Related papers: Descriptional Complexity of Semi-Simple Splicing S…
The automatic complexity of a finite word (string) is an analogue for finite automata of Sipser's distinguishing complexity (1983) and was introduced by Shallit and Wang (2001). For a finite alphabet $\Sigma$ of at least two elements, we…
We describe software and a language for quasibiological computations. Its theoretical basis is a unified theory of complex (adaptive) systems where all laws are regularities of relations between things or agents, and dynamics is made from…
The design of complex engineering systems is an often long and articulated process that highly relies on engineers' expertise and professional judgment. As such, the typical pitfalls of activities involving the human factor often manifest…
Gene assembly is an intricate biological process that has been studied formally and modeled through string and graph rewriting systems. Recently, a restriction of the general (intramolecular) model, called simple gene assembly, has been…
Algorithms which learn environments represented by automata in the past have had complexity scaling with the number of states in the automaton, which can be exponentially large even for automata recognizing regular expressions with a small…
Infinite words, also known as streams, hold significant interest in computer science and mathematics, raising the natural question of how their complexity should be measured. We introduce cellular automaton reducibility as a measure of…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…
This paper outlines an application of iterated version of generalised sequential crossover of two languages (which in some sense, an abstraction of the crossover of chromosomes in living organisms) in studying some classes of the newly…
An RNA sequence is a word over an alphabet on four elements $\{A,C,G,U\}$ called bases. RNA sequences fold into secondary structures where some bases match one another while others remain unpaired. Pseudoknot-free secondary structures can…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the effect of knocking…
To solve hard problems, AI relies on a variety of disciplines such as logic, probabilistic reasoning, machine learning and mathematical programming. Although it is widely accepted that solving real-world problems requires an integration…
Separation Logic with inductive definitions is a well-known approach for deductive verification of programs that manipulate dynamic data structures. Deciding verification conditions in this context is usually based on user-provided lemmas…
Freely available and easy-to-use audio editing tools make it straightforward to perform audio splicing. Convincing forgeries can be created by combining various speech samples from the same person. Detection of such splices is important…
Verifying the integrity of voice recording evidence for criminal investigations is an integral part of an audio forensic analyst's work. Here, one focus is on detecting deletion or insertion operations, so called audio splicing. While this…
We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including: part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This…
The identification of syllables within phonetic sequences is known as syllabification. This task is thought to play an important role in natural language understanding, speech production, and the development of speech recognition systems.…
The development of novel high-throughput sequencing (HTS) methods for RNA (RNA-Seq) has provided a very powerful mean to study splicing under multiple conditions at unprecedented depth. However, the complexity of the information to be…
We construct a family of exactly solvable spin models that illustrate a novel mechanism for fractionalization in topologically ordered phases, dubbed the string flux mechanism. The essential idea is that an anyon of a topological phase can…
Designers of statistical machine translation (SMT) systems have begun to employ tree-structured translation models. Systems involving tree-structured translation models tend to be complex. This article aims to reduce the conceptual…