalls as well, such as excessive article processing charges. We discuss the decision that an author faces when choosing to submit to...
Conference Paper
Designing software for exploring hierarchical data sets is challenging because users can easily become lost in large hierarchies. We present a novel interface, the hoptree, to assist users with navigating large hierarchies. The hoptree preserves navigational history and context and allows one-click navigation to recently-visited locations. We descr...
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Abstract In many species, nongenetic phenotypic variation helps mitigate risk associated with an uncertain environment. In some cases, developmental cues can be used to match phenotype to environment-a strategy known as predictive plasticity. When environmental conditions are entirely unpredictable, generating random phenotypic diversity may improv...
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Costly signalling theory is commonly invoked as an explanation for how honest communication can be stable when interests conflict. However, the signal costs predicted by costly signalling models often turn out to be unrealistically high. These models generally assume that signal cost is determinate. Here, we consider the case where signal cost is i...
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Gender disparities appear to be decreasing in academia according to a number of metrics, such as grant funding, hiring, acceptance at scholarly journals, and productivity, and it might be tempting to think that gender inequity will soon be a problem of the past. However, a large-scale analysis based on over eight million papers across the natural s...
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Biogeographic patterns of survival help constrain the causal factors responsible for mass extinction. To test whether biogeography influenced end-Cretaceous (K-Pg) extinction patterns, we used a network approach to delimit biogeographic units (BUs) above the species level in a global Maastrichtian database of 329 bivalve genera. Geographic range is...
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The authors describe a classroom experiment designed to present the idea of two-sided matching, the concept of a stable assignment, and the Gale-Shapley deferred-acceptance mechanism. Participants need no prior training in economics or game theory, but the exercise will also interest trained economists and game theorists.
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One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change by the opponent. To study how...
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Costly signalling theory has become a common explanation for honest communication when interests conflict. In this paper, we provide an alternative explanation for partially honest communication that does not require significant signal costs. We show that this alternative is at least as plausible as traditional costly signalling, and we suggest a n...
Article
Carl Bergstrom assesses the power of scientometrics in predicting the shifts and shelf-life of knowledge.
Article
In this paper, we show how the Eigenfactor(R) score, originally designed for ranking scholarly journals, can be adapted to rank the scholarly output of authors, institutions, and countries based on authorlevel citation data. Using the methods described herein, we provide Eigenfactor rankings for 84,808 disambiguated authors of 240,804 papers in the...
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Structural controllability has been proposed as an analytical framework for making predictions regarding the control of complex networks across myriad disciplines in the physical and life sciences (Liu et al., Nature:473(7346):167-173, 2011). Although the integration of control theory and network analysis is important, we argue that the application...
Article
Full-text available
One strategy for winning a coevolutionary struggle is to evolve rapidly. Most of the literature on host-pathogen coevolution focuses on this phenomenon, and looks for consequent evidence of coevolutionary arms races. An alternative strategy, less often considered in the literature, is to deter rapid evolutionary change by the opponent. To study how...
Article
The interface between evolutionary biology and the biomedical sciences promises to advance understanding of the origins of genetic and infectious diseases in humans, potentially leading to improved medical diagnostics, therapies, and public health practices. The biomedical sciences also provide unparalleled examples for evolutionary biologists to e...
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Evolutionary biology provides an essential perspective on the determinants of health and disease, believe Peter Gluckman and Carl Bergstrom. It needs to be further integrated into medical research and teaching
Article
When a group needs to reach a consensus decision, uninformed members can help to reduce the infl uence of a manipulative minority.
Article
We use an information-theoretic approach to describe changes in lending relationships between federal funds market participants around the time of the Lehman Brothers failure. Unlike previous work that conducts maximum-likelihood estimation on undirected networks, our analysis distinguishes between borrowers and lenders and looks for broader lendin...
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Full-text available
To comprehend the hierarchical organization of large integrated systems, we introduce the hierarchical map equation, which reveals multilevel structures in networks. In this information-theoretic approach, we exploit the duality between compression and pattern detection; by compressing a description of a random walker as a proxy for real flow on a...
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Evolutionary principles are now routinely incorporated into medicine and agriculture. Examples include the design of treatments that slow the evolution of resistance by weeds, pests, and pathogens, and the design of breeding programs that maximize crop yield or quality. Evolutionary principles are also increasingly incorporated into conservation bi...
