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Mitigating Biases in CORD-19 for Analyzing COVID-19 Literature

Authors

  • Anshul Kanakia
  • Kuansan Wang
  • Yuxiao Dong
  • Boya Xie
  • Kyle Lo
  • Zhihong Shen
  • Lucy Lu Wang
  • Chiyuan Huang
  • Darrin Eide
  • Sebastian Kohlmeier
  • Chieh-Han Wu
  • Frontiers in Research Metrics and Analytics
  • 2020
  • View in Semantic Scholar

Abstract

On the behest of the Office of Science and Technology Policy in the White House, six institutions, including ours, have created an open research dataset called COVID-19 Research Dataset (CORD-19) to facilitate the development of question-answering systems that can assist researchers in finding relevant research on COVID-19. As of May 27, 2020, CORD-19 includes more than 100,000 open access publications from major publishers and PubMed as well as preprint articles deposited into medRxiv, bioRxiv, and arXiv. Recent years, however, have also seen question-answering and other machine learning systems exhibit harmful behaviors to humans due to biases in the training data. It is imperative and only ethical for modern scientists to be vigilant in inspecting and be prepared to mitigate the potential biases when working with any datasets. This article describes a framework to examine biases in scientific document collections like CORD-19 by comparing their properties with those derived from the citation behaviors of the entire scientific community. In total, three expanded sets are created for the analyses: 1) the enclosure set CORD-19E composed of CORD-19 articles and their references and citations, mirroring the methodology used in the renowned “A Century of Physics” analysis; 2) the full closure graph CORD-19C that recursively includes references starting with CORD-19; and 3) the inflection closure CORD-19I, that is, a much smaller subset of CORD-19C but already appropriate for statistical analysis based on the theory of the scale-free nature of the citation network. Taken together, all these expanded datasets show much smoother trends when used to analyze global COVID-19 research. The results suggest that while CORD-19 exhibits a strong tilt toward recent and topically focused articles, the knowledge being explored to attack the pandemic encompasses a much longer time span and is very interdisciplinary. A question-answering system with such expanded scope of knowledge may perform better in understanding the literature and answering related questions. However, while CORD-19 appears to have topical coverage biases compared to the expanded sets, the collaboration patterns, especially in terms of team sizes and geographical distributions, are captured very well already in CORD-19 as the raw statistics and trends agree with those from larger datasets.

Introduction

Since first reported to the WHO in December 2019, the COVID-19 pandemic has been wreaking havoc around the globe, causing staggering loss of lives and livelihood. A key reason for its lasting power is that modern medicine has yet to find effective means to prevent or treat COVID-19 caused by a novel coronavirus. Nevertheless, the response from the research community has been swift and intense since the onset of the outbreak. Major publishers have all expedited the peer review and publication of research on COVID-19 (Horbach, 2020) , resulting in an impressive growth in the literature on this subject that has surpassed 3,500 new titles per week by mid-March (Microsoft Research, 2020) . After 3 months, the growth in the research literature only sees acceleration and no sign of abating (Hutson, 2020) . Facing the daunting task of tracking the voluminous new studies arriving at an unprecedented rate and motivated by the remarkable advancements in artificial intelligence (AI) in recent years, the U.S. Office of Science and Technology Policy in the White House (WH/OSTP) has challenged the research community to develop intelligent agents that can effectively sift through the literature and assist scientists and policy makers alike. Specifically, the WH/OSTP has led the launch of an open question-answering challenge hosted on Kaggle (Kaggle, 2020) and three new tracks in the long-running Text REtrieval Conference organized by the National Institute of Standards and Technology that has given birth to pivotal theoretical and technological components behind modern Web search engines and conversational systems. The has been created to support these efforts. It is comprised of research articles whose fulltext contents are made publicly available for the purpose of text and data mining without infringing on the rights of the owners. The genesis and the details of CORD-19 are described in Wang L. L. et al. (2020) , and a comparison to other collections (Colavizza et al., 2020) indicates many relevant articles still are not included into . The study of Colavizza et al. (2020) is based on running the same article retrieval query used for CORD-19 on other commercial search engines from Web of Science and Dimensions. As noted in , the keyword search approach can inadvertently include biases from the search engine designers and their content curators. Because the biases are implicit and undisclosed, it is difficult to tease apart whether the differences in corpus coverage are merely the result of search engines having different design approaches or whether substantive contents are indeed missing from An approach to mitigate the search and the curation biases is to crowdsource to the domain experts by exploiting their citation behaviors in their scholarly communications. This is the method employed by Sinatra et al. (2015) to analyze physics literature in "A Century of Physics." Their approach starts with a seed collection of research articles from a few hand-picked journals that is then expanded to include articles citing and cited by the seed collection. In other words, the corpus is constructed by a single-step traversal on the citation network in either direction, effectively forming an "enclosure" of the seed collection. The enclosure provides a more holistic view into how pivotal research is inspired by the prior art and how the impact is felt throughout the research community. The larger size also lends itself to more robust analytics using statistical methods. The motivation behind creating the CORD-19 corpus shares the same objectives, namely, to understand what knowledge has been exploited to attack the COVID-19 pandemic, where the potentially impactful research activities are taking place, and what opportunities exist for broader collaborations. These studies, however, must be conducted with extreme caution, especially given recent years have seen ample instances in which biases in datasets or methodologies have led to unintended and sometimes harmful consequences to the societies (Ntoutsi et al., 2020) . While the rest of this article is devoted to the data biases of CORD-19, the enclosure corpus using CORD-19 as the seed collection, called CORD-19E below, appears to be a reasonable starting point but with important drawbacks:

