Related papers: QUBODock: A Pip-Installable QUBO Tool for Ligand P…
The Quadratic Unconstrained Binary Optimization (QUBO) model has gained prominence in recent years with the discovery that it unifies a rich variety of combinatorial optimization problems. By its association with the Ising problem in…
We demonstrate that the search space of the quadratic assignment problem (QAP), known as an NP-hard combinatorial optimization problem, can be reduced using Grover adaptive search (GAS) with permutation preparation operator (PPO). To that…
Quadratic Unconstrained Binary Optimization (QUBO) is a standard NP-hard optimization problem. Recently, it has gained renewed interest through quantum computing, as QUBOs directly reduce to the Ising model, on which quantum annealing…
Combinatorial optimization problems represent a wide range of real-world scenarios where complicated interactions make it difficult to find the best solution. One example is the quadratic assignment problem (QAP), which involves determining…
The Quadratic Unconstrained Binary Optimization (QUBO) modeling and solution framework is a requirement for quantum and digital annealers. However optimality for QUBO problems of any practical size is extremely difficult to achieve. In…
We extend the family of problems that may be implemented on an adiabatic quantum optimizer (AQO). When a quadratic optimization problem has at least one set of discrete controls and the constraints are linear, we call this a quadratic…
Understanding the structure of the protein-ligand complex is crucial to drug development. Existing virtual structure measurement and screening methods are dominated by docking and its derived methods combined with deep learning. However,…
Diagnosing the minimal set of faults capable of explaining a set of given observations, e.g., from sensor readouts, is a hard combinatorial optimization problem usually tackled with artificial intelligence techniques. We present the mapping…
Adiabatic Quantum Computing (AQC) is an attractive paradigm for solving hard integer polynomial optimization problems. Available hardware restricts the Hamiltonians to be of a structure that allows only pairwise interactions. This requires…
In this proceedings we present Qibocal, an open-source software package for calibration and characterization of quantum processing units (QPUs) based on the Qibo framework. Qibocal is specifically designed for self-hosted QPUs and provides…
De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance…
Bin picking in real industrial environments remains challenging due to severe clutter, occlusions, and the high cost of traditional 3D sensing setups. We present Pickalo, a modular 6D pose-based bin-picking pipeline built entirely on…
Quadratic Unconstrained Binary Optimization (QUBO) is a generic technique to model various NP-hard Combinatorial Optimization problems (CO) in the form of binary variables. Ising Hamiltonian is used to model the energy function of a system.…
SkeleDock is a scaffold docking algorithm which uses the structure of a protein-ligand complex as a template to model the binding mode of a chemically similar system. This algorithm was evaluated in the D3R Grand Challenge 4 pose prediction…
The broad applicability of Quadratic Unconstrained Binary Optimization (QUBO) constitutes a general-purpose modeling framework for combinatorial optimization problems and are a required format for gate array and quantum annealing computers.…
Gaussian Processes are used in many applications to model spatial phenomena. Within this context, a key issue is to decide the set of locations where to take measurements so as to obtain a better approximation of the underlying function.…
We study a Grover-type method for Quadratic Unconstrained Binary Optimization (QUBO) problems. For an $n$-dimensional QUBO problem with $m$ nonzero terms, we construct a marker oracle for such problems with a tuneable parameter, $\Lambda…
The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…
Recent advances in quantum computing and the increasing availability of quantum hardware have substantially enhanced the practical relevance of quantum approaches to discrete optimization. Among these, the Quadratic Unconstrained Binary…
Quantum approaches to combinatorial optimization problems (COPs) are often limited by the resource demands of Quadratic Unconstrained Binary Optimization (QUBO) encodings, which enlarge circuits through penalty terms and increase qubit and…