Modified Tabu search to solve complex, continuous-variable problems through gradient analysis and contour jumps

This paper introduces a method of solving np-hard problems with continuous random variables by using a modified Tabu search algorithm. Traditionally, Tabu search is a metaheuristic that deals with binary or integer variable type problems and finds "good" solutions to the problem. This study explores the Tabu search algorithm and presents a methodology by with the algorithm can be modified to handle continuous random variables as well as integer and binary. The modifications include an appropriate method of defining the neighborhood solution sets and then an effective manner of moving through the neighborhood to converge to an acceptable solution as quickly as possible. In addition to moving through the neighborhood, a method of locating and moving to local optima is included. From there this technique will incorporate a method of "jumping" to the base of a new, improving local optima in the state space. From there the algorithm will return to locating and reaching the local optima point. In this fashion, the modified Tabu search will explore the state space for continually improving points and will "jump over" areas that, while feasible, are not worth exploring. This method saves computation time as well as achieving a more direct route to an acceptably good solution. In addition, it is proposed that with enough time, the optimal point will be found

Addressing the challenges of modeling the scattering from bottlebrush polymers in solution

Small‐angle scattering measurements of complex macromolecules in solution are used to establish relationships between chemical structure and conformational properties. Interpretation of the scattering data requires an inverse approach where a model is chosen and the simulated scattering intensity from that model is iterated to match the experimental scattering intensity. This raises challenges in the case where the model is an imperfect approximation of the underlying structure, or where there are significant correlations between model parameters. We examine three bottlebrush polymers (consisting of polynorbornene backbone and polystyrene side chains) in a good solvent using a model commonly applied to this class of polymers: the flexible cylinder model. Applying a series of constrained Monte‐Carlo Markov Chain analyses demonstrates the severity of the correlations between key parameters and the presence of multiple close minima in the goodness of fit space. We demonstrate that a shape‐agnostic model can fit the scattering with significantly reduced parameter correlations and less potential for complex, multimodal parameter spaces. We provide recommendations to improve the analysis of complex macromolecules in solution, highlighting the value of Bayesian methods. This approach provides richer information for understanding parameter sensitivity compared to methods which produce a single, best fit

Examining MEDLINE Search Query Reproducibility and Resulting Variation in Search Results

The MEDLINE database is publicly available through the National Library of Medicine’s PubMed but the data file itself is also licensed to a number of vendors, who may offer their versions to institutional and other parties as part of a database platform. These vendors provide their own interface to the MEDLINE file and offer other technologies that attempt to make their version useful to subscribers. However, little is known about how vendor platforms ingest and interact with MEDLINE data files, nor how these changes influence the construction of search queries and the results they produce. This poster presents a longitudinal study of five MEDLINE databases involving 29 sets of logically and semantically consistent search queries (five search queries for each set). The goal is to understand whether it is possible to reproduce search queries by: a) analyzing search query syntax per database, and b) controlling for total search results. We also highlight the barriers to creating reproducible queries across MEDLINE databases

Search Results Outliers Among MEDLINE Platforms

Objective: Hypothetically, content in MEDLINE records is consistent across multiple platforms. Though platforms have different interfaces and requirements for query syntax, results should be similar when the syntax is controlled for across the platforms. The authors investigated how search result counts varied when searching records among five MEDLINE platforms. Methods: We created 29 sets of search queries targeting various metadata fields and operators. Within search sets, we adapted 5 distinct, compatible queries to search 5 MEDLINE platforms (PubMed, ProQuest, EBSCOhost, Web of Science, and Ovid), totaling 145 final queries. The 5 queries were designed to be logically and semantically equivalent and were modified only to match platform syntax requirements. We analyzed the result counts and compared PubMed’s MEDLINE result counts to result counts from the other platforms. We identified outliers by measuring the result count deviations using modified z-scores centered around PubMed’s MEDLINE results. Results: Web of Science and ProQuest searches were the most likely to deviate from the equivalent PubMed searches. EBSCOhost and Ovid were less likely to deviate from PubMed searches. Ovid’s results were the most consistent with PubMed’s but appeared to apply an indexing algorithm that resulted in lower retrieval sets among equivalent searches in PubMed. Web of Science exhibited problems with exploding or not exploding Medical Subject Headings (MeSH) terms. Conclusion: Platform enhancements among interfaces affect record retrieval and challenge the expectation that MEDLINE platforms should, by default, be treated as MEDLINE. Substantial inconsistencies in search result counts, as demonstrated here, should raise concerns about the impact of platform-specific influences on search results

