相关论文: Barcoding-free BAC Pooling Enables Combinatorial S…

We propose Bayesian Conformal Prediction (BCP), a framework that combines Bayesian posterior predictive distributions with PAC-style conformal risk control to produce prediction sets with finite-sample coverage guarantees. Standard…

We introduce a parallel algorithmic architecture for metagenomic sequence assembly, termed MetaPar, which allows for significant reductions in assembly time and consequently enables the processing of large genomic datasets on computers with…

Blind deconvolution (BD) arises in many applications. Without assumptions on the signal and the filter, BD does not admit a unique solution. In practice, subspace or sparsity assumptions have shown the ability to reduce the search space and…

An important preprocessing step in most data analysis pipelines aims to extract a small set of sources that explain most of the data. Currently used algorithms for blind source separation (BSS), however, often fail to extract the desired…

DNA methylation (DNAme) is a critical component of the epigenetic regulatory machinery and aberrations in DNAme patterns occur in many diseases, such as cancer. Mapping and understanding DNAme profiles offers considerable promise for…

Polar codes are a class of linear block codes that provably achieves channel capacity. They have been selected as a coding scheme for the control channel of enhanced mobile broadband (eMBB) scenario for $5^{\text{th}}$ generation wireless…

In this paper, we introduce a deep learning-based decoder designed for concatenated coding schemes over a deletion/substitution channel. Specifically, we focus on serially concatenated codes, where the outer code is either a convolutional…

We present a bracketing-based encoding that can be used to represent any 2-planar dependency tree over a sentence of length n as a sequence of n labels, hence providing almost total coverage of crossing arcs in sequence labeling parsing.…

Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire…

Learning ensembles by bagging can substantially improve the generalization performance of low-bias, high-variance estimators, including those evolved by Genetic Programming (GP). To be efficient, modern GP algorithms for evolving (bagging)…

We consider error-correcting coding for deoxyribonucleic acid (DNA)-based storage using nanopore sequencing. We model the DNA storage channel as a sampling noise channel where the input data is chunked into $M$ short DNA strands, which are…

Convolutional precoding in polarization-adjusted convolutional (PAC) codes can reduce the number of minimum weight codewords (a.k.a error coefficient) of polar codes. This can result in improving the error correction performance of (near)…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

Coded polynomial aggregation (CPA) in distributed computing systems enables the master to directly recover a weighted aggregation of polynomial computations without individually decoding each term, thereby reducing the number of required…

Due to the sequential nature of the successive-cancellation (SC) algorithm, the decoding of polar codes suffers from significant decoding latencies. Fast SC decoding is able to speed up the SC decoding process, by implementing parallel…

Identification of every single genome present in a microbial sample is an important and challenging task with crucial applications. It is challenging because there are typically millions of cells in a microbial sample, the vast majority of…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

This paper introduces a new family of reconstruction codes which is motivated by applications in DNA data storage and sequencing. In such applications, DNA strands are sequenced by reading some subset of their substrings. While previous…

Two concatenated coding schemes incorporating algebraic Reed-Solomon (RS) codes and polarization-adjusted convolutional (PAC) codes are proposed. Simulation results show that at a bit error rate of $10^{-5}$, a concatenated scheme using RS…

In convolutional neural networks (CNNs), pooling operations play important roles such as dimensionality reduction and deformation compensation. In general, max pooling, which is the most widely used operation for local pooling, is performed…