Reuse of imputed data in microarray analysis increases imputation efficiency

BACKGROUND: The imputation of missing values is necessary for the efficient use of DNA microarray data, because many clustering algorithms and some statistical analysis require a complete data set. A few imputation methods for DNA microarray data have been introduced, but the efficiency of the methods was low and the validity of imputed values in these methods had not been fully checked. RESULTS: We developed a new cluster-based imputation method called sequential K-nearest neighbor (SKNN) method. This imputes the missing values sequentially from the gene having least missing values, and uses the imputed values for the later imputation. Although it uses the imputed values, the efficiency of this new method is greatly improved in its accuracy and computational complexity over the conventional KNN-based method and other methods based on maximum likelihood estimation. The performance of SKNN was in particular higher than other imputation methods for the data with high missing rates and large number of experiments. Application of Expectation Maximization (EM) to the SKNN method improved the accuracy, but increased computational time proportional to the number of iterations. The Multiple Imputation (MI) method, which is well known but not applied previously to microarray data, showed a similarly high accuracy as the SKNN method, with slightly higher dependency on the types of data sets. CONCLUSIONS: Sequential reuse of imputed data in KNN-based imputation greatly increases the efficiency of imputation. The SKNN method should be practically useful to save the data of some microarray experiments which have high amounts of missing entries. The SKNN method generates reliable imputed values which can be used for further cluster-based analysis of microarray data

Inference of missing spectrographic features for robust speech recognition

Two types of algorithms are introduced that recover missing time-frequency regions of log-spectral representations of speech. These compensation algorithms modify the incoming feature vector without any changes to the speech recognition system, in contrast to previously-described approaches. The first approach clusters the log-spectral vectors representing clean speech. Missing data are recovered by estimating the spectral cluster in each analysis frame on the basis of the feature values that are present. The second approach uses MAP procedures to estimate the values of missing data elements based on their correlation with the features that are present. Greatest recognition accuracy was obtained using the correlation-based approach, presumably because of its ability to exploit the temporal as well as spectral structure of speech. The recognition accuracy provided by these algorithms approaches but does not exceed that obtained by traditional marginalization. Nevertheless, it is believed that these algorithms provide greater computational efficiency and enable greater flexibility in recognition system structure. 1