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Motivation Phage–host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage–host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH. Results On the validation set, ContigNet achieves 72–85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60–70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts. Availability and implementation The source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet. [ABSTRACT FROM AUTHOR]

The emerging resistive random-access memory (RRAM) has been widely applied in accelerating the computing of deep neural networks. However, it is challenging to achieve high-precision computations based on RRAM due to the limits of the resistance level and the interfaces. Low bit-width convolutional neural networks (CNNs) provide promising solutions to introduce low bit-width RRAM devices and low bit-width interfaces in RRAM-based computing system (RCS). While open questions still remain regarding: 1) how to make matrix splitting when a single crossbar is not large enough to hold all parameters of one weight matrix; 2) how to design a pipeline to accelerate the inference based on line buffer structure; and 3) how to reduce the accuracy drop due to the parameter splitting and data quantization. In this paper, we propose an RRAM crossbar-based low bit-width CNN (LB-CNN) accelerator. We make detailed discussion on the system design, including the matrix splitting strategies to enhance the scalability, and the pipelined implementation based on line buffers to accelerate the inference. In addition, we propose a splitting and quantizing while training method to incorporate the actual hardware constraints with the training. In our experiments, low bit-width LeNet-5 on RRAM show much better robustness than multibit models with device variation. The pipeline strategy achieves approximately $6.0\times $ speedup to process each image on ResNet-18. For low-bit VGG-8 on CIFAR-10, the proposed accelerator saves 54.9% of the energy consumption and 48.3% of the area compared with the multibit VGG-8 structure. [ABSTRACT FROM AUTHOR]