MEDLINE Search Retrieval Issues: A Longitudinal Query Analysis of Five Vendor Platforms

This study compared the results of data collected from a longitudinal query analysis of the MEDLINE database hosted on multiple platforms that include PubMed, EBSCOHost, Ovid, ProQuest, and Web of Science. The goal was to identify variations among the search results on the platforms after controlling for search query syntax. We devised twenty-nine cases of search queries comprised of five semantically equivalent queries per case to search against the five MEDLINE database platforms. We ran our queries monthly for a year and collected search result count data to observe changes. We found that search results varied considerably depending on MEDLINE platform. Reasons for variations were due to trends in scholarly publication such as publishing individual papers online first versus complete issues. Some other reasons were metadata differences in bibliographic records; differences in the levels of specificity of search fields provided by the platforms and large fluctuations in monthly search results based on the same query. Database integrity and currency issues were observed as each platform updated its MEDLINE data throughout the year. Specific biomedical bibliographic databases are used to inform clinical decision-making, create systematic reviews, and construct knowledge bases for clinical decision support systems. They serve as essential information retrieval and discovery tools to help identify and collect research data and are used in a broad range of fields and as the basis of multiple research designs. This study should help clinicians, researchers, librarians, informationists, and others understand how these platforms differ and inform future work in their standardization

Addressing the challenges of modeling the scattering from bottlebrush polymers in solution

Small‐angle scattering measurements of complex macromolecules in solution are used to establish relationships between chemical structure and conformational properties. Interpretation of the scattering data requires an inverse approach where a model is chosen and the simulated scattering intensity from that model is iterated to match the experimental scattering intensity. This raises challenges in the case where the model is an imperfect approximation of the underlying structure, or where there are significant correlations between model parameters. We examine three bottlebrush polymers (consisting of polynorbornene backbone and polystyrene side chains) in a good solvent using a model commonly applied to this class of polymers: the flexible cylinder model. Applying a series of constrained Monte‐Carlo Markov Chain analyses demonstrates the severity of the correlations between key parameters and the presence of multiple close minima in the goodness of fit space. We demonstrate that a shape‐agnostic model can fit the scattering with significantly reduced parameter correlations and less potential for complex, multimodal parameter spaces. We provide recommendations to improve the analysis of complex macromolecules in solution, highlighting the value of Bayesian methods. This approach provides richer information for understanding parameter sensitivity compared to methods which produce a single, best fit

Concentration Dependence of the Size and Symmetry of a Bottlebrush Polymer in a Good Solvent

Bottlebrush polymers consist of a linear backbone with densely grafted side chains which impact the rigidity of the molecule. The persistence length of the bottlebrush backbone in solution is influenced by both the intrinsic structure of the polymer and the local environment, such as the solvent quality and concentration. Increasing the concentration reduces the overall size of the molecule because of the reduction in backbone stiffness. In this study, we map out the size of a bottlebrush polymer as a function of concentration for a single backbone length. Small-angle neutron scattering measurements are conducted on a polynorbornene-based bottlebrush with polystyrene side chains in a good solvent. The data are fit using a model which provides both the long and short axis radius of gyration (R_(g,2) and R_(g,1), respectively), providing a measure for how the conformation changes as a function of concentration. At low concentrations, a highly anisotropic structure is observed (R_(g,2)/R_(g,1) ≈ 4), becoming more isotropic at higher concentrations (R_(g,2)/R_(g,1) ≈ 1.5). The concentration scaling for both R_(g,2) and the overall Rg is evaluated and compared with predictions in the literature. Coarse-grained molecular dynamics simulations were also conducted to probe the impact of concentration on bottlebrush conformation, showing qualitative agreement with the experimental results