Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A Mixed User-Equilibrium and System-Optimal Traffic Flow for Connected Vehicles Stated as a Complementarity Problem

Connected vehicles (CVs), be they autonomous vehicles or a fleet of cargo carriers or Uber, are a matter of when they become a reality and not if. It is not unreasonable to think that CV technology may have a far-reaching impact, even to the genesis of a completely new traffic pattern. To this end, the literature has yet to address the routing behavior of the CVs, namely traffic assignment problem (TAP) (perhaps it is assumed, they ought to follow the traditional shortest possible paths, known as user equilibrium [UE]). It is possible that real-time data could be derived from the vehicles\u27 communications that in turn could be used to achieve a better traffic circulation. In this article, we propose a mathematical formulation to ensure the CVs are seeking the system optimal (SO) principles, while the remainder continue to pursue the old-fashioned UE pattern. The model is formulated as a nonlinear complementarity problem (NCP). This article contributes to the literature in three distinct ways: (i) mathematical formulation for the CVs\u27 routing, stated as a mixed UE-SO traffic pattern, is proposed; (ii) a variety of realistic features are explicitly considered in the solution to the TAP including road capacity, elastic demand, multiclass and asymmetric travel time; and (iii) formal proof of the existence and uniqueness of the solutions are also presented. The proposed methodology is applied to the networks of Sioux-Falls and Melbourne

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical science. © The Author(s) 2019. Published by Oxford University Press