State-of-the art data normalization methods improve NMR-based metabolomic analysis

Extracting biomedical information from large metabolomic datasets by multivariate data analysis is of considerable complexity. Common challenges include among others screening for differentially produced metabolites, estimation of fold changes, and sample classification. Prior to these analysis steps, it is important to minimize contributions from unwanted biases and experimental variance. This is the goal of data preprocessing. In this work, different data normalization methods were compared systematically employing two different datasets generated by means of nuclear magnetic resonance (NMR) spectroscopy. To this end, two different types of normalization methods were used, one aiming to remove unwanted sample-to-sample variation while the other adjusts the variance of the different metabolites by variable scaling and variance stabilization methods. The impact of all methods tested on sample classification was evaluated on urinary NMR fingerprints obtained from healthy volunteers and patients suffering from autosomal polycystic kidney disease (ADPKD). Performance in terms of screening for differentially produced metabolites was investigated on a dataset following a Latin-square design, where varied amounts of 8 different metabolites were spiked into a human urine matrix while keeping the total spike-in amount constant. In addition, specific tests were conducted to systematically investigate the influence of the different preprocessing methods on the structure of the analyzed data. In conclusion, preprocessing methods originally developed for DNA microarray analysis, in particular, Quantile and Cubic-Spline Normalization, performed best in reducing bias, accurately detecting fold changes, and classifying samples

Multi-domain stain normalization for digital pathology: A cycle-consistent adversarial network for whole slide images

The variation in histologic staining between different medical centers is one of the most profound challenges in the field of computer-aided diagnosis. The appearance disparity of pathological whole slide images causes algorithms to become less reliable, which in turn impedes the wide-spread applicability of downstream tasks like cancer diagnosis. Furthermore, different stainings lead to biases in the training which in case of domain shifts negatively affect the test performance. Therefore, in this paper we propose MultiStain-CycleGAN, a multi-domain approach to stain normalization based on CycleGAN. Our modifications to CycleGAN allow us to normalize images of different origins without retraining or using different models. We perform an extensive evaluation of our method using various metrics and compare it to commonly used methods that are multi-domain capable. First, we evaluate how well our method fools a domain classifier that tries to assign a medical center to an image. Then, we test our normalization on the tumor classification performance of a downstream classifier. Furthermore, we evaluate the image quality of the normalized images using the Structural similarity index and the ability to reduce the domain shift using the Fr\'echet inception distance. We show that our method proves to be multi-domain capable, provides the highest image quality among the compared methods, and can most reliably fool the domain classifier while keeping the tumor classifier performance high. By reducing the domain influence, biases in the data can be removed on the one hand and the origin of the whole slide image can be disguised on the other, thus enhancing patient data privacy.Comment: 19 pages, 11 figures, 3 table

A Framework for Evaluating Land Use and Land Cover Classification Using Convolutional Neural Networks

Analyzing land use and land cover (LULC) using remote sensing (RS) imagery is essential for many environmental and social applications. The increase in availability of RS data has led to the development of new techniques for digital pattern classification. Very recently, deep learning (DL) models have emerged as a powerful solution to approach many machine learning (ML) problems. In particular, convolutional neural networks (CNNs) are currently the state of the art for many image classification tasks. While there exist several promising proposals on the application of CNNs to LULC classification, the validation framework proposed for the comparison of different methods could be improved with the use of a standard validation procedure for ML based on cross-validation and its subsequent statistical analysis. In this paper, we propose a general CNN, with a fixed architecture and parametrization, to achieve high accuracy on LULC classification over RS data from different sources such as radar and hyperspectral. We also present a methodology to perform a rigorous experimental comparison between our proposed DL method and other ML algorithms such as support vector machines, random forests, and k-nearest-neighbors. The analysis carried out demonstrates that the CNN outperforms the rest of techniques, achieving a high level of performance for all the datasets studied, regardless of their different characteristics.Ministerio de Economía y Competitividad TIN2014-55894-C2-1-RMinisterio de Economía y Competitividad TIN2017-88209-C2-2-

Inference and Evaluation of the Multinomial Mixture Model for Text Clustering

In this article, we investigate the use of a probabilistic model for unsupervised clustering in text collections. Unsupervised clustering has become a basic module for many intelligent text processing applications, such as information retrieval, text classification or information extraction. The model considered in this contribution consists of a mixture of multinomial distributions over the word counts, each component corresponding to a different theme. We present and contrast various estimation procedures, which apply both in supervised and unsupervised contexts. In supervised learning, this work suggests a criterion for evaluating the posterior odds of new documents which is more statistically sound than the "naive Bayes" approach. In an unsupervised context, we propose measures to set up a systematic evaluation framework and start with examining the Expectation-Maximization (EM) algorithm as the basic tool for inference. We discuss the importance of initialization and the influence of other features such as the smoothing strategy or the size of the vocabulary, thereby illustrating the difficulties incurred by the high dimensionality of the parameter space. We also propose a heuristic algorithm based on iterative EM with vocabulary reduction to solve this problem. Using the fact that the latent variables can be analytically integrated out, we finally show that Gibbs sampling algorithm is tractable and compares favorably to the basic expectation maximization approach

Statistically Motivated Second Order Pooling

Second-order pooling, a.k.a.~bilinear pooling, has proven effective for deep learning based visual recognition. However, the resulting second-order networks yield a final representation that is orders of magnitude larger than that of standard, first-order ones, making them memory-intensive and cumbersome to deploy. Here, we introduce a general, parametric compression strategy that can produce more compact representations than existing compression techniques, yet outperform both compressed and uncompressed second-order models. Our approach is motivated by a statistical analysis of the network's activations, relying on operations that lead to a Gaussian-distributed final representation, as inherently used by first-order deep networks. As evidenced by our experiments, this lets us outperform the state-of-the-art first-order and second-order models on several benchmark recognition datasets.Comment: Accepted to ECCV 2018. Camera ready version. 14 page, 5 figures, 3 table

Best Practices in Convolutional Networks for Forward-Looking Sonar Image Recognition

Convolutional Neural Networks (CNN) have revolutionized perception for color images, and their application to sonar images has also obtained good results. But in general CNNs are difficult to train without a large dataset, need manual tuning of a considerable number of hyperparameters, and require many careful decisions by a designer. In this work, we evaluate three common decisions that need to be made by a CNN designer, namely the performance of transfer learning, the effect of object/image size and the relation between training set size. We evaluate three CNN models, namely one based on LeNet, and two based on the Fire module from SqueezeNet. Our findings are: Transfer learning with an SVM works very well, even when the train and transfer sets have no classes in common, and high classification performance can be obtained even when the target dataset is small. The ADAM optimizer combined with Batch Normalization can make a high accuracy CNN classifier, even with small image sizes (16 pixels). At least 50 samples per class are required to obtain $90\%$ test accuracy, and using Dropout with a small dataset helps improve performance, but Batch Normalization is better when a large dataset is available.Comment: Author version; IEEE/MTS Oceans 2017 Aberdee