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GenoREC:交互式基因组学数据可视化推荐系统。

GenoREC: A Recommendation System for Interactive Genomics Data Visualization.

出版信息

IEEE Trans Vis Comput Graph. 2023 Jan;29(1):570-580. doi: 10.1109/TVCG.2022.3209407. Epub 2022 Dec 21.


DOI:10.1109/TVCG.2022.3209407
PMID:36191105
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10067538/
Abstract

Interpretation of genomics data is critically reliant on the application of a wide range of visualization tools. A large number of visualization techniques for genomics data and different analysis tasks pose a significant challenge for analysts: which visualization technique is most likely to help them generate insights into their data? Since genomics analysts typically have limited training in data visualization, their choices are often based on trial and error or guided by technical details, such as data formats that a specific tool can load. This approach prevents them from making effective visualization choices for the many combinations of data types and analysis questions they encounter in their work. Visualization recommendation systems assist non-experts in creating data visualization by recommending appropriate visualizations based on the data and task characteristics. However, existing visualization recommendation systems are not designed to handle domain-specific problems. To address these challenges, we designed GenoREC, a novel visualization recommendation system for genomics. GenoREC enables genomics analysts to select effective visualizations based on a description of their data and analysis tasks. Here, we present the recommendation model that uses a knowledge-based method for choosing appropriate visualizations and a web application that enables analysts to input their requirements, explore recommended visualizations, and export them for their usage. Furthermore, we present the results of two user studies demonstrating that GenoREC recommends visualizations that are both accepted by domain experts and suited to address the given genomics analysis problem. All supplemental materials are available at https://osf.io/y73pt/.

摘要

基因组学数据的解释严重依赖于广泛应用各种可视化工具。大量的基因组学数据可视化技术和不同的分析任务对分析师来说是一个重大挑战:哪种可视化技术最有可能帮助他们深入了解数据?由于基因组学分析师通常在数据可视化方面的培训有限,他们的选择通常基于反复试验或受技术细节的指导,例如特定工具可以加载的特定数据格式。这种方法使他们无法为工作中遇到的许多数据类型和分析问题的组合做出有效的可视化选择。可视化推荐系统通过根据数据和任务特征推荐适当的可视化来帮助非专家创建数据可视化。然而,现有的可视化推荐系统并不是为处理特定领域的问题而设计的。为了解决这些挑战,我们设计了 GenoREC,这是一种针对基因组学的新型可视化推荐系统。GenoREC 使基因组学分析师能够根据其数据和分析任务的描述选择有效的可视化。在这里,我们介绍了使用基于知识的方法选择适当可视化的推荐模型和一个 web 应用程序,该应用程序使分析师能够输入他们的要求,探索推荐的可视化,并将其导出以供使用。此外,我们还介绍了两项用户研究的结果,这些结果表明 GenoREC 推荐的可视化不仅被领域专家所接受,而且适合解决给定的基因组学分析问题。所有补充材料均可在 https://osf.io/y73pt/ 上获取。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/b1c408991e5f/nihms-1846026-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/e18585da5c19/nihms-1846026-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/3698af9234dc/nihms-1846026-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/76aabe62655c/nihms-1846026-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/a512666f4c14/nihms-1846026-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/a8aed92089cb/nihms-1846026-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/d74cd3be6b86/nihms-1846026-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/b1c408991e5f/nihms-1846026-f0007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/e18585da5c19/nihms-1846026-f0001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/3698af9234dc/nihms-1846026-f0002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/76aabe62655c/nihms-1846026-f0003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/a512666f4c14/nihms-1846026-f0004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/a8aed92089cb/nihms-1846026-f0005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/d74cd3be6b86/nihms-1846026-f0006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/536a/10067538/b1c408991e5f/nihms-1846026-f0007.jpg

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引用本文的文献

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Understanding Visualization Authoring Techniques for Genomics Data in the Context of Personas and Tasks.

IEEE Trans Vis Comput Graph. 2025-1

[2]
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[5]
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[6]
Gos: a declarative library for interactive genomics visualization in Python.

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[7]
Multi-View Design Patterns and Responsive Visualization for Genomics Data.

IEEE Trans Vis Comput Graph. 2023-1

本文引用的文献

[1]
Gos: a declarative library for interactive genomics visualization in Python.

Bioinformatics. 2023-1-1

[2]
Multi-View Design Patterns and Responsive Visualization for Genomics Data.

IEEE Trans Vis Comput Graph. 2023-1

[3]
Gosling: A Grammar-based Toolkit for Scalable and Interactive Genomics Data Visualization.

IEEE Trans Vis Comput Graph. 2022-1

[4]
Semantic Snapping for Guided Multi-View Visualization Design.

IEEE Trans Vis Comput Graph. 2022-1

[5]
An Evaluation-Focused Framework for Visualization Recommendation Algorithms.

IEEE Trans Vis Comput Graph. 2022-1

[6]
GEViTRec: Data Reconnaissance Through Recommendation Using a Domain-Specific Visualization Prevalence Design Space.

IEEE Trans Vis Comput Graph. 2022-12

[7]
MobileVisFixer: Tailoring Web Visualizations for Mobile Phones Leveraging an Explainable Reinforcement Learning Framework.

IEEE Trans Vis Comput Graph. 2021-2

[8]
Comparative Layouts Revisited: Design Space, Guidelines, and Future Directions.

IEEE Trans Vis Comput Graph. 2021-2

[9]
Tasks, Techniques, and Tools for Genomic Data Visualization.

Comput Graph Forum. 2019-6

[10]
Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study.

Nat Med. 2019-9-30

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