Related papers: Fundamental Limits of Multiple Sequence Reconstruc…
The merit factor problem is of practical importance to manifold domains, such as digital communications engineering, radars, system modulation, system testing, information theory, physics, chemistry. However, the merit factor problem is…
The sequence a_1,...,a_m is a common subsequence in the set of permutations S = {p_1,...,p_k} on [n] if it is a subsequence of p_i(1),...,p_i(n) and p_j(1),...,p_j(n) for some distinct p_i, p_j in S. Recently, Beame and Huynh-Ngoc (2008)…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…
Recent advances in unsupervised learning have highlighted the possibility of learning to reconstruct signals from noisy and incomplete linear measurements alone. These methods play a key role in medical and scientific imaging and sensing,…
The coded trace reconstruction problem asks to construct a code $C\subset \{0,1\}^n$ such that any $x\in C$ is recoverable from independent outputs ("traces") of $x$ from a binary deletion channel (BDC). We present binary codes of rate…
We consider a branching random walk with binary state space and index set $T^k$, the infinite rooted tree in which each node has k children (also known as the model of "broadcasting on a tree"). The root of the tree takes a random value 0…
The sequence reconstruction problem, introduced by Levenshtein in 2001, considers a communication setting in which a sender transmits a codeword and the receiver observes K independent noisy versions of this codeword. In this work, we study…
The paper investigates possibility of recovery of sequences from their decimated subsequences. It is shown that this recoverability is associated with certain spectrum degeneracy of a new kind, and that a sequences of a general kind can be…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
A two-dimensional string is simply a two-dimensional array. We continue the study of the combinatorial properties of repetitions in such strings over the binary alphabet, namely the number of distinct tandems, distinct quartics, and runs.…
We investigate the longest common substring problem for encoded sequences and its asymptotic behaviour. The main result is a strong law of large numbers for a re-scaled version of this quantity, which presents an explicit relation with the…
This paper investigates the approximability of the Longest Common Subsequence (LCS) problem. The fastest algorithm for solving the LCS problem exactly runs in essentially quadratic time in the length of the input, and it is known that under…
One possible data encryption scheme is related to stream ciphers, which use a sufficiently long pseudo-random sequence. To increase the cryptographic strength of the cipher, linear shift algorithms (generated by linear recurrent sequences…
State-of-the-art (SOTA) Generative Models (GMs) can synthesize photo-realistic images that are hard for humans to distinguish from genuine photos. Identifying and understanding manipulated media are crucial to mitigate the social concerns…
We use the replica method of statistical mechanics to examine a typical performance of correctly reconstructing $N$-dimensional sparse vector $bx=(x_i)$ from its linear transformation $by=bF bx$ of $P$ dimensions on the basis of…
The form of the primordial power spectrum has the potential to differentiate strongly between competing models of perturbation generation in the early universe and so is of considerable importance. The recent release of five years of WMAP…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
Assume that for some $\alpha<1$ and for all nutural $n$ a set $F_n$ of at most $2^{\alpha n}$ "forbidden" binary strings of length $n$ is fixed. Then there exists an infinite binary sequence $\omega$ that does not have (long) forbidden…
We revisit parallel-innermost term rewriting as a model of parallel computation on inductive data structures and provide a corresponding notion of runtime complexity parametric in the size of the start term. We propose automatic techniques…