Transmembrane proteins (TMPs) constitute approximately 30% of the mammalian proteome and are critical targets in biomedical research due to their involvement in signaling, transport, and drug interactions. However, their unique structural characteristics pose significant challenges for conventional multiple sequence alignment (MSA) methods, which are typically optimized for soluble proteins. In this paper, we propose TMP-M2Align, a novel topology-aware multiobjective algorithm specifically designed for the multiple alignment of TMPs. The method simultaneously optimizes two complementary objectives: (i) a topology-aware Sum-of-Pairs (SPs) score that integrates region-specific substitution matrices and gap penalties, and (ii) an Aligned Regions (ARs) score that rewards consistent alignment of functional and topological domains. By combining these objectives, TMP-M2Align generates Pareto front approximations of alignment solutions, enabling researchers to select trade-offs that best suit their biological questions. We evaluated TMP-M2Align on BAliBASE Reference Set 7 and on complete datasets of human G protein-coupled receptors (GPCRs) from classes A, B1, and C. Experimental results demonstrate that TMP-M2Align consistently outperforms both traditional alignment tools and specialized TM-specific methods in terms of SPs and Total Column metrics. Moreover, qualitative topological analyses confirm that TMP-M2Align preserves the integrity of transmembrane helices and loop boundaries more effectively than competing approaches. These findings highlight the effectiveness of integrating topology-aware scoring with multiobjective optimization for achieving accurate and biologically meaningful alignments of TMPs.

Julia is a programming language suitable for data analysis and scientific computing that combines simplicity of productivity languages with characteristics of performance-oriented languages. In this paper, we are interested in studying the use of Julia to implement Multi-Objective MetaHeuristics. Concretely, we use the Java-based jMetal framework as a reference support and investigate how Julia could be used to design and develop the component-based architecture for multi-objective evolutionary algorithms that jMetal provides. By using the NSGA-II algorithm as an example, we analyze the advantages and shortcomings of using Julia in this context, including aspects related to reusing jMetal code and a performance comparison.

The application of semantic technologies, particularly ontologies, in the realm of multi-objective evolutionary algorithms is overlook despite their effectiveness in knowledge representation. In this paper, we introduce MOODY, an ontology specifically tailored to formalize these kinds of algorithms, encompassing their respective parameters, and multi-objective optimization problems based on a characterization of their search space landscapes. MOODY is designed to be particularly applicable in automatic algorithm configuration, which involves the search of the parameters of an optimization algorithm to optimize its performance. In this context, we observe a notable absence of standardized components, parameters, and related considerations, such as problem characteristics and algorithm configurations. This lack of standardization introduces difficulties in the selection of valid component combinations and in the re-use of algorithmic configurations between different algorithm implementations. MOODY offers a means to infuse semantic annotations into the configurations found by automatic tools, enabling efficient querying of the results and seamless integration across diverse sources through their incorporation into a knowledge graph. We validate our proposal by presenting four case studies.

The automatic design of multi-objective metaheuristics is an active research line aimed at, given a set of problems used as training set, to find the configuration of a multi-objective optimizer able of solving them efficiently. The expected outcome is that the auto-configured algorithm can be used of find accurate Pareto front approximations for other problems. In this paper, we conduct a study on the meta-optimization of the well-known NSGA-II algorithm, i.e., we intend to use NSGA-II as an automatic configuration tool to find configurations of NSGA-II. This search can be formulated as a multi-objective problem where the decision variables are the NSGA-II components and parameters and the objectives are quality indicators that have to be minimized. To develop this study, we rely on the jMetal framework. The analysis we propose is aimed at answering the following research questions: RQ1 - how complex is to build the meta-optimization package?, and RQ2 - can accurate configurations be found? We conduct an experimentation to give an answer to these questions.

Evolver is a tool based on the formulation of the automatic configuration and design of multi-objective metaheuristics as a multi-objective optimization problem that can be solved by using the same kind of algorithms; i.e., we are applying a meta-optimization approach. Evolver provides highly configurable implementations of representative multi-objective solvers which can be automatically configured from a number of multi-objective problems used as the training set and a list of quality indicators which are the objectives to be optimized. Our tool is based on the jMetal framework, so a large number of existing algorithms can be used as meta-optimizers. A graphical user interface allows scientists to easily define auto-configuration scenarios, thus simplifying the complex process of finding high-quality algorithm settings.

