Related papers: An Ansatz for computational undecidability in RNA …
In modern machine (ML) learning systems, Transformer-based architectures have achieved milestone success across a broad spectrum of tasks, yet understanding their operational mechanisms remains an open problem. To improve the transparency…
One-dimensional quantum cellular automata (QCA) consist in a line of identical, finite dimensional quantum systems. These evolve in discrete time steps according to a local, shift-invariant unitary evolution. By local we mean that no…
A data tree is an unranked ordered tree whose every node is labelled by a letter from a finite alphabet and an element ("datum") from an infinite set, where the latter can only be compared for equality. The article considers alternating…
Agda is a dependently-typed programming language and a proof assistant, pivotal in proof formalization and programming language theory. This paper extends the Agda ecosystem into machine learning territory, and, vice versa, makes…
This paper connects the classes of weighted alternating finite automata (WAFA), weighted finite tree automata (WFTA), and polynomial automata (PA). First, we investigate the use of trees in the run semantics for weighted alternating…
In this conceptual paper we propose to explore the analogy between ontic/epistemic description of quantum phenomena and interrelation between dynamics of conformational and functional states of proteins. Another new idea is to apply theory…
Minimizing finite automata, proving trace equivalence of labelled transition systems or representing sofic subshifts involve very similar arguments, which suggests the possibility of a unified formalism. We propose finite states…
We give a one-dimensional quantum cellular automaton (QCA) capable of simulating all others. By this we mean that the initial configuration and the local transition rule of any one-dimensional QCA can be encoded within the initial…
RNA co-transcriptionality, where RNA is spliced or folded during transcription from DNA templates, offers promising potential for molecular programming. It enables programmable folding of nano-scale RNA structures and has recently been…
We introduce and study the repetitive variants of the deterministic and the nondeterministic finite automaton with translucent words (DFAwtw and NFAwtw). On seeing the right sentinel, a repetitive NFAwtw need not halt immediately, accepting…
Cognitive computing models offer a formal and interpretable way to characterize human's deliberation and decision-making, yet their development remains labor-intensive. In this paper, we propose NL2CA, a novel method for auto-formalizing…
Zero automata are a probabilistic extension of parity automata on infinite trees. The satisfiability of a certain probabilistic variant of mso, called tmso + zero, reduces to the emptiness problem for zero automata. We introduce a variant…
Automatic verification of concurrent programs faces state explosion due to the exponential possible interleavings of its sequential components coupled with large or infinite state spaces. An alternative is deductive verification, where…
Automata play important roles in wide area of computing and the growth of multicores calls for their efficient parallel implementation. Though it is known in theory that we can perform the computation of a finite automaton in parallel by…
This thesis investigates the central role of homomorphism problems (structure-preserving maps) in two complementary domains: database querying over finite, graph-shaped data, and constraint solving over (potentially infinite) structures.…
Very recently, the Neural Cellular Automata (NCA) has been proposed to simulate the morphogenesis process with deep networks. NCA learns to grow an image starting from a fixed single pixel. In this work, we show that the neural network (NN)…
We introduce the class of Interrupt Timed Automata (ITA), a subclass of hybrid automata well suited to the description of timed multi-task systems with interruptions in a single processor environment. While the reachability problem is…
Hyperproperties lift conventional trace properties from a set of execution traces to a set of sets of execution traces. Hyperproperties have been shown to be a powerful formalism for expressing and reasoning about information-flow security…
There are many types of automata and grammar models that have been studied in the literature, and for these models, it is common to determine whether certain problems are decidable. One problem that has been difficult to answer throughout…
It is the first step for understanding how RNA structure folds from base sequences that to know how its secondary structure is formed. Traditional energy-based algorithms are short of precision, particularly for non-nested sequences, while…