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This study develops an algorithm to solve a variation of the Shortest Common Superstring (SCS) problem. There are two modifications to the base SCS problem. First, one string in the set S is allowed to have up to K mistakes, defined as not…
Exponential error bounds achievable by universal coding and decoding are derived for frame-asynchronous discrete memoryless %asynchronous multiple access channels with two senders, via the method of subtypes, a refinement of the method of…
Model transformations operate on models conforming to precisely defined metamodels. Consequently, it often seems relatively easy to chain them: the output of a transformation may be given as input to a second one if metamodels match.…
A change points detection aims to catch an abrupt disorder in data distribution. Common approaches assume that there are only two fixed distributions for data: one before and another after a change point. Real-world data are richer than…
Individual cancer cells carry a bewildering number of distinct genomic alterations i.e., copy number variations and mutations, making it a challenge to uncover genomic-driven mechanisms governing tumorigenesis. Here we performed…
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
We develop Bayesian inference methods for a recently-emerging type of epigenetic data to study the transmission fidelity of DNA methylation patterns over cell divisions. The data consist of parent-daughter double-stranded DNA methylation…
In this paper we study a variant of string pattern matching which deals with tuples of strings known as \textit{multi-track strings}. Multi-track strings are a generalisation of strings (or \textit{single-track strings}) that have primarily…
Many structured prediction tasks in machine vision have a collection of acceptable answers, instead of one definitive ground truth answer. Segmentation of images, for example, is subject to human labeling bias. Similarly, there are multiple…
Sequencing by tunneling is a next-generation approach to read single-base information using electronic tunneling transverse to the single-stranded DNA (ssDNA) backbone while the latter is translocated through a narrow channel. The original…
Already in the 1960s, Levenshtein and others studied error-correcting codes that protect against synchronization errors, such as symbol insertions and deletions. However, despite significant efforts, progress on designing such codes has…
Chain-like macromolecules in solution, whether biological or synthetic, transform from a spatially extended conformation to a compact one upon change of temperature or solvent qualities. This sharp transition plays a key role in various…
We study data structures in the presence of adversarial noise. We want to encode a given object in a succinct data structure that enables us to efficiently answer specific queries about the object, even if the data structure has been…
An insdel refers to a deletion or an insertion, and an edit refers to an insdel or a substitution. In this paper, we consider the segmented single-insdel (resp. single-edit) channel, where the channel's input bit stream is partitioned into…
A binary string transmitted via a memoryless i.i.d. deletion channel is received as a subsequence of the original input. From this, one obtains a posterior distribution on the channel input, corresponding to a set of candidate…
The process of translation is ambiguous, in that there are typically many valid trans- lations for a given sentence. This gives rise to significant variation in parallel cor- pora, however, most current models of machine translation do not…
Motivated by the sequence reconstruction problem from traces in DNA-based storage, we consider the problem of designing codes for the deletion channel when multiple observations (or traces) are available to the decoder. We propose simple…
DNA polymerase (DNAP) is a dual-purpose enzyme that plays two opposite roles in two different situations during DNA replication. It plays its normal role as a {\it polymerase} catalyzing the elongation of a new DNA molecule by adding a…
Deadlock detection in recursive programs that admit dynamic resource creation is extremely complex and solutions either give imprecise answers or do not scale. We define an algorithm for detecting deadlocks of "linear recursive programs" of…
In this paper, we consider the problem of variable packet-error coding, which emerges in network communication scenarios where a source transmits information to a destination through multiple disjoint paths. The objective is to design codes…