Simple Strategies in Multi-Objective MDPs
Ontology highlight
ABSTRACT:
SUBMITTER: Biere A
PROVIDER: S-EPMC7439746 | biostudies-literature | 2020 Mar
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The purpose of breeding programs is to obtain sustainable gains in multiple traits while controlling the loss of genetic variation. The decisions at each breeding cycle involve multiple, usually competing, objectives; these complex decisions can be supported by the insights that are gained by applying multi-objective optimization principles to breeding. The discussion in this manuscript includes the definition of several multi-objective optimized breeding approaches within the phenotypic or genomic breeding frameworks and the comparison of these approaches with the standard multi-trait breeding schemes such as tandem selection, independent culling and index selection. Proposed methods are demonstrated with two empirical data sets and simulations. In addition, we have described several graphical tools that can aid breeders in arriving at a compromise decision. The results show that the proposed methodology is a viable approach to answer several real breeding problems. In simulations, the newly proposed methods resulted in gains larger than the methods previously proposed including index selection: Compared to the best alternative breeding strategy, the gains from multi-objective optimized parental proportions approaches were about 20-30% higher at the end of long-term simulations of breeding cycles. In addition, the flexibility of the multi-objective optimized breeding strategies were displayed with methods and examples covering non-dominated selection, assignment of optimal parental proportions, using genomewide marker effects in producing optimal mating designs, and finally in selection of training populations for genomic prediction.
| S-EPMC6461918 | biostudies-literature
Project description:Background:Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information about the behaviour of genetic information on different conditions. In order to analyse this data, clustering arises as one of the main techniques used, and it aims at finding groups of genes that have some criterion in common, like similar expression profile. However, the problem of finding groups is normally multi dimensional, making necessary to approach the clustering as a multi-objective problem where various cluster validity indexes are simultaneously optimised. They are usually based on criteria like compactness and separation, which may not be sufficient since they can not guarantee the generation of clusters that have both similar expression patterns and biological coherence. Method:We propose a Multi-Objective Clustering algorithm Guided by a-Priori Biological Knowledge (MOC-GaPBK) to find clusters of genes with high levels of co-expression, biological coherence, and also good compactness and separation. Cluster quality indexes are used to optimise simultaneously gene relationships at expression level and biological functionality. Our proposal also includes intensification and diversification strategies to improve the search process. Results:The effectiveness of the proposed algorithm is demonstrated on four publicly available datasets. Comparative studies of the use of different objective functions and other widely used microarray clustering techniques are reported. Statistical, visual and biological significance tests are carried out to show the superiority of the proposed algorithm. Conclusions:Integrating a-priori biological knowledge into a multi-objective approach and using intensification and diversification strategies allow the proposed algorithm to find solutions with higher quality than other microarray clustering techniques available in the literature in terms of co-expression, biological coherence, compactness and separation.
| S-EPMC6081857 | biostudies-literature
Project description:Many real-world engineering problems need to balance different objectives and can be formatted as multi-objective optimization problem. An effective multi-objective algorithm can achieve a set of optimal solutions that can make a tradeoff between different objectives, which is valuable to further explore and design. In this paper, an improved multi-objective differential evolution algorithm (MOEA/D/DEM) based on a decomposition strategy is proposed to improve the performance of differential evolution algorithm for practical multi-objective nutrition decision problems. Firstly, considering the neighborhood characteristic, a neighbor intimacy factor is designed in the search process for enhancing the diversity of the population, then a new Gaussian mutation strategy with variable step size is proposed to reduce the probability of escaping local optimum area and improve the local search ability. Finally, the proposed algorithm is tested by classic test problems (DTLZ1-7 and WFG1-9) and applied to the multi-objective nutrition decision problems, compared to the other reported multi-objective algorithms, the proposed algorithm has a better search capability and obtained competitive results.
| S-EPMC9729643 | biostudies-literature
Project description:A new software tool making use of a genetic algorithm for multi-objective experimental optimization (GAME.opt) was developed based on a strength Pareto evolutionary algorithm. The software deals with high dimensional variable spaces and unknown interactions of design variables. This approach was evaluated by means of multi-objective test problems replacing the experimental results. A default parameter setting is proposed enabling users without expert knowledge to minimize the experimental effort (small population sizes and few generations).