In recent years, the application of artificial intelligence has been revolutionizing the manufacturing industry, becoming one of the key pillars of what has been called Industry 4.0. In this context, we focus on the job shop scheduling problem (JSP), which aims at productions orders to be carried out, but considering the reduction of energy consumption as a key objective to fulfill. Finding the best combination of machines and jobs to be performed is not a trivial problem and becomes even more involved when several objectives are taken into account. Among them, the improvement of energy savings may conflict with other objectives, such as the minimization of the makespan. In this paper, we provide an in-depth review of the existing literature on multi-objective job shop scheduling optimization with metaheuristics, in which one of the objectives is the minimization of energy consumption. We systematically reviewed and critically analyzed the most relevant features of both problem formulations and algorithms to solve them effectively. The manuscript also informs with empirical results the main findings of our bibliographic critique with a performance comparison among representative multi-objective evolutionary solvers applied to a diversity of synthetic test instances. The ultimate goal of this article is to carry out a critical analysis, finding good practices and opportunities for further improvement that stem from current knowledge in this vibrant research area.

NSGA-II is, by far, the most popular metaheuristic that has been adopted for solving multi-objective optimization problems. However, its most common usage, particularly when dealing with continuous problems, is circumscribed to a standard algorithmic configuration similar to the one described in its seminal paper. In this work, our aim is to show that the performance of NSGA-II, when properly configured, can be significantly improved in the context of large-scale optimization. It leverages a combination of tools for automated algorithmic tuning called irace, and a highly configurable version of NSGA-II available in the jMetal framework. Two scenarios are devised: first, by solving the Zitzler–Deb–Thiele (ZDT) test problems, and second, when dealing with a binary real-world problem of the telecommunications domain. Our experiments reveal that an auto-configured version of NSGA-II can properly address test problems ZDT1 and ZDT2 with up to 217=131,072 decision variables. The same methodology, when applied to the telecommunications problem, shows that significant improvements can be obtained with respect to the original NSGA-II algorithm when solving problems with thousands of bits.

Many Pareto-based multiobjective evolutionary algorithms require ranking the solutions of the population in each iteration according to the dominance principle, which can become a costly operation particularly in the case of dealing with many-objective optimization problems. In this article, we present a new efficient algorithm for computing the nondominated sorting procedure, called merge nondominated sorting (MNDS), which has a best computational complexity of O(NlogN) and a worst computational complexity of O(MN2) , with N being the population size and M being the number of objectives. Our approach is based on the computation of the dominance set, that is, for each solution, the set of solutions that dominate it, by taking advantage of the characteristics of the merge sort algorithm. We compare MNDS against six well-known techniques that can be considered as the state-of-the-art. The results indicate that the MNDS algorithm outperforms the other techniques in terms of the number of comparisons as well as the total running time.

In the field of complex problem optimization with metaheuristics, semantics has been used for modeling different aspects, such as: problem characterization, parameters, decision-maker's preferences, or algorithms. However, there is a lack of approaches where ontologies are applied in a direct way into the optimization process, with the aim of enhancing it by allowing the systematic incorporation of additional domain knowledge. This is due to the high level of abstraction of ontologies, which makes them difficult to be mapped into the code implementing the problems and/or the specific operators of metaheuristics. In this paper, we present a strategy to inject domain knowledge (by reusing existing ontologies or creating a new one) into a problem implementation that will be optimized using a metaheuristic. Thus, this approach based on accepted ontologies enables building and exploiting complex computing systems in optimization problems. We describe a methodology to automatically induce user choices (taken from the ontology) into the problem implementations provided by the jMetal optimization framework. With the aim of illustrating our proposal, we focus on the urban domain. Concretely, we start from defining an ontology representing the domain semantics for a city (e.g., building, bridges, point of interest, routes, etc.) that allows defining a-priori preferences by a decision maker in a standard, reusable, and formal (logic-based) way. We validate our proposal with several instances of two use cases, consisting in biobjective formulations of the Traveling Salesman Problem (TSP) and the Radio Network Design problem (RND), both in the context of an urban scenario. The results of the experiments conducted show how the semantic specification of domain constraints are effectively mapped into feasible solutions of the tackled TSP and RND scenarios. This proposal aims at representing a step forward towards the automatic modeling and adaptation of optimization problems guided by semantics, where the annotation of a human expert can be now considered during the optimization process.

