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Domain Adaption for Genomic Sequence Analysis

Supplementary material for publication "An Empirical Analysis of Domain Adaptation Algorithms for Genomic Sequence Analysis" by Gabriele Schweikert, Christian Widmer, Bernhard Schölkopf und Gunnar Rätsch at NIPS 2008

Abstract

We study the problem of domain transfer for a supervised classification task in mRNA splicing. We consider a number of recent domain transfer methods from machine learning, including some that are novel, and evaluate them on genomic sequence data from model organisms of varying evolutionary distance. We find that in cases where the organisms are not closely related, the use of domain adaptation methods can help improve classification performance.

The paper is available, (here).

The data splits, additional information on model selection, the predictions as well as the stand-alone prediction tool are available on request. If there are questions, please contact Gunnar.Raetsch@tuebingen.mpg.de.

Results

Graphical Results

remanei
pacificus
drosophila
thaliana


Tabular Single Source Results



2500 6500 16000 40000 100000
SVMS,T 77.06 (±2.13) 77.80 (±2.89) 77.89 (±0.29) 79.02 (±0.09) 80.49 (±0.0)
SVMS+SVMT 71.61 (±2.39) 76.58 (±0.52) 77.50 (±0.77) 78.19 (±0.44) 80.19 (±0.0)
SVMSxT 75.37 (±2.56) 76.10 (±2.62) 76.76 (±0.28) 77.82 (±0.23) 79.75 (±0.0)
SVMS->T 75.78 (±8.43) 75.55 (±1.08) 77.23 (±0.37) 78.11 (±0.49) 79.84 (±0.0)
SVMS+T 75.49 (±1.88) 75.87 (±0.25) 77.23 (±0.47) 77.33 (±0.83) 79.96 (±0.0)
SVMS 75.52 (±0.44) 76.27 (±0.42) 75.65 (±0.23) 75.65 (±0.4) 75.65 (±0.0)
SVMT 24.04 (±4.53) 46.45 (±2.29) 60.51 (±1.01) 70.50 (±0.85) 78.04 (±0.0)
C.remanei


2500 6500 16000 40000 100000
SVMS,T 64.72 (±3.75) 66.39 (±0.66) 68.44 (±0.67) 71.00 (±0.38) 74.88 (±0.0)
SVMS+SVMT 64.74 (±3.49) 67.30 (±1.38) 66.58 (±1.82) 71.82 (±0.97) 75.39 (±0.0)
SVMSxT 57.67 (±26.14) 66.33 (±0.28) 67.29 (±2.24) 71.46 (±0.21) 74.99 (±0.0)
SVMS->T 63.52 (±14.05) 66.07 (±0.07) 67.59 (±1.7) 70.90 (±0.95) 75.11 (±0.0)
SVMS+T 62.99 (±1.48) 65.87 (±0.83) 68.02 (±0.97) 70.85 (±0.37) 74.73 (±0.0)
SVMS 62.73 (±0.62) 63.77 (±0.04) 63.75 (±0.75) 63.77 (±0.36) 63.83 (±0.0)
SVMT 20.36 (±3.94) 38.16 (±3.21) 57.28 (±3.46) 67.90 (±1.35) 74.10 (±0.0)
P.pacificus


2500 6500 16000 40000 100000
SVMS,T 40.80 (±2.18) 37.87 (±3.77) 52.33 (±0.91) 58.17 (±1.5) 63.26 (±0.0)
SVMS+SVMT 37.23 (±1.58) 40.36 (±3.32) 48.64 (±0.99) 54.38 (±1.57) 62.26 (±0.0)
SVMSxT 38.71 (±7.67) 41.23 (±1.4) 49.58 (±0.91) 56.20 (±1.86) 62.22 (±0.0)
SVMS->T 35.29 (±6.72) 40.15 (±2.47) 48.98 (±2.19) 54.60 (±1.99) 63.53 (±0.0)
SVMS+T 36.43 (±1.18) 37.98 (±4.05) 49.46 (±1.38) 56.56 (±2.36) 62.07 (±0.0)
SVMS 32.95 (±0.38) 33.05 (±0.07) 33.07 (±0.25) 33.07 (±0.01) 33.74 (±0.0)
SVMT 14.59 (±1.02) 26.69 (±0.58) 38.33 (±2.06) 51.32 (±2.86) 61.26 (±0.0)
D.melanogaster


