Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning

doi:10.1093/molbev/msaf260

CSpace

	Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning
	Zhang, Xinru 1,2; Ding, Shizhe 1,2; Yu, Chungong 1,2,3; Zhao, Jianquan 1,2; Bu, Dongbo 1,2,3
	2025-11-01
发表期刊	MOLECULAR BIOLOGY AND EVOLUTION
ISSN	0737-4038
卷号	42 期号:11 页码:14
摘要	Accurate phylogenetic inference is crucial for understanding evolutionary relationships among species. Deep learning technique has been introduced for phylogenetic inference; however, the existing deep learning-based approaches either suffer from limited accuracy as they split inference into several disjoint stages, or exhibit low efficiency and hardly apply to the cases with over 20 species. Here, we present an accurate and efficient approach to phylogenetic inference. Our approach, called NeuralNJ, employs an end-to-end framework that directly constructs phylogenetic trees from the input taxa, thus effectively avoiding the inaccuracy incurred by the split inference stages. The key innovation of NeuralNJ lies in its learnable neighbor joining mechanism, which iteratively joins neighbors guided by learned priority scores and thereby achieves accurate tree reconstruction. The inference accuracy is further enhanced through incorporating reinforcement learning-based tree search. Using both simulated and empirical data as representatives, we demonstrate that NeuralNJ can effectively infer phylogenetic tree with improved computational efficiency and reconstruction accuracy. The study paves the way to accurate and efficient phylogenetic inference for hundreds of taxa in complex evolutionary scenarios.
关键词	phylogenetic inference phylogenetic tree deep learning
DOI	10.1093/molbev/msaf260
收录类别	SCI
语种	英语
WOS研究方向	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS类目	Biochemistry & Molecular Biology ; Evolutionary Biology ; Genetics & Heredity
WOS记录号	WOS:001615870300001
出版者	OXFORD UNIV PRESS
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/43096
专题	中国科学院计算技术研究所
通讯作者	Ding, Shizhe; Bu, Dongbo
作者单位	1.Chinese Acad Sci, Inst Comp Technol, SKLP, Beijing 100190, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100049, Peoples R China 3.Henan Acad Sci, Cent China Artificial Intelligence Res Inst, Zhengzhou 450046, Peoples R China
推荐引用方式 GB/T 7714	Zhang, Xinru,Ding, Shizhe,Yu, Chungong,et al. Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning[J]. MOLECULAR BIOLOGY AND EVOLUTION,2025,42(11):14.
APA	Zhang, Xinru,Ding, Shizhe,Yu, Chungong,Zhao, Jianquan,&Bu, Dongbo.(2025).Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning.MOLECULAR BIOLOGY AND EVOLUTION,42(11),14.
MLA	Zhang, Xinru,et al."Accurate and Efficient Phylogenetic Inference through End-To-End Deep Learning".MOLECULAR BIOLOGY AND EVOLUTION 42.11(2025):14.