An Adaptive Scheme to Generate the Pareto Front Based on the Epsilon-Constraint Method

We discuss methods for generating or approximating the Pareto set of multiobjective optimization problems by solving a sequence of constrained single-objective problems. The necessity of determining the constraint value a priori is shown to be a serious drawback of the original epsilon-constraint method. We therefore propose a new, adaptive scheme to generate appropriate constraint values during the run. A simple example problem is presented, where the running time (measured by the number of constrained single-objective sub-problems to be solved) of the original epsilon-constraint method is exponential in the problem size (number of decision variables), although the size of the Pareto set grows only linearly. We prove that --- independent of the problem or the problem size --- the time complexity of the new scheme is O(k^{m-1}), where k is the number of Pareto-optimal solutions to be found and m the number of objectives. Simulation results for the example problem as well as for different instances of the multiobjective knapsack problem demonstrate the behavior of the method, and links to reference implementations are provided

Pattern Identification in Pareto-Set Approximations

In a multiobjective setting, evolutionary algorithms can be used to generate a set of compromise solutions. This makes decision making easier for the user as he has alternative solutions at hand which he can directly compare. However, if the number of solutions and the number of decision variables which define the solutions are large, such an analysis may be difficult and corresponding tools are desirable to support a human in separating relevant from irrelevant information. In this paper, we present a method to extract structural information from Pareto-set approximations which offers the possibility to present and visualize the trade-off surface in a compressed form. The main idea is to identify modules of decision variables that are strongly related to each other. Thereby, the set of decision variables can be reduced to a smaller number of significant modules. Furthermore, at the same time the solutions are grouped in a hierarchical manner according to their module similarity. Overall, the output is a dendrogram where the leaves are the solutions and the nodes are annotated with modules. As will be shown on knapsack problem instances and a network processor design application, this method can be highly useful to reveal hidden structures in compromise solution sets

Evolutionary algorithms for the selection of single nucleotide polymorphisms

BACKGROUND: Large databases of single nucleotide polymorphisms (SNPs) are available for use in genomics studies. Typically, investigators must choose a subset of SNPs from these databases to employ in their studies. The choice of subset is influenced by many factors, including estimated or known reliability of the SNP, biochemical factors, intellectual property, cost, and effectiveness of the subset for mapping genes or identifying disease loci. We present an evolutionary algorithm for multiobjective SNP selection. RESULTS: We implemented a modified version of the Strength-Pareto Evolutionary Algorithm (SPEA2) in Java. Our implementation, Multiobjective Analyzer for Genetic Marker Acquisition (MAGMA), approximates the set of optimal trade-off solutions for large problems in minutes. This set is very useful for the design of large studies, including those oriented towards disease identification, genetic mapping, population studies, and haplotype-block elucidation. CONCLUSION: Evolutionary algorithms are particularly suited for optimization problems that involve multiple objectives and a complex search space on which exact methods such as exhaustive enumeration cannot be applied. They provide flexibility with respect to the problem formulation if a problem description evolves or changes. Results are produced as a trade-off front, allowing the user to make informed decisions when prioritizing factors. MAGMA is open source and available at . Evolutionary algorithms are well suited for many other applications in genomics

Evolutionary Algorithms for

Many real-world problems involve two types of problem difficulty: i) multiple, conflicting objectives and ii) a highly complex search space. On the one hand, instead of a single optimal solution competing goals give rise to a set of compromise solutions, generally denoted as Pareto-optimal. In the absence of preference information, none of the corresponding trade-offs can be said to be better than the others. On the other hand, the search space can be too large and too complex to be solved by exact methods. Thus, efficient optimization strategies are required that are able to deal with both difficulties. Evolutionary algorithms possess several characteristics that are desirable for this kind of problem and make them preferable to classical optimization methods. In fact, various evolutionary approaches to multiobjective optimization have been proposed since 1985, capable of searching for multiple Paretooptimal solutions concurrently in a single simulation run. However, in spite of this variety, there is a lack of extensive comparative studies in the literature. Therefore, it has remained open up to now

BicAT: a biclustering analysis toolbox

Summary: Besides classical clustering methods such as hierarchical clustering, in recent years biclustering has become a popular approach to analyze biological data sets, e.g. gene expression data. The Biclustering Analysis Toolbox (BicAT) is a software platform for clustering-based data analysis that integrates various biclustering and clustering techniques in terms of a common graphical user interface. Furthermore, BicAT provides different facilities for data preparation, inspection and postprocessing such as discretization, filtering of biclusters according to specific criteria or gene pair analysis for constructing gene interconnection graphs. The possibility to use different biclustering algorithms inside a single graphical tool allows the user to compare clustering results and choose the algorithm that best fits a specific biological scenario. The toolbox is described in the context of gene expression analysis, but is also applicable to other types of data, e.g. data from proteomics or synthetic lethal experiments. Availability: The BicAT toolbox is freely available at and runs on all operating systems. The Java source code of the program and a developer's guide is provided on the website as well. Therefore, users may modify the program and add further algorithms or extensions. Contact: [email protected]