| S-EPMC1705497 | biostudies-other
Project description:In this work we formulate and formally characterize group fairness as a multi-objective optimization problem, where each sensitive group risk is a separate objective. We propose a fairness criterion where a classifier achieves minimax risk and is Pareto-efficient w.r.t. all groups, avoiding unnecessary harm, and can lead to the best zero-gap model if policy dictates so. We provide a simple optimization algorithm compatible with deep neural networks to satisfy these constraints. Since our method does not require test-time access to sensitive attributes, it can be applied to reduce worst-case classification errors between outcomes in unbalanced classification problems. We test the proposed methodology on real case-studies of predicting income, ICU patient mortality, skin lesions classification, and assessing credit risk, demonstrating how our framework compares favorably to other approaches.
| S-EPMC7912461 | biostudies-literature
Project description:Artificially synthesized RNA molecules have recently come under study since such molecules have a potential for creating a variety of novel functional molecules. When designing artificial RNA sequences, secondary structure should be taken into account since functions of noncoding RNAs strongly depend on their structure. RNA inverse folding is a methodology for computationally exploring the RNA sequences folding into a user-given target structure. In the present study, we developed a multi-objective genetic algorithm, MODENA (Multi-Objective DEsign of Nucleic Acids), for RNA inverse folding. MODENA explores the approximate set of weak Pareto optimal solutions in the objective function space of 2 objective functions, a structure stability score and structure similarity score. MODENA can simultaneously design multiple different RNA sequences at 1 run, whose lowest free energies range from a very stable value to a higher value near those of natural counterparts. MODENA and previous RNA inverse folding programs were benchmarked with 29 target structures taken from the Rfam database, and we found that MODENA can successfully design 23 RNA sequences folding into the target structures; this result is better than those of the other benchmarked RNA inverse folding programs. The multi-objective genetic algorithm gives a useful framework for a functional biomolecular design. Executable files of MODENA can be obtained at http://rna.eit.hirosaki-u.ac.jp/modena/.
| S-EPMC3169953 | biostudies-literature
Project description:Data classification is a fundamental task in data mining. Within this field, the classification of multi-labeled data has been seriously considered in recent years. In such problems, each data entity can simultaneously belong to several categories. Multi-label classification is important because of many recent real-world applications in which each entity has more than one label. To improve the performance of multi-label classification, feature selection plays an important role. It involves identifying and removing irrelevant and redundant features that unnecessarily increase the dimensions of the search space for the classification problems. However, classification may fail with an extreme decrease in the number of relevant features. Thus, minimizing the number of features and maximizing the classification accuracy are two desirable but conflicting objectives in multi-label feature selection. In this article, we introduce a multi-objective optimization algorithm customized for selecting the features of multi-label data. The proposed algorithm is an enhanced variant of a decomposition-based multi-objective optimization approach, in which the multi-label feature selection problem is divided into single-objective subproblems that can be simultaneously solved using an evolutionary algorithm. This approach leads to accelerating the optimization process and finding more diverse feature subsets. The proposed method benefits from a local search operator to find better solutions for each subproblem. We also define a pool of genetic operators to generate new feature subsets based on old generation. To evaluate the performance of the proposed algorithm, we compare it with two other multi-objective feature selection approaches on eight real-world benchmark datasets that are commonly used for multi-label classification. The reported results of multi-objective method evaluation measures, such as hypervolume indicator and set coverage, illustrate an improvement in the results obtained by the proposed method. Moreover, the proposed method achieved better results in terms of classification accuracy with fewer features compared with state-of-the-art methods.
