Comparative analyses of graph structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given k graphs as input, alignment algorithms use topological information to assign a similarity score to each k-tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs, and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method, and show that it can deliver exponential speedups over conventional (non-quantum) methods. I.
Comparative analyses of graph structured datasets underly diverse problems. Examples of these problems include identification of conserved functional components (biochemical interactions) across species, structural similarity of large biomolecules, and recurring patterns of interactions in social networks. A large class of such analyses methods quantify the topological similarity of nodes across networks. The resulting correspondence of nodes across networks, also called node alignment, can be used to identify invariant subgraphs across the input graphs. Given k graphs as input, alignment algorithms use topological information to assign a similarity score to each k-tuple of nodes, with elements (nodes) drawn from each of the input graphs. Nodes are considered similar if their neighbors are also similar. An alternate, equivalent view of these network alignment algorithms is to consider the Kronecker product of the input graphs, and to identify high-ranked nodes in the Kronecker product graph. Conventional methods such as PageRank and HITS (Hypertext Induced Topic Selection) can be used for this purpose. These methods typically require computation of the principal eigenvector of a suitably modified Kronecker product matrix of the input graphs. We adopt this alternate view of the problem to address the problem of multiple network alignment. Using the phase estimation algorithm, we show that the multiple network alignment problem can be efficiently solved on quantum computers. We characterize the accuracy and performance of our method, and show that it can deliver exponential speedups over conventional (non-quantum) methods. I.
Comparative analyses of protein-protein interaction networks play important roles in the understanding of biological processes. However, the growing enormity of available data on the networks becomes a computational challenge for the conventional alignment algorithms. Quantum algorithms generally provide greater efficiency over their classical counterparts in solving various problems. One of such algorithms is the quantum phase estimation algorithm which generates the principal eigenvector of a stochastic matrix with probability one. Using the quantum phase estimation algorithm, we introduce a quantum computing approach for the alignment of protein-protein interaction networks by following the classical algorithm IsoRank which uses the principal eigenvector of the stochastic matrix representing the Kronecker product of the normalized adjacency matrices of networks for the pairwise alignment. We also present a greedy quantum measurement scheme to efficiently procure the alignment from the output state of the phase estimation algorithm where the eigenvector is encoded as the amplitudes of this state. The complexity of the quantum approach outperforms the classical running time.
Protein-protein interaction (PPI) network alignment combines topological and sequence information to identify conserved modules across species, but global alignment remains challenging: heuristics sacrifice optimality, while exact methods lack scalability. We model the alignment as a weighted maximum common induced subgraph problem and reformulate it through the modular product graph to a minimum-weight vertex cover on the complement, with node weights carrying sequence similarity. To solve this problem, we develop a hybrid framework combining kernelisation, branch-and-bound, and seven Quantum Approximate Optimisation Algorithm (QAOA) formulations. These formulations differ in how the cover constraints are enforced, from penalty terms in the cost Hamiltonian to mixers confined to the feasible subspace. For single round QAOA, we derive closed-form expressions for the expected cost of four circulant mixer variants, enabling performance characterisation without circuit simulation. Applied to synthetic and real-world networks reduced to KEGG pathways, the QAOA formulations achieve high topological conservation on the aligned core while at least maintaining biological conservation comparable to leading classical aligners, at the cost of reduced node coverage. Across selected KEGG pathways, the aligned subnetworks retain disease-associated proteins, preserving biologically relevant information. Cheaper formulations leave more edges uncovered, while enforcing feasibility in the mixer raises circuit depth by one to two orders of magnitude. Together, these results highlight the potential of quantum optimisation for PPI network alignment and the resource trade-offs that will shape its scalability as quantum hardware matures.
Graph partitioning is a crucial problem in computer science with applications in diverse areas like VLSI design, image segmentation, and network analysis. Traditional classical algorithms often face significant challenges when dealing with large and complex graphs, leading to increased computational time and memory requirements. This paper explores the potential of quantum walk algorithms to address this issue. We propose a framework for leveraging quantum walk algorithms to efficiently explore the connectivity structure of a graph and identify optimal partitions. The core idea involves mapping the graph's nodes and edges onto a quantum system and utilizing the inherent parallelism of quantum walks to traverse the graph. We present a theoretical analysis of the algorithm's potential speedup compared to classical approaches, focusing on scenarios where quantum computation offers a significant advantage. Specifically, we formulate the graph partitioning problem as a search problem on a graph represented as a quantum walk, considering the Hamiltonian operator and its eigenstates for efficient traversal. The effectiveness of the algorithm is dependent on the graph's structure and the ability to accurately simulate the quantum walk. The presented methodology provides a novel approach to graph partitioning, potentially leading to substantial performance improvements for large, complex graphs.
Simulating quantum mechanical evolutions in general is difficult on classical computers because the size of the Hilbert space grows exponentially with the number of particles involved in the simulations. However, a quantum computer, which obeys the laws of quantum mechanics, is believed to perform such simulations more efficiently. The time evolution operator, a unitary matrix, of a quantum system acts as a quantum gate changing the state of the system in time. Therefore, any computation on quantum computers can be interpreted as a unitary transformation on quantum state vectors. Generally, quantum gates are sufficiently simple operations so as to avoid difficulty in the physical implementation. The implementation of a general given computation represented by a unitary matrix on quantum computers requires finding an array of elementary quantum gates describing the desired computation. This describes a matrix decomposition problem known as the quantum circuit design problem. In this dissertation, we address the following questions concerning quantum circuit designs: How hard is it to find suitable quantum circuits for a given computation? What are the possible circuit design methods? How do we apply these to simulations of quantum problems, in particular quantum chemistry problems? To answer these questions, we categorize methods for designing quantum circuits as evolutionary algorithms and deterministic methods. We apply our developed group leaders optimization algorithm, an evolutionary algorithm, to find quantum circuits for known quantum algorithms and the simulation of molecular Hamiltonians. Then, we present a deterministic circuit design approach to produce universal circuits, which can be programmable. Moreover, we show how to use these programmable circuit designs within the quantum phase estimation algorithm to find eigenvalues of nonunitary matrices and study resonances in quantum systems. Finally, the quantum phase estimation algorithm is employed to efficiently solve ranking problems: in particular, multiple network alignment is considered to find the similarities between protein-protein interaction networks and molecular networks.
We review the main ndings on the ranking capabilities of the recently proposed Quantum PageRank algorithm (1,2) applied to large complex networks. The algorithm has been shown to identify unambiguously the underlying topology of the network and to be capable of clearly highlighting the struc- ture of secondary hubs of networks. Furthermore it can resolve the degeneracy in importance of the low lying part of the list of rankings. Examples of applications include real world instances from the WWW, which typically display a scale-free network structure and models of hierarchical networks. The quantum algorithm has been shown to display an increased stability with respect to a variation of the damping parameter, present in the Google algorithm, and a more clearly pronounced power-law behaviour in the distribution of importance among the nodes, as compared to the classical algorithm.
HodgeRank generalizes ranking algorithms, e.g. Google PageRank, to rank alternatives based on real-world (often incomplete) data using graphs and discrete exterior calculus. It analyzes multipartite interactions on high-dimensional networks with a complexity that scales exponentially with dimension. We develop a quantum algorithm that approximates the HodgeRank solution with complexity independent of dimension. Our algorithm extracts relevant information from the state such as the ranking consistency, which achieves a superpolynomial speedup over similar classical methods.