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In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…

Genomics · Quantitative Biology 2007-05-23 Kerstin Hoef-Emden

It is common practice to compare the computational power of different models of computation. For example, the recursive functions are strictly more powerful than the primitive recursive functions, because the latter are a proper subset of…

Logic in Computer Science · Computer Science 2020-06-11 Udi Boker , Nachum Dershowitz

Computational phylogenetics has become an established tool in historical linguistics, with many language families now analyzed using likelihood-based inference. However, standard approaches rely on expert-annotated cognate sets, which are…

Computation and Language · Computer Science 2026-03-30 Gerhard Jäger

Automated theorem proving has long been a key task of artificial intelligence. Proofs form the bedrock of rigorous scientific inquiry. Many tools for both partially and fully automating their derivations have been developed over the last…

Artificial Intelligence · Computer Science 2018-10-15 Brian Groenke

The philosophy of mathematical practice (PMP) looks to evidence from working mathematics to help settle philosophical questions. One prominent program under the PMP banner is the study of explanation in mathematics, which aims to understand…

History and Overview · Mathematics 2025-07-08 William D'Alessandro

We employ computer algebra algorithms to prove a collection of identities involving Bessel functions with half-integer orders and other special functions. These identities appear in the famous Handbook of Mathematical Functions, as well as…

Symbolic Computation · Computer Science 2013-07-22 Stefan Gerhold , Manuel Kauers , Christoph Koutschan , Peter Paule , Carsten Schneider , Burkhard Zimmermann

Inductive proofs can be represented as proof schemata, i.e. as parameterized sequences of proofs defined in a primitive recursive way. Applications of proof schemata can be found in the area of automated proof analysis where the schemata…

Logic in Computer Science · Computer Science 2025-06-09 Alexander Leitsch , Anela Lolić , Stella Mahler

In the logic programming paradigm, a program is defined by a set of methods, each of which can be executed when specific conditions are met during the current state of an execution. The semantics of these programs can be elegantly…

Logic in Computer Science · Computer Science 2024-10-02 Matteo Acclavio , Roberto Maieli

Biology is data-rich, and it is equally rich in concepts and hypotheses. Part of trying to understand biological processes and systems is therefore to confront our ideas and hypotheses with data using statistical methods to determine the…

Quantitative Methods · Quantitative Biology 2022-06-22 Sean T. Vittadello , Michael P. H. Stumpf

We present an alternative cyclic proof system for Peano arithmetic that could be simpler than the existing ones and well-adapted both for proof analysis and for automatizing inductive proof search. In addition, we will show how various…

Logic · Mathematics 2025-02-11 Lev D. Beklemishev , Daniyar S. Shamkanov , Ivan N. Smirnov

The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…

Computational Engineering, Finance, and Science · Computer Science 2013-10-01 Daniela Besozzi , Giulio Caravagna , Paolo Cazzaniga , Marco Nobile , Dario Pescini , Alessandro Re

Argumentation frameworks, consisting of arguments and an attack relation representing conflicts, are fundamental for formally studying reasoning under conflicting information. We use methods from mathematical logic, specifically…

Artificial Intelligence · Computer Science 2025-12-01 Uri Andrews , Luca San Mauro

Discrete mixture models provide a well-known basis for effective clustering algorithms, although technical challenges have limited their scope. In the context of gene-expression data analysis, a model is presented that mixes over a finite…

Methodology · Statistics 2012-11-12 Michael A. Newton , Lisa M. Chung

Several formal systems, such as resolution and minimal model semantics, provide a framework for logic programming. In this paper, we will survey the use of structural proof theory as an alternative foundation. Researchers have been using…

Logic in Computer Science · Computer Science 2021-11-02 Dale Miller

Proof assistants enable users to develop machine-checked proofs regarding software-related properties. Unfortunately, the interactive nature of these proof assistants imposes most of the proof burden on the user, making formal verification…

Software Engineering · Computer Science 2024-05-08 Pedro Carrott , Nuno Saavedra , Kyle Thompson , Sorin Lerner , João F. Ferreira , Emily First

Large Language Models (LLMs) have demonstrated significant promise in formal theorem proving. In this study, we investigate the ability of LLMs to discover novel theorems and produce verified proofs. We propose a pipeline called…

Machine Learning · Computer Science 2026-05-07 Kazumi Kasaura , Naoto Onda , Yuta Oriike , Masaya Taniguchi , Akiyoshi Sannai , Sho Sonoda

We note the significance of hypergraphic planted clique (HPC) detection in the investigation of computational hardness for a range of tensor problems. We ask if more evidence for the computational hardness of HPC detection can be developed.…

Machine Learning · Statistics 2020-09-15 Yuetian Luo , Anru R. Zhang

We explore the geometric notion of prolongations in the setting of computational algebra, extending results of Landsberg and Manivel which relate prolongations to equations for secant varieties. We also develop methods for computing…

Commutative Algebra · Mathematics 2008-04-03 Jessica Sidman , Seth Sullivant

Through case studies, we demonstrate how multiverse analysis can strengthen the robustness and transparency of computational social science findings against alternative methodological decisions. We conduct multiverse analyses of three…

Other Statistics · Statistics 2026-05-20 Maximilian Linde , Jun Sun , Paul Balluff , Danica Radovanović , Chung-hong Chan

Hypothesis formulation and testing are central to empirical research. A strong hypothesis is a best guess based on existing evidence and informed by a comprehensive view of relevant literature. However, with exponential increase in the…

Computation and Language · Computer Science 2024-03-27 Sai Koneru , Jian Wu , Sarah Rajtmajer