Methodologically Grounded SemanticAnalysis of Large Volume of Chilean Medical Literature Data Applied to the Analysis of Medical Research Funding Efficiency in Chile

Background Medical knowledge is accumulated in scientific research papers along time. In order to exploit this knowledge by automated systems, there is a growing interest in developing text mining methodologies to extract, structure, and analyze in the shortest time possible the knowledge encoded in the large volume of medical literature. In this paper, we use the Latent Dirichlet Allocation approach to analyze the correlation between funding efforts and actually published research results in order to provide the policy makers with a systematic and rigorous tool to assess the efficiency of funding programs in the medical area. Results We have tested our methodology in the Revista Medica de Chile, years 2012-2015. 50 relevant semantic topics were identified within 643 medical scientific research papers. Relationships between the identified semantic topics were uncovered using visualization methods. We have also been able to analyze the funding patterns of scientific research underlying these publications. We found that only 29% of the publications declare funding sources, and we identified five topic clusters that concentrate 86% of the declared funds. Conclusions Our methodology allows analyzing and interpreting the current state of medical research at a national level. The funding source analysis may be useful at the policy making level in order to assess the impact of actual funding policies, and to design new policies.This research was partially funded by CONICYT, Programa de Formacion de Capital Humano avanzado (CONICYT-PCHA/Doctorado Nacional/2015-21150115). MG work in this paper has been partially supported by FEDER funds for the MINECO project TIN2017-85827-P, and projects KK-2018/00071 and KK2018/00082 of the Elkartek 2018 funding program. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 777720. No role has been played by funding bodies in the design of the study and collection, analysis, or interpretation of data or in writing the manuscript

Finding semantically valid and relevant topics by association-based topic selection model

Topic modelling methods such as Latent Dirichlet Allocation (LDA) have been successfully applied to various fields, since these methods can effectively characterize document collections by using a mixture of semantically rich topics. So far, many models have been proposed. However, the existing models typically outperform on full analysis on the whole collection to find all topics but difficult to capture coherent and specifically meaningful topic representations. Furthermore, it is very challenging to incorporate user preferences into existing topic modelling methods to extract relevant topics. To address these problems, we develop a novel personalized Association-based Topic Selection (ATS) model, which can identify semantically valid and relevant topics from a set of raw topics based on the semantical relatedness between users’ preferences and the structured patterns captured in topics. The advantage of the proposed ATS model is that it enables an interactive topic modelling process driven by users’ specific interests. Based on three benchmark datasets, namely, RCV1, R8, and WT10G under the context of information filtering (IF) and information retrieval (IR), our rigorous experiments show that the proposed ATS model can effectively identify relevant topics with respect to users’ specific interests, and hence to improve the performance of IF and IR