Coupled VAE: Improved Accuracy and Robustness of a Variational Autoencoder.

We present a coupled variational autoencoder (VAE) method, which improves the accuracy and robustness of the model representation of handwritten numeral images. The improvement is measured in both increasing the likelihood of the reconstructed images and in reducing divergence between the posterior and a prior latent distribution. The new method weighs outlier samples with a higher penalty by generalizing the original evidence lower bound function using a coupled entropy function based on the principles of nonlinear statistical coupling. We evaluated the performance of the coupled VAE model using the Modified National Institute of Standards and Technology (MNIST) dataset and its corrupted modification C-MNIST. Histograms of the likelihood that the reconstruction matches the original image show that the coupled VAE improves the reconstruction and this improvement is more substantial when seeded with corrupted images. All five corruptions evaluated showed improvement. For instance, with the Gaussian corruption seed the accuracy improves by 1014 (from 10-57.2 to 10-42.9) and robustness improves by 1022 (from 10-109.2 to 10-87.0). Furthermore, the divergence between the posterior and prior distribution of the latent distribution is reduced. Thus, in contrast to the ß-VAE design, the coupled VAE algorithm improves model representation, rather than trading off the performance of the reconstruction and latent distribution divergence.

Classification of malignant and benign tumors of the lung by infrared spectral histopathology (SHP).

We report results of a study utilizing a novel tissue classification method, based on label-free spectral techniques, for the classification of lung cancer histopathological samples on a tissue microarray. The spectral diagnostic method allows reproducible and objective classification of unstained tissue sections. This is accomplished by acquiring infrared data sets containing thousands of spectra, each collected from tissue pixels ∼6 µm on edge; these pixel spectra contain an encoded snapshot of the entire biochemical composition of the pixel area. The hyperspectral data sets are subsequently decoded by methods of multivariate analysis that reveal changes in the biochemical composition between tissue types, and between various stages and states of disease. In this study, a detailed comparison between classical and spectral histopathology is presented, suggesting that spectral histopathology can achieve levels of diagnostic accuracy that is comparable to that of multipanel immunohistochemistry.

Biomedical informatics for computer-aided decision support systems: a survey.

The volumes of current patient data as well as their complexity make clinical decision making more challenging than ever for physicians and other care givers. This situation calls for the use of biomedical informatics methods to process data and form recommendations and/or predictions to assist such decision makers. The design, implementation, and use of biomedical informatics systems in the form of computer-aided decision support have become essential and widely used over the last two decades. This paper provides a brief review of such systems, their application protocols and methodologies, and the future challenges and directions they suggest.

Top scoring pairs for feature selection in machine learning and applications to cancer outcome prediction.

BACKGROUND: The widely used k top scoring pair (k-TSP) algorithm is a simple yet powerful parameter-free classifier. It owes its success in many cancer microarray datasets to an effective feature selection algorithm that is based on relative expression ordering of gene pairs. However, its general robustness does not extend to some difficult datasets, such as those involving cancer outcome prediction, which may be due to the relatively simple voting scheme used by the classifier. We believe that the performance can be enhanced by separating its effective feature selection component and combining it with a powerful classifier such as the support vector machine (SVM). More generally the top scoring pairs generated by the k-TSP ranking algorithm can be used as a dimensionally reduced subspace for other machine learning classifiers. RESULTS: We developed an approach integrating the k-TSP ranking algorithm (TSP) with other machine learning methods, allowing combination of the computationally efficient, multivariate feature ranking of k-TSP with multivariate classifiers such as SVM. We evaluated this hybrid scheme (k-TSP+SVM) in a range of simulated datasets with known data structures. As compared with other feature selection methods, such as a univariate method similar to Fisher's discriminant criterion (Fisher), or a recursive feature elimination embedded in SVM (RFE), TSP is increasingly more effective than the other two methods as the informative genes become progressively more correlated, which is demonstrated both in terms of the classification performance and the ability to recover true informative genes. We also applied this hybrid scheme to four cancer prognosis datasets, in which k-TSP+SVM outperforms k-TSP classifier in all datasets, and achieves either comparable or superior performance to that using SVM alone. In concurrence with what is observed in simulation, TSP appears to be a better feature selector than Fisher and RFE in some of the cancer datasets CONCLUSIONS: The k-TSP ranking algorithm can be used as a computationally efficient, multivariate filter method for feature selection in machine learning. SVM in combination with k-TSP ranking algorithm outperforms k-TSP and SVM alone in simulated datasets and in some cancer prognosis datasets. Simulation studies suggest that as a feature selector, it is better tuned to certain data characteristics, i.e. correlations among informative genes, which is potentially interesting as an alternative feature ranking method in pathway analysis.