Related papers: Sequence Reconstruction for the Single-Deletion Si…
We present strategies how to reconstruct (estimate) properties of a quantum channel described by the map E based on incomplete measurements. In a particular case of a qubit channel a complete reconstruction of the map E can be performed via…
Line spectral estimation is a classical signal processing problem that aims to estimate the line spectra from their signal which is contaminated by deterministic or random noise. Despite a large body of research on this subject, the…
Insertion-deletion codes (insdel codes for short) are used for correcting synchronization errors in communications, and in other many interesting fields such as DNA storage, date analysis, race-track memory error correction and language…
We study near optimal error correction codes for real-time communication. In our setup the encoder must operate on an incoming source stream in a sequential manner, and the decoder must reconstruct each source packet within a fixed playback…
The shift distance $\mathsf{sh}(S_1,S_2)$ between two strings $S_1$ and $S_2$ of the same length is defined as the minimum Hamming distance between $S_1$ and any rotation (cyclic shift) of $S_2$. We study the problem of sketching the shift…
We extend Ziv and Lempel's model of finite-state encoders to the realm of lossy compression of individual sequences. In particular, the model of the encoder includes a finite-state reconstruction codebook followed by an information lossless…
Sum-rank Hamming codes are introduced in this work. They are essentially defined as the longest codes (thus of highest information rate) with minimum sum-rank distance at least $ 3 $ (thus one-error-correcting) for a fixed redundancy $ r $,…
The construction of deletion codes for the Levenshtein metric is reduced to the construction of codes over the integers for the Manhattan metric by run length coding. The latter codes are constructed by expurgation of translates of…
Motivated by applications in in-vivo DNA storage, we study codes for correcting duplications. A reverse-complement duplication of length $k$ is the insertion of the reversed and complemented copy of a substring of length $k$ adjacent to its…
Like classical block codes, a locally repairable code also obeys the Singleton-type bound (we call a locally repairable code {\it optimal} if it achieves the Singleton-type bound). In the breakthrough work of \cite{TB14}, several classes of…
Common intervals have been defined as a modelisation of gene clusters in genomes represented either as permutations or as sequences. Whereas optimal algorithms for finding common intervals in permutations exist even for an arbitrary number…
List decoding of insertions and deletions in the Levenshtein metric is considered. The Levenshtein distance between two sequences is the minimum number of insertions and deletions needed to turn one of the sequences into the other. In this…
In this paper, we consider a class of symmetry groups associated to communication channels, which can informally be viewed as the transformations of the set of inputs that ``commute'' with the action of the channel. These groups were first…
Let $K_q(n,r)$ denote the minimum size of a $q$-ary covering code of word length $n$ and covering radius $r$. In other words, $K_q(n,r)$ is the minimum size of a set of $q$-ary codewords of length $n$ such that the Hamming balls of radius…
A quantum channel is sufficient with respect to a set of input states if it can be reversed on this set. In the approximate version, the input states can be recovered within an error bounded by the decrease of the relative entropy under the…
We prove that every $1$-error-correcting code over a finite field can be embedded in a $1$-perfect code of some larger length. Embedding in this context means that the original code is a subcode of the resulting $1$-perfect code and can be…
We propose a new algorithm to identify a Wiener-Hammerstein system. This model represents a communication channel where two linear filters are separated by a non-linear function modelling an amplifier. The algorithm enables to recover each…
We propose a list-decoding scheme for reconstruction codes in the context of uniform-tandem-duplication noise, which can be viewed as an application of the associative memory model to this setting. We find the uncertainty associated with…
In this article, we investigate different parsimony-based approaches towards finding recombination breakpoints in a multiple sequence alignment. This recombination detection task is crucial in order to avoid errors in evolutionary analyses…
We study the tandem duplication distance between binary sequences and their roots. In other words, the quantity of interest is the number of tandem duplication operations of the form $\seq x = \seq a \seq b \seq c \to \seq y = \seq a \seq b…