Solving a large-scale Poisson system is computationally expensive for most of the Eulerian fluid simulation applications. We propose a novel machine learning-based approach to accelerate this process. At the heart of our approach is a deep convolutional neural network (CNN), with the capability of predicting the solution (pressure) of a Poisson system given the discretization structure and the intermediate velocities as input. Our system consists of four main components, namely, a deep neural network to solve the large linear equations, a geometric structure to describe the spatial hierarchies of the input vector, a Principal Component Analysis (PCA) process to reduce the dimension of input in training, and a novel loss function to control the incompressibility constraint. We have demonstrated the efficacy of our approach by simulating a variety of high-resolution smoke and liquid phenomena. In particular, we have shown that our approach accelerates the projection step in a conventional Eulerian fluid simulator by two orders of magnitude. In addition, we have also demonstrated the generality of our approach by producing a diversity of animations deviating from the original datasets.

BACKGROUND: Removing duplicates might be considered as a well-resolved problem in next-generation sequencing (NGS) data processing domain. However, as NGS technology gains more recognition in clinical application, researchers start to pay more attention to its sequencing errors, and prefer to remove these errors while performing deduplication operations. Recently, a new technology called unique molecular identifier (UMI) has been developed to better identify sequencing reads derived from different DNA fragments. Most existing duplicate removing tools cannot handle the UMI-integrated data. Some modern tools can work with UMIs, but are usually slow and use too much memory. Furthermore, existing tools rarely report rich statistical results, which are very important for quality control and downstream analysis. These unmet requirements drove us to develop an ultra-fast, simple, little-weighted but powerful tool for duplicate removing and sequence error suppressing, with features of handling UMIs and reporting informative results. RESULTS: This paper presents an efficient tool gencore for duplicate removing and sequence error suppressing of NGS data. This tool clusters the mapped sequencing reads and merges reads in each cluster to generate one single consensus read. While the consensus read is generated, the random errors introduced by library construction and sequencing can be removed. This error-suppressing feature makes gencore very suitable for the application of detecting ultra-low frequency mutations from deep sequencing data. When unique molecular identifier (UMI) technology is applied, gencore can use them to identify the reads derived from same original DNA fragment. Gencore reports statistical results in both HTML and JSON formats. The HTML format report contains many interactive figures plotting statistical coverage and duplication information. The JSON format report contains all the statistical results, and is interpretable for downstream programs. CONCLUSIONS: Comparing to the conventional tools like Picard and SAMtools, gencore greatly reduces the output data's mapping mismatches, which are mostly caused by errors. Comparing to some new tools like UMI-Reducer and UMI-tools, gencore runs much faster, uses less memory, generates better consensus reads and provides simpler interfaces. To our best knowledge, gencore is the only duplicate removing tool that generates both informative HTML and JSON reports. This tool is available at: https://github.com/OpenGene/gencore.

Calibration is a key step for on-vehicle AR-HUD systems to ensure the augmented information to be correctly viewed by the driver. State-of-art calibration methods require setting up of spatial tracking devices or attaching markers on vehicles, which is time-consuming and error-prone. In this paper, we present a novel multi-viewpoints calibration method for AR-HUD using only a mixed reality glasses such as HoloLens. The full calibration process can be done in one minute and provides high precise calibration result, while no markers need to be attached on vehicle.

Motivation: Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Traditionally, a different tool is used for each operation, such as quality control, adapter trimming and quality filtering. These tools are often insufficiently fast as most are developed using high-level programming languages (e.g. Python and Java) and provide limited multi-threading support. Reading and loading data multiple times also renders preprocessing slow and I/O inefficient. Results: We developed fastp as an ultra-fast FASTQ preprocessor with useful quality control and data-filtering features. It can perform quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data. This tool is developed in C++ and has multi-threading support. Based on our evaluation, fastp is 2-5 times faster than other FASTQ preprocessing tools such as Trimmomatic or Cutadapt despite performing far more operations than similar tools. Availability and implementation: The open-source code and corresponding instructions are available at https://github.com/OpenGene/fastp.

Mastitis is the major cause of loss in dairy farming. Somatic cells are one of most important standards to detect this infection. This paper proposes a novel image processing algorithm to recognize four types of somatic cells in bovine milk automatically. First, cloud model uses to segment cell images. Second, a variety of features are extracted from regions of interest. Finally, most differential features are selected using ReliefF algorithm and performances of two classifiers, Back propagation networks (BPN) and support vector machine (SVM), are compared. The experimental results are obtained using a large set of images from different sources. The results of our proposed method is not only efficient in accuracy and speed, but also robust to illumination in bovine mastitis via optical microscopy.

BACKGROUND: Some applications, especially those clinical applications requiring high accuracy of sequencing data, usually have to face the troubles caused by unavoidable sequencing errors. Several tools have been proposed to profile the sequencing quality, but few of them can quantify or correct the sequencing errors. This unmet requirement motivated us to develop AfterQC, a tool with functions to profile sequencing errors and correct most of them, plus highly automated quality control and data filtering features. Different from most tools, AfterQC analyses the overlapping of paired sequences for pair-end sequencing data. Based on overlapping analysis, AfterQC can detect and cut adapters, and furthermore it gives a novel function to correct wrong bases in the overlapping regions. Another new feature is to detect and visualise sequencing bubbles, which can be commonly found on the flowcell lanes and may raise sequencing errors. Besides normal per cycle quality and base content plotting, AfterQC also provides features like polyX (a long sub-sequence of a same base X) filtering, automatic trimming and K-MER based strand bias profiling. RESULTS: For each single or pair of FastQ files, AfterQC filters out bad reads, detects and eliminates sequencer's bubble effects, trims reads at front and tail, detects the sequencing errors and corrects part of them, and finally outputs clean data and generates HTML reports with interactive figures. AfterQC can run in batch mode with multiprocess support, it can run with a single FastQ file, a single pair of FastQ files (for pair-end sequencing), or a folder for all included FastQ files to be processed automatically. Based on overlapping analysis, AfterQC can estimate the sequencing error rate and profile the error transform distribution. The results of our error profiling tests show that the error distribution is highly platform dependent. CONCLUSION: Much more than just another new quality control (QC) tool, AfterQC is able to perform quality control, data filtering, error profiling and base correction automatically. Experimental results show that AfterQC can help to eliminate the sequencing errors for pair-end sequencing data to provide much cleaner outputs, and consequently help to reduce the false-positive variants, especially for the low-frequency somatic mutations. While providing rich configurable options, AfterQC can detect and set all the options automatically and require no argument in most cases.

In this paper, we propose a novel approach of Gabor feature based on bi-directional two-dimensional principal component analysis ((2D)2PCA) for somatic cells recognition. Firstly, Gabor features of different orientations and scales are extracted by the convolution of Gabor filter bank. Secondly, dimensionality reduction of the feature space applies (2D)2PCA in both row and column. Finally, the classifier uses Support Vector Machine (SVM) to achieve our goal. The experimental results are obtained using a large set of images from different sources. The results of our proposed method are not only efficient in accuracy and speed, but also robust to illumination in bovine mastitis via optical microscopy.