scholarly journals Efficiently Sparse Listing of Classes of Optimal Cophylogeny Reconciliations

2021 ◽  
Author(s):  
Yishu Wang ◽  
Arnaud Mary ◽  
Marie-France Sagot ◽  
Blerina Sinaimeri
Keyword(s):  
Optimization Problem ◽  
Practical Importance ◽  
Biological Information ◽  
Optimal Solutions ◽  
Powerful Method ◽  
New Approach ◽  
Significant Research ◽  
Whole Space ◽  
Polynomial Delay ◽  
Host Parasite

Abstract Background: Cophylogeny reconciliation is a powerful method for analyzing host-parasite (or host-symbiont) co-evolution. It models co-evolution as an optimization problem where the set of all optimal solutions may represent different biological scenarios which thus need to be analyzed separately. Despite the significant research done in the area, few approaches have addressed the problem of helping the biologist deal with the often huge space of optimal solutions.Results: In this paper, we propose a new approach to tackle this problem. We introduce three different criteria under which two solutions may be considered biologically equivalent, and then we propose polynomial-delay algorithms that enumerate only one representative per equivalence class (without listing all the solutions).Conclusions: Our results are of both theoretical and practical importance. Indeed, as shown by the experiments, we are able to significantly reduce the space of optimal solutions while still maintaining important biological information about the whole space.

scholarly journals A new approach to optimality in a class of nonconvex smooth optimization problems

2018 ◽  
Vol 34 (1) ◽  
pp. 01-07
Author(s):  
TADEUSZ ANTCZAK ◽  
Keyword(s):  
Approximation Method ◽  
Optimization Problem ◽  
Optimization Problems ◽  
Extremum Problem ◽  
Optimal Solutions ◽  
New Approach ◽  
Smooth Optimization

In this paper, a new approximation method for a characterization of optimal solutions in a class of nonconvex differentiable optimization problems is introduced. In this method, an auxiliary optimization problem is constructed for the considered nonconvex extremum problem. The equivalence between optimal solutions in the considered differentiable extremum problem and its approximated optimization problem is established under (Φ, ρ)-invexity hypotheses.

scholarly journals A Fast and Exact Greedy Algorithm for the Core–Periphery Problem

Symmetry ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 94 ◽  
Author(s):  
Dario Fasino ◽  
Franca Rinaldi
Keyword(s):  
Structural Analysis ◽  
Optimization Problem ◽  
Polynomial Time Algorithm ◽  
Time Algorithm ◽  
Combinatorial Optimization Problem ◽  
Connected Subgraph ◽  
Optimal Solutions ◽  
The Core ◽  
Core Set ◽  
Key Concepts

The core–periphery structure is one of the key concepts in the structural analysis of complex networks. It consists of a partitioning of the node set of a given graph or network into two groups, called core and periphery, where the core nodes induce a well-connected subgraph and share connections with peripheral nodes, while the peripheral nodes are loosely connected to the core nodes and other peripheral nodes. We propose a polynomial-time algorithm to detect core–periphery structures in networks having a symmetric adjacency matrix. The core set is defined as the solution of a combinatorial optimization problem, which has a pleasant symmetry with respect to graph complementation. We provide a complete description of the optimal solutions to that problem and an exact and efficient algorithm to compute them. The proposed approach is extended to networks with loops and oriented edges. Numerical simulations are carried out on both synthetic and real-world networks to demonstrate the effectiveness and practicability of the proposed algorithm.

Adaptive Grouping Brain Storm Optimization for Multimodal Optimization Problems

2021 ◽  
Vol 12 (4) ◽  
pp. 81-100
Author(s):  
Yao Peng ◽  
Zepeng Shen ◽  
Shiqi Wang
Keyword(s):  
Optimization Problem ◽  
Optimization Problems ◽  
Optimal Algorithm ◽  
Peak Detection ◽  
Multimodal Optimization ◽  
Optimal Solutions ◽  
Grouping Strategy ◽  
Different Dimensions ◽  
Global Optimal ◽  
Localization Ability

Multimodal optimization problem exists in multiple global and many local optimal solutions. The difficulty of solving these problems is finding as many local optimal peaks as possible on the premise of ensuring global optimal precision. This article presents adaptive grouping brainstorm optimization (AGBSO) for solving these problems. In this article, adaptive grouping strategy is proposed for achieving adaptive grouping without providing any prior knowledge by users. For enhancing the diversity and accuracy of the optimal algorithm, elite reservation strategy is proposed to put central particles into an elite pool, and peak detection strategy is proposed to delete particles far from optimal peaks in the elite pool. Finally, this article uses testing functions with different dimensions to compare the convergence, accuracy, and diversity of AGBSO with BSO. Experiments verify that AGBSO has great localization ability for local optimal solutions while ensuring the accuracy of the global optimal solutions.

scholarly journals New Cancer Stochastic Models Involving Both Hereditary and Nonhereditary Cancer Cases: A New Approach

2013 ◽  
Vol 2013 ◽  
pp. 1-19
Author(s):  
Wai-Yuan Tan ◽  
Hong Zhou
Keyword(s):  
Cancer Incidence ◽  
Stochastic Models ◽  
Biological Information ◽  
Cancer Genes ◽  
New Approach ◽  
Human Cancers ◽  
Seer Data ◽  
Sampling Procedures ◽  
And Control ◽  
Better Than

To incorporate biologically observed epidemics into multistage models of carcinogenesis, in this paper we have developed new stochastic models for human cancers. We have further incorporated genetic segregation of cancer genes into these models to derive generalized mixture models for cancer incidence. Based on these models we have developed a generalized Bayesian approach to estimate the parameters and to predict cancer incidence via Gibbs sampling procedures. We have applied these models to fit and analyze the SEER data of human eye cancers from NCI/NIH. Our results indicate that the models not only provide a logical avenue to incorporate biological information but also fit the data much better than other models. These models would not only provide more insights into human cancers but also would provide useful guidance for its prevention and control and for prediction of future cancer cases.