In the last few years, the formulation of real-world optimization problems and their efficient solution via metaheuristic algorithms has been a catalyst for a myriad of research studies. In spite of decades of historical advancements on the design and use of metaheuristics, large difficulties still remain in regards to the understandability, algorithmic design uprightness, and performance verifiability of new technical achievements. A clear example stems from the scarce replicability of works dealing with metaheuristics used for optimization, which is often infeasible due to ambiguity and lack of detail in the presentation of the methods to be reproduced. Additionally, in many cases, there is a questionable statistical significance of their reported results. This work aims at providing the audience with a proposal of good practices which should be embraced when conducting studies about metaheuristics methods used for optimization in order to provide scientific rigor, value and transparency. To this end, we introduce a step by step methodology covering every research phase that should be followed when addressing this scientific field. Specifically, frequently overlooked yet crucial aspects and useful recommendations will be discussed in regards to the formulation of the problem, solution encoding, implementation of search operators, evaluation metrics, design of experiments, and considerations for real-world performance, among others. Finally, we will outline important considerations, challenges, and research directions for the success of newly developed optimization metaheuristics in their deployment and operation over real-world application environments.

Modern applications of Big Data are transcending from being scalable solutions of data processing and analysis, to now provide advanced functionalities with the ability to exploit and understand the underpinning knowledge. This change is promoting the development of tools in the intersection of data processing, data analysis, knowledge extraction and management. In this paper, we propose TITAN, a software platform for managing all the life cycle of science workflows from deployment to execution in the context of Big Data applications. This platform is characterised by a design and operation mode driven by semantics at different levels: data sources, problem domain and workflow components. The proposed platform is developed upon an ontological framework of meta-data consistently managing processes and models and taking advantage of domain knowledge. TITAN comprises a well-grounded stack of Big Data technologies including Apache Kafka for inter-component communication, Apache Avro for data serialisation and Apache Spark for data analytics. A series of use cases are conducted for validation, which comprises workflow composition and semantic meta-data management in academic and real-world fields of human activity recognition and land use monitoring from satellite images.

A number of streaming technologies have appeared in the last years as a result of the rising of Big Data applications. Nowadays, deciding which technology to adopt is not an easy task due not only to the number of available data streaming processing projects, but also because they are continuously evolving. In this paper, we focus on how these issues have affected jMetalSP, a framework for dynamic multi-objective optimization that incorporates streaming features. jMetalSP allows the development of three tier optimization workflows where the central component is an optimizer that is continuously solving a dynamic multi-objective optimization problem. This problem can change as a consequence of the analysis of data streams carried out by components that use the Apache Spark streaming engine. A third kind of components receive and process the Pareto front approximations being yielded by the optimization algorithm. However, all jMetalSP elements are tightly coupled and linked to Spark, making it difficult to use a different streaming system. To overcome this issue, we have redesigned the jMetalSP architecture to make it flexible enough to avoid the dependence of any particular streaming system. This way, popular Apache projects such as Spark Structured Streaming, Kafka Streams, or Flink can be used without requiring to change the rest of components of the application. Furthermore, Kafka can be used for inter-process communication, what enables the execution of components in different nodes of a cluster, independently of their implementation languages thanks to the serialization of data streams with Apache Avro. We show how the embraced solution provides a high degree of flexibility that enhances the usability of jMetalSP. To this end, a representative case study based on a transport problem is conducted that focuses on data representation and performance evaluation of the Spark, Flink, and Kafka systems.

