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Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…

Molecular Networks · Quantitative Biology 2018-10-10 Ines Abdeljaoued-Tej , Alia BenKahla , Ghassen Haddad , Annick Valibouze

What do large language models actually model? Do they tell us something about human capacities, or are they models of the corpus we've trained them on? I give a non-deflationary defence of the latter position. Cognitive science tells us…

Computation and Language · Computer Science 2025-08-27 Colin Klein

Large Language Models (LLMs), such as ChatGPT, have taken the world by storm and have passed certain forms of the Turing test. However, LLMs are not limited to human language and analyze sequential data, such as DNA, protein, and gene…

Genomics · Quantitative Biology 2024-01-08 Hilbert Yuen In Lam , Xing Er Ong , Marek Mutwil

LLMs have revolutionized the field of artificial intelligence and have emerged as the de-facto tool for many tasks. The current established technology of LLMs is to process input and generate output at the token level. This is in sharp…

Nobody knows how language works, but many theories abound. Transformers are a class of neural networks that process language automatically with more success than alternatives, both those based on neural computations and those that rely on…

Computation and Language · Computer Science 2024-08-08 Felix Hill

In 1975, Ladner showed that under the hypothesis that P is not equal to NP, there exists a language which is neither in P, nor NP-complete. This result was latter generalized by Schoning and several authors to various polynomial-time…

Computational Complexity · Computer Science 2007-05-23 Philippe Chapdelaine

The Language of Thought (LOT) hypothesis posits that at least some important cognitive processes involve language-like representations. These representations must be processed by appropriate hardware. Since the organ of biological cognition…

Neurons and Cognition · Quantitative Biology 2025-10-14 Gualtiero Piccinini

Deterministic 2-head finite automata which are machines that process an input word from both ends are analyzed for their ability to perform reversible computations. This implies that the automata are backward deterministic, enabling unique…

Formal Languages and Automata Theory · Computer Science 2025-07-22 Benedek Nagy , Walaa Yasin

A notion of alternating timed automata is proposed. It is shown that such automata with only one clock have decidable emptiness problem over finite words. This gives a new class of timed languages which is closed under boolean operations…

Logic in Computer Science · Computer Science 2007-05-23 Slawomir Lasota , Igor Walukiewicz

A set of integers is $S$-recognizable in an abstract numeration system $S$ if the language made up of the representations of its elements is accepted by a finite automaton. For abstract numeration systems built over bounded languages with…

Discrete Mathematics · Computer Science 2008-09-16 Emilie Charlier , Michel Rigo , Wolfgang Steiner

Soft linear logic ([Lafont02]) is a subsystem of linear logic characterizing the class PTIME. We introduce Soft lambda-calculus as a calculus typable in the intuitionistic and affine variant of this logic. We prove that the (untyped) terms…

Logic in Computer Science · Computer Science 2007-05-23 Patrick Baillot , Virgile Mogbil

Bi-directional LSTMs are a powerful tool for text representation. On the other hand, they have been shown to suffer various limitations due to their sequential nature. We investigate an alternative LSTM structure for encoding text, which…

Computation and Language · Computer Science 2018-05-08 Yue Zhang , Qi Liu , Linfeng Song

The article suggests a description of a system of tables with a set of special lists absorbing a semantics of data and reflects a fullness of data. It shows how their parallel processing can be constructed based on the descriptions. The…

Distributed, Parallel, and Cluster Computing · Computer Science 2008-11-03 R. Nuriyev

The idea of representing symbolic knowledge in connectionist systems has been a long-standing endeavour which has attracted much attention recently with the objective of combining machine learning and scalable sound reasoning. Early work…

Artificial Intelligence · Computer Science 2021-12-15 Son N. Tran , Artur d'Avila Garcez

Human languages have evolved to be structured through repeated language learning and use. These processes introduce biases that operate during language acquisition and shape linguistic systems toward communicative efficiency. In this paper,…

Computation and Language · Computer Science 2024-12-16 Tom Kouwenhoven , Max Peeperkorn , Tessa Verhoef

The Turing machine is one of the simple abstract computational devices that can be used to investigate the limits of computability. In this paper, they are considered from several points of view that emphasize the importance and the…

Computational Complexity · Computer Science 2012-03-16 Yaroslav D. Sergeyev , Alfredo Garro

Hofmann (1999) introduced the functional programming language LFPL to characterize the functions computable in polynomial time using an affine type system. LFPL enables a natural programming style, including nested recursion, and has…

Programming Languages · Computer Science 2026-05-19 Nathaniel Glover , Jan Hoffmann

We show that transformer-based large language models are computationally universal when augmented with an external memory. Any deterministic language model that conditions on strings of bounded length is equivalent to a finite automaton,…

Computation and Language · Computer Science 2023-01-12 Dale Schuurmans

We present extensions to a continuous-state dependency parsing method that makes it applicable to morphologically rich languages. Starting with a high-performance transition-based parser that uses long short-term memory (LSTM) recurrent…

Computation and Language · Computer Science 2015-08-12 Miguel Ballesteros , Chris Dyer , Noah A. Smith

This paper concerns $\mu$-limit sets of cellular automata: sets of configurations made of words whose probability to appear does not vanish with time, starting from an initial $\mu$-random configuration. More precisely, we investigate the…

Discrete Mathematics · Computer Science 2015-06-23 Laurent Boyer , Martin Delacourt , Victor Poupet , Mathieu Sablik , Guillaume Theyssier