Related papers: Improving MSA Estimation through Adaptive Weight V…
The Multi-Objective Evolutionary Algorithm based on Decomposition (MOEA/D) is a popular algorithm for solving Multi-Objective Problems (MOPs). The main component of MOEA/D is to decompose a MOP into easier sub-problems using a set of weight…
Decomposition-based multi-objective evolutionary algorithms (MOEAs) are widely used for solving multi-objective optimisation problems. However, their effectiveness depends on the consistency between the problems Pareto front shape and the…
When working with decomposition-based algorithms, an appropriate set of weights might improve quality of the final solution. A set of uniformly distributed weights usually leads to well-distributed solutions on a Pareto front. However,…
Evolutionary algorithms based on modeling the statistical dependencies (interactions) between the variables have been proposed to solve a wide range of complex problems. These algorithms learn and sample probabilistic graphical models able…
We study the multi-objective minimum weight base problem, an abstraction of classical NP-hard combinatorial problems such as the multi-objective minimum spanning tree problem. We prove some important properties of the convex hull of the…
The major difficulty in Multi-objective Optimization Evolutionary Algorithms (MOEAs) is how to find an appropriate solution that is able to converge towards the true Pareto Front with high diversity. Most existing methodologies, which have…
Decomposition-based multiobjective evolutionary algorithms (MOEAs) with clustering-based reference vector adaptation show good optimization performance for many-objective optimization problems (MaOPs). Especially, algorithms that employ a…
Parallel batch processing machines have extensive applications in the semiconductor manufacturing process. However, the problem models in previous studies regard parallel batch processing as a fixed processing stage in the machining…
Multiobjective evolutionary algorithms (MOEAs) have been successfully applied to a number of constrained optimization problems. Many of them adopt mutation and crossover operators from differential evolution. However, these operators do not…
Many real-world optimization problems such as engineering design can be eventually modeled as the corresponding multiobjective optimization problems (MOPs) which must be solved to obtain approximate Pareto optimal fronts. Multiobjective…
We theorize that phylogenetic profiles provide a quantitative method that can relate the structural and functional properties of proteins, as well as their evolutionary relationships. A key feature of phylogenetic profiles is the…
The effectiveness of Constrained Multi-Objective Evolutionary Algorithms (CMOEAs) depends on their ability to reach the different feasible regions during evolution, by exploiting the information present in infeasible solutions, in addition…
The field of protein folding research has been greatly advanced by deep learning methods, with AlphaFold2 (AF2) demonstrating exceptional performance and atomic-level precision. As co-evolution is integral to protein structure prediction,…
Multi-objective evolutionary algorithms (MOEAs) are widely used for searching optimal solutions in complex multi-component applications. Traditional MOEAs for multi-component deep learning (MCDL) systems face challenges in enhancing the…
Sequence alignment is common nowadays as it is used in many fields to determine how closely two sequences are related and at times to see how little they differ. In computational biology / Bioinformatics, there are many algorithms developed…
A preference based multi-objective evolutionary algorithm is proposed for generating solutions in an automatically detected knee point region. It is named Automatic Preference based DI-MOEA (AP-DI-MOEA) where DI-MOEA stands for…
Variable division and optimization (D\&O) is a frequently utilized algorithm design paradigm in Evolutionary Algorithms (EAs). A D\&O EA divides a variable into partial variables and then optimize them respectively. A complicated problem is…
Recent generative learning models applied to protein multiple sequence alignment (MSA) datasets include simple and interpretable physics-based Potts covariation models and other machine learning models such as MSA-Transformer (MSA-T). The…
Multiple Sequence Alignment (MSA) is one of the most computationally intensive tasks in Computational Biology. Existing best known solutions for multiple sequence alignment take several hours (in some cases days) of computation time to…
Variant effect predictors (VEPs) aim to assess the functional impact of protein variants, traditionally relying on multiple sequence alignments (MSAs). This approach assumes that naturally occurring variants are fit, an assumption…