Generalizable Architectures and Principles of Informatics for Scalable Personalized and Precision Medicine (PPM) Decision Support

Author(s):  
Steven G. Johnson ◽  
Pamala Jacobson ◽  
Susan M. Wolf ◽  
Kingshuk K. Sinha ◽  
Douglas Yee ◽  
...  
2021 ◽  
Author(s):  
Weifeng Qin ◽  
Xudong Lu ◽  
Qiang Shu ◽  
Huilong Duan ◽  
Haomin Li

Pharmacogenomics clinical decision support (PGx-CDS) is an important tool to incorporate PGx information into existing clinical workflows and facilitate PGx clinical translation. However, due to the lack of a computable formalization to represent the primary PGx knowledge, the complexity of genomics information and the lag of current commercial electronic health record (EHR) system for precision medicine, it is difficult to develop computerized PGx-CDS. Therefore, we explored a novel approach to build an information system, named the Pharmacogenomics Clinical Translation Platform (PCTP), for PGx clinical implementation. The PCTP can represent, store, and manage the primary PGx knowledge in a structured and computable format. Moreover, it has the potential to provide various PGx-CDS services and simplify the integration of PGx-CDS into EHRs.


2021 ◽  
Author(s):  
zicheng zhang

Abstract Background: Retrieving gene and disease information from a vast collection of biomedical abstracts to provide doctors with clinical decision support is one of the important research directions of Precision Medicine. Method: We propose a novel article retrieval method based on expanded word and co-word analyses, also conducting Cuckoo Search to optimize parameters of the retrieval function. The main goal is to retrieve the abstracts of biomedical articles that refer to treatments. The methods mentioned in this manuscript adopt the BM25 algorithm to calculate the score of abstracts. We, however, propose an improved version of BM25 that computes the scores of expanded words and co-word leading to a composite retrieval function, which is then optimized using the Cuckoo Search. The proposed method aims to find both disease and gene information in the abstract of the same biomedical article. This is to achieve higher relevance and hence score of articles. Besides, we investigate the influence of different parameters on the retrieval algorithm and summarize how they meet various retrieval needs. Results: The data used in this manuscript is sourced from medical articles presented in Text Retrieval Conference (TREC):Clinical Decision Support (CDS) Tracks of 2017, 2018, and 2019 in Precision Medicine. A total of 120 topics are tested. Three indicators are employed for the comparison of utilized methods, which are selected among the ones based only on the BM25 algorithm and its improved version to conduct comparable experiments. The results showed that the proposed algorithm achieves better results.Conclusion: The proposed method, an improved version of the BM25 algorithm, utilizes both co-word implementation and Cuckoo Search, which has been verified achieving better results on a large number of experimental sets. Besides, a relatively simple query expansion method is implemented in this manuscript. Future research will focus on ontology and semantic networks to expand the query vocabulary.


2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Hyo Jung Kim ◽  
Hyeong Joon Kim ◽  
Yoomi Park ◽  
Woo Seung Lee ◽  
Younggyun Lim ◽  
...  

2020 ◽  
Author(s):  
Zicheng Zhang

Abstract Background: Retrieving gene and disease information from a very large collection of biomedical abstracts to provide doctors with clinical decision support is one of the important research directions of Precision Medicine.Method: We propose a new method for the retrieval of biomedical articles utilizing expanded word and co-word implementations and conducting Cuckoo Search to optimize parameters of the retrieval function in the final stage of the proposed method. The specific goal is to retrieve biomedical abstracts of articles addressing treatments. The method employed in this manuscript first implements the BM25 algorithm to compute the score of the abstract, then we propose a method utilizing the BM25, an improved version of BM25, to compute the scores of expanded words and co-word that lead to a composite retrieval function. Afterward, the retrieval function is optimized using Cuckoo Search. The proposed method is utilized to find both disease and gene in the abstract of the same biomedical article. By doing so, the relevance of articles would tend to increase so would the score of the biomedical article. Besides, the manuscript discusses the influence of different parameters on the retrieval algorithm and summarizes the parameters to meet various retrieval needs.Results: All data are taken from medical articles provided in the Text Retrieval Conference (TREC) utilizing Clinical Decision Support (CDS) Tracks of 2017, 2018, and 2019 in Precision Medicine. 120 standard topics are tested. Three test indicators are employed to make comparisons among the methods utilized. To conduct comparable experiments, only the BM25 algorithm and its improved version of it are utilized. The experimental results show that the proposed algorithm achieves both better results and ranking outcomes.Conclusion: The proposed algorithm, an improved version of the BM25 algorithm, utilizes both co-word implementation and Cuckoo Search and verifies that the proposed algorithm produces better results on a large number of experimental sets. On the other hand, a relatively simple query expansion method is implemented in this manuscript. As a future direction of this research, both the ontology and semantic network to expand the query vocabulary is planned to be conducted.


2019 ◽  
pp. 1-9 ◽  
Author(s):  
Seán Walsh ◽  
Evelyn E.C. de Jong ◽  
Janna E. van Timmeren ◽  
Abdalla Ibrahim ◽  
Inge Compter ◽  
...  

Precision medicine is the future of health care: please watch the animation at https://vimeo.com/241154708 . As a technology-intensive and -dependent medical discipline, oncology will be at the vanguard of this impending change. However, to bring about precision medicine, a fundamental conundrum must be solved: Human cognitive capacity, typically constrained to five variables for decision making in the context of the increasing number of available biomarkers and therapeutic options, is a limiting factor to the realization of precision medicine. Given this level of complexity and the restriction of human decision making, current methods are untenable. A solution to this challenge is multifactorial decision support systems (DSSs), continuously learning artificial intelligence platforms that integrate all available data—clinical, imaging, biologic, genetic, cost—to produce validated predictive models. DSSs compare the personalized probable outcomes—toxicity, tumor control, quality of life, cost effectiveness—of various care pathway decisions to ensure optimal efficacy and economy. DSSs can be integrated into the workflows both strategically (at the multidisciplinary tumor board level to support treatment choice, eg, surgery or radiotherapy) and tactically (at the specialist level to support treatment technique, eg, prostate spacer or not). In some countries, the reimbursement of certain treatments, such as proton therapy, is already conditional on the basis that a DSS is used. DSSs have many stakeholders—clinicians, medical directors, medical insurers, patient advocacy groups—and are a natural consequence of big data in health care. Here, we provide an overview of DSSs, their challenges, opportunities, and capacity to improve clinical decision making, with an emphasis on the utility in oncology.


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