用深度学习自动判断法医DNA样本来自多少人,准确率超89%。
deepNoC: A deep learning system to assign the number of contributors to a short tandem repeat DNA profile
- 通过模拟电泳信号生成百万级带标签数据,训练深度网络识别贡献者人数
- 在1到10人范围内准确率达89%,少量实测数据即可微调适配实验室
- 内置可解释性输出,结果可视化直观,适合法医和司法场景使用
法医生物学中常见的任务是解读和评估短串联重复(STR)DNA图谱。首要步骤是确定图谱的贡献者人数,这一工作通常由科学家基于对DNA图谱行为的经验手动完成。已有研究显示,随着图谱复杂度增加、贡献者人数增多,科学家的判断能力显著下降。尽管已有多种机器学习算法尝试自动识别贡献者人数,但由于实验生成真实图谱存在实际限制,这些算法多依赖于现有信息的摘要。本文构建了一个分析流程,能够模拟STR图谱的电泳信号,从而生成理论上无限量且预先标注的训练数据。我们通过模拟10万份图谱,并采用深度神经网络架构(命名为deepNoC)进行训练,实现了1至10名贡献者情况下89%的高准确率。该训练模型还可通过仅几百个真实样本进行微调,在特定实验室中保持相同精度。此外,deepNoC还集成辅助输出,提供用户可理解的解释性信息,并展示出直观的可视化方式。
原文摘要 · Abstract (English)
A common task in forensic biology is to interpret and evaluate short tandem repeat DNA profiles. The first step in these interpretations is to assign a number of contributors to the profiles, a task that is most often performed manually by a scientist using their knowledge of DNA profile behaviour. Studies using constructed DNA profiles have shown that as DNA profiles become more complex, and the number of DNA-donating individuals increases, the ability for scientists to assign the target number. There have been a number of machine learning algorithms developed that seek to assign the number of contributors to a DNA profile, however due to practical limitations in being able to generate DNA profiles in a laboratory, the algorithms have been based on summaries of the available information. In this work we develop an analysis pipeline that simulates the electrophoretic signal of an STR profile, allowing virtually unlimited, pre-labelled training material to be generated. We show that by simulating 100 000 profiles and training a number of contributors estimation tool using a deep neural network architecture (in an algorithm named deepNoC) that a high level of performance is achieved (89% for 1 to 10 contributors). The trained network can then have fine-tuning training performed with only a few hundred profiles in order to achieve the same accuracy within a specific laboratory. We also build into deepNoC secondary outputs that provide a level of explainability to a user of algorithm, and show how they can be displayed in an intuitive manner.
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