Related papers: Descriptional Complexity of Semi-Simple Splicing S…
The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…
Scoring systems are linear classification models that only require users to add, subtract and multiply a few small numbers in order to make a prediction. These models are in widespread use by the medical community, but are difficult to…
Semantically meaningful sentence embeddings are important for numerous tasks in natural language processing. To obtain such embeddings, recent studies explored the idea of utilizing synthetically generated data from pretrained language…
Separation Logic (SL) with inductive definitions is a natural formalism for specifying complex recursive data structures, used in compositional verification of programs manipulating such structures. The key ingredient of any automated…
In computational biology, tandem duplication is an important biological phenomenon which can occur either at the genome or at the DNA level. A tandem duplication takes a copy of a genome segment and inserts it right after the segment - this…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
Geometric folding processes are ubiquitous in natural systems ranging from protein biochemistry to patterns of insect wings and leaves. In a previous study, a folding operation between strings of formal languages was introduced as a model…
Historical linguists have long written "programs" that convert reconstructed words in an ancestor language into their attested descendants via ordered string rewrite functions (called sound laws) However, writing these programs is…
Modern language models define distributions over strings, but downstream tasks often require different output formats. For instance, a model that generates byte-pair strings does not directly produce word-level predictions, and a DNA model…
In this paper, we propose Selection and Pooling with Large Language Models (SPILL), an intuitive and domain-adaptive method for intent clustering without fine-tuning. Existing embeddings-based clustering methods rely on a few labeled…
We present an approach for recursively splitting and rephrasing complex English sentences into a novel semantic hierarchy of simplified sentences, with each of them presenting a more regular structure that may facilitate a wide variety of…
We study random string-duplication systems, which we call P\'olya string models. These are motivated by DNA storage in living organisms, and certain random mutation processes that affect their genome. Unlike previous works that study the…
Word segmentation is the task of inserting or deleting word boundary characters in order to separate character sequences that correspond to words in some language. In this article we propose an approach based on a beam search algorithm and…
Scoring systems are classification models that only require users to add, subtract and multiply a few meaningful numbers to make a prediction. These models are often used because they are practical and interpretable. In this paper, we…
We study the polyregular string-to-string functions, which are certain functions of polynomial output size that can be described using automata and logic. We describe a system of combinators that generates exactly these functions. Unlike…
We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly.…
Machine learning models make mistakes, yet sometimes it is difficult to identify the systematic problems behind the mistakes. Practitioners engage in various activities, including error analysis, testing, auditing, and red-teaming, to form…
In this note we consider a new variant of network of splicing processors which simplifies the general model such that filters remain associated with nodes but the input and output filters of every node coincide. This variant is called {\it…
Descriptive complexity may be useful to design programs in a natural declarative way. This is important for parallel computation models such as cellular automata, because designing parallel programs is considered difficult. Our paper…
Indexed languages are a classical notion in formal language theory, which has attracted attention in recent decades due to its role in higher-order model checking: They are precisely the languages accepted by order-2 pushdown automata. The…