(1) By design, the enclosure is susceptible to selection bias in the seed collection: just consider the extreme case where the seed collection consists of a single article, which is unlikely to cite all the relevant prior art. (2) Following both citations and references over multiple expansion steps from a seed collection quickly results in an explosion of the included literature that quickly loses topical focus. Furthermore, there does not seem to be a straightforward enhancement to generalize the single-step traversal as described in Sinatra et al. (2015) to a multi-step algorithm that can systemically augment the article collection without immediate topical digression from the seeds.

The latter problem is particularly noticeable when CORD-19 articles utilize advanced techniques from other fields like optics, instrumentation, big data analytics, or machine learning and cite the pertinent literature. More than one-hop traversal of the citation and reference networks together-a bidirectional graph-quickly grows the collection to include articles that bear little relevance to COVID-19 research as these techniques are widely adopted in diverse fields of study. For example, if an article in the original CORD-19 dataset utilizes the ImageNet technique for medical image analysis and references (Russakovsky et al., 2015; Krizhevsky et al., 2017) and this citation is subsequently bidirectionally expanded, the resulting dataset would include all 80,000 plus articles that also cite ImageNet that have little to do with the problem of COVID-19. Simply put, the bidirectional citation enclosure for more than one hops generalizes the resultant collection too quickly and loses the focus of the initial seed literature in just two iterations.

To overcome this difficulty, we posit that even though articles sometimes reference work outside of their main theme, their references overall are dominated by relevant work. This observation motivates another method to follow only the references but not the citations, iteratively, thereby augment the seed collection with unidirectional multi-step traversals on the citation network. The iterative traversal will eventually converge to an article collection, known as the "closure graph" (Cook et al., 1997) in the network science literature, where all references are made to articles within the collection itself.

The motivation of using a closure graph is further bolstered by a widely observed phenomenon that citation networks assume a power law distribution (Redner, 1998) , that is, appear to be scalefree. The mechanisms toward forming scale-free networks have seen many theoretical developments, ranging from the preferential attachment (Barabasi and Albert, 1999), homophily (McPherson et al., 2001) , node fitness (Caldarelli et al., 2002) to temporal stochastic models (Leskovec et al., 2007) , just to name a few. Despite remnant controversies (Broido and Clauset, 2019; Holme, 2019) , these theories have recently been unified into a single mathematical framework, called a discrete choice model (Overgoor et al., 2019) , in which a new member is modeled to connect to an existing network by employing a logit utility function that evaluates the plausible choices. In the context of citation networks, this mechanism is consistent with the notion that a scholarly article will primarily reference the prior art that is most important and relevant to its contents. One can thus trace COVID-19 research by following the references recursively from articles in a seed collection, turning the quest into a problem of solving the closure of CORD-19. Any initial selection bias in the seed collection may thus be alleviated by following the iterative expansion to a closure, provided the assumption about citing predominantly relevant work holds. Due to these desirable theoretical and mathematical properties, the closure graph of CORD-19-henceforth called CORD-19C-is discussed and primarily analyzed in this work.

