TY - GEN
T1 - More powerful discriminants for classifying phylogenetic signals in dinucleotide frequencies
AU - Baran, Robert H.
AU - Jeon, Changwon
AU - Han, David K.
AU - Ko, Hanseok
PY - 2008
Y1 - 2008
N2 - Microbial DNA fragments are classified according to species using compositional features and "genomic signatures" the oldest of which is the dinucleotide relative abundance profile defined by Karlin et al. More informative features, including higher order signatures, have demonstrated greater species-specificity in comparison to the baseline established by the dinucleotide signature using "delta-distance" to assess dissimilarity; but lack of standard methods has precluded rigorous comparison. We describe a new method for classifier evaluation that reduces any number of pair-wise inter-genomic comparisons to a single performance measure. To illustrate the method, we compare delta-distance to quadratic and linear discriminants prescribed by elementary pattern recognition theory, and find that the quadratic form is significantly more powerful.
AB - Microbial DNA fragments are classified according to species using compositional features and "genomic signatures" the oldest of which is the dinucleotide relative abundance profile defined by Karlin et al. More informative features, including higher order signatures, have demonstrated greater species-specificity in comparison to the baseline established by the dinucleotide signature using "delta-distance" to assess dissimilarity; but lack of standard methods has precluded rigorous comparison. We describe a new method for classifier evaluation that reduces any number of pair-wise inter-genomic comparisons to a single performance measure. To illustrate the method, we compare delta-distance to quadratic and linear discriminants prescribed by elementary pattern recognition theory, and find that the quadratic form is significantly more powerful.
KW - Biomedical signal processing
KW - DNA
KW - Error analysis
KW - Pattern classification
KW - Software performance
UR - http://www.scopus.com/inward/record.url?scp=51449100134&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=51449100134&partnerID=8YFLogxK
U2 - 10.1109/ICASSP.2008.4517682
DO - 10.1109/ICASSP.2008.4517682
M3 - Conference contribution
AN - SCOPUS:51449100134
SN - 1424414849
SN - 9781424414840
T3 - ICASSP, IEEE International Conference on Acoustics, Speech and Signal Processing - Proceedings
SP - 605
EP - 608
BT - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
T2 - 2008 IEEE International Conference on Acoustics, Speech and Signal Processing, ICASSP
Y2 - 31 March 2008 through 4 April 2008
ER -