19 research outputs found

    Large expert-curated database for benchmarking document similarity detection in biomedical literature search

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    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

    Optimal Hermite Collocation Applied to a One-Dimensional Convection-Diffusion Equation Using an Adaptive Hybrid Optimization Algorithm

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    Purpose – The Hermite collocation method of discretization can be used to determine highly accurate solutions to the steady-state one-dimensional convection-diffusion equation (which can be used to model the transport of contaminants dissolved in groundwater). This accuracy is dependent upon sufficient refinement of the finite-element mesh as well as applying upstream or downstream weighting to the convective term through the determination of collocation locations which meet specified constraints. Owing to an increase in computational intensity of the application of the method of collocation associated with increases in the mesh refinement, minimal mesh refinement is sought. Very often this optimization problem is the one where the feasible region is not connected and as such requires a specialized optimization search technique. This paper aims to focus on this method. Design/methodology/approach – An original hybrid method that utilizes a specialized adaptive genetic algorithm followed by a hill-climbing approach is used to search for the optimal mesh refinement for a number of models differentiated by their velocity fields. The adaptive genetic algorithm is used to determine a mesh refinement that is close to a locally optimal mesh refinement. Following the adaptive genetic algorithm, a hill-climbing approach is used to determine a local optimal feasible mesh refinement. Findings – In all cases the optimal mesh refinements determined with this hybrid method are equally optimal to, or a significant improvement over, mesh refinements determined through direct search methods. Research limitations – Further extensions of this work could include the application of the mesh refinement technique presented in this paper to non-steady-state problems with time-dependent coefficients with multi-dimensional velocity fields. Originality/value – The present work applies an original hybrid optimization technique to obtain highly accurate solutions using the method of Hermite collocation with minimal mesh refinement

    Efficient groundwater remediation system designs with flow and concentration constraints subject to uncertainty

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    Δημοσίευση σε επιστημονικό περιοδικόSummarization: A nested optimization problem that utilizes a multiscenario approach based upon a method known as robust optimization is employed to determine a groundwater remediation design that considers the uncertainty in the hydraulic conductivity in the flow and transport model. This optimization approach reduces a complicated multiscenario approach to a simple deterministic method for optimization. The parameter values associated with the final deterministic model represent not the true physical model, but rather a model that results in a conservatively designed remediation system that accounts for the uncertainty in the hydraulic conductivity. Both flow constraints and concentration constraints are considered in this approach, and as such the optimization problem is nonlinear in both its objective function and its constraints. A search method that combines simulated annealing and a downhill simplex algorithm is used to determine the solution to this optimization problem.Presented on: Journal of Water Resources Planning and Managemen
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