The closure graph method is a variant of the community detection approaches based on network traversing, with a difference that the manner in which the underlying network is explored here is systematic and deterministic as opposed to random walks (e.g., Girvan and Newman, 2002; Rosvall and Bergstrom, 2008; Fortunato and Hric, 2016) . Network traversing, while being straightforward from a computational point of view, does have an unsolved problem in overgeneralization, namely, how to avoid including the entire network by drawing a clear boundary within which a community shares strong common properties among its constituents. This issue is particularly critical here because, modern research being highly interdisciplinary in nature, a full closure inevitably will contain articles that are rather remote to the core research topics of the seeds, and this can take place as early as the first hop as noted previously in To address this issue, this work further proposes a pragmatic yet theoretically well-motivated approach by using the rate of encountering new articles during network traversal as a stop criterion to avoid overgeneralization. If scholarly articles indeed make predominantly relevant references as hypothesized in the discrete choice model, the acceleration of reaching new articles by walking the citation networks should decrease from the initial quasi-exponential expansions to an inflection point beyond which the newly encountered articles are less relevant to the seeds. The empirical evidence below suggests a partial closure terminated at the inflection point, called the "inflection closure" or CORD-19I, which leads to a collection that maintains topical focus on the initial seed while retaining many desirable properties of the full closure. Namely, the inflection closure already provides a large enough landscape from which broader trends, lineages, and other aggregate properties of the research represented by the seeds can be derived.

The main contribution of this work is to provide a critical inspection on the CORD-19 dataset and demonstrate the areas in which CORD-19 will be a biased source for literature analyses. Most interestingly, the method of using the full closure to identify biases in CORD-19 leads to a discovery that a partial closure at the infection point seems to be an economic, yet effective, means to mitigate these biases. In the following, the citation data and the methods of computing the closure graphs are first described in detail before demonstrating their effectiveness. As there are potentially unlimited areas for which CORD-19 and its expanded datasets can be used, this article is scoped to mainly demonstrate a few rudimentary areas where the biases can emerge, especially for the purposes of identifying important publication venues to follow and vital trending topics to track. To balance the unintended perception that CORD-19 is a totally biased dataset, an area that it seems to sample the research articles well, namely, in describing the patterns of collaborations, is also provided. The raw data behind these analyses are embedded into the figures included in the Supplementary Materials.

Data And Methods

As the research activities on COVID-19 are ongoing, CORD-19 is a fast-growing dataset. Since its first release on March 16, 2020, CORD-19 has more than doubled its size from 29,000 articles to more than 60,000 on April 17, 2020, and then again to almost 120,000 articles in May 2020. Although the analyses reported in this article are solely based on the April 17, 2020 release of CORD-19, the most up-to-date versions of CORD-19 and the corresponding closure graphs are released regularly at https://www.semanticscholar.org/cord19 and https://aka.ms/ magcord19mapping, respectively.

For this work, the snapshot of Microsoft Academic Graph (Sinha et al., 2015; , or MAG, taken on the same date is used to obtain the enclosure, the inflection, and the closure graphs. The articles in CORD-19 are first identified in MAG for expanding their citation network. Once CORD-19 articles are mapped to MAG, the citation network in MAG is traversed for creating the enclosure CORD-19E as well as the full/ inflection closures CORD-19C/CORD-19I using a breadth-first search algorithm. The articles in the April 17 version of CORD-19 are mapped to 48,526 unique seed articles in MAG. The discrepancies can be largely attributed to the following:

(1) MAG is updated approximately on a weekly basis based on the Web crawl from the week before (Wang et al., 2019) . Therefore, the April 17, 2020 version of MAG only contains contents published before April 10, 2020. Articles published after April 10 are not available in the April 17 version of MAG. (2) Unlike CORD-19 in which articles with distinct DOIs are treated as unique articles, MAG combines articles of the same contents into a single entity even though they are assigned distinct DOIs. The motivations behind this design choice are described in Wang L. L. et al. (2020) . Consequently, multiple articles in CORD-19 may be mapped to the same article in MAG. (3) Similarly, articles with the same contents, but significantly different publication dates are treated as a single entity in MAG but as distinct in . A major source of the discrepancies can be observed between the records in PubMed and from the publishers themselves. (4) CORD-19 honors unique identification assignments on articles tracked by the WHO. Unfortunately, the WHO's data systematically treats Chinese journals in English translation and transliteration as they are distinct (e.g., "Chinese Journal of Stomatology" vs. "Zhonghua Kou Qiang Yi Xue Za Zhi"), leading to duplicate entries for every article in those journals from MAG's perspective. (5) MAG fails to recognize some articles as distinct mostly because they have same titles and author lists (e.g., "Infectious disease surveillance update" by R. Heald).