Articulating User Preferences in Many-Objective Problems by Sampling the Weighted Hypervolume

International audienceThe hypervolume indicator has become popular in recent years both for performance assessment and to guide the search of evolutionary multiobjective optimizers. Two critical research topics can be emphasized with respect to hyper\-volume-based search: (i) the hypervolume indicator inherently introduces a specific preference and the question is how arbitrary user preferences can be incorporated; (ii) the exact calculation of the hypervolume indicator is expensive and efficient approaches to tackle many-objective problems are needed. In two previous studies, we addressed both issues independently: a study proposed the weighted hypervolume indicator with which user-defined preferences can be articulated; other studies exist that propose to estimate the hypervolume indicator by Monte-Carlo sampling. Here, we combine these two approaches for the first time and extend them, i.e., we present an approach of sampling the weighted hypervolume to incorporate user-defined preferences into the search for problems with many objectives. In particular, we propose weight distribution functions to stress extreme solutions and to define preferred regions of the objective space in terms of so-called preference points; sampling them allows to tackle problems with many objectives. Experiments on several test functions with up to 25 objectives show the usefulness of the approach in terms of decision making and search

A systematic comparison and evaluation of biclustering methods for gene expression data

Motivation: In recent years, there have been various efforts to overcome the limitations of standard clustering approaches for the analysis of gene expression data by grouping genes and samples simultaneously. The underlying concept, which is often referred to as biclustering, allows to identify sets of genes sharing compatible expression patterns across subsets of samples, and its usefulness has been demonstrated for different organisms and datasets. Several biclustering methods have been proposed in the literature; however, it is not clear how the different techniques compare with each other with respect to the biological relevance of the clusters as well as with other characteristics such as robustness and sensitivity to noise. Accordingly, no guidelines concerning the choice of the biclustering method are currently available. Results: First, this paper provides a methodology for comparing and validating biclustering methods that includes a simple binary reference model. Although this model captures the essential features of most biclustering approaches, it is still simple enough to exactly determine all optimal groupings; to this end, we propose a fast divide-and-conquer algorithm (Bimax). Second, we evaluate the performance of five salient biclustering algorithms together with the reference model and a hierarchical clustering method on various synthetic and real datasets for Saccharomyces cerevisiae and Arabidopsis thaliana. The comparison reveals that (1) biclustering in general has advantages over a conventional hierarchical clustering approach, (2) there are considerable performance differences between the tested methods and (3) already the simple reference model delivers relevant patterns within all considered settings. Availability: The datasets used, the outcomes of the biclustering algorithms and the Bimax implementation for the reference model are available at Contact: [email protected] Supplementary information: Supplementary data are available a

Peningkatan Kemampuan Guru dalam Penerapan Model Pembelajaran pada Matematika melalui Supervisi Akademik di SDN 1 Setanggor

Tujuan utama dalam penelitian ini adalah untuk mengetahui Peningkatan Kemampuan Guru Dalam Penerapan Model Pembelajaran Pada Matematika Melalui Supervisi Akademik Di SDN 1 Setanggor Kecamatan Sukamulia Tahun Pelajaran 2018/2019. Subyek dalam penelitian ini adalah guru-guru kelas tinggi di SDN 1 Setanggor Kecamatan Sukamulia Tahun Pelajaran 2018/2019. Dalam penelitian Tindakan kepengawasan ini variabel yang diteliti adalah Peningkatan kemampuan guru dalam penerapan model pembelajaran pada SDN 1 Setanggor kecamatan Sukamulia. Berdasarkan  hasil penelitian ini menunjukkan bahwa penerapan model pembelajaran memiliki dampak positif dalam meningkatkan kemampuan guru hal ini dapat dilihat dari semakin mantapnya pemahaman guru dari pembinaan yang diberikan oleh kepala sekolah ( ketuntasan pembinaan meningkat dari siklus I, II, dan III ) yaitu masing-masing 33,33% ; 66,67 % ; 100 %  Pada siklus III ketuntasan pembinaan guru secara kelompok telah tercapai

Product Knowledge Graph Embedding for E-commerce

In this paper, we propose a new product knowledge graph (PKG) embedding approach for learning the intrinsic product relations as product knowledge for e-commerce. We define the key entities and summarize the pivotal product relations that are critical for general e-commerce applications including marketing, advertisement, search ranking and recommendation. We first provide a comprehensive comparison between PKG and ordinary knowledge graph (KG) and then illustrate why KG embedding methods are not suitable for PKG learning. We construct a self-attention-enhanced distributed representation learning model for learning PKG embeddings from raw customer activity data in an end-to-end fashion. We design an effective multi-task learning schema to fully leverage the multi-modal e-commerce data. The Poincare embedding is also employed to handle complex entity structures. We use a real-world dataset from grocery.walmart.com to evaluate the performances on knowledge completion, search ranking and recommendation. The proposed approach compares favourably to baselines in knowledge completion and downstream tasks