The efficient calibration of hydrologic models allows experts to evaluate past events in river basins, as well as to describe new scenarios and predict possible future floodings. A difficulty in this context is the need to adjust a large number of parameters in the model to reduce prediction errors. In this work, we address this issue with two complementary contributions. First, we propose a new lumped rainfall-runoff hydrologic model—called Qom—which is featured by a limited set of continuous decision variables associated with soil moisture and direct runoff. Qom allows to separate and quantify the volume of losses and excesses of the rainwater falling in a hydrographic basin, while a Clark’s model is used to determine output hydrograms. Second, we apply a multi-objective optimization approach to find accurate calibrations of the model in a systematic and automatic way. The idea is to formulate the process as a bi-objective optimization problem where the Nash-Sutcliffe Efficiency coefficient and percent bias have to be minimized, and to combine the results found by a set of metaheuristics used to solve it. For validation purposes, we apply our proposal in six hydrographic scenarios, comprising river basins located in Spain, USA, Brazil and Argentina. The proposed approach is shown to minimize prediction errors of simulated streamflows with regards to those observed in these real-world basins.

MOTIVATION:Multiple sequence alignment (MSA) consists of finding the optimal alignment of three or more biological sequences to identify highly conserved regions that may be the result of similarities and relationships between the sequences. MSA is an optimization problem with NP-hard complexity (non-deterministic polynomial-time hardness), because the time needed to find optimal alignments raises exponentially along with the number of sequences and their length. Furthermore, the problem becomes multiobjective when more than one score is considered to assess the quality of an alignment, such as maximizing the percentage of totally conserved columns and minimizing the number of gaps. Our motivation is to provide a Python tool for solving MSA problems using evolutionary algorithms, a nonexact stochastic optimization approach that has proven to be effective to solve multiobjective problems.RESULTS:The software tool we have developed, called Sequoya, is written in the Python programming language, which offers a broad set of libraries for data analysis, visualization and parallelism. Thus, Sequoya offers a graphical tool to visualize the progress of the optimization in real time, the ability to guide the search toward a preferred region in run-time, parallel support to distribute the computation among nodes in a distributed computing system, and a graphical component to assist in the analysis of the solutions found at the end of the optimization.AVAILABILITY AND IMPLEMENTATION:Sequoya can be freely obtained from the Python Package Index (pip) or, alternatively, it can be downloaded from Github at https://github.com/benhid/Sequoya.SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

Industry 4.0 is revolutionizing decision making processes within the manufacturing industry. Among the technological portfolio enabling this revolution, the late literature has capitalized on the potential of data analytics for improving the production cycle at different stages, from resource provisioning to planning, delivery and storage. However, such a promising role of data analytics has been so far explored without a proper, quantitative inspection of the cost-improvement trade-off, nor has the process of acquiring sensors and extracting valuable information from their captured data formalized in a series of methodological steps. This paper introduces the Analyze, Sense, Preprocess, Predict, Implement and Deploy (ASPPID) methodology, an iterative decision workflow that spans from the acquisition of sensing equipment to the quantitative assessment of the contribution of their captured data to enhance the production step under focus. By placing the data scientist at the core of the workflow, this methodology helps improvement teams make informed decisions about which parts of the process need to be sensed, and how to exploit this information towards a verifiable improvement of the production cycle. The implementation of this methodology is exemplified in a real use case within the automotive industry, where the detection of defects in an annealing process can be modeled as a classification problem over a highly imbalanced dataset. Results obtained after applying the proposed ASPPID methodology show that the scrap ratio is reduced by sensing the correct part of the process at minimal investment costs, thus highlighting the crucial role of the data scientist in the management team of manufacturing plants.

Reverse engineering of biochemical networks remains an important open challenge in computational systems biology. The goal of model inference is to, based on time-series gene expression data, obtain the sparse topological structure and parameters that quantitatively understand and reproduce the dynamics of biological systems. In this paper, we propose a multi-objective approach for the inference of S-System structures for Gene Regulatory Networks (GRNs) based on Pareto dominance and Pareto optimality theoretical concepts instead of the conventional single-objective evaluation of Mean Squared Error (MSE). Our motivation is that, using a multi-objective formulation for the GRN, it is possible to optimize the sparse topology of a given GRN as well as the kinetic order and rate constant parameters in a decoupled S-System, yet avoiding the use of additional penalty weights. A flexible and robust Multi-Objective Cellular Evolutionary Algorithm is adapted to perform the tasks of parameter learning and network topology inference for the proposed approach. The resulting software, called MONET, is evaluated on real-based academic and synthetic time-series of gene expression taken from the DREAM3 challenge and the IRMA in vivo datasets. The ability to reproduce biological behavior and robustness to noise is assessed and compared. The results obtained are competitive and indicate that the proposed approach offers advantages over previously used methods. In addition, MONET is able to provide experts with a set of trade-off solutions involving GRNs with different typologies and MSEs.