Construction Of Covid-19 Research Dataset-19E

All referenced articles are admitted into the collection for the purpose of computing the enclosure, regardless of the properties-such as citation count, venue, and importance-of the citing or the cited articles. In total, the CORD-19E contains 926,281 references and 505,060 citations, that is, articles cited by and citing CORD-19, respectively. In total, these 1,479,867 articles correspond to 0.6% of articles indexed by MAG. Within CORD-19E, the citation edges terminated at the seed articles, the references, and the citations are 1,362,025, 136,692,815, and 7,903,302, accounting for 0.085, 8.5, and 0.5% of the citation edges in MAG, respectively. Please note that the terms "references" and "citations" are not interchangeable in this article: when article A cites article B, A is called a citation of B while B, a reference of A.

Construction And Convergence Of Covid-19 Research Dataset-19I And Covid-19 Research Dataset-19C

To construct the closure graphs, the literature abounds with iterative algorithmic designs, for example, beam search, bestfirst, or the mathematically optimal A* search (Cook et al., 1997) , but those algorithms require additional heuristics that can accurately assess the importance of each article, itself an actively researched topic. This study reports only the results for with the most straightforward breadth-first algorithm as no material differences have been observed in the converged outcomes from these other alternatives for this application. Each iterative citation expansion step of the current collection of articles in the graph is called a "hop." Figure 1 shows the cumulative number of articles at the end of each hop, with hop 0 being the CORD-19 collection. Not surprisingly, the collection exhibits an exponential growth pattern in the early hops because each article typically cites more than one other article. However, as elaborated earlier, the growth eventually slows when most important articles are encountered after a few hops. Based on the recent CORD-19 releases, the inflection point leading to CORD-19I typically takes place after three hops, although it takes approximately 11 hops to see the growth rate reaching below 0.5% of the total article counts, at which point the closure is considered reached in this work. As shown in Figure 1 , the inflection and the closure graphs, denoted for the rest of the article as respectively, have more than 22 million and 59 million nodes (articles), and 731 million and 966 million edges (citation links). In other words, they cover approximately 9 and 25% of the articles but 45 and 60% of the citation links of MAG, respectively. In addition to different search algorithms, variations in the seed document collection, such as the experiments mentioned in Colavizza et al. (2020) , are also replicated with MAG, and no substantial differences are observed in the converged closure, suggesting the closure graphs are relatively stable and reliable bases to broadly understand the COVID-19 research.

FIGURE 1 | Accumulated paper and citation counts per hop of the closure graph expansion. The callouts are article counts for COVID-19 Research Dataset (CORD-19) (seed), CORD-19I (hop 3), and CORD-19C (hop 11).

It is long known that citation networks must be analyzed carefully because not all nodes and edges are equally important (Price, 1965) . Particularly, since it takes time for a publication to receive its due recognition, using the simple citation count as a measure for article importance has an intrinsic age bias favoring older articles. To mitigate this bias, MAG uses a measure, called saliency, that utilizes reinforcement learning to acquire the optimal strategy in assessing article importance (Wang et al., 2019) . Figure 2 shows the aggregate saliencies of articles from the seed collection to the closure graphs. As saliency is a probabilistic measure, the information theoretical entropy that quantifies the information amount can be computed from it and shown also in Figure 2 . As can be seen, the full closure CORD-19C eventually accounts for 68.1% of all the probability mass and its information amount reaches 11.68 nits, out of 16.0 nits of the entire MAG, or 73%. In contrast, the partial closure at the inflection point, amounts to 38.6% and 6.46/16 40.37% of the saliencies and information of the entire MAG. These measures show CORD-19I and CORD-19C account for more important contents out of the entire scholarly publications in MAG than their portion of the node and edge counts may suggest.

FIGURE 2 | Information density represented as entropy in nits, and saliency for each hop in the COVID-19 Research Dataset (CORD-19) closure graph expansion. As a reference, the entropy of the entire Microsoft Academic Graph dataset is 16 nits.

