基于机器学习的汉族人群地域来源推断模型

doi:10.16288/j.yczz.25-261

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Hereditas(Beijing) ›› 2026, Vol. 48 ›› Issue (7): 726-740.doi: 10.16288/j.yczz.25-261

• Technique and Method • Previous Articles Next Articles

Machine learning-based geographical ancestry inference model for the Han Chinese population

Shuaiqi Wang¹^,²(), Chunnian Wang¹^,², Deqin Zhang²^,³, Linlin Lou²^,⁴, Yiting Ban², Li Jiang²(), Caixia Li¹^,²()

¹ School of Investigation, People’s Public Security University of China, Beijing 100038, China
² Institute of Forensic Science, Ministry of Public Security & Beijing Engineering Research Center of Crime Scene Evidence Examination & National Engineering Laboratory for Forensic Science, Beijing 100038, China
³ Department of Forensic Medicine, Guizhou Medical University, Guiyang 550004, China
⁴ School of Forensic Medicine, Shanxi Medical University, Jinzhong 030600, China

Received:2025-12-23 Revised:2026-02-18 Online:2026-07-20 Published:2026-03-06
Contact: Li Jiang, Caixia Li E-mail:qwert0019155@gmail.com;jl@mail.bnu.edu.cn;licaixia@tsinghua.org.cn
Supported by:
National Key R&D Program of China(2022YFC3341004);National Natural Science Foundation of China(82171870);Science and Technology Program of the Ministry of Public Security(2023JSZ02);Beijing Nova Program of Science and Technology(20220484149)

Abstract

Abstract:

The Han Chinese population exhibits a complex genetic structure characterized by subtle yet discernible regional differentiation. Elucidating this fine-scale population structure and developing robust models for biogeographical ancestry inference are of great significance for revealing population evolutionary patterns and achieving precise ancestry inference. However, ancestry inference models specifically tailored to the genetic diversity within the domestic Han Chinese population remain scarce. In this study, we analyzed high-density SNP data from 1,229 Han Chinese individuals across eight provinces to investigate the correlation between genetic variation and geographic distribution, and to construct a machine learning-based model for regional ancestry prediction. After stringent quality control (including linkage disequilibrium pruning), we retained 208,193 SNPs for downstream analysis. Principal component analysis (PCA) and ADMIXTURE clustering revealed measurable genetic stratification corresponding to geography, supporting the delineation of seven distinct genetic clusters within the Han population. Leveraging the top principal components as features, we trained and compared multiple classifiers—XGBoost, random forest, and K-nearest neighbors—via five-fold cross-validation on the reference set, with model performance evaluated using both top-rank prediction accuracy and likelihood ratio (LR)-based metrics. The results showed that the PCA-XGBoost model achieved the optimal prediction performance in the reference set, with a first-rank prediction accuracy of 87.66% and an LR-based accuracy of 96.87%. In independent test sets, the PCA-XGBoost model maintained strong performance (first-rank prediction accuracy >85%; LR-based accuracy >95%), demonstrating excellent generalizability and stability. In summary, the PCA-XGBoost predictive model developed in this study demonstrates high efficiency, robustness, and accuracy, offering a reliable methodological tool for research in population genetics and forensic genetics.

Key words: Han Chinese, biogeographic ancestry inference, high-density SNP, principal component analysis, machine learning

Shuaiqi Wang, Chunnian Wang, Deqin Zhang, Linlin Lou, Yiting Ban, Li Jiang, Caixia Li. Machine learning-based geographical ancestry inference model for the Han Chinese population[J]. Hereditas(Beijing), 2026, 48(7): 726-740.

