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

BACKGROUND: Accurate methods for extraction of meaningful patterns in high dimensional data have become increasingly important with the recent generation of data types containing measurements across thousands of variables. Principal components analysis (PCA) is a linear dimensionality reduction (DR) method that is unsupervised in that it relies only on the data; projections are calculated in Euclidean or a similar linear space and do not use tuning parameters for optimizing the fit to the data. However, relationships within sets of nonlinear data types, such as biological networks or images, are frequently mis-rendered into a low dimensional space by linear methods. Nonlinear methods, in contrast, attempt to model important aspects of the underlying data structure, often requiring parameter(s) fitting to the data type of interest. In many cases, the optimal parameter values vary when different classification algorithms are applied on the same rendered subspace, making the results of such methods highly dependent upon the type of classifier implemented. RESULTS: We present the results of applying the spectral method of Lafon, a nonlinear DR method based on the weighted graph Laplacian, that minimizes the requirements for such parameter optimization for two biological data types. We demonstrate that it is successful in determining implicit ordering of brain slice image data and in classifying separate species in microarray data, as compared to two conventional linear methods and three nonlinear methods (one of which is an alternative spectral method). This spectral implementation is shown to provide more meaningful information, by preserving important relationships, than the methods of DR presented for comparison. Tuning parameter fitting is simple and is a general, rather than data type or experiment specific approach, for the two datasets analyzed here. Tuning parameter optimization is minimized in the DR step to each subsequent classification method, enabling the possibility of valid cross-experiment comparisons. CONCLUSION: Results from the spectral method presented here exhibit the desirable properties of preserving meaningful nonlinear relationships in lower dimensional space and requiring minimal parameter fitting, providing a useful algorithm for purposes of visualization and classification across diverse datasets, a common challenge in systems biology

A biomimetic algorithm for the improved detection of microarray features,

One the major difficulties of microarray technology relate to the processing of large and - importantly - error-loaded images of the dots on the chip surface. Whatever the source of these errors, those obtained in the first stage of data acquisition - segmentation - are passed down to the subsequent processes, with deleterious results. As it has been demonstrated recently that biological systems have evolved algorithms that are mathematically efficient, this contribution attempts to test an algorithm that mimics a bacterial-"patented" algorithm for the search of available space and nutrients to find, "zero-in" and eventually delimitate the features existent on the microarray surface

A Study Of Factors Contributing To Self-reported Anomalies In Civil Aviation

A study investigating what factors are present leading to pilots submitting voluntary anomaly reports regarding their flight performance was conducted. The study employed statistical methods, text mining, clustering, and dimensional reduction techniques in an effort to determine relationships between factors and anomalies. A review of the literature was conducted to determine what factors are contributing to these anomalous incidents, as well as what research exists on human error, its causes, and its management. Data from the NASA Aviation Safety Reporting System (ASRS) was analyzed using traditional statistical methods such as frequencies and multinomial logistic regression. Recently formalized approaches in text mining such as Knowledge Based Discovery (KBD) and Literature Based Discovery (LBD) were employed to create associations between factors and anomalies. These methods were also used to generate predictive models. Finally, advances in dimensional reduction techniques identified concepts or keywords within records, thus creating a framework for an unsupervised document classification system. Findings from this study reinforced established views on contributing factors to civil aviation anomalies. New associations between previously unrelated factors and conditions were also found. Dimensionality reduction also demonstrated the possibility of identifying salient factors from unstructured text records, and was able to classify these records using these identified features