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We have extended the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to support directional bonds and dynamic bonding. The framework supports stochastic formation of new bonds, breakage of existing bonds, and conversion…

Soft Condensed Matter · Physics 2015-05-30 Carsten Svaneborg

Neuroscience is experiencing a data revolution in which many hundreds or thousands of neurons are recorded simultaneously. Currently, there is little consensus on how such data should be analyzed. Here we introduce LFADS (Latent Factor…

Machine Learning · Computer Science 2016-08-24 David Sussillo , Rafal Jozefowicz , L. F. Abbott , Chethan Pandarinath

We introduce an algebraic analogue of dynamical systems, based on term rewriting. We show that a recursive function applied to the output of an iterated rewriting system defines a formal class of models into which all the main architectures…

Category Theory · Mathematics 2023-11-07 Iolo Jones , Jerry Swan , Jeffrey Giansiracusa

Autonomous systems require the management of several model views to assure properties such as safety and security among others. A crucial issue in autonomous systems design assurance is the notion of emergent behavior; we cannot use their…

Logic in Computer Science · Computer Science 2022-03-31 Georgios Bakirtzis , Ufuk Topcu

Real-world structural optimisation problems involve multiple loading conditions and design constraints, with responses typically depending on states of discretised governing equations. Generally, one uses gradient-based nested analysis and…

Computational Engineering, Finance, and Science · Computer Science 2022-02-23 Stijn Koppen , Max van der Kolk , Sanne van den Boom , Matthijs Langelaar

We present semantic correctness proofs of automatic differentiation (AD). We consider a forward-mode AD method on a higher-order language with algebraic data types and we characterise it as the unique structure-preserving macro given a…

Programming Languages · Computer Science 2026-05-07 Mathieu Huot , Sam Staton , Matthijs Vákár

We present a new design for an algebraic simplification library structured around concepts from universal algebra: theories, models, homomorphisms, and universal properties of free algebras and free extensions of algebras. The library's…

Programming Languages · Computer Science 2025-07-21 Guillaume Allais , Edwin Brady , Nathan Corbyn , Ohad Kammar , Jeremy Yallop

Dependency pairs are one of the most powerful techniques to analyze termination of term rewrite systems (TRSs) automatically. We adapt the dependency pair framework to the probabilistic setting in order to prove almost-sure innermost…

Logic in Computer Science · Computer Science 2023-06-06 Jan-Christoph Kassing , Jürgen Giesl

Functional dependencies restrict the potential interactions among variables connected in a probabilistic network. This restriction can be exploited in qualitative probabilistic reasoning by introducing deterministic variables and modifying…

Artificial Intelligence · Computer Science 2013-04-05 Michael P. Wellman

This short note presents a new formal language, lambda dependency-based compositional semantics (lambda DCS) for representing logical forms in semantic parsing. By eliminating variables and making existential quantification implicit, lambda…

Artificial Intelligence · Computer Science 2013-09-19 Percy Liang

Finite dynamical systems (FDSs) are commonly used to model systems with a finite number of states that evolve deterministically and at discrete time steps. Considered up to isomorphism, those correspond to functional graphs. As such, FDSs…

Discrete Mathematics · Computer Science 2022-12-15 Émile Naquin , Maximilien Gadouleau

We propose a probabilistic semantic filtering framework in which parameters of a dynamical system are inferred and associated with a closed set of semantic classes in a map. We extend existing methods to a multi-parameter setting using a…

Systems and Control · Electrical Eng. & Systems 2026-01-15 Marcus Greiff , Ray Zhang , Thomas Lew , John Subosits

A data language is a set of finite words defined on an infinite alphabet. Data languages are used to express properties associated with data values (domain defined over a countably infinite set). In this paper, we introduce set augmented…

Formal Languages and Automata Theory · Computer Science 2023-11-14 Ansuman Banerjee , Kingshuk Chatterjee , Shibashis Guha

A study of assisted problem solving formalized via decompositions of deterministic finite automata is initiated. The landscape of new types of decompositions of finite automata this study uncovered is presented. Languages with various…

Computational Complexity · Computer Science 2007-07-04 Peter Gaži , Branislav Rovan

This contribution deals with identification of fractional-order dynamical systems. We consider systems whose mathematical description is a three-member differential equation in which the orders of derivatives can be real numbers. We give a…

Optimization and Control · Mathematics 2007-05-23 L. Dorcak , V. Lesko , I. Kostial

Temporal and dynamic extensions of Answer Set Programming (ASP) have played an important role in addressing dynamic problems, as they allow the use of temporal operators to reason with dynamic scenarios in a very effective way. In my Ph.D.…

Artificial Intelligence · Computer Science 2021-09-20 Susana Hahn

The Algebraic lambda-calculus and the Linear-Algebraic lambda-calculus extend the lambda-calculus with the possibility of making arbitrary linear combinations of terms. In this paper we provide a fine-grained, System F-like type system for…

Logic in Computer Science · Computer Science 2015-07-01 Pablo Arrighi , Alejandro Diaz-Caro

Transformer-based pre-trained models like BERT have achieved great progress on Semantic Sentence Matching. Meanwhile, dependency prior knowledge has also shown general benefits in multiple NLP tasks. However, how to efficiently integrate…

Computation and Language · Computer Science 2023-08-25 Jian Song , Di Liang , Rumei Li , Yuntao Li , Sirui Wang , Minlong Peng , Wei Wu , Yongxin Yu

We present an Augmented Lagrangian formulation and its real-space implementation for non-periodic orbital-free Density Functional Theory (OF-DFT) calculations. In particular, we rewrite the constrained minimization problem of OF-DFT as a…

Computational Physics · Physics 2015-06-19 Phanish Suryanarayana , Deepa Phanish

We propose a new method to design adaptation algorithms that guarantee a certain prescribed level of performance and are applicable to systems with nonconvex parameterization. The main idea behind the method is, given the desired…

Optimization and Control · Mathematics 2007-05-23 I. Y. Tyukin , D. V. Prokhorov , Cees van Leeuwen