SMARTString Matching Algorithms Research Tool

by Simone Faro - www.dmi.unict.it/~faro/smart/ - email: faro@dmi.unict.it

Report of Experimental Results

Test Code EXP1712145140

Date 2024:04:03 22:38:11

Text protein (alphabet : 64 - size : 1048576 bytes)

	2	4	8	16	32	64	128	256	512	1024	2048	4096
TVSBS	0.23 3.64 2.12 - 9.10	0.23 2.78 1.61 - 6.07	0.23 2.09 1.18 - 5.32	0.20 1.41 0.95 - 3.49	0.25 1.44 0.82 - 2.75	0.22 1.10 0.72 - 2.52	0.21 0.99 0.67 - 2.36	0.23 1.07 0.63 - 2.42	0.22 1.14 0.76 - 2.73	0.24 1.21 0.73 - 2.38	0.25 1.20 0.67 - 2.43	0.26 1.27 0.62 - 2.18
FJS	0.02 3.70 2.05 - 8.18	0.02 2.89 1.51 - 6.51	0.02 2.03 1.10 - 5.15	0.02 1.49 0.86 - 3.65	0.02 2.01 0.78 - 2.97	0.02 1.16 0.61 - 2.95	0.02 1.24 0.58 - 3.01	0.02 1.20 0.59 - 3.02	0.02 1.07 0.61 - 3.36	0.02 1.14 0.59 - 2.86	0.03 1.14 0.62 - 2.83	0.06 1.57 0.62 - 3.23
HASH8	0.01 1.97 1.45 - 5.59	0.02 2.19 1.45 - 5.60	0.02 14.68 8.90 - 28.82	0.02 2.64 1.42 - 5.34	0.02 1.59 0.83 - 5.06	0.02 1.08 0.63 - 2.35	0.01 0.83 0.56 - 2.02	0.01 0.80 0.52 - 1.94	0.02 0.96 0.60 - 2.05	0.02 0.94 0.59 - 1.74	0.02 0.88 0.62 - 2.01	0.04 1.41 0.50 - 2.11
SO	0.01 1.90 1.20 - 5.23	0.02 2.20 1.20 - 5.58	0.02 2.08 1.20 - 5.78	0.02 2.17 1.19 - 5.13	0.02 2.80 1.18 - 5.70	0.01 1.61 1.08 - 4.39	0.02 1.70 1.07 - 9.77	0.02 1.73 1.08 - 4.26	0.02 1.77 1.07 - 4.22	0.02 1.65 1.07 - 4.05	0.01 1.57 1.08 - 4.42	0.02 2.33 1.08 - 3.97
SBNDM	0.03 3.31 1.81 - 7.58	0.02 1.38 0.91 - 3.25	0.03 1.23 0.66 - 2.66	0.02 0.87 0.53 - 2.20	0.03 1.06 0.50 - 1.85	0.02 0.89 0.55 - 2.03	0.02 0.95 0.56 - 2.11	0.02 0.91 0.54 - 2.08	0.02 1.00 0.56 - 2.39	0.02 0.81 0.55 - 2.26	0.02 0.92 0.59 - 2.41	0.03 1.29 0.57 - 2.44
LBNDM	0.01 2.67 1.31 - 7.80	0.01 2.29 1.04 - 6.36	0.02 2.08 0.88 - 8.22	0.01 1.32 0.75 - 2.84	0.02 1.37 0.58 - 2.23	0.01 0.82 0.52 - 2.13	0.01 0.79 0.50 - 2.05	0.01 0.78 0.53 - 2.21	0.02 0.87 0.51 - 1.97	0.02 0.86 0.53 - 2.07	0.02 1.61 0.54 - 5.24	0.03 4.72 1.04 - 8.95