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群体信息	人群缩写	样本量		地理分区	ChinaMAP遗传分区^c)	WBBC遗传分区^d)
群体信息	人群缩写	参考集	测试集	地理分区	ChinaMAP遗传分区^c)	WBBC遗传分区^d)
黑龙江汉族^a)	HLJ	123	30	东北	北方汉族	北方汉族
河北汉族^a)	HEB	123	30	华北
辽宁汉族^b)	LN	/	30	东北
山西汉族^b)	SX	/	30	华北
甘肃汉族^a)	GS	124	30	西北	西北汉族
青海汉族^b)	QH	/	30	西北	西北汉族
江苏汉族^a)	JS	123	30	华东	东部汉族	中部汉族
上海汉族^b)	SH	/	30	华东	东部汉族	中部汉族
湖北汉族^a)	HUB	125	30	华中	中部汉族	南方汉族
云南汉族^a)	YN	124	30	西南	南方汉族
贵州汉族^b)	GZ	/	30	西南	南方汉族
福建汉族^a)	FJ	123	30	华东	东南汉族
广西汉族^a)	GX	124	30	华南	岭南汉族	岭南汉族
广东汉族^b)	GD	/	30	华南	岭南汉族	岭南汉族

遗传分区	群体信息	人群缩写	样本量		来源参考集	测序方法
遗传分区	群体信息	人群缩写	参考集	测试集	来源参考集	GSA	CGA	sequencing (5×)	sequencing (15×)
北方汉族	黑龙江汉族^a)	HLJ	123	30	本实验室	125	27	1	/
	河北汉族^a)	HEB	123	30	本实验室	136	3	14	/
	辽宁汉族^b)	LN	/	30	本实验室	26	3	/	1
	山西汉族^b)	SX	/	30	本实验室	29	1	/	/
西北汉族	甘肃汉族^a)	GS	124	30	本实验室	151	2	/	1
西北汉族	青海汉族^b)	QH	/	30	本实验室	11	/	/	19
中部汉族	湖北汉族^a)	HUB	125	30	本实验室	116	39	/	/
东部汉族	江苏汉族^a)	JS	123	30	本实验室	149	/	/	4
东部汉族	上海汉族^b)	SH	/	30	本实验室	24	6	/	/
西南汉族	云南汉族^a)	YN	124	30	本实验室	98	55	1	/
西南汉族	贵州汉族^b)	GZ	/	30	本实验室	20	9	/	1
东南汉族	福建汉族^a)	FJ	123	30	本实验室	151	/	1	1
岭南汉族	广西汉族^a)	GX	124	30	本实验室	99	42		13
岭南汉族	广东汉族^b)	GD	/	30	本实验室	30	/	/	/

分类器	参数	参数范围	最优参数
XGBoost	learning_rate	range(0.1,1)	0.1406
	gamma	range(0.01,1)	0.8593
	lambda	range(1,10)	5.4916
	max_depth	range(1,10)	10
	min_child_weight	range(1,5)	1
	num_boost_round	range(10,500)	170
	early_stopping_rounds	range(10,100)	18

方法	1stAcc	Acc_LR	Err_LR	Cons_LR	Incc_LR
XGBoost	87.06%	96.66%	3.34%	59.96%	36.70%
随机森林	85.54%	95.55%	4.45%	58.44%	37.11%
K近邻	71.08%	94.03%	5.97%	16.78%	77.25%

真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	215(73)	16(13)	2(2)	13(13)				246	87.40%	98.78%	57.72%
西北汉族	18(10)	103(59)	1(1)			2(2)		124	83.06%	93.55%	35.48%
中部汉族	2(1)		106(51)	9(7)	5(3)	3(2)		125	84.80%	95.20%	44.00%
东部汉族	19(13)	1(0)	10(9)	93(42)				123	75.61%	93.50%	41.46%
东南汉族			8(5)	2(1)	109(16)	3(3)	1(1)	123	88.62%	96.75%	75.61%
西南汉族			7(4)		2(2)	114(17)	1(1)	124	91.94%	97.58%	78.23%
岭南汉族					1(1)	2(1)	121(10)	124	97.58%	99.19%	89.52%
总计								989	87.06%	96.66%	59.96%

