Genome signatures, self-organizing maps and higher order phylogenies: a parametric analysis

Genome signatures are data vectors derived from the compositional statistics of DNA. The self-organizing map (SOM) is a neural network method for the conceptualisation of relationships within complex data, such as genome signatures. The various parameters of the SOM training phase are investigated for their effect on the accuracy of the resulting output map. It is concluded that larger SOMs, as well as taking longer to train, are less sensitive in phylogenetic classification of unknown DNA sequences. However, where a classification can be made, a larger SOM is more accurate. Increasing the number of iterations in the training phase of the SOM only slightly increases accuracy, without improving sensitivity. The optimal length of the DNA sequence k-mer from which the genome signature should be derived is 4 or 5, but shorter values are almost as effective. In general, these results indicate that small, rapidly trained SOMs are generally as good as larger, longer trained ones for the analysis of genome signatures. These results may also be more generally applicable to the use of SOMs for other complex data sets, such as microarray data

Group Analysis of Self-organizing Maps based on Functional MRI using Restricted Frechet Means

Studies of functional MRI data are increasingly concerned with the estimation of differences in spatio-temporal networks across groups of subjects or experimental conditions. Unsupervised clustering and independent component analysis (ICA) have been used to identify such spatio-temporal networks. While these approaches have been useful for estimating these networks at the subject-level, comparisons over groups or experimental conditions require further methodological development. In this paper, we tackle this problem by showing how self-organizing maps (SOMs) can be compared within a Frechean inferential framework. Here, we summarize the mean SOM in each group as a Frechet mean with respect to a metric on the space of SOMs. We consider the use of different metrics, and introduce two extensions of the classical sum of minimum distance (SMD) between two SOMs, which take into account the spatio-temporal pattern of the fMRI data. The validity of these methods is illustrated on synthetic data. Through these simulations, we show that the three metrics of interest behave as expected, in the sense that the ones capturing temporal, spatial and spatio-temporal aspects of the SOMs are more likely to reach significance under simulated scenarios characterized by temporal, spatial and spatio-temporal differences, respectively. In addition, a re-analysis of a classical experiment on visually-triggered emotions demonstrates the usefulness of this methodology. In this study, the multivariate functional patterns typical of the subjects exposed to pleasant and unpleasant stimuli are found to be more similar than the ones of the subjects exposed to emotionally neutral stimuli. Taken together, these results indicate that our proposed methods can cast new light on existing data by adopting a global analytical perspective on functional MRI paradigms.Comment: 23 pages, 5 figures, 4 tables. Submitted to Neuroimag

Can Self-Organizing Maps accurately predict photometric redshifts?

We present an unsupervised machine learning approach that can be employed for estimating photometric redshifts. The proposed method is based on a vector quantization approach called Self--Organizing Mapping (SOM). A variety of photometrically derived input values were utilized from the Sloan Digital Sky Survey's Main Galaxy Sample, Luminous Red Galaxy, and Quasar samples along with the PHAT0 data set from the PHoto-z Accuracy Testing project. Regression results obtained with this new approach were evaluated in terms of root mean square error (RMSE) to estimate the accuracy of the photometric redshift estimates. The results demonstrate competitive RMSE and outlier percentages when compared with several other popular approaches such as Artificial Neural Networks and Gaussian Process Regression. SOM RMSE--results (using $\Delta$z=z$_{phot}$--z$_{spec}$) for the Main Galaxy Sample are 0.023, for the Luminous Red Galaxy sample 0.027, Quasars are 0.418, and PHAT0 synthetic data are 0.022. The results demonstrate that there are non--unique solutions for estimating SOM RMSEs. Further research is needed in order to find more robust estimation techniques using SOMs, but the results herein are a positive indication of their capabilities when compared with other well-known methods.Comment: 5 pages, 3 figures, submitted to PAS

Multiple object tracking using a neural cost function

This paper presents a new approach to the tracking of multiple objects in CCTV surveillance using a combination of simple neural cost functions based on Self-Organizing Maps, and a greedy assignment algorithm. Using a reference standard data set and an exhaustive search algorithm for benchmarking, we show that the cost function plays the most significant role in realizing high levels of performance. The neural cost function’s context-sensitive treatment of appearance, change of appearance and trajectory yield better tracking than a simple, explicitly designed cost function. The algorithm matches 98.8% of objects to within 15 pixels