RAPID: Automated discovery of COVID-19 related hypotheses using publicly available scientific literature

现代数据库（例如美国国家医学图书馆的 MEDLINE）中积累的大量生物医学信息给研究人员进行有效的广泛调查带来了很大的困难，即使使用先进的信息搜索引擎，研究人员也试图根据现有的生物医学文献来评估新信息。自动假设生成系统旨在帮助科学家克服这些困难并加速他们的研究。 COVID-19大流行正是此类系统在应对冠状病毒方面发挥极其重要作用的案例之一。使用两种不同的人工智能方法，我们开发了两个系统来发现生物医学领域的合理假设。在该项目中，我们将部署 COVID-19 定制假设生成和知识发现系统，在与本研究查询相关的任何相关问题上大规模运行该系统，并在开放领域向广大科学界发布结果（包括经过训练的 AI 模型和发现的信息），目标是加速 COVID-19 研究。这项工作主要侧重于通过使用生物医学领域的公开信息建模和制定科学假设来解决基础知识发现问题。然而，总的来说，这些方法并不局限于任何特定的信息领域，即它们可以广泛地用于发现文本中的知识。尽管我们的实验工作将与 COVID-19 有关，但这些方法可以在有保留的情况下应用于任何基于文献的分析。例如，在材料科学计划中，目标之一是建立对材料特性的系统理解并发现可以通过使用大量论文进行分析来完成的新材料。在法律领域，可以使用类似的假设建模方法来识别相关专利。所提出的方法的核心在于从国家医学图书馆的各种异构数据库中提取的所有生物医学对象的大型多模式和多关系语义知识网络。这些对象包括但不限于科学论文、摘要、关键词、短语、同义词库元素、基因、蛋白质、突变、途径、疾病和诊断。我们将利用两个系统，即 MOLIERE 和 AGATHA，分别基于结构学习和深度学习。我们将使用快速更新的新论文数据集来定制它们，这些数据集尚未被国家医学图书馆处理，但已经存在于开放领域，例如各种预印本档案和报告中。 MOLIERE 系统基于网络分析技术，该技术应用于使用论文的低维嵌入构建的图，以及基于概率主题建模的结果解释方法。 AGATHA 系统以更细的粒度处理文本，并使用更准确的嵌入技术创建语义知识网络，然后进行知识发现的深度学习训练。两个系统相辅相成。虽然《AGATHA》的质量更高，但《莫里哀》的解释性更强。这项研究将综合利用两者。该奖项反映了 NSF 的法定使命，并通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。

The vast amounts of biomedical information that accumulate in modern databases (such as MEDLINE of the National Library of Medicine) impose a great difficulty for efficient wide surveying by researchers who try to evaluate new information considering existing biomedical literature even when advanced information search engines are used. Automated hypotheses generation systems are designed to help scientists to overcome these difficulties and accelerate their research. The pandemic situation with COVID-19 is precisely one of the cases when such systems can play an extremely important role in coping with the coronavirus. Using two different AI approaches, we have developed two systems to discover plausible hypotheses in the biomedical domain. In this project, we will will deploy the COVID-19 customized hypothesis generation and knowledge discovery system, massively run it on any relevant to this research queries, and publish the results (including trained AI models, and discovered information) in the open domain for broad scientific community with the goal to accelerate the COVID-19 research. This work focuses heavily on addressing fundamental knowledge discovery questions by modeling and formulating scientific hypotheses using the publicly available information in the biomedical domain. However, in general, these methods are not restricted to any specific information domain, i.e., they can be broadly used to discover knowledge in texts. Although our experimental work will be related to COVID-19, the methods can be applied with some reservations to any literature-based analysis. For example, in the Materials Science Initiative, one of the goals is to establish a systematic understanding of the material properties and discover new materials which can be done by analyzing using the massive corpus of papers. In the legal world, identifying related patents can be done using a similar hypothesis modeling methodology.In the heart of the proposed approach lies a big multi-modal and multi-relational semantic knowledge network of all biomedical objects extracted from a variety of heterogeneous databases of the National Library of Medicine. These objects include but are not limited to scientific papers, abstracts, keywords, phrases, elements of thesaurus, genes, proteins, mutations, pathways, diseases, and diagnoses. We will leverage two systems, namely MOLIERE and AGATHA, that are based on structural and deep learning, respectively. We will customize them using the rapidly updated dataset of new papers that has not been yet processed by the National Library of Medicine but already exists in the open domain such as in various preprint archives and reports. The MOLIERE system is based on the network analysis techniques applied on the graph constructed using the low-dimensional embedding of the papers with the result interpretation methods that are based on the probabilistic topic modeling. The AGATHA system processes texts at much finer granularity, and creates a semantic knowledge network using more accurate embedding techniques followed by the deep learning training for knowledge discovery. Two systems complement each other. While the AGATHA is of higher quality, the MOLIERE is more interpretable. A combination of both will be leveraged in this research.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.