SBNDM2	0.02 2.08 1.22 - 5.73	0.02 1.19 0.73 - 3.45	0.02 0.98 0.57 - 2.40	0.02 0.86 0.51 - 2.08	0.02 1.00 0.49 - 2.08	0.01 0.76 0.48 - 1.93	0.01 0.74 0.47 - 1.93	0.02 0.75 0.48 - 1.91	0.02 0.79 0.48 - 2.12	0.02 0.78 0.48 - 1.90	0.02 0.80 0.49 - 1.90	0.02 1.03 0.48 - 1.78
SBNDM-BMH	0.02 2.93 1.71 - 7.34	0.02 2.30 1.16 - 6.17	0.02 1.69 0.85 - 4.13	0.02 1.17 0.73 - 3.24	0.03 1.22 0.55 - 2.20	0.02 0.98 0.54 - 5.11	0.02 0.91 0.58 - 2.27	0.02 0.85 0.56 - 2.42	0.02 0.97 0.56 - 2.41	0.02 0.96 0.56 - 2.22	0.03 1.38 0.56 - 2.21	0.03 1.16 0.58 - 2.16
FNDM	0.01 2.61 1.38 - 6.47	0.02 2.30 1.07 - 5.63	0.02 1.91 0.93 - 4.15	0.02 1.28 0.73 - 3.06	0.02 1.41 0.59 - 2.15	0.02 0.92 0.54 - 2.27	0.02 1.00 0.54 - 2.29	0.01 0.84 0.57 - 2.46	0.02 1.01 0.56 - 2.32	0.02 0.96 0.55 - 3.94	0.02 1.33 0.57 - 2.84	0.02 1.14 0.57 - 2.06
FSBNDM	0.01 1.82 0.97 - 5.36	0.02 1.44 0.74 - 3.74	0.02 1.11 0.59 - 2.44	0.01 0.86 0.52 - 2.02	0.02 1.07 0.48 - 2.34	0.01 0.83 0.49 - 2.08	0.02 0.86 0.48 - 2.69	0.02 0.87 0.49 - 2.01	0.01 0.79 0.48 - 2.00	0.02 0.82 0.48 - 1.90	0.02 1.11 0.49 - 1.97	0.02 1.12 0.52 - 2.13
SBNDMQ8	0.01 2.09 1.44 - 5.68	0.02 2.42 1.43 - 5.79	0.02 5.10 3.04 - 11.82	0.01 1.21 0.74 - 3.36	0.02 1.32 0.54 - 2.34	0.01 0.84 0.55 - 2.59	0.02 0.89 0.55 - 2.29	0.01 0.84 0.55 - 2.35	0.02 0.92 0.55 - 2.27	0.02 0.88 0.55 - 2.41	0.02 1.13 0.58 - 2.53	0.02 1.12 0.55 - 2.32
UFNDMQ2	0.02 1.63 1.00 - 4.54	0.02 1.21 0.74 - 3.14	0.02 0.99 0.61 - 2.73	0.02 0.88 0.54 - 2.31	0.01 0.97 0.50 - 2.01	0.01 0.75 0.50 - 1.95	0.01 0.79 0.49 - 2.02	0.01 0.70 0.49 - 1.88	0.01 0.88 0.49 - 1.89	0.01 0.80 0.49 - 2.03	0.01 1.13 0.50 - 1.95	0.01 0.82 0.49 - 4.98