| S-EPMC7924502 | biostudies-literature
Project description:Molecular docking is a hard optimization problem that has been tackled in the past with metaheuristics, demonstrating new and challenging results when looking for one objective: the minimum binding energy. However, only a few papers can be found in the literature that deal with this problem by means of a multi-objective approach, and no experimental comparisons have been made in order to clarify which of them has the best overall performance. In this paper, we use and compare, for the first time, a set of representative multi-objective optimization algorithms applied to solve complex molecular docking problems. The approach followed is focused on optimizing the intermolecular and intramolecular energies as two main objectives to minimize. Specifically, these algorithms are: two variants of the non-dominated sorting genetic algorithm II (NSGA-II), speed modulation multi-objective particle swarm optimization (SMPSO), third evolution step of generalized differential evolution (GDE3), multi-objective evolutionary algorithm based on decomposition (MOEA/D) and S-metric evolutionary multi-objective optimization (SMS-EMOA). We assess the performance of the algorithms by applying quality indicators intended to measure convergence and the diversity of the generated Pareto front approximations. We carry out a comparison with another reference mono-objective algorithm in the problem domain (Lamarckian genetic algorithm (LGA) provided by the AutoDock tool). Furthermore, the ligand binding site and molecular interactions of computed solutions are analyzed, showing promising results for the multi-objective approaches. In addition, a case study of application for aeroplysinin-1 is performed, showing the effectiveness of our multi-objective approach in drug discovery.
| S-EPMC6272647 | biostudies-literature
Project description:This study aimed to demonstrate that the simple tracing test (STT) is useful for assessing the hand dexterity in patients with cervical spondylotic myelopathy (CSM) by comparing STT scores between healthy volunteers and CSM patients. This study included 25 CSM patients and 38 healthy volunteers. In the STT, the participants traced a sine wave displayed on a tablet device at a comfortable pace, and the tracing accuracy, changes in the total sum of pen pressures, and tracing duration were assessed. Data were analyzed using an artificial neural networks (ANN) model to obtain STT scores. All participants were evaluated using the subsection for the upper extremity function of the Japanese Orthopaedic Association (JOA) scoring system for cervical myelopathy (JOA subscore for upper extremity function) and the grip and release test (GRT). The results were compared with the STT scores. The mean STT scores were 24.4 ± 32.8 in the CSM patients and 84.9 ± 31.3 in the healthy volunteers, showing a significant difference. The STT scores showed highly positive correlations with both the JOA subscore for upper extremity function (r = 0.66; P < 0.001) and GRT values (r = 0.74; P < 0.001). Furthermore, receiver operating characteristic analysis showed an area under the curve of 0.89 (95% confidence interval, 0.76-1.00), demonstrating that STT has excellent discriminative ability. This study revealed that STT enables accurate assessment of the hand dexterity in CSM patients.
| S-EPMC6616365 | biostudies-literature
Project description:BackgroundIn the field of computational biology, analyzing complex data helps to extract relevant biological information. Sample classification of gene expression data is one such popular bio-data analysis technique. However, the presence of a large number of irrelevant/redundant genes in expression data makes a sample classification algorithm working inefficiently. Feature selection is one such high-dimensionality reduction technique that helps to maximize the effectiveness of any sample classification algorithm. Recent advances in biotechnology have improved the biological data to include multi-modal or multiple views. Different 'omics' resources capture various equally important biological properties of entities. However, most of the existing feature selection methodologies are biased towards considering only one out of multiple biological resources. Consequently, some crucial aspects of available biological knowledge may get ignored, which could further improve feature selection efficiency.ResultsIn this present work, we have proposed a Consensus Multi-View Multi-objective Clustering-based feature selection algorithm called CMVMC. Three controlled genomic and proteomic resources like gene expression, Gene Ontology (GO), and protein-protein interaction network (PPIN) are utilized to build two independent views. The concept of multi-objective consensus clustering has been applied within our proposed gene selection method to satisfy both incorporated views. Gene expression data sets of Multiple tissues and Yeast from two different organisms (Homo Sapiens and Saccharomyces cerevisiae, respectively) are chosen for experimental purposes. As the end-product of CMVMC, a reduced set of relevant and non-redundant genes are found for each chosen data set. These genes finally participate in an effective sample classification.ConclusionsThe experimental study on chosen data sets shows that our proposed feature-selection method improves the sample classification accuracy and reduces the gene-space up to a significant level. In the case of Multiple Tissues data set, CMVMC reduces the number of genes (features) from 5565 to 41, with 92.73% of sample classification accuracy. For Yeast data set, the number of genes got reduced to 10 from 2884, with 95.84% sample classification accuracy. Two internal cluster validity indices - Silhouette and Davies-Bouldin (DB) and one external validity index Classification Accuracy (CA) are chosen for comparative study. Reported results are further validated through well-known biological significance test and visualization tool.
| S-EPMC7495900 | biostudies-literature