Abstract Maximum Satisfiability (MaxSAT) is a prototypical constraint optimization problem,
and its generalized version is the (Weighted) Partial MaxSAT problem, denoted as (W) PMS …

By representing the constraints and objective function in factorized form, graphical models
can concisely define various NP-hard optimization problems. They are therefore extensively …

Proteins are chains of simple molecules called amino acids. The three-dimensional shape of
a protein and its amino acid composition define its biological function. Over millions of years …

Weighted maximum satisfiability and (unweighted) partial maximum satisfiability (PMS) are
two significant generalizations of maximum satisfiability (MAX-SAT), and weighted partial …

Motivation: The main challenge for structure-based computational protein design (CPD)
remains the combinatorial nature of the search space. Even in its simplest fixed-backbone …

Motivation Multistate protein design addresses real-world challenges, such as multi-
specificity design and backbone flexibility, by considering both positive and negative protein …

Computational protein design (CPD) aims to predict amino acid sequences that fold to
specific structures and perform desired functions. CPD depends on a rotamer library, an …

Soft neighborhood substitutability (SNS) is a powerful technique to automatically detect and
prune dominated solutions in combinatorial optimization. Recently, it has been shown in [26] …

The (weighted) partial maximum satisfiability ((W) PMS) problem is an important
generalization of the classic problem of propositional (Boolean) satisfiability with a wide …

Application tools for the crop allocation problem (CAP) are required for agricultural advisors
to design more efficient farming systems. Despite the extensive treatment of this issue by …