jMetal is a Java-based framework for multi-objective optimization with metaheuristics providing, among other features, a wide set of algorithms that are representative of the state-of-the-art. Although it has become a widely used tool in the area, it lacks support for automatic tuning of algorithm parameter settings, which can prevent obtaining accurate Pareto front approximations, especially for inexperienced users. In this paper, we present a first approach to combine jMetal and irace, a package for automatic algorithm configuration; the NSGA-II is chosen as the target algorithm to be tuned. The goal is to facilitate the combined use of both tools to jMetal users to avoid wasting time in adjusting manually the parameters of the algorithms. Our proposal involves the definition of a new algorithm template for evolutionary algorithms, which allows the flexible composition of multi-objective evolutionary algorithms from a set of configurable components, as well as the generation of configuration files for adjusting the algorithm parameters with irace. To validate our approach, NSGA-II is tuned with a benchmark problems and compared with the same algorithm using standard settings, resulting in a new variant that shows a competitive behavior.

Molecular docking is a Bioinformatics method based on predicting the position and orientation of a small molecule or ligand when it is bound to a target macromolecule. This method can be modeled as an optimization problem where one or more objectives can be defined, typically around an energy scoring function. This paper reviews developments in the field of single- and multi-objective meta-heuristics for efficiently addressing molecular docking optimization problems. We comprehensively analyze both problem formulations and applied techniques from Evolutionary Computation and Swarm Intelligence, jointly referred to as Bio-inspired Optimization. Our prospective analysis is supported by an experimental study dealing with a molecular docking problem driven by three conflicting objectives, which is tackled by using different multi-objective heuristics. We conclude that genetic algorithms are the most widely used techniques by far, with a noted increasing prevalence of particle swarm optimization in the last years, being these last techniques particularly adequate when dealing with multi-objective formulations of molecular docking problems. We end this experimental survey by outlining future research paths that should be under target in this vibrant area.

This paper describes jMetalPy, an object-oriented Python-based framework for multi-objective optimization with metaheuristic techniques. Building upon our experiences with the well-known jMetal framework, we have developed a new multi-objective optimization software platform aiming not only at replicating the former one in a different programming language, but also at taking advantage of the full feature set of Python, including its facilities for fast prototyping and the large amount of available libraries for data processing, data analysis, data visualization, and high-performance computing. As a result, jMetalPy provides an environment for solving multi-objective optimization problems focused not only on traditional metaheuristics, but also on techniques supporting preference articulation, constrained and dynamic problems, along with a rich set of features related to the automatic generation of statistical data from the results generated, as well as the real-time and interactive visualization of the Pareto front approximations produced by the algorithms. jMetalPy offers additionally support for parallel computing in multicore and cluster systems. We include some use cases to explore the main features of jMetalPy and to illustrate how to work with it.

The problem of molecular docking focuses on minimizing the binding energy of a complex composed by a ligand and a receptor. In this paper, we propose a new approach based on the joint optimization of three conflicting objectives: Einter that relates to the ligand-receptor affinity, the Eintra characterizing the ligand deformity and the RMSD score (Root Mean Square Deviation), which measures the difference of atomic distances between the co-crystallized ligand and the computed ligand. In order to deal with this multi-objective problem, three different metaheuristic solvers (SMPSO, MOEA/D and MPSO/D) are used to evolve a numerical representation of the ligand's conformation. An experimental benchmark is designed to shed light on the comparative performance of these multi-objective heuristics, comprising a set of HIV-proteases/inhibitors complexes where flexibility was applied. The obtained results are promising, and pave the way towards embracing the proposed algorithms for practical multi-criteria in the docking problem.