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Table 2 LOO-CV classification error rates for six DR methods and three classifiers (fibroblast data)

From: Spectral embedding finds meaningful (relevant) structure in image and microarray data

   PCA (cor) PCA (cov) Nonmetric MDS kernel PCA Spectral Ng et al. Spectral Lafon
*KNN ( k = 2) Pan paniscus 27.27%–41.02% 0%–13.71% 0%–13.69% 0%–9.13% 0%–9.02% 0%
  Gorilla gorilla 8.33%–29.39% 8.33%–12.61% 8.33%–12.42% 8.33%–12.49% 8.33%–29.33% 0%
  Homo sapiens 4.55% 0%–2.28% 0%–2.22% 0%–2.26% 0%–4.66% 0%
  Total 20.09% 2.22%–7.83% 2.22%–7.74% 2.22%–6.79% 2.22%–13.93% 0%
*KNN ( k = 3) Pan paniscus 27.27% 18.18% 18.18% 9.09% 9.09% 0%
  Gorilla gorilla 8.33% 16.67% 16.67% 16.67% 25% 0%
  Homo sapiens 4.55% 4.55% 4.55% 0% 0%–3.04% 0%
  Total 11.11% 11.11% 11.11% 8.56% 8.88%–13.79% 0%
QDA Pan paniscus 72.73% 9.09% 9.09% 0% 0% 0%
  Gorilla gorilla 16.67% 8.33% 8.33% 0% 8.33% 0%
  Homo sapiens 4.55% 0% 0% 0% 0% 0%
  Total 24.44% 4.44% 4.44% 0% 2.22% 0%
LDA Pan paniscus 18.18% 9.09% 9.09% 0% 0% **9.09%
  Gorilla gorilla 25% 8.33% 8.33% 8.33% 41.67% 0%
  Homo sapiens 0% 0% 0% 0% 9.09% 0%
  Total 11.11% 4.44% 4.44% 2.22% 15.56% **2.22%
  1. *The k-nearest neighbors (KNN) classifier was calculated over 1,000 independent trials for the mean error rates to be determined. Range of error values indicate that one or more trials provided a smaller error rate, though the average was computed.
  2. † KNN k = 2: ε = 174,000; KNN k = 3: ε = 57,000; QDA: ε = 67,000; LDA: ε = 73,000
  3. KNN k = 2: ε = 21,000; KNN k = 3: ε = 21,000; QDA: ε = 20,000; LDA: ε = 20,000
  4. **The 9.09% error rate corresponds to a single Pan paniscus sample that is misclassified by LOO-CV using LDA as a classifier.