In this work we show that convolutional neural networks (CNNs) can be efficiently used to classify vibrational spectroscopic data and identify important spectral regions. CNNs are the current state-of-the-art in image classification and speech recognition and can learn interpretable representations of the data. These characteristics make CNNs a good candidate for reducing the need for preprocessing and for highlighting important spectral regions, both of which are crucial steps in the analysis of vibrational spectroscopic data. Chemometric analysis of vibrational spectroscopic data often relies on preprocessing methods involving baseline correction, scatter correction and noise removal, which are applied to the spectra prior to model building. Preprocessing is a critical step because even in simple problems using 'reasonable' preprocessing methods may decrease the performance of the final model. We develop a new CNN based method and provide an accompanying publicly available software. It is based on a simple CNN architecture with a single convolutional layer (a so-called shallow CNN). Our method outperforms standard classification algorithms used in chemometrics (e.g. PLS) in terms of accuracy when applied to non-preprocessed test data (86% average accuracy compared to the 62% achieved by PLS), and it achieves better performance even on preprocessed test data (96% average accuracy compared to the 89% achieved by PLS). For interpretability purposes, our method includes a procedure for finding important spectral regions, thereby facilitating qualitative interpretation of results.

Spectral-spatial classification of hyperspectral images has been the subject of many studies in recent years. When there are only a few labeled pixels for training and a skewed class label distribution, this task becomes very challenging because of the increased risk of overfitting when training a classifier. In this paper, we show that in this setting, a convolutional neural network with a single hidden layer can achieve state-of-the-art performance when three tricks are used: a spectrallocality-aware regularization term and smoothing-and label-based data augmentation. The shallow network architecture prevents overfitting in the presence of many features and few training samples. The locality-aware regularization forces neighboring wavelengths to have similar contributions to the features generated during training. The new data augmentation procedure favors the selection of pixels in smaller classes, which is beneficial for skewed class label distributions. The accuracy of the proposed method is assessed on five publicly available hyperspectral images, where it achieves state-of-the-art results. As other spectral-spatial classification methods, we use the entire image (labeled and unlabeled pixels) to infer the class of its unlabeled pixels. To investigate the positive bias induced by the use of the entire image, we propose a new learning setting where unlabeled pixels are not used for building the classifier. Results show the beneficial effect of the proposed tricks also in this setting and substantiate the advantages of using labeled and unlabeled pixels from the image for hyperspectral image classification.

Purpose To evaluate the value of convolutional neural network (CNN) in the diagnosis of human brain tumor or Alzheimer’s disease by MR spectroscopic imaging (MRSI) and to compare its Matthews correlation coefficient (MCC) score against that of other machine learning methods and previous evaluation of the same data. We address two challenges: 1) limited number of cases in MRSI datasets and 2) interpretability of results in the form of relevant spectral regions. Methods A shallow CNN with only one hidden layer and an ad-hoc loss function was constructed involving two branches for processing spectral and image features of a brain voxel respectively. Each branch consists of a single convolutional hidden layer. The output of the two convolutional layers is merged and fed to a classification layer that outputs class predictions for the given brain voxel. Results Our CNN method separated glioma grades 3 and 4 and identified Alzheimer’s disease patients using MRSI and complementary MRI data with high MCC score (Area Under the Curve were 0.87 and 0.91 respectively). The results demonstrated superior effectiveness over other popular methods as Partial Least Squares or Support Vector Machines. Also, our method automatically identified the spectral regions most important in the diagnosis process and we show that these are in good agreement with existing biomarkers from the literature. Conclusion Shallow CNNs models integrating image and spectral features improved quantitative and exploration and diagnosis of brain diseases for research and clinical purposes. Software is available at https://bitbucket.org/TeslaH2O/cnn_mrsi.

Abstract. Constrained non-negative matrix factorization (CNMF) is an effective machine learning technique to cluster documents in the presence of class label constraints. In this work, we provide a novel application of this technique in research on neuro-degenerative diseases. Specifically, we consider a dataset of documents from the Netherlands Brain Bank containing free text describing clinical and pathological information about donors affected by Multiple Sclerosis. The goal is to use CNMF for identifying clinical profiles with pathological information as constraints. After pre-processing the documents by means of standard filtering techniques, a feature representation of the documents in terms of bi-grams is constructed. The high dimensional feature space is reduced by applying a trimming procedure. The resulting datasets of clinical and pathological bi-grams are then clustered using non-negative matrix factorization (NMF) and, next, clinical data are clustered using CNMF with constraints induced by the clustering of pathological data. Results indicate the presence of interesting clinical profiles, for instance related to vision or movement problems. In particular, the use of CNMF leads to the identification of a clinical profile related to diabetes mellitus. Pathological characteristics and duration of disease of the identified profiles are analysed. Although highly promising, results of this investigation should be interpreted with care due to the relatively small size of the considered datasets.