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      Constructing a finer-grained representation of clinical trial results from ClinicalTrials.gov

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          Abstract

          Randomized controlled trials are essential for evaluating clinical interventions; however, selective reporting and publication bias in medical journals have undermined the integrity of the clinical evidence system. ClinicalTrials.gov serves as a valuable and complementary repository, yet synthesizing information from it remains challenging. This study introduces a curated dataset that extends beyond the traditional PICO framework. It links efficacy with safety results at the experimental arm group level within each trial, and connects them across all trials through a knowledge graph. This novel representation effectively bridges the gap between generally described searchable information and specifically detailed yet underutilized reported results, and promotes a dual-faceted understanding of interventional effects. Adhering to the “calculate once, use many times” principle, the structured dataset will enhance the reuse and interpretation of ClinicalTrials.gov results data. It aims to facilitate more systematic evidence synthesis and health technology assessment, by incorporating both positive and negative results, distinguishing biomarkers, patient-reported outcomes, and clinical endpoints, while also balancing both efficacy and safety outcomes for a given medical intervention.

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          Most cited references26

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          BioBERT: a pre-trained biomedical language representation model for biomedical text mining

          Abstract Motivation Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. Results We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. Availability and implementation We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.
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            Gephi: An Open Source Software for Exploring and Manipulating Networks

            Gephi is an open source software for graph and network analysis. It uses a 3D render engine to display large networks in real-time and to speed up the exploration. A flexible and multi-task architecture brings new possibilities to work with complex data sets and produce valuable visual results.  We present several key features of Gephi in the context of interactive exploration and interpretation of networks. It provides easy and broad access to network data and allows for spatializing, filtering, navigating, manipulating and clustering. Finally, by presenting dynamic features of Gephi, we highlight key aspects of dynamic network visualization.
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              New evidence pyramid

              A pyramid has expressed the idea of hierarchy of medical evidence for so long, that not all evidence is the same. Systematic reviews and meta-analyses have been placed at the top of this pyramid for several good reasons. However, there are several counterarguments to this placement. We suggest another way of looking at the evidence-based medicine pyramid and explain how systematic reviews and meta-analyses are tools for consuming evidence—that is, appraising, synthesising and applying evidence.
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                Author and article information

                Contributors
                dujian@bjmu.edu.cn
                Journal
                Sci Data
                Sci Data
                Scientific Data
                Nature Publishing Group UK (London )
                2052-4463
                6 January 2024
                6 January 2024
                2024
                : 11
                : 41
                Affiliations
                [1 ]Institute of Medical Technology, Peking University, ( https://ror.org/02v51f717) Beijing, 100191 China
                [2 ]National Institute of Health Data Science, Peking University, ( https://ror.org/02v51f717) Beijing, 100191 China
                Author information
                http://orcid.org/0009-0009-5261-6863
                http://orcid.org/0000-0001-8436-778X
                Article
                2869
                10.1038/s41597-023-02869-7
                10771511
                38184674
                4722c80b-831b-4bed-b3b1-6635be2b7b21
                © The Author(s) 2024

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 3 October 2023
                : 17 December 2023
                Funding
                Funded by: National Key R&D Program for Young Scientists (2022YFF0712000)
                Funded by: National Key R&D Program for Young Scientists (2022YFF0712000)
                Categories
                Data Descriptor
                Custom metadata
                © Springer Nature Limited 2024

                outcomes research,drug development,data publication and archiving,statistical methods

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