UFNDMQ8	0.02 2.42 1.45 - 5.71	0.02 2.37 1.44 - 5.64	0.02 1.25 0.78 - 3.67	0.02 1.03 0.62 - 2.99	0.01 1.14 0.57 - 2.22	0.01 0.88 0.56 - 2.68	0.01 0.87 0.55 - 2.33	0.01 0.87 0.56 - 2.22	0.01 0.84 0.55 - 2.34	0.01 0.92 0.56 - 2.48	0.01 1.05 0.57 - 2.31	0.01 1.11 0.56 - 2.41
KBNDM	0.02 3.64 2.12 - 7.98	0.01 1.96 1.30 - 5.38	0.01 1.23 0.88 - 3.59	0.01 0.94 0.69 - 3.34	0.02 1.29 0.60 - 2.18	0.02 0.91 0.55 - 2.09	0.02 0.79 0.50 - 2.04	0.02 0.83 0.51 - 2.11	0.02 0.84 0.50 - 1.90	0.02 0.89 0.52 - 1.93	0.02 1.12 0.52 - 2.10	0.02 1.13 0.51 - 1.88
FS-W2	0.04 2.78 1.55 - 6.74	0.04 1.81 1.02 - 4.61	0.04 1.21 0.79 - 3.22	0.04 1.06 0.67 - 3.01	0.07 1.47 0.61 - 2.37	0.05 0.98 0.57 - 2.32	0.05 0.89 0.53 - 2.30	0.05 0.86 0.51 - 2.04	0.05 0.85 0.55 - 2.21	0.06 0.85 0.53 - 2.46	0.10 1.16 0.53 - 2.08	0.15 1.26 0.60 - 2.54
LWFR5	0.02 2.25 1.45 - 5.66	0.01 2.25 1.44 - 5.67	0.06 2.65 1.76 - 7.01	0.06 0.88 0.59 - 2.55	0.09 1.09 0.54 - 2.41	0.07 0.72 0.50 - 1.86	0.08 0.81 0.49 - 1.78	0.07 0.71 0.48 - 1.72	0.09 0.77 0.46 - 2.41	0.10 0.72 0.46 - 1.90	0.17 0.99 0.48 - 1.95	0.25 1.10 0.54 - 2.61
QF43	0.01 2.18 1.39 - 5.35	0.01 2.13 1.45 - 6.16	0.02 1.00 0.71 - 4.45	0.03 1.13 0.55 - 3.90	0.03 1.12 0.49 - 1.91	0.02 0.74 0.46 - 1.85	0.02 0.70 0.45 - 2.10	0.02 0.69 0.44 - 1.72	0.02 0.64 0.42 - 1.59	0.03 0.70 0.41 - 1.96	0.03 0.75 0.41 - 2.42	0.04 0.93 0.40 - 4.52
SBNDM-W2	0.01 2.56 1.21 - 7.62	0.02 1.72 0.86 - 4.98	0.01 1.25 0.68 - 3.45	0.02 1.19 0.60 - 2.34	0.02 1.06 0.51 - 2.12	0.02 0.84 0.53 - 2.18	0.01 0.81 0.52 - 2.05	0.02 0.83 0.51 - 2.09	0.02 0.92 0.53 - 2.15	0.02 0.82 0.52 - 2.24	0.02 1.03 0.53 - 2.22	0.02 1.06 0.53 - 2.32
WFR2	0.07 2.70 1.51 - 6.77	0.07 1.55 0.93 - 3.89	0.07 1.20 0.72 - 2.85	0.07 1.11 0.63 - 2.43	0.09 1.28 0.59 - 2.54	0.06 0.81 0.55 - 2.79	0.06 0.77 0.50 - 2.13	0.07 0.78 0.51 - 2.55	0.08 0.76 0.47 - 3.33	0.08 0.71 0.46 - 2.52	0.16 1.13 0.46 - 8.58	0.20 1.23 0.48 - 16.19