Article
Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and...
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We continue investigation of the effect of position in announcements of newly received articles, a single day artifact, with citations received over the course of ensuing years. Earlier work focused on the “visibility” effect for positions ...
Article
The Eigenfactor Metrics provide an alternative way of evaluating scholarly journals based on an iterative ranking procedure analogous to Google's PageRank algorithm. These metrics have recently been adopted by Thomson-Reuters and are listed alongside the Impact Factor in the Journal Citation Reports. But do these metrics differ sufficiently so as t...
Article
Limited time and budgets have created a legitimate need for quantitative measures of scholarly work. The well-known journal impact factor is the leading measure of this sort; here we describe an alternative approach based on the full structure of the scholarly citation network. The Eigenfactor Metrics-Eigenfactor Score and Article Influence Score-u...
Article
Communication and information are central concepts in evolutionary biology. In fact, it is hard to find an area of biology where these concepts are not used. However, quantifying the information transferred in biological interactions has been difficult. How much information is transferred when the first spring rainfall hits a dormant seed, or when...
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Change is a fundamental ingredient of interaction patterns in biology, technology, the economy, and science itself: Interactions within and between organisms change; transportation patterns by air, land, and sea all change; the global financial flow changes; and the frontiers of scientific research change. Networks and clustering methods have becom...
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Mapping change in physics & chemistry 1997–2007 (0.06 MB PDF)
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Mapping change in medicine 1997–2007 (0.07 MB PDF)
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Here we briefly review our information theoretic approach to revealing community structure in weighted and directed networks and present a new fast stochastic and recursive search algorithm to minimize the map equation — the objective function of our method. (0.14 MB PDF)
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New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to utilize them fully. This article summarizes suggestions from several groups who have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and...
Article
Control measures used to limit the spread of infectious disease often generate externalities. Vaccination for transmissible diseases can reduce the incidence of disease even among the unvaccinated, whereas antimicrobial chemotherapy can lead to the evolution of antimicrobial resistance and thereby limit its own effectiveness over time. We integrate...
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Control measures used to limit the spread of infectious disease often generate externalities. Vaccination for transmissible diseases can reduce the incidence of disease even among the unvaccinated, whereas antimicrobial chemotherapy can lead to the evolution of antimicrobial resistance and thereby limit its own effectiveness over time. We integrate...
Article
Full-text available
New applications of evolutionary biology in medicine are being discovered at an accelerating rate, but few physicians have sufficient educational background to use them fully. This article summarizes suggestions from several groups that have considered how evolutionary biology can be useful in medicine, what physicians should learn about it, and wh...
Article
Although powerful, list searches have their limitations. Using second order bibliometric operators \citep{kurtz02} in the SAO/NASA Astrophysics Data System (ADS), one is able to easily find review papers or the most popular papers on a given subject. Because of their one-dimensionality, lists cannot display a rich context for a given paper. The bes...
Conference Paper
well--formed.eigenfactor presents interactive visualizations to explore emerging patterns in scientific citation networks. The Eigenfactor project calculates a measure of importance for individual journals -- the Eigenfactor score -- as well as measures of citation flow and a hierarchical clustering based thereon. Moritz Stefaner turns this informa...
Conference Paper
well-formed.eigenfactor presents interactive visualizations to explore emerging patterns in scientific citation networks. The Eigenfactor project calculates a measure of importance for individual journals (the Eigenfactor score), measures citation flow, and creates a hierarchical clustering. Moritz Stefaner turns this information into a set of four...
Article
Many real-world networks are so large that we must simplify their structure before we can extract useful information about the systems they represent. As the tools for doing these simplifications proliferate within the network literature, researchers would benefit from some guidelines about which of the so-called community detection algorithms are...
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Social function and organization are predicated on effective coordination and cooperation; these in turn require honest communication among the participants in a social group. But in order to facilitate any sort of social structure and interaction, there has to be some way to deal with the threat of deception. We see this not only at the level of c...
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We provide simple formulas that can be used to calculate ideal bootstrap or exact recombination estimates of group statistics from experimental data.
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The bibliometric measure impact factor is a leading indicator of journal influence, and impact factors are routinely used in making decisions ranging from selecting journal subscriptions to allocating research funding to deciding tenure cases. Yet journal impact factors have increased gradually over time, and moreover impact factors vary widely acr...
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