9 papers
High-Order Epistasis Detection Using Factorization Machine with Quadratic Optimization Annealing and MDR-Based Evaluation
Shuta Kikuchi, Shu Tanaka
Detecting high-order epistasis is a fundamental challenge in genetic association studies due to the combinatorial explosion of candidate locus combinations. Although multifactor di…
Improving FMQA via Initial Training Data Design Considering Marginal Bit Coverage in One-Hot Encoding
Taiga Hayashi, Yuya Seki, Kotaro Terada +3
Factorization machine with quadratic-optimization annealing (FMQA) is a black-box optimization method that combines a factorization machine (FM) surrogate with QUBO-based search by…
Parallelizable Search-Space Decomposition for Large-Scale Combinatorial Optimization Problems Using Ising Machines
Eiji Kawase, Shuta Kikuchi, Hideaki Tamai +1
Combinatorial optimization problems are crucial in industry. However, many COPs are NP-hard, causing the search space to grow exponentially with problem size and rendering large-sc…
Factorization Machine with Quadratic-Optimization Annealing for RNA Inverse Folding and Evaluation of Binary-Integer Encoding and Nucleotide Assignment
Shuta Kikuchi, Shu Tanaka
The RNA inverse folding problem aims to identify nucleotide sequences that preferentially adopt a given target secondary structure. While various heuristic and machine learning-bas…
SWIFT-FMQA: Enhancing Factorization Machine with Quadratic-Optimization Annealing via Sliding Window
Mayumi Nakano, Yuya Seki, Shuta Kikuchi +1
Black-box (BB) optimization problems aim to identify an input that maximizes or minimizes the output of a function (the BB function) whose input-output relationship is unknown. Fac…
Extending Sample Persistence Variable Reduction for Constrained Combinatorial Optimization Problems
Shunta Ide, Shuta Kikuchi, Shu Tanaka
Constrained combinatorial optimization problems (CCOPs) are challenging to solve due to the exponential growth of the solution space. When tackled with Ising machines, constraints…