相关论文: Fundamental Bounds and Approaches to Sequence Reco…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
Automatic 3D neuron reconstruction is critical for analysing the morphology and functionality of neurons in brain circuit activities. However, the performance of existing tracing algorithms is hinged by the low image quality. Recently, a…
Expanding genetic codes from natural standard nucleotides to artificial non-standard nucleotides marks a significant advancement in synthetic biology, with profound implications for biotechnology and medicine. Decoding the biological…
The Levenshtein sequence reconstruction problem studies the reconstruction of a transmitted sequence from multiple erroneous copies of it. A fundamental question in this field is to determine the minimum number of erroneous copies required…
Modern technology for producing extremely bright and coherent X-ray laser pulses provides the possibility to acquire a large number of diffraction patterns from individual biological nanoparticles, including proteins, viruses, and DNA.…
Nanopore sequencing technology remains highly error-prone, making efficient error correction essential in DNA-based data storage. Prior work addressed high error rates using convolutional codes with their decoder coupled with the…
Undersampled inverse problems occur everywhere in the sciences including medical imaging, radar, astronomy etc., yielding underdetermined linear or non-linear reconstruction problems. There are now a myriad of techniques to design decoders…
Systematic techniques to improve quality of deep neural networks (DNNs) are critical given the increasing demand for practical applications including safety-critical ones. The key challenge comes from the little controllability in updating…
Correcting insertions/deletions as well as substitution errors simultaneously plays an important role in DNA-based storage systems as well as in classical communications. This paper deals with the fundamental task of constructing codes that…
Motivated by average-case trace reconstruction and coding for portable DNA-based storage systems, we initiate the study of \emph{coded trace reconstruction}, the design and analysis of high-rate efficiently encodable codes that can be…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
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…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
Insertion and deletion (insdel for short) errors are synchronization errors in communication systems caused by the loss of positional information in the message. Reed-Solomon codes have gained a lot of interest due to its encoding…
The {\em insertion-deletion channel} takes as input a binary string $x \in\{0, 1\}^n$, and outputs a string $\widetilde{x}$ where some of the bits have been deleted and others inserted independently at random. In the {\em trace…
In the emerging field of DNA storage, data is encoded as DNA sequences and stored. The data is read out again by sequencing the stored DNA. Nanopore sequencing is a new sequencing technology that has many advantages over other methods; in…
This paper introduces a new solution to DNA storage that integrates all three steps of retrieval, namely clustering, reconstruction, and error correction. DNA-correcting codes are presented as a unique solution to the problem of ensuring…
We consider the problem of identifying jointly the ancestral sequence, the phylogeny and the parameters in models of DNA sequence evolution with insertion and deletion (indel). Under the classical TKF91 model of sequence evolution, we…
The determination of a patient's DNA sequence can, in principle, reveal an increased risk to fall ill with particular diseases [1,2] and help to design "personalized medicine" [3]. Moreover, statistical studies and comparison of genomes [4]…