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

Radiative forcing by well-mixed greenhouse gases: Estimates from climate models in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4)

The radiative effects from increased concentrations of well-mixed greenhouse gases (WMGHGs) represent the most significant and best understood anthropogenic forcing of the climate system. The most comprehensive tools for simulating past and future climates influenced by WMGHGs are fully coupled atmosphere-ocean general circulation models (AOGCMs). Because of the importance of WMGHGs as forcing agents it is essential that AOGCMs compute the radiative forcing by these gases as accurately as possible. We present the results of a radiative transfer model intercomparison between the forcings computed by the radiative parameterizations of AOGCMs and by benchmark line-by-line (LBL) codes. The comparison is focused on forcing by CO2, CH4, N2O, CFC-11, CFC-12, and the increased H2O expected in warmer climates. The models included in the intercomparison include several LBL codes and most of the global models submitted to the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4). In general, the LBL models are in excellent agreement with each other. However, in many cases, there are substantial discrepancies among the AOGCMs and between the AOGCMs and LBL codes. In some cases this is because the AOGCMs neglect particular absorbers, in particular the near-infrared effects of CH4 and N2O, while in others it is due to the methods for modeling the radiative processes. The biases in the AOGCM forcings are generally largest at the surface level. We quantify these differences and discuss the implications for interpreting variations in forcing and response across the multimodel ensemble of AOGCM simulations assembled for the IPCC AR4