Evaluating global and local sequence alignment methods for comparing patient medical records

Huang, Ming; Shah, Nilay D.; Yao, Lixia

doi:10.1186/s12911-019-0965-y

BMC Medical Informatics and Decision Making

Table 4 Similarity scores of pairwise local sequence alignments

From: Evaluating global and local sequence alignment methods for comparing patient medical records

ID	Operation	Seed Patient 1 (N = 9)					Seed Patient 2 (N = 84)					Seed Patient 3 (N = 224)					Seed Patient 4 (N = 458)
		DTWL		SWA		REF	DTWL		SWA		REF	DTWL		SWA		REF	DTWL		SWA		REF
		C	S_n	C	S_n	C (S_n)	C	S_n	C	S_n	C (S_n)	C	S_n	C	S_n	C (S_n)	C	S_n	C	S_n	C (S_n)
1	x	1.000	0.819	1.000	0.778	0.667	1.000	0.980	1.000	0.976	0.738	1.000	0.991	1.000	0.991	0.571	1.000	0.998	1.000	0.996	0.500
2	x x	1.000	0.597	1.000	0.556	0.333	1.000	0.976	1.000	0.952	0.452	1.000	0.987	1.000	0.982	0.509	1.000	0.994	1.000	0.991	0.511
3	u	1.000	0.852	1.000	0.852	0.444	1.000	0.988	1.000	0.988	0.964	1.000	0.996	1.000	0.996	0.741	1.000	0.996	1.000	0.996	0.917
4	u u	1.000	0.714	1.000	0.714	0.333	1.000	0.952	1.000	0.952	0.667	1.000	0.984	1.000	0.984	0.549	1.000	0.993	1.000	0.993	0.502
5	s	0.778	0.556	0.778	0.556	0.556	0.976	0.976	0.976	0.976	0.976	1.000	0.991	1.000	0.991	0.665	1.000	0.991	1.000	0.991	0.472
6	s s	1.000	0.286	1.000	0.286	0.222	1.000	0.905	1.000	0.905	0.333	1.000	0.988	1.000	0.988	0.969	0.998	0.985	0.998	0.985	0.469
7	x u	0.889	0.667	0.889	0.667	0.556	1.000	0.964	1.000	0.952	0.405	1.000	0.988	1.000	0.987	0.411	1.000	0.993	1.000	0.991	0.541
8	x s	1.000	0.611	1.000	0.556	0.444	1.000	0.929	1.000	0.929	0.369	1.000	0.978	1.000	0.973	0.652	1.000	0.989	1.000	0.987	0.526
9	u s	1.000	0.457	1.000	0.457	0.333	1.000	0.929	1.000	0.929	0.893	1.000	0.981	1.000	0.981	0.487	1.000	0.987	1.000	0.987	0.373
10	x u s	0.444	0.400	0.444	0.400	0.222	1.000	0.905	1.000	0.905	0.560	1.000	0.969	1.000	0.964	0.335	1.000	0.984	1.000	0.983	0.648
11	X	0.778	0.778	0.778	0.778	0.778	1.000	0.869	1.000	0.810	0.560	1.000	0.877	0.804	0.804	0.804	0.891	0.891	0.891	0.891	0.891
12	X X	0.333	0.333	0.333	0.333	0.333	1.000	0.702	1.000	0.667	0.619	1.000	0.708	1.000	0.625	0.509	1.000	0.657	1.000	0.633	0.618
13	U	0.667	0.667	0.667	0.667	0.667	1.000	0.821	1.000	0.821	0.762	0.835	0.835	0.835	0.835	0.835	0.893	0.893	0.893	0.893	0.893
14	U U	1.000	0.551	1.000	0.551	0.222	0.952	0.826	0.952	0.826	0.821	1.000	0.711	1.000	0.709	0.634	1.000	0.695	1.000	0.695	0.445
15	S	0.778	0.401	0.333	0.333	0.333	0.893	0.714	0.893	0.708	0.548	1.000	0.729	0.862	0.711	0.545	0.838	0.650	0.838	0.650	0.478
16	S S	0.556	0.389	0.556	0.333	0.222	0.690	0.500	0.690	0.500	0.452	0.728	0.463	0.728	0.460	0.335	0.782	0.417	0.782	0.408	0.389
17	X U	0.556	0.556	0.556	0.556	0.556	1.000	0.702	0.679	0.679	0.679	1.000	0.679	1.000	0.668	0.317	0.939	0.756	0.939	0.745	0.535
18	X S	0.222	0.222	0.222	0.222	0.222	1.000	0.539	1.000	0.530	0.262	1.000	0.577	0.821	0.561	0.362	0.734	0.569	0.734	0.567	0.476
19	U S	0.222	0.222	0.222	0.222	0.111	1.000	0.526	0.833	0.518	0.310	1.000	0.689	1.000	0.685	0.625	1.000	0.646	1.000	0.640	0.498
20	X U S	0.222	0.222	0.222	0.222	0.111	0.857	0.706	0.857	0.706	0.571	0.795	0.608	0.795	0.598	0.576	0.893	0.731	0.893	0.731	0.618

a. ID is the synthetic patient index. N is the number of daily events in a seed patient sequence
b. DTWL, SWA and REF refer to as modified Dynamic Time Warping for Local alignment, Smith-Waterman Algorithm, and baseline reference, respectively. C is the coverage of the seed patient sequence aligned to a synthetic patient sequence. S_n is normalized highest alignment score (i.e., the highest alignment score divided by N). C (S_n) denotes that S_n = C
c. The lower case letters “x”, “u”, and “s” denote deleting, updating and switching a daily event, respectively. The upper case letters “X”, “U”, and “S” stand for deleting, updating and switching multi-day events (event block)

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