2500 6500 16000 40000 100000
SVMS,T 24.21 (±3.41) 27.30 (±1.46) 38.49 (±1.59) 49.75 (±1.46) 56.54 (±0.0)
SVMS+SVMT 21.70 (±2.77) 28.55 (±1.96) 35.80 (±1.48) 44.07 (±2.99) 54.06 (±0.0)
SVMSxT 24.62 (±3.07) 27.33 (±3.17) 38.20 (±1.32) 47.05 (±2.39) 53.60 (±0.0)
SVMS->T 17.09 (±6.79) 26.41 (±4.81) 36.83 (±1.74) 47.98 (±2.25) 55.99 (±0.0)
SVMS+T 20.06 (±3.23) 24.71 (±3.25) 37.72 (±1.74) 47.31 (±2.55) 53.41 (±0.0)
SVMS 14.07 (±0.46) 14.85 (±0.1) 14.23 (±0.53) 14.83 (±0.49) 14.33 (±0.0)
SVMT 10.23 (±1.56) 19.07 (±2.53) 32.56 (±1.91) 45.34 (±2.83) 53.63 (±0.0)
A.thaliana

Tabular Multi Source Results



2500 6500 16000 40000 100000
M-SVMS,T 69.45 (±0.17) 71.44 (±1.5) 71.03 (±1.8) 76.21 (±0.2) 79.11 (±0.0)
M-SVMS+SVMT 68.51 (±2.95) 72.69 (±0.86) 72.78 (±0.8) 75.75 (±0.64) 79.06 (±0.0)
M-SVMS->T 63.23 (±5.61) 70.11 (±0.52) 72.09 (±0.19) 75.32 (±0.32) 79.24 (±0.0)
SVMT 24.04 (±4.53) 46.45 (±2.29) 60.51 (±1.01) 70.50 (±0.85) 78.04 (±0.0)
C.remanei


2500 6500 16000 40000 100000
M-SVMS,T 61.38 (±2.05) 64.07 (±1.07) 67.81 (±2.0) 71.05 (±1.26) 75.15 (±0.0)
M-SVMS+SVMT 62.88 (±0.3) 64.77 (±0.52) 65.52 (±0.81) 70.50 (±0.94) 74.20 (±0.0)
M-SVMS->T 61.46 (±0.49) 62.48 (±0.41) 64.78 (±1.7) 70.14 (±0.56) 74.43 (±0.0)
SVMT 20.36 (±3.94) 38.16 (±3.21) 57.28 (±3.46) 67.90 (±1.35) 74.10 (±0.0)
P.pacificus


2500 6500 16000 40000 100000
M-SVMS,T 46.32 (±0.39) 47.71 (±1.03) 53.17 (±0.45) 57.56 (±1.54) 62.66 (±0.0)
M-SVMS+SVMT 46.61 (±3.27) 48.15 (±3.02) 52.12 (±0.73) 57.01 (±1.64) 62.12 (±0.0)
M-SVMS->T 40.89 (±2.28) 44.61 (±1.51) 53.29 (±1.47) 56.35 (±1.57) 61.57 (±0.0)
SVMT 14.59 (±1.02) 26.69 (±0.58) 38.33 (±2.06) 51.32 (±2.86) 61.26 (±0.0)
D.melanogaster


2500 6500 16000 40000 100000
M-SVMS,T 30.90 (±2.12) 36.43 (±3.46) 43.63 (±1.92) 49.49 (±1.92) 56.57 (±0.0)
M-SVMS+SVMT 26.61 (±2.29) 35.58 (±0.31) 39.43 (±1.98) 46.98 (±3.73) 54.11 (±0.0)
M-SVMS->T 27.17 (±1.33) 33.18 (±3.32) 39.32 (±2.07) 47.53 (±2.2) 55.50 (±0.0)
SVMT 10.23 (±1.56) 19.07 (±2.53) 32.56 (±1.91) 45.34 (±2.83) 53.63 (±0.0)
A.thaliana

Data


Download Dataset in MATLAB format

Model Selection

hyperpar


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