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

Modeling human expertise on a cheese ripening industrial process using GP

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Cooperative coevolution for agrifood process modeling

On the contrary to classical schemes of evolutionary optimisations algorithms, single population Cooperative Co-evolution techniques (CCEAs, also called "Parisian" approaches) make it possible to represent the evolved solution as an aggregation of several individuals (or even as a whole population). In other words, each individual represents only a part of the solution. This scheme allows simulating the principles of Darwinian evolution in a more economic way, which results in gain in robustness and efficiency. The counterpart however is a more complex design phase. In this chapter, we detail the design of efficient CCEAs schemes on two applications related to the modeling of an industrial agri-food process. The experiments correspond to complex optimisations encountered in the modeling of a Camembert-cheese ripening process. Two problems are considered: A deterministic modeling problem, phase prediction, for which a search for a closed form tree expression is performed using genetic programming (GP). A Bayesian network structure estimation problem. The novelty of the proposed approach is based on the use of a two step process based on an intermediate representation called independence model. The search for an independence model is formulated as a complex optimisation problem, for which the CCEA scheme is particularly well suited. A Bayesian network is finally deduced using a deterministic algorithm, as a representative of the equivalence class figured by the independence model