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Barcodes are ubiquitous and have been used in most of critical daily activities for decades. However, most of traditional decoders require well-founded barcode under a relatively standard condition. While wilder conditioned barcodes such as…

String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…

A scheme for concatenating the recently invented polar codes with interleaved block codes is considered. By concatenating binary polar codes with interleaved Reed-Solomon codes, we prove that the proposed concatenation scheme captures the…

Motivation: New long read sequencers promise to transform sequencing and genome assembly by producing reads tens of kilobases long. However their high error rate significantly complicates assembly and requires expensive correction steps to…

In single-molecule super-resolution microscopy, engineered point-spread functions (PSFs) are designed to efficiently encode new molecular properties, such as 3D orientation, into complex spatial features captured by a camera. To fully…

(An updated version of this manuscript has been accepted to Scientific Reports in 2016, please refer to http://www.nature.com/articles/srep31900) The highly anticipated transition from next generation sequencing (NGS) to third generation…

A number of recent studies have shown that a Deep Convolutional Neural Network (DCNN) pretrained on a large dataset can be adopted as a universal image description which leads to astounding performance in many visual classification tasks.…

Despite the superior performance of CNN, deploying them on low computational power devices is still limited as they are typically computationally expensive. One key cause of the high complexity is the connection between the convolution…

The high incidence rate of prostate disease poses a requirement in early detection for diagnosis. As one of the main imaging methods used for prostate cancer detection, Magnetic Resonance Imaging (MRI) has wide range of appearance and…

We consider the problem of multivariate density deconvolution where the distribution of a random vector needs to be estimated from replicates contaminated with conditionally heteroscedastic measurement errors. We propose a conceptually…

Second-generation sequencing technologies have replaced array-based technologies and become the default method for genomics and epigenomics analysis. Second-generation sequencing technologies sequence tens of millions of DNA/cDNA fragments…

Coded computing is an effective technique to mitigate "stragglers" in large-scale and distributed matrix multiplication. In particular, univariate polynomial codes have been shown to be effective in straggler mitigation by making the…

We tackle the problem of sequential brick assembly with LEGO bricks to create combinatorial 3D structures. This problem is challenging since this brick assembly task encompasses the characteristics of combinatorial optimization problems. In…

It is known that the bit errors of polar codes with successive cancellation (SC) decoding are coupled. However, existing concatenation schemes of polar codes with other error correction codes rarely take this coupling effect into…

This paper describes a novel approach of packing sparse convolutional neural networks for their efficient systolic array implementations. By combining subsets of columns in the original filter matrix associated with a convolutional layer,…

We developed a low-cost, high-throughput microbiome profiling method that uses combinatorial sequence tags attached to PCR primers that amplify the rRNA V6 region. Amplified PCR products are sequenced using an Illumina paired-end protocol…

The rapidly improving performance of modern hardware renders convolutional codes obsolete, and allows for the practical implementation of more sophisticated correction codes such as low density parity check (LDPC) and turbo codes (TC). Both…

One of the major challenges in using distributed learning to train complicated models with large data sets is to deal with stragglers effect. As a solution, coded computation has been recently proposed to efficiently add redundancy to the…

Fast SC decoding overcomes the latency caused by the serial nature of the SC decoding by identifying new nodes in the upper levels of the SC decoding tree and implementing their fast parallel decoders. In this work, we first present a novel…

Background. Models of ancestral gene order reconstruction have progressively integrated different evolutionary patterns and processes such as unequal gene content, gene duplications, and implicitly sequence evolution via reconciled gene…