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

The Hubble Space Telescope Survey of M31 Satellite Galaxies. II. The Star Formation Histories of Ultrafaint Dwarf Galaxies

We present the lifetime star formation histories (SFHs) for six ultrafaint dwarf (UFD; M V > − 7.0, 4.9 < log 10 ( M * ( z = 0 ) / M ⊙ ) < 5.5 ) satellite galaxies of M31 based on deep color-magnitude diagrams constructed from Hubble Space Telescope imaging. These are the first SFHs obtained from the oldest main-sequence turnoff of UFDs outside the halo of the Milky Way (MW). We find that five UFDs formed at least 50% of their stellar mass by z = 5 (12.6 Gyr ago), similar to known UFDs around the MW, but that 10%-40% of their stellar mass formed at later times. We uncover one remarkable UFD, And xiii, which formed only 10% of its stellar mass by z = 5, and 75% in a rapid burst at z ∼ 2-3, a result that is robust to choices of underlying stellar model and is consistent with its predominantly red horizontal branch. This “young” UFD is the first of its kind and indicates that not all UFDs are necessarily quenched by reionization, which is consistent with predictions from several cosmological simulations of faint dwarf galaxies. SFHs of the combined MW and M31 samples suggest reionization did not homogeneously quench UFDs. We find that the least-massive MW UFDs (M *(z = 5) ≲ 5 × 104 M ⊙) are likely quenched by reionization, whereas more-massive M31 UFDs (M *(z = 5) ≳ 105 M ⊙) may only have their star formation suppressed by reionization and quench at a later time. We discuss these findings in the context of the evolution and quenching of UFDs. © 2023. The Author(s). Published by the American Astronomical Society.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]