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

Dynamic analysis of a viscoelastic orthotropic cracked body using the extended finite element method

The extended finite element method (XFEM) is found promising in approximating solutions to locally non-smooth features such as jumps, kinks, high gradients, inclusions, voids, shocks, boundary layers or cracks in solid or fluid mechanics problems. The XFEM uses the properties of the partition of unity finite element method (PUFEM) to represent the discontinuities without the corresponding finite element mesh requirements. In the present study numerical simulations of a dynamically loaded orthotropic viscoelastic cracked body are performed using XFEM and the J-integral and stress intensity factors (SIF’s) are calculated. This is achieved by fully (reproducing elements) or partially (blending elements) enriching the elements in the vicinity of the crack tip or body. The enrichment type is restricted to extrinsic mesh-based topological local enrichment in the current work. Thus two types of enrichment functions are adopted viz. the Heaviside step function replicating a jump across the crack and the asymptotic crack tip function particular to the element containing the crack tip or its immediately adjacent ones. A constitutive model for strain-rate dependent moduli and Poisson ratios (viscoelasticity) is formulated. A symmetric double cantilever beam (DCB) of a generic orthotropic material (mixed mode fracture) is studied using the developed XFEM code. The same problem is studied using the viscoelastic constitutive material model implemented in ABAQUS through an implicit user defined material subroutine (UMAT). The results from XFEM correlate well with those of the finite element method (FEM). Three cases viz. static, dynamic and viscoelastic dynamic are studied. It is shown that there is an increase in the value of maximum J-integral when the material exhibits strain rate sensitivity