Developing novel time-varying phenotype representations for clinical systems

为临床系统开发新颖的时变表型表征

• 批准号: RGPIN-2018-06778
• 负责人: Ghassemi, Marzyeh
• 金额: $ 1.68万
• 依托单位: University of Toronto
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2018
• 资助国家: 加拿大
• 起止时间: 2018-01-01 至 2019-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=651781
• 关键词: Developing; novel; time; varying; phenotype

Representation learning has prompted some of the greatest advances seen in machine learning; for example, the lower dimensional, qualitatively meaningful representations of imaging datasets learned by convolutional networks (CNNs). Clinical data lacks such natural representations, which is a limiting factor to the progress of relevant machine learning. This is especially problematic in the realm of decision making, where there is much uncertainty about what is best for a particular patient. Most interventions have potentially harmful side-effects, and even well-established intensive care unit are associated with improved outcomes in randomized controlled. It is therefore critical to develop representations or health phenotypes that are robust representations of patient state. Our goal is to develop health phenotypes, and pioneer their use to understand what it means to be healthy, identify similar patients, improve healthcare delivery, and quantify the impact of possible interventions. ******In order to develop health phenotypes, we need to integrate data that span free text notes, coded procedures and diagnoses, timeseries of vitals like blood pressure, and high-frequency signals like ECG. For any given patient, different data may be important for a specific task. While prior work has targeted specific tasks (e.g., the prediction of longitudinal outcomes or diagnostic codes, we plan to focus instead on representations that integrate distinct data types, including coded billing data (sparse binary tensors), vitals and labs (dense irregularly sampled time series data), clinical narratives (variable length text vectors), and genomics data (dense binary matrices). Learned phenotypes must be reliable and robust as there are many potential unintended consequences that may result from the application machine learning in clinical practice. Incorporating these data into phenotypic latent state estimates requires mapping across time-scales and granularity. ******The proposed research will have a strong impact on our understanding of what it means to be healthy, and variance within the human phenotype. The importance of representation learning in other fields has increased along with the intent to use the machine learning systems in a practical setting. Our focus on meaningful phenotypes discovery in heterogeneous data is also powerful in many other application areas where justifications about the robustness of a learned representation in machine learning methods are expected by collaborators.

表示学习促进了机器学习中的一些最大进步;例如，卷积网络（CNN）学习的成像数据集的低维，定性意义的表示。临床数据缺乏这样的自然表示，这是相关机器学习进展的限制因素。这在决策领域尤其成问题，因为对于特定患者来说，什么是最好的，存在很大的不确定性。大多数干预措施都有潜在的有害副作用，即使是完善的重症监护病房也与随机对照结局的改善有关。因此，开发作为患者状态的稳健表示的表示或健康表型是至关重要的。我们的目标是开发健康表型，并率先使用它们来了解健康意味着什么，识别相似的患者，改善医疗服务，并量化可能的干预措施的影响。** 为了开发健康表型，我们需要整合数据，这些数据包括自由文本注释、编码程序和诊断、血压等生命体征的时间序列以及ECG等高频信号。对于任何给定的患者，不同的数据对于特定任务可能是重要的。虽然先前的工作针对特定的任务（例如，纵向结果或诊断代码的预测，我们计划专注于整合不同数据类型的表示，包括编码的账单数据（稀疏二进制张量），生命体征和实验室（密集不规则采样时间序列数据），临床叙述（可变长度文本向量）和基因组学数据（密集二进制矩阵）。学习的表型必须可靠和稳健，因为在临床实践中应用机器学习可能会导致许多潜在的非预期后果。将这些数据转化为表型潜在状态估计值需要跨时间尺度和粒度进行映射。** 这项拟议中的研究将对我们理解健康意味着什么以及人类表型的差异产生重大影响。随着在实际环境中使用机器学习系统的意图，表示学习在其他领域的重要性沿着增加。我们专注于在异构数据中发现有意义的表型，在许多其他应用领域也是强大的，在这些应用领域中，合作者预计机器学习方法中学习表示的鲁棒性是合理的。