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In this paper we present a new approach to solve the satisfiability problem (SAT), based on boolean networks (BN). We define a mapping between a SAT instance and a BN, and we solve SAT problem by simulating the BN dynamics. We prove that BN…
In the continuum limit (large number of qubits), adiabatic quantum algorithms display a remarkable similarity to sweeps through quantum phase transitions. We find that transitions of second or higher order are advantageous in comparison to…
Gene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one…
Constraint satisfiability problems, crucial to several applications, are solved on a quantum computer using Grover's search algorithm, leading to a quadratic improvement over the classical case. The solutions are obtained with high…
The aim of the paper is to answer a long-standing open problem on the relationship between NP and BQP. The paper shows that BQP contains NP by proposing a BQP quantum algorithm for the MAX-E3-SAT problem which is a fundamental NP-hard…
Accurately predicting protein structures from amino acid sequences remains a fundamental challenge in computational biology, with profound implications for understanding biological functions and enabling structure-based drug discovery.…
Predicting the three-dimensional (3D) structure of a protein from its primary sequence of amino acids is known as the protein folding (PF) problem. Due to the central role of proteins' 3D structures in chemistry, biology and medicine…
There has been increasing interest in developing efficient quantum algorithms for hard classical problems. The Network Signal Coordination (NSC) problem is one such problem known to be NP complete. We implement Grover's search algorithm to…
Quantum search algorithms are considered in the context of protein sequence comparison in biocomputing. Given a sample protein sequence of length m (i.e m residues), the problem considered is to find an optimal match in a large database…
The Boolean constraint satisfaction problem 3-SAT is arguably the canonical NP-complete problem. In contrast, 2-SAT can not only be decided in polynomial time, but in fact in deterministic linear time. In 2006, Bravyi proposed a physically…
Identifying a biclique with the maximum number of edges bears considerable implications for numerous fields of application, such as detecting anomalies in E-commerce transactions, discerning protein-protein interactions in biology, and…
Boolean satisfiability (SAT) problem is of fundamental importance in computer science and many application domains. For Grover's algorithm, solving the SAT problem requires $\mathcal{O}(\sqrt{2^n})$ queries--where n denotes the number of…
Modern neural networks obtain information about the problem and calculate the output solely from the input values. We argue that it is not always optimal, and the network's performance can be significantly improved by augmenting it with a…
In this paper, we present a novel algorithm to solve the Boolean Satisfiability (SAT) problem, using noise-based logic (NBL). Contrary to what the name may suggest, NBL is not a random/fuzzy logic system. In fact, it is a completely…
In this contribution, we provide a comprehensive evaluation of graph neural networks applied to Boolean satisfiability problems, accompanied by an intuitive explanation of the mechanisms enabling the model to generalize to different…
Computational models of biological processes provide one of the most powerful methods for a detailed analysis of the mechanisms that drive the behavior of complex systems. Logic-based modeling has enhanced our understanding and…
Quantum algorithm design plays a crucial role in exploiting the computational advantage of quantum devices. Here we develop a deep-reinforcement-learning based approach for quantum adiabatic algorithm design. Our approach is generically…
While accelerated computing has transformed many domains of computing, its impact on logical reasoning, specifically Boolean satisfiability (SAT), remains limited. State-of-the-art SAT solvers rely heavily on inherently sequential…
This paper introduces a new Boolean-based methodology for constructing Segment Display Problems (SDPs) in the quantum domain and solving them using Grover's quantum search algorithm. In the classical domain, the SDPs are typically solved…
The problem of P vs. NP is very serious, and solutions to the problem can help save lives. This article is an attempt at solving the problem using a computer algorithm. It is presented in a fashion that will hopefully allow for easy…