Collaborative Research: ABI Innovation: A Scalable Framework for Visual Exploration and Hypotheses Extraction of Phenomics Data using Topological Analytics

了解基因与环境的相互作用如何导致特定的表型是现代生物学的核心目标，并对作物管理等方面产生现实影响。发展和管理成功的作物措施是一个从根本上与我们的国家粮食安全相关的目标。通过应用新的计算视觉分析方法，该项目试图识别和解开连接基因型、环境和表型的复杂的相互作用网络。这些方法首先需要被设计和开发成可以处理大量作物表现学数据的可用的软件应用程序。高通量传感技术收集了与作物发育和生产相关的许多植物性状的大量田间数据，如开花时间。这里使用的玉米品种来自于在各种环境条件下生长的多种基因类型，以便为理解相互作用提供最广泛的条件。由此产生的数据集在规模和复杂性上都在迅速增长，但提取知识和催化科学发现所需的分析工具明显落后。本项目将制定的方法是为弥合这一迅速扩大的鸿沟所作的系统尝试。该项目本质上是跨学科的，涉及计算机科学家、植物科学家和数学家之间密切的研究伙伴关系。研究成果将与教育紧密结合，采用多管齐下的方法，除其他外，包括博士后和学生培训(毕业生和本科生)，新的校园范围内数据分析跨学科本科学位的课程开发，培训表型组学数据从业者的会议教程，以及通过太平洋西北路易斯·斯托克斯少数民族参与联盟在STEM领域招募和留住未被充分代表的少数民族(尤其是女性)的贡献。该项目将导致设计和开发一个新的、可扩展的、可视化分析平台，适合从复杂的表型组学数据集中提取和完善假设。在表现学数据集的背景下，专注于假设提取是至关重要的，因为在农作物田地中产生的许多高通量传感数据是在没有专门制定的假设的情况下产生的。从数据中提取可信的假设是一项重要但乏味的任务。为此，该项目将利用新兴的高级算法原理，特别是来自研究复杂数据形状和结构的数学分支代数拓扑学的原理，应用和开发新的能力。研究目标有三个方面。首先，该项目将使用和扩展代数拓扑学中的新兴算法技术，以解码大型、复杂的表型组学数据的结构。其次，将开发一个交互式可视化分析平台，以便于使用提取的拓扑结构进行知识发现。最后，该团队设计的一个新的视觉分析平台的质量和有效性将使用真实世界的玉米数据集以及模拟输入作为试验床进行测试。开发的框架将对科学家描述三种假说的功能进行编码：i)单一复杂性状的遗传特征；ii)共享潜在多效性效应的多个性状的基因特征；iii)通过对玉米开花和生长性状的合作试点研究，解码和详细描述基因型与环境的交互作用。这项工作的预期意义是，生物学家将能够通过使用一类新的可视化分析工具从植物表型组学数据集中提取不同类型的可测试假说，从而对基因型、环境和表型之间的相互作用有更深入的了解。该项目在两个方面具有潜在的变革性：i)它将把先进的数学和计算原理引入主流的表象数据分析；ii)它将开创一个新时代，在这个时代，生物学家将借助交互式、信息量大和直观的工具，带头进行数据驱动的假说提取和发现。该项目将对基础数据驱动发现的表型组学软件的状态产生直接影响。为了促进更广泛的社区采用，该项目将把这些工具整合到CyVerse研究所和一个社区表现学软件网点。它还将导致自动化科学工作流程的发展。项目网站：http://tdaphenomics.eecs.wsu.edu/

Understanding how gene by environment interactions result in specific phenotypes is a core goal of modern biology and has real-world impacts on such things as crop management. Developing and managing successful crop practices is a goal that is fundamentally tied to our national food security. By applying novel computational visual analytical methods, this project seeks to identify and unravel the complex web of interactions linking genotypes, environments and phenotypes. These methods will first need to be designed and developed into usable software applications that can handle large volumes of crop phenomics data. High-throughput sensing technologies collect large volumes of field data for many plant traits, such as flowering time, related to crop development and production. The maize cultivars used here come from multiple genotypes that have been grown under a variety of environmental conditions, in order to give the widest range of conditions for understanding the interactions. The resulting data sets are growing quickly, both in size and complexity, but the analytical tools needed to extract knowledge and catalyze scientific discoveries have significantly lagged behind. The methodologies to be developed in this project represent a systematic attempt at bridging this rapidly widening divide. The project is inherently interdisciplinary, involving close research partnerships among computer scientists, plant scientists, and mathematicians. The research outcomes will be tightly integrated with education using a multipronged approach that includes, among others, postdoctoral and student training (graduates and undergraduates), curriculum development for a new campus-wide interdisciplinary undergraduate degree in Data Analytics, conference tutorials for training phenomics data practitioners, and contribution to the recruitment and retention of underrepresented minorities (particularly women) in STEM fields through the Pacific Northwest Louis Stokes Alliance for Minority Participation.This project will lead to the design and development of a new, scalable, visual analytics platform suitable for hypothesis extraction and refinement from complex phenomics data sets. Focus on hypothesis extraction is critical in the context of phenomics data sets because much of the high-throughput sensing data being generated in crop fields are generated in the absence of specifically formulated hypotheses. Extracting plausible hypotheses from the data represents an important but tedious task. To this end, this project will apply and develop new capabilities using emerging advanced algorithmic principles, particularly from the branch of mathematics called algebraic topology that studies shapes and structure of complex data. The research objectives are three-fold. First, the project will employ and extend emerging algorithmic techniques from algebraic topology to decode the structure of large, complex phenomics data. Second, an interactive visual analytic platform will be developed to facilitate knowledge discovery using the extracted topological structures. Lastly, the quality and validity of a new visual analytic platform designed by this team will be tested using real-world maize data sets as well as simulated inputs as testbeds. The developed framework will encode functions for scientists to delineate hypotheses of three kinds: i) genetic characterization of single complex traits; ii) genetic characterization of multiple traits that share potentially pleiotropic effects; and iii) decoding and detailed characterization of genotype-by-environmental interactions, in particular, through a collaborative pilot study of maize flowering and growth traits. The expected significance of the proposed work is that biologists will be able to extract different types of testable hypotheses from plant phenomics data sets by employing a new class of visual analytic tools, and thus obtain a deeper understanding of the interactions among genotypes, environments and phenotypes. The project is potentially transformative in two ways: i) it will introduce advanced mathematical and computational principles into mainstream phenomic data analysis; and ii) it will usher in a new era where biologists spearhead data-driven hypothesis extraction and discovery with the aid of interactive, informative, and intuitive tools. The project will have a direct impact on the state of software in phenomics for fundamental data-driven discovery. To facilitate broader community adoption, the project will integrate the tools into the CyVerse Institute, and to a community phenomics software outlet. It will also lead to the development of automated scientific workflows. Project website: http://tdaphenomics.eecs.wsu.edu/