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Table 3 CK-36-SEQ

From: Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment

CK-36-SEQ

UCD

NCD

CD

 

UPGMA

NJ

UPGMA

NJ

UPGMA

NJ

Gzip

0.8500

0.9030

0.8500

0.7600

0.9030

0.7600

Bzip2

0.8585

0.6970

0.8265

0.7236

0.9030

0.7462

PPMd16

0.9030

0.7827

0.9030

0.7600

0.9030

0.7827

PPMd8

0.9030

0.8407

0.9030

0.7600

0.5501

0.5456

PPMd4

0.9030

0.7069

0.9030

0.7600

0.5389

0.5517

PPMd2

0.8500

0.7069

0.8500

0.7069

0.5449

0.5386

Huffman

0.8188

0.7609

0.8645

0.7609

0.8161

0.7066

Ac fast

0.8392

0.6770

0.8392

0.6770

0.8410

0.7324

Rc fast

0.8706

0.7275

0.8706

0.7275

0.8734

0.7268

Ac med.

0.8518

0.6718

0.8518

0.6718

0.8584

0.7288

Rc med.

0.8780

0.7674

0.8466

0.6825

0.7936

0.6621

Ac slow

0.8518

0.7009

0.8392

0.7009

0.8584

0.7268

Rc slow

0.9030

0.7357

0.9030

0.7188

0.8734

0.7288

BwtRleHuff

0.8319

0.6970

0.8585

0.8442

0.7840

0.7440

BwtMtfRleHuff

0.8501

0.8355

0.8253

0.6770

0.7971

0.6692

BwtRleAc fast

0.8706

0.7008

0.8706

0.8026

0.9030

0.7515

BwtMtfRleAc fast

0.8382

0.7217

0.8126

0.7336

0.8706

0.8001

BwtRleRc fast

0.8706

0.7343

0.8706

0.6889

0.9030

0.7950

BwtMtfRleRc fast

0.8500

0.7217

0.8500

0.7217

0.8500

0.7515

BwtRleRc med.

0.8500

0.7074

0.8706

0.7336

0.9066

0.8762

BwtMtfRleRc med.

0.8252

0.6951

0.8252

0.6951

0.8252

0.6657

BwtRleRc slow

0.9030

0.7357

0.8585

0.7297

0.9030

0.7084

BwtMtfRleRc slow

0.8706

0.7480

0.8126

0.7910

0.8706

0.6825

BwtWavelet

0.8706

0.6887

0.8706

0.7993

0.8647

0.7066

  1. Experimental results for the CK-36-SEQ data set, with the UCD (left), NCD (middle), and CD (right) distance. For each compression algorithm, we report the F-measure for both UPGMA and NJ methods.