TWFRQ2	0.07 2.37 1.27 - 6.03	0.07 1.44 0.82 - 3.45	0.07 1.11 0.67 - 2.73	0.09 1.32 0.64 - 2.64	0.07 0.89 0.58 - 2.97	0.07 0.93 0.55 - 2.19	0.07 0.80 0.52 - 2.14	0.08 0.90 0.51 - 3.61	0.07 0.75 0.48 - 1.95	0.07 0.65 0.45 - 2.01	0.10 0.85 0.45 - 8.42	0.13 1.13 0.46 - 19.42
TWFRQ4	0.02 2.30 1.43 - 5.88	0.06 2.47 1.58 - 6.66	0.07 1.17 0.70 - 2.92	0.10 1.40 0.57 - 2.37	0.07 0.79 0.51 - 2.11	0.07 0.80 0.49 - 1.99	0.06 0.73 0.49 - 1.78	0.08 0.85 0.48 - 2.11	0.07 0.74 0.46 - 1.90	0.08 0.73 0.46 - 1.78	0.11 0.97 0.46 - 7.58	0.13 1.15 0.47 - 13.72
WOM	0.02 3.50 2.09 - 9.34	0.02 2.58 1.47 - 5.89	0.02 1.83 1.04 - 5.00	0.02 1.65 0.83 - 3.51	0.02 1.12 0.70 - 3.17	0.02 1.05 0.62 - 2.61	0.02 0.93 0.56 - 2.61	0.02 1.07 0.55 - 2.41	0.02 0.92 0.55 - 2.12	0.02 0.84 0.55 - 2.31	0.04 1.24 0.55 - 2.48	0.04 1.01 0.56 - 2.15
LIBC1	0.01 1.62 1.09 - 4.05	0.01 1.37 0.83 - 3.66	0.01 1.01 0.62 - 2.81	0.01 1.10 0.53 - 2.27	0.01 0.77 0.49 - 2.16	0.01 0.82 0.51 - 1.99	0.01 0.80 0.51 - 2.13	0.01 0.82 0.50 - 1.94	0.01 1.09 0.57 - 2.63	0.01 1.05 0.56 - 2.56	0.01 1.27 0.59 - 2.38	0.01 1.41 0.60 - 2.40
MUSL1	0.00 0.01 0.00 - 0.05	0.00 0.18 0.01 - 2.00	0.00 1.03 0.01 - 4.18	0.00 1.26 0.01 - 3.94	0.00 0.59 0.01 - 2.37	0.00 0.50 0.01 - 1.93	0.00 0.52 0.01 - 1.99	0.01 0.50 0.01 - 2.30	0.01 0.52 0.02 - 2.25	0.01 0.51 0.02 - 2.15	0.03 0.89 0.03 - 2.52	0.05 0.81 0.05 - 2.55
SIMDKR	0.02 0.80 0.49 - 2.08	0.01 0.79 0.49 - 1.96	0.01 0.84 0.49 - 1.95	0.02 0.92 0.49 - 2.43	0.01 0.73 0.48 - 1.83	0.01 0.79 0.50 - 1.96	0.02 0.91 0.51 - 1.93	0.01 0.88 0.51 - 2.02	0.01 0.78 0.49 - 2.21	0.01 0.83 0.48 - 1.89	0.02 1.26 0.50 - 1.94	0.02 1.17 0.51 - 2.06
EPSM	0.01 0.82 0.50 - 1.77	0.01 0.92 0.52 - 1.99	0.02 0.86 0.58 - 2.73	0.03 1.35 0.67 - 2.44	0.02 0.73 0.53 - 1.82	0.02 0.72 0.49 - 1.86	0.03 0.79 0.47 - 1.74	0.04 0.75 0.47 - 1.84	0.05 0.71 0.49 - 1.88	0.09 0.84 0.49 - 2.12	0.19 1.11 0.53 - 2.12	0.39 1.35 0.67 - 2.80