To understand how relevant the articles are to the CORD-19 throughout the hops toward the closure convergence, Figure 3 shows the average "embeddedness," as defined in Fortunato and Hric (2016) , of the articles, namely, the average ratio of citations received from within and outside of CORD-19C for articles encountered at each hop. The embeddedness of CORD-19 is 71.4%, and articles cited up to the inflection point have the average embeddedness above 64%. After the inflection point, the embeddedness monotonically decreases, finally reaching 19% at the closure. This observation is consistent with the explanations offered by various models unified under the discrete choice theory (Overgoor et al., 2019) where scholars use topical closeness as a criterion for choosing articles to cite.

FIGURE 3 | Embeddedness, as defined in (Fortunato and Hric, 2016), of the closure graph expansion per hop.

To further verify this observation, the distribution of article fields of study, using the algorithm described in Shen et al. (2018) , is shown in Figure 4 . Throughout the citation hopping process, the fields of biology, medicine, and chemistry dominate, with the portion of these three fields accounting for 50.4, 38.0, and 3.9% of the articles at CORD-19, respectively. By the inflection point at , articles in medicine, at 28.3%, have overtaken biology at 26.7%, with the portion of articles in chemistry grown to 17.9%. Taken together, these top three fields comprise 92.3 and 73.9% of the articles in respectively. Agreeing with the trend shown with the embeddedness measure ( Figure 3) , articles from outside of the three fields start to increase in volume after the inflection point, eventually reaching 55.10% at the closure CORD-19C. Age Distributions of the COVID-19 Literature CORD-19 has a strong bias toward newer articles, while its three expanded datasets capture better how the current research is built on knowledge discovered in the years past. Figure 5 illustrates the article age distributions in these four collections by showing the percentage of articles versus their publication years. Note that all areas under the curve are normalized to 100% even though their volumes are orders of magnitude apart (cf. Figure 1) . Specifically, in CORD-19 where articles are dated back to the discovery of coronavirus in late 1960s, a whopping 12% of the articles are published in 2020. A steep jump in article counts can be seen in year 2003, corresponding to the major outbreak of SARS that is also caused by a novel coronavirus. In contrast, the expanded sets all show a gradual rise in articles from the decades before 2010, suggesting the scientific knowledge contributing to COVID-19 research today is accumulated over a long period of time. Based on the two closure graphs, CORD-19I or CORD-19C that bear remarkable identical results, the body of the research literature of year 2020 still accounts for 0.02% even with the flurry of the publications on the subject in the first few months of year. CORD-19E, which includes articles citing CORD-19, contains more articles in the recent years than the closure graphs. Still, CORD-19E has less than 2% of articles published in year 2020 and shows the literature of the past decades accounts for a larger presence than those in recent years as suggested by Aside from analyses based on article counts alone, Figure 6 shows the publication year distribution where the articles are further weighted by their respective importance. Again, while CORD-19 strongly emphasizes the importance of recent articles, the expanded datasets recognize more the contributions from the past decades. Specifically, both the citation counts (shown as dotted lines) and the saliencies are first computed as measurements for article importance before being aggregated for each publication year in Figure 6 . Here, the age bias in citations, reported to be 7-10 years as first noted in Price (1965) , manifests itself as the visibly lower citation counts for articles from the most recent decade. Their saliencies, designed to mitigate the age bias somewhat, shift the distribution toward more recent years. All expanded datasets indicate the articles in the decade before 2018 are more likely to be considered as important in the near future, as opposed to the CORD-19 results that suggest articles published in 2020 have an outsized probability, 13.2%, being cited against other CORD-19 articles, for example, 3.9% for those published in 2019 and 4.6% for 2018.

FIGURE 4 | Distribution of the top three high-level fields of study using Microsoft Academic Graph field stamping algorithm (Shen et al., 2018) on each expansion hop of the closure graph.
FIGURE 5 | Distribution of articles in percent per year for COVID-19 Research Dataset (CORD-19) (seed), CORD-19I (inflection), CORD-19C (closure), and the enclosure graph CORD-19E generated by the bidirectional citation expansion. Callouts are percentages for CORD-19 and CORD-19C for the years 2002, 2012, and 2019–2020, corresponding to the SARS, MERS, and COVID-19 outbreaks, respectively.