Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Adaptive Blind Channel Estimation for MIMO-OFDM Systems Based on PARAFAC

In order to track the changing channel in multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) systems, it is prior to estimate channel impulse response adaptively. In this paper, we proposed an adaptive blind channel estimation method based on parallel factor analysis (PARAFAC). We used an exponential window to weight the past observations; thus, the cost function can be constructed via a weighted least squares criterion. The minimization of the cost function is equivalent to the decomposition of third-order tensor which consists of the weighted OFDM data symbols. To reduce the computational load, we adopt a recursive singular value decomposition method for tensor decomposition; then, the channel parameters can be estimated adaptively. Simulation results validate the effectiveness of the proposed algorithm under diverse signalling conditions

Joint Adaptive Blind Channel Estimation and Data Detection for MIMO-OFDM Systems

In order to track a changing channel in multiple-input multiple-output orthogonal frequency division multiplexing (MIMO-OFDM) systems, it is a priority to estimate channel impulse response adaptively. In this paper, we propose an adaptive blind channel estimation method based on parallel factor analysis (PARAFAC). We used an exponential window to weigh the past observations; thus, the cost function can be constructed via a weighted least squares criterion. The minimization of the cost function is equivalent to the decomposition of a third-order tensor, which consists of the weighted OFDM data symbols. By preserving the Khatri-Rao product, we used a recursive least squares solution to update the estimated subspace at each time instant, then the channel parameters can be estimated adaptively, and the algorithm achieves superior convergence performance. Simulation results validate the effectiveness of the proposed algorithm

Crop Classification Using MSCDN Classifier and Sparse Auto-Encoders with Non-Negativity Constraints for Multi-Temporal, Quad-Pol SAR Data

Accurate and reliable crop classification information is a significant data source for agricultural monitoring and food security evaluation research. It is well-known that polarimetric synthetic aperture radar (PolSAR) data provides ample information for crop classification. Moreover, multi-temporal PolSAR data can further increase classification accuracies since the crops show different external forms as they grow up. In this paper, we distinguish the crop types with multi-temporal PolSAR data. First, due to the “dimension disaster” of multi-temporal PolSAR data caused by excessive scattering parameters, a neural network of sparse auto-encoder with non-negativity constraint (NC-SAE) was employed to compress the data, yielding efficient features for accurate classification. Second, a novel crop discrimination network with multi-scale features (MSCDN) was constructed to improve the classification performance, which is proved to be superior to the popular classifiers of convolutional neural networks (CNN) and support vector machine (SVM). The performances of the proposed method were evaluated and compared with the traditional methods by using simulated Sentinel-1 data provided by European Space Agency (ESA). For the final classification results of the proposed method, its overall accuracy and kappa coefficient reaches 99.33% and 99.19%, respectively, which were almost 5% and 6% higher than the CNN method. The classification results indicate that the proposed methodology is promising for practical use in agricultural applications