Machine learning-based geographical ancestry inference model for the Han Chinese population

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真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	220(203)	9(8)	1(1)	15(12)		1(1)		246	89.43%	98.37%	6.91%
西北汉族	69(53)	50(48)				5(4)		124	40.32%	86.29%	1.61%
中部汉族	23(20)	2(1)	59(59)	29(25)	6(5)	6(5)		125	42.70%	92.00%	0.00%
东部汉族	32(22)		21(19)	66(65)	3(3)	1(1)		123	53.66%	90.24%	0.81%
东南汉族	1(0)		17(14)	7(6)	98(56)			123	79.67%	95.93%	34.15%
西南汉族	5(4)	7(6)	16(10)	4(1)	1(1)	90(60)	1(1)	124	72.58%	91.13%	24.19%
岭南汉族	1(1)		1(1)		1(1)	1(1)	120(46)	124	96.77%	100.00%	59.58%
总计								989	71.08%	94.03%	16.78%

真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	213(56)	13(7)		20(18)				246	86.59%	96.75%	63.82%
西北汉族	24(11)	100(25)						124	80.65%	89.52%	60.48%
中部汉族	1(0)	1(0)	101(81)	11(11)	4(2)	7(6)		125	80.80%	96.00%	16.00%
东部汉族	19(11)	1(1)	9(8)	98(78)				123	76.42%	92.68%	13.01%
东南汉族			16(15)	1(0)	102(6)	2(2)	2(1)	123	82.93%	97.56%	78.05%
西南汉族		1(1)	5(2)		4(3)	114(15)		124	91.94%	96.77%	79.84%
岭南汉族					1(0)	1(0)	122(7)	124	98.39%	98.39%	92.74%
总计								989	85.54%	95.55%	58.44%

真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	212(73)	18(16)	1(1)	15(12)				246	86.18%	97.97%	59.50%
西北汉族	16(11)	106(53)		1(1)		1(0)		124	85.48%	95.16%	42.74%
中部汉族	2(1)		103(40)	10(8)	6(4)	4(4)		125	82.40%	96.00%	50.40%
东部汉族	18(12)		6(6)	99(46)				123	80.49%	95.12%	43.09%
东南汉族			7(3)	3(2)	110(14)	2(2)	1(1)	123	89.43%	95.93%	78.04%
西南汉族			6(4)		3(2)	115(21)		124	92.74%	97.58%	78.81%
岭南汉族						2(1)	122(3)	124	98.39%	99.19%	95.97%
总计								989	87.66%	96.87%	62.39%

真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	49(17)	7(7)		4(4)				60	81.67%	100.00%	53.33%
西北汉族	4(2)	25(12)		1(0)				30	83.33%	93.33%	43.33%
中部汉族	1(0)		23(11)	3(2)	3(3)			30	76.67%	93.33%	40.00%
东部汉族	4(0)			26(12)				30	86.67%	86.67%	46.67%
东南汉族			2(0)		27(5)		1(1)	30	90.00%	93.33%	73.33%
西南汉族			2(1)			28(4)		30	93.33%	96.67%	80.00%
岭南汉族						1(1)	29(1)	30	96.67%	100.00%	93.33%
总计								240	86.25%	95.42%	60.41%

真实/预测	北方汉族	西北汉族	中部汉族	东部汉族	东南汉族	西南汉族	岭南汉族	总计	1stAcc	Acc_LR	Cons_LR
北方汉族	53(23)	5(5)	1(1)			1(1)		60	88.33%	100.00%	50.00%
西北汉族	1(1)	28(8)	1(1)					30	93.33%	100.00%	66.67%
东部汉族			5(5)	25(9)				30	83.33%	100.00%	53.33%
西南汉族			10(7)		3(3)	17(6)		30	56.67%	90.00%	36.67%
岭南汉族							30(1)	30	100.00%	100.00%	96.67%
总计								180	85.00%	98.33%	58.89%

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