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253. High fidelity single-pixel imaging

Author

Deng, Chao, Hu, Xuemei, Li, Xiaoxu, Suo, Jinli, Zhang, Zhili, and Dai, Qionghai

Subjects
Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Single-pixel imaging (SPI) is an emerging technique which has attracts wide attention in various research fields. However, restricted by the low reconstruction quality and large amount of measurements, the practical application is still in its infancy. Inspired by the fact that natural scenes exhibit unique degenerate structures in the low dimensional subspace, we propose to take advantage of the local prior in convolutional sparse coding to implement high fidelity single-pixel imaging. Specifically, by statistically learning strategy, the target scene can be sparse represented on an overcomplete dictionary. The dictionary is composed of various basis learned from a natural image database. We introduce the above local prior into conventional SPI framework to promote the final reconstruction quality. Experiments both on synthetic data and real captured data demonstrate that our method can achieve better reconstruction from the same measurements, and thus consequently reduce the number of required measurements for same reconstruction quality., Comment: 5 pages, 6 figures

Published
2018

254. Identifying viruses from metagenomic data by deep learning

Author

Ren, Jie, Song, Kai, Deng, Chao, Ahlgren, Nathan A., Fuhrman, Jed A., Li, Yi, Xie, Xiaohui, and Sun, Fengzhu

Subjects
Quantitative Biology - Genomics
Abstract

The recent development of metagenomic sequencing makes it possible to sequence microbial genomes including viruses in an environmental sample. Identifying viral sequences from metagenomic data is critical for downstream virus analyses. The existing reference-based and gene homology-based methods are not efficient in identifying unknown viruses or short viral sequences. Here we have developed a reference-free and alignment-free machine learning method, DeepVirFinder, for predicting viral sequences in metagenomic data using deep learning techniques. DeepVirFinder was trained based on a large number of viral sequences discovered before May 2015. Evaluated on the sequences after that date, DeepVirFinder outperformed the state-of-the-art method VirFinder at all contig lengths. Enlarging the training data by adding millions of purified viral sequences from environmental metavirome samples significantly improves the accuracy for predicting under-represented viruses. Applying DeepVirFinder to real human gut metagenomic samples from patients with colorectal carcinoma (CRC) identified 51,138 viral sequences belonging to 175 bins. Ten bins were associated with the cancer status, indicating their potential use for non-invasive diagnosis of CRC. In summary, DeepVirFinder greatly improved the precision and recall rates of viral identification, and it will significantly accelerate the discovery rate of viruses.

Published
2018

255. Snapshot hyperspectral imaging via spectral basis multiplexing in Fourier domain

Author

Deng, Chao, Hu, Xuemei, Suo, Jinli, Zhang, Yuanlong, Zhang, Zhili, and Dai, Qionghai

Subjects
Physics - Instrumentation and Detectors, Physics - Optics
Abstract

Hyperspectral imaging is an important tool having been applied in various fields, but still limited in observation of dynamic scenes. In this paper, we propose a snapshot hyperspectral imaging technique which exploits both spectral and spatial sparsity of natural scenes. Under the computational imaging scheme, we conduct spectral dimension reduction and spatial frequency truncation to the hyperspectral data cube and snapshot it in a low cost manner. Specifically, we modulate the spectral variations by several broadband spectral filters, and then map these modulated images into different regions in the Fourier domain. The encoded image compressed in both spectral and spatial are finally collected by a monochrome detector. Correspondingly, the reconstruction is essentially a Fourier domain extraction and spectral dimensional back projection with low computational load. This Fourier-spectral multiplexing in a 2D sensor simplifies both the encoding and decoding process, and makes hyperspectral data captured in a low cost manner. We demonstrate the high performance of our method by quantitative evaluation on simulation data and build a prototype system experimentally for further validation., Comment: 13 pages, 8 figures

Published
2018
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