Table 1. Running times of experimental tests n.EXP1712145140. Each time value is the mean of 500 runs. Running times are in milliseconds.

Best mean times

Heatmap top 5%

Heatmap top 10%

Heatmap top 25%

Heatmap top 50%

Show pre-processing times

Show best and worst running times

Average Running Times

TVSBS

FJS

HASH8

SBNDM

LBNDM

SBNDM2

SBNDM-BMH

FNDM

FSBNDM

SBNDMQ8

UFNDMQ2

UFNDMQ8

KBNDM

FS-W2

LWFR5

QF43

SBNDM-W2

WFR2

TWFRQ2

TWFRQ4

WOM

LIBC1

MUSL1

SIMDKR

EPSM

Chart 1. Plot of the running times of experimental tests n.EXP1712145140. The x axes reports the length of the pattern (in a log scale) while the y axes reports the running time in milliseconds.

Worst Running Times

Best Running Times

TVSBS - Thathoo-Virmani-Sai-Balakrishnan-Sekar

Detailed plot of the running times relative to the TVSBS algorithm. The plot reports the mean and the distribution of the running times.

FJS - Franek-Jennings-Smyth

Detailed plot of the running times relative to the FJS algorithm. The plot reports the mean and the distribution of the running times.

HASH8 - Wu-Manber for Single Pattern Matching (q=8)

Detailed plot of the running times relative to the HASH8 algorithm. The plot reports the mean and the distribution of the running times.

SO - Shift-Or

Detailed plot of the running times relative to the SO algorithm. The plot reports the mean and the distribution of the running times.

SBNDM - Simplified BNDM

Detailed plot of the running times relative to the SBNDM algorithm. The plot reports the mean and the distribution of the running times.

LBNDM - long patterns bndm

Detailed plot of the running times relative to the LBNDM algorithm. The plot reports the mean and the distribution of the running times.

SBNDM2 - simplified bndm with loop-unrolling

Detailed plot of the running times relative to the SBNDM2 algorithm. The plot reports the mean and the distribution of the running times.

SBNDM-BMH - sbndm with horspool shift

Detailed plot of the running times relative to the SBNDM-BMH algorithm. The plot reports the mean and the distribution of the running times.

FNDM - forward nondeterministic dawg matching

Detailed plot of the running times relative to the FNDM algorithm. The plot reports the mean and the distribution of the running times.

FSBNDM - forward sbndm

Detailed plot of the running times relative to the FSBNDM algorithm. The plot reports the mean and the distribution of the running times.

SBNDMQ8 - simplified bndm with q-grams

Detailed plot of the running times relative to the SBNDMQ8 algorithm. The plot reports the mean and the distribution of the running times.

UFNDMQ2 - Upper bits fndm with q-grams

Detailed plot of the running times relative to the UFNDMQ2 algorithm. The plot reports the mean and the distribution of the running times.

UFNDMQ8 - Upper bits fndm with q-grams

Detailed plot of the running times relative to the UFNDMQ8 algorithm. The plot reports the mean and the distribution of the running times.

KBNDM - Factorized BNDM

Detailed plot of the running times relative to the KBNDM algorithm. The plot reports the mean and the distribution of the running times.

FS-W2 - Multiple Sliding Windows

Detailed plot of the running times relative to the FS-W2 algorithm. The plot reports the mean and the distribution of the running times.

LWFR5 - Weak Factor Recognizer, Linear Version

Detailed plot of the running times relative to the LWFR5 algorithm. The plot reports the mean and the distribution of the running times.

QF43 - Q-gram Filtering q=4 s=3

Detailed plot of the running times relative to the QF43 algorithm. The plot reports the mean and the distribution of the running times.

SBNDM-W2 - SBNDM with lookahead

Detailed plot of the running times relative to the SBNDM-W2 algorithm. The plot reports the mean and the distribution of the running times.

WFR2 - Weak Factor Recognizer (m>=2)

Detailed plot of the running times relative to the WFR2 algorithm. The plot reports the mean and the distribution of the running times.

TWFRQ2 - Tuned Weak Factor Recognizer with q-grams

Detailed plot of the running times relative to the TWFRQ2 algorithm. The plot reports the mean and the distribution of the running times.

TWFRQ4 - Tuned Weak Factor Recognizer with q-grams

Detailed plot of the running times relative to the TWFRQ4 algorithm. The plot reports the mean and the distribution of the running times.

WOM - Worst Occurrence Matcher

Detailed plot of the running times relative to the WOM algorithm. The plot reports the mean and the distribution of the running times.

LIBC1 - memmem

Detailed plot of the running times relative to the LIBC1 algorithm. The plot reports the mean and the distribution of the running times.

MUSL1 - musl memmem

Detailed plot of the running times relative to the MUSL1 algorithm. The plot reports the mean and the distribution of the running times.

SIMDKR - SIMD generic Rabin-Karp variants

Detailed plot of the running times relative to the SIMDKR algorithm. The plot reports the mean and the distribution of the running times.

EPSM - SSE4 Exact Packed String Matching

Detailed plot of the running times relative to the EPSM algorithm. The plot reports the mean and the distribution of the running times.