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

E ?? B flow velocity deduced from the poloidal motion of fluctuation patterns in neutral beam injected L-mode plasmas on KSTAR

A method for direct assessment of the equilibrium E ?? B flow velocity (E??B flow shear is responsible for the turbulence suppression and transport reduction in tokamak plasmas) is investigated based on two facts. The first one is that the apparent poloidal rotation speed of density fluctuation patterns is close to the turbulence rotation speed in the direction perpendicular to the local magnetic field line within the flux surface. And the second well-known fact is that the turbulence rotation velocity consists of the equilibrium E ?? B flow velocity and intrinsic phase velocity of turbulence in the E ?? B flow frame. In the core region of the low confinement (L-mode) discharges where a strong toroidal rotation is induced by neutral beam injection, the apparent poloidal velocities (and turbulence rotation velocities) are good approximations of the E??B flow velocities since linear gyrokinetic simulations suggest that the intrinsic phase velocity of the dominant turbulence is significantly lower than the apparent poloidal velocity. In the neutral beam injected L-mode plasmas, temporal and spatial scales of the measured turbulence are studied by comparing with the local equilibrium parameters relevant to the ion-scale turbulence.clos

Study of ion-gyroscale fluctuations in low-density L-mode plasmas heated by NBI on KSTAR

Broadband density fluctuations with peak frequency ranging from 150 to 400 kHz were measured using a multichannel microwave imaging reflectometer in core region of the low-density L-mode plasmas heated by neutral beam injection on KSTAR. These fluctuations have been studied by comparing the dominant mode scales estimated from the measurement with those predicted from linear gyrokinetic simulation. The measured poloidal wavenumbers are qualitatively comparable to those of the 'fastest growing modes' from simulations, whereas they are larger than those of the 'transport-dominant modes' by about a factor of three. The agreement on wavenumbers between the measurement and linear simulation (for the fastest growing modes) is probably due to sufficiently weak E x B flow shear compared to the maximum linear growth rate. Meanwhile, the transport-dominant modes seem to be related to the fluctuations in lower frequencies (similar to 80-150 kHz) observed in some of the measurement