Related papers: On the Reverse-Complement String-Duplication Syste…
Despite strong performance on a variety of tasks, neural sequence models trained with maximum likelihood have been shown to exhibit issues such as length bias and degenerate repetition. We study the related issue of receiving…
Backtracking (i.e., reverse execution) helps the user of a debugger to naturally think backwards along the execution path of a program, and thinking backwards makes it easy to locate the origin of a bug. So far backtracking has been…
We introduce a new two-sided type system for verifying the correctness and incorrectness of functional programs with atoms and pattern matching. A key idea in the work is that types should range over sets of normal forms, rather than sets…
In this paper we study error-correcting codes for the storage of data in synthetic deoxyribonucleic acid (DNA). We investigate a storage model where a data set is represented by an unordered set of $M$ sequences, each of length $L$. Errors…
The doubly shortened perfect codes of length 13 are classified utilizing the classification of perfect codes in [P.R.J. \"Osterg{\aa}rd and O. Pottonen, The perfect binary one-error-correcting codes of length 15: Part I - Classification,…
The binary Defect Combination Problem consists in finding a fully working subset from a given ensemble of imperfect binary components. We determine the typical properties of the model using methods of statistical mechanics, in particular,…
Despite their significant advantages over competing technologies, nanopore sequencers are plagued by high error rates, due to physical characteristics of the nanopore and inherent noise in the biological processes. It is thus paramount not…
Motivated from the fact that universal source coding on countably infinite alphabets is not feasible, this work introduces the notion of almost lossless source coding. Analog to the weak variable-length source coding problem studied by Han…
We present a new recursive generation algorithm for prefix normal words. These are binary strings with the property that no substring has more 1s than the prefix of the same length. The new algorithm uses two operations on binary strings,…
In this paper, we consider pattern avoidance in a subset of words on $\{1,1,2,2,\dots,n,n\}$ called reverse double lists. In particular a reverse double list is a word formed by concatenating a permutation with its reversal. We enumerate…
The (bitwise) complement $\overline{x}$ of a binary word $x$ is obtained by changing each $0$ in $x$ to $1$ and vice versa. An $\textit{antisquare}$ is a nonempty word of the form $x\, \overline{x}$. In this paper, we study infinite binary…
The minimum average number of bits need to describe a random variable is its entropy, assuming knowledge of the underlying statistics On the other hand, universal compression supposes that the distribution of the random variable, while…
A complete classification of the perfect binary one-error-correcting codes of length 15 as well as their extensions of length 16 is presented. There are 5983 such inequivalent perfect codes and 2165 extended perfect codes. Efficient…
Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the…
We derive a massive double copy construction within string theory. To this end, we use massive vectors of the open string spectrum that appear in compactifications to four dimensions and construct massive spin-2 tensors as closed string…
We consider the problem of correcting mass readout errors in information encoded in binary polymer strings. Our work builds on results for string reconstruction problems using composition multisets [Acharya et al., 2015] and the unique…
In this work, we derive upper bounds on the cardinality of tandem duplication and palindromic deletion correcting codes by deriving the generalized sphere packing bound for these error types. We first prove that an upper bound for tandem…
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…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
Since some years, non-overlapping sets of strings (also called cross-bifix-free sets) have had an increasing interest in the frame of the researches about Theory of Codes. Recently some non-overlapping sets of strings with variable length…