NBLDA: Negative Binomial Linear Discriminant Analysis for RNA-Seq Data

RNA-sequencing (RNA-Seq) has become a powerful technology to characterize gene expression profiles because it is more accurate and comprehensive than microarrays. Although statistical methods that have been developed for microarray data can be applied to RNA-Seq data, they are not ideal due to the discrete nature of RNA-Seq data. The Poisson distribution and negative binomial distribution are commonly used to model count data. Recently, Witten (2011) proposed a Poisson linear discriminant analysis for RNA-Seq data. The Poisson assumption may not be as appropriate as negative binomial distribution when biological replicates are available and in the presence of overdispersion (i.e., when the variance is larger than the mean). However, it is more complicated to model negative binomial variables because they involve a dispersion parameter that needs to be estimated. In this paper, we propose a negative binomial linear discriminant analysis for RNA-Seq data. By Bayes' rule, we construct the classifier by fitting a negative binomial model, and propose some plug-in rules to estimate the unknown parameters in the classifier. The relationship between the negative binomial classifier and the Poisson classifier is explored, with a numerical investigation of the impact of dispersion on the discriminant score. Simulation results show the superiority of our proposed method. We also analyze four real RNA-Seq data sets to demonstrate the advantage of our method in real-world applications

Multi-level Feature Fusion-based CNN for Local Climate Zone Classification from Sentinel-2 Images: Benchmark Results on the So2Sat LCZ42 Dataset

As a unique classification scheme for urban forms and functions, the local climate zone (LCZ) system provides essential general information for any studies related to urban environments, especially on a large scale. Remote sensing data-based classification approaches are the key to large-scale mapping and monitoring of LCZs. The potential of deep learning-based approaches is not yet fully explored, even though advanced convolutional neural networks (CNNs) continue to push the frontiers for various computer vision tasks. One reason is that published studies are based on different datasets, usually at a regional scale, which makes it impossible to fairly and consistently compare the potential of different CNNs for real-world scenarios. This study is based on the big So2Sat LCZ42 benchmark dataset dedicated to LCZ classification. Using this dataset, we studied a range of CNNs of varying sizes. In addition, we proposed a CNN to classify LCZs from Sentinel-2 images, Sen2LCZ-Net. Using this base network, we propose fusing multi-level features using the extended Sen2LCZ-Net-MF. With this proposed simple network architecture and the highly competitive benchmark dataset, we obtain results that are better than those obtained by the state-of-the-art CNNs, while requiring less computation with fewer layers and parameters. Large-scale LCZ classification examples of completely unseen areas are presented, demonstrating the potential of our proposed Sen2LCZ-Net-MF as well as the So2Sat LCZ42 dataset. We also intensively investigated the influence of network depth and width and the effectiveness of the design choices made for Sen2LCZ-Net-MF. Our work will provide important baselines for future CNN-based algorithm developments for both LCZ classification and other urban land cover land use classification