现代计算机技术在遗传学实验教学中的应用——移动端轻量级高精度果蝇遗传性状批量识别系统的开发

doi:10.16288/j.yczz.22-409

遗传 ›› 2023, Vol. 45 ›› Issue (4): 354-363.doi: 10.16288/j.yczz.22-409

• 遗传学教学 • 上一篇

现代计算机技术在遗传学实验教学中的应用——移动端轻量级高精度果蝇遗传性状批量识别系统的开发

安钧浩(), 赵雪莹, 乔守怡, 卢大儒, 皮妍()

复旦大学生命科学学院，生物科学国家级实验教学示范中心，上海 200433

收稿日期:2022-12-12 修回日期:2023-01-13 出版日期:2023-04-20 发布日期:2023-03-17
通讯作者: 皮妍 E-mail:anjunhao_16@outlook.com;yanpi@fudan.edu.cn
作者简介:安钧浩，本科在读，专业方向：生物信息学。E-mail: anjunhao_16@outlook.com
基金资助:
复旦大学本科教学研究与改革实践项目(课程思政，编号)(FD2021E002);复旦大学本科教学研究与改革实践项目(课程思政，编号)(FD2021E003);复旦大学本科教学研究与改革实践项目(课程思政，编号)(FD2021E004)

Application of modern computer technology in classical genetics lab course——Development of a mobile, lightweight and high-precision batch identification system for genetic traits of Drosophila

Junhao An(), Xueying Zhao, Shouyi Qiao, Daru Lu, Yan Pi()

National Demonstration Center for Experimental Biology Education, School of Life Sciences, Fudan University, Shanghai 200433, China

Received:2022-12-12 Revised:2023-01-13 Online:2023-04-20 Published:2023-03-17
Contact: Pi Yan E-mail:anjunhao_16@outlook.com;yanpi@fudan.edu.cn
Supported by:
Supported by Fudan University Undergraduate Teaching Research and Reform Practice Project Nos(FD2021E002);Supported by Fudan University Undergraduate Teaching Research and Reform Practice Project Nos(FD2021E003);Supported by Fudan University Undergraduate Teaching Research and Reform Practice Project Nos(FD2021E004)

摘要/Abstract

摘要：

果蝇是实验教学中最常用的重要生物材料之一。在果蝇实验教学中，每个学生通常需要针对上百只果蝇进行手工辨认，并记录每只果蝇身上的数个不同性状，工作量大且分类标准参差不齐。为了解决这一问题，本文将现代计算机技术融入到遗传学实验教学中，使用深度卷积神经网络来自动统计每只果蝇的性状。采用的是目标检测模型+分类模型的两阶段策略模式。在分类模型的训练设计过程中，创新性利用了关键点辅助分类的方法，有效地提升了模型的可解释性。此外，还针对任务特性改善了RandAugment方法，利用渐进式学习与适应性正则化策略，在有限的计算资源下训练了MobileNetV3架构下的多标签分类任务，并最终在每只果蝇3对性状(红/白眼、长/小翅、雌/雄)的分类任务下分别达到了97.5%、97.5%和98%的准确率。模型经过优化后，可以在手机端10 s内完成600个果蝇性状的分类，该模型具有轻量化的特点，大小不到5 MB，易于在各类安卓系统手机上安装使用。该系统的开发有利于推进以果蝇为研究对象的遗传规律验证等实验的教学，也可用于涉及大量果蝇分类统计分析的科研工作。

关键词: 现代计算机技术, 实验教学, 移动端, 果蝇性状识别系统

Abstract:

Drosophila is a crucial biological experimental teaching material extensively utilized in experimental teaching. In this experimental teaching, each student typically needs to manually identify hundreds of fruit flies and record multiple of each fly. This task involves substantial workload, and the classification standards can be inconsistent. To address this issue, we introduce a deep convolutional neural network that classifies the traits of every fruit fly, using a two-stage consisting of an object detector and a trait classifier. We propose a keypoint-assisted classification model with tailored training session for the trait classification task and significantly enhanced the model interpretability. Additionally, we’ve enhanced the RandAugment method to better fit the features of our task. The model is trained with progressive learning and adaptive regularization under limited computational resources. The final classification model, which utilizes MobileNetV3 as backbone, achieves an accuracy of 97.5%, 97.5% and 98% for the eyes, wings, gender tasks, respectively. After optimization, the model is highly lightweight, classifying 600 fruit fly traits from raw images in 10 seconds and having a size less than 5 MB. It can be easily deployed on any android device. The development of this system is conducive to promoting the experimental teaching, such as verifying genetic laws with Drosophila as the research object. It can also be used for scientific research involving a large number of Drosophila classifications, statistics and analyses.

Key words: modern computer technology, experiment teaching, mobile terminal, Drosophila character recognition system

安钧浩, 赵雪莹, 乔守怡, 卢大儒, 皮妍. 现代计算机技术在遗传学实验教学中的应用——移动端轻量级高精度果蝇遗传性状批量识别系统的开发[J]. 遗传, 2023, 45(4): 354-363.

Junhao An, Xueying Zhao, Shouyi Qiao, Daru Lu, Yan Pi. Application of modern computer technology in classical genetics lab course——Development of a mobile, lightweight and high-precision batch identification system for genetic traits of Drosophila[J]. Hereditas(Beijing), 2023, 45(4): 354-363.

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现代计算机技术在遗传学实验教学中的应用——移动端轻量级高精度果蝇遗传性状批量识别系统的开发

Application of modern computer technology in classical genetics lab course——Development of a mobile, lightweight and high-precision batch identification system for genetic traits of Drosophila

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