Related papers: An Ansatz for computational undecidability in RNA …
The paper studies defeasible reasoning in rule-based systems, in particular about legal norms and contracts. We identify rule modifiers that specify how rules interact and how they can be overridden. We then define rule transformations that…
We present results from an experiment similar to one performed by Packard (1988), in which a genetic algorithm is used to evolve cellular automata (CA) to perform a particular computational task. Packard examined the frequency of evolved CA…
In this paper, we investigate the problem of synthesizing computable functions of infinite words over an infinite alphabet (data $\omega$-words). The notion of computability is defined through Turing machines with infinite inputs which can…
Cellular automata have been useful artificial models for exploring how relatively simple rules combined with spatial memory can give rise to complex emergent patterns. Moreover, studying the dynamics of how rules emerge under artificial…
Atomic-accuracy structure prediction of macromolecules is a long-sought goal of computational biophysics. Accurate modeling should be achievable by optimizing a physically realistic energy function but is presently precluded by incomplete…
We exhibit the construction of a deterministic automaton that, given k > 0, recognizes the (regular) language of k-differentiable words. Our approach follows a scheme of Crochemore et al. based on minimal forbidden words. We extend this…
The determinisation problem for min-plus (tropical) weighted automata was recently shown to be decidable. However, the proof is purely existential, relying on several non-constructive arguments. Our contribution in this work is twofold:…
We introduce Neural Particle Automata (NPA), a Lagrangian generalization of Neural Cellular Automata (NCA) from static lattices to dynamic particle systems. Unlike classical Eulerian NCA where cells are pinned to pixels or voxels, NPA model…
To study relationship between quantum finite automata and probabilistic finite automata, we introduce a notion of probabilistic reversible automata (PRA, or doubly stochastic automata). We find that there is a strong relationship between…
We explore language semantics for automata combining probabilistic and nondeterministic behavior. We first show that there are precisely two natural semantics for probabilistic automata with nondeterminism. For both choices, we show that…
Number-conserving cellular automata (NCCA) are particularly interesting, both because of their natural appearance as models of real systems, and because of the strong restrictions that number-conservation implies. Here we extend the…
For non-uniform cellular automata (NUCA) with finite memory over an arbitrary universe with multiple local transition rules, we show that pointwise nilpotency, pointwise periodicity, and pointwise eventual periodicity properties are…
A rationally dynamically algebraic (RDA) power series is one that arises as (a component of) the solution of a system of differential equations of the form $\boldsymbol{y}' = F(\boldsymbol{y})$, where $F$ is a vector of rational functions…
In the field of computational logic, two classes of finite automata are considered fundamental: deterministic and nondeterministic automata (DFAs and NFAs). In a more fine-grained approach three natural intermediate classes were introduced,…
Threshold automata are a formalism for modeling and analyzing fault-tolerant distributed algorithms, recently introduced by Konnov, Veith, and Widder, describing protocols executed by a fixed but arbitrary number of processes. We conduct…
We study decidability of verification problems for timed automata extended with unbounded discrete data structures. More detailed, we extend timed automata with a pushdown stack. In this way, we obtain a strong model that may for instance…
Real-world computers have operational constraints that cause nonzero entropy production (EP). In particular, almost all real-world computers are ``periodic'', iteratively undergoing the same physical process; and ``local", in that…
We propose a theoretical formalism, molecular finite automata (MFA), to describe individual proteins as rule-based computing machines. The MFA formalism provides a framework for modeling individual protein behaviors and systems-level…
We present a complete theoretical and empirical framework establishing feedforward neural networks as universal finite-state machines (N-FSMs). Our results prove that finite-depth ReLU and threshold networks can exactly simulate…
We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called…