Related papers: Combining Insertion and Deletion in RNA-editing Pr…
Discrete biological sequence optimization requires iterative refinement under strict syntactic constraints. Diffusion models offer progressive refinement but do not naturally expose controllable discrete edit operations, while…
Tools that effectively analyze and compare sequences are of great importance in various areas of applied computational research, especially in the framework of molecular biology. In the present paper, we introduce simple geometric criteria…
Large language models (LLMs) often exhibit flawed reasoning ability that undermines reliability. Existing approaches to improving reasoning typically treat it as a general and monolithic skill, applying broad training which is inefficient…
Relating formal grammars is a hard problem that balances between language equivalence (which is known to be undecidable) and grammar identity (which is trivial). In this paper, we investigate several milestones between those two extremes…
The prevalent technique for DNA sequencing consists of two main steps: shotgun sequencing, where many randomly located fragments, called reads, are extracted from the overall sequence, followed by an assembly algorithm that aims to…
Text-driven motion editing and intra-structural retargeting, where source and target share topology but may differ in bone lengths, are traditionally handled by fragmented pipelines with incompatible inputs and representations: editing…
String Edit Distance is a more-than-classical problem whose behavior in the dynamic setting, where the strings are updated over time, is well studied. A single-character substitution, insertion, or deletion can be processed in time…
This paper presents a novel approach to recurrent neural network (RNN) regularization. Differently from the widely adopted dropout method, which is applied to \textit{forward} connections of feed-forward architectures or RNNs, we propose to…
In this paper we show how string rewriting methods can be applied to give a new method of computing double cosets. Previous methods for double cosets were enumerative and thus restricted to finite examples. Our rewriting methods do not…
Ancestral sequence reconstruction (ASR) aims to infer extinct protein sequences at internal nodes of a phylogenetic tree. Classical ASR methods are typically based on continuous-time Markov substitution models, but they treat sites largely…
Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper…
We propose a generic termination proof method for rewriting under strategies, based on an explicit induction on the termination property. Rewriting trees on ground terms are modeled by proof trees, generated by alternatively applying…
We propose a new approach for modelling the process of RNA folding as a graph transformation guided by the global value of free energy. Since the folding process evolves towards a configuration in which the free energy is minimal, the…
The synthesis of DNA strands remains the most costly part of the DNA storage system. Thus, to make DNA storage system more practical, the time and materials used in the synthesis process have to be optimized. We consider the most common…
Multiset rewriting systems provide a formalism particularly suitable for the description of biological systems. We present an extension of this formalism with additional controls on the derivations as a tool for reducing possible…
We introduce Noise Injection Node Regularization (NINR), a method of injecting structured noise into Deep Neural Networks (DNN) during the training stage, resulting in an emergent regularizing effect. We present theoretical and empirical…
The continuity of life and its evolution, we proposed, emerge from an interactive group process manifested in networks of interaction. We term this process \textit{survival-of-the-fitted}. Here, we reason that survival of the fitted results…
Writing is, by nature, a strategic, adaptive, and more importantly, an iterative process. A crucial part of writing is editing and revising the text. Previous works on text revision have focused on defining edit intention taxonomies within…
RNA can be used as a high-density medium for data storage and transmission; however, an important RNA process -- replication -- is noisy. This paper presents an error analysis for RNA as a data transmission medium, analyzing how deletion…
We discuss various formalisms to describe string-to-string transformations. Many are based on automata and can be seen as operational descriptions, allowing direct implementations when the input scanner is deterministic. Alternatively, one…