scholarly journals Brain Cancer Prediction Based on Novel Interpretable Ensemble Gene Selection Algorithm and Classifier

Diagnostics ◽  
2021 ◽  
Vol 11 (10) ◽  
pp. 1936
Author(s):  
Abdulqader M. Almars ◽  
Majed Alwateer ◽  
Mohammed Qaraad ◽  
Souad Amjad ◽  
Hanaa Fathi ◽  
...  
Keyword(s):  
Gene Selection ◽  
Ensemble Methods ◽  
Cancer Classification ◽  
Biological Information ◽  
Gradient Boosting ◽  
New Approach ◽  
Biological Studies ◽  
Abnormal Cells ◽  
Gene Selection Algorithm ◽  
Gene Expression Levels

The growth of abnormal cells in the brain causes human brain tumors. Identifying the type of tumor is crucial for the prognosis and treatment of the patient. Data from cancer microarrays typically include fewer samples with many gene expression levels as features, reflecting the curse of dimensionality and making classifying data from microarrays challenging. In most of the examined studies, cancer classification (Malignant and benign) accuracy was examined without disclosing biological information related to the classification process. A new approach was proposed to bridge the gap between cancer classification and the interpretation of the biological studies of the genes implicated in cancer. This study aims to develop a new hybrid model for cancer classification (by using feature selection mRMRe as a key step to improve the performance of classification methods and a distributed hyperparameter optimization for gradient boosting ensemble methods). To evaluate the proposed method, NB, RF, and SVM classifiers have been chosen. In terms of the AUC, sensitivity, and specificity, the optimized CatBoost classifier performed better than the optimized XGBoost in cross-validation 5, 6, 8, and 10. With an accuracy of 0.91±0.12, the optimized CatBoost classifier is more accurate than the CatBoost classifier without optimization, which is 0.81± 0.24. By using hybrid algorithms, SVM, RF, and NB automatically become more accurate. Furthermore, in terms of accuracy, SVM and RF (0.97±0.08) achieve equivalent and higher classification accuracy than NB (0.91±0.12). The findings of relevant biomedical studies confirm the findings of the selected genes.

Space Contraction and Partition Algorithm for Combinatorial Optimization

2011 ◽  
Vol 421 ◽  
pp. 559-563
Author(s):  
Yong Chao Gao ◽  
Li Mei Liu ◽  
Heng Qian ◽  
Ding Wang
Keyword(s):  
Combinatorial Optimization ◽  
Optimization Problem ◽  
Optimization Problems ◽  
Solution Space ◽  
Search Space ◽  
Small Scale ◽  
Optimal Solutions ◽  
Solution Quality ◽  
Intelligent Algorithms ◽  
Combinatorial Optimization Problems

The scale and complexity of search space are important factors deciding the solving difficulty of an optimization problem. The information of solution space may lead searching to optimal solutions. Based on this, an algorithm for combinatorial optimization is proposed. This algorithm makes use of the good solutions found by intelligent algorithms, contracts the search space and partitions it into one or several optimal regions by backbones of combinatorial optimization solutions. And optimization of small-scale problems is carried out in optimal regions. Statistical analysis is not necessary before or through the solving process in this algorithm, and solution information is used to estimate the landscape of search space, which enhances the speed of solving and solution quality. The algorithm breaks a new path for solving combinatorial optimization problems, and the results of experiments also testify its efficiency.

scholarly journals Evaluation Method of Multiobjective Functions’ Combination and Its Application in Hydrological Model Evaluation

2020 ◽  
Vol 2020 ◽  
pp. 1-23 ◽  
Author(s):  
Jiuyuan Huo ◽  
Liqun Liu
Keyword(s):  
Objective Function ◽  
Parameter Optimization ◽  
Optimization Problem ◽  
Hydrological Model ◽  
Pareto Optimal ◽  
Pareto Optimal Solutions ◽  
Optimal Solutions ◽  
Objective Functions ◽  
Hydrological Forecasting ◽  
Model Parameter Optimization

Parameter optimization of a hydrological model is intrinsically a high dimensional, nonlinear, multivariable, combinatorial optimization problem which involves a set of different objectives. Currently, the assessment of optimization results for the hydrological model is usually made through calculations and comparisons of objective function values of simulated and observed variables. Thus, the proper selection of objective functions’ combination for model parameter optimization has an important impact on the hydrological forecasting. There exist various objective functions, and how to analyze and evaluate the objective function combinations for selecting the optimal parameters has not been studied in depth. Therefore, to select the proper objective function combination which can balance the trade-off among various design objectives and achieve the overall best benefit, a simple and convenient framework for the comparison of the influence of different objective function combinations on the optimization results is urgently needed. In this paper, various objective functions related to parameters optimization of hydrological models were collected from the literature and constructed to nine combinations. Then, a selection and evaluation framework of objective functions is proposed for hydrological model parameter optimization, in which a multiobjective artificial bee colony algorithm named RMOABC is employed to optimize the hydrological model and obtain the Pareto optimal solutions. The parameter optimization problem of the Xinanjiang hydrological model was taken as the application case for long-term runoff prediction in the Heihe River basin. Finally, the technique for order preference by similarity to ideal solution (TOPSIS) based on the entropy theory is adapted to sort the Pareto optimal solutions to compare these combinations of objective functions and obtain the comprehensive optimal objective functions’ combination. The experiments results demonstrate that the combination 2 of objective functions can provide more comprehensive and reliable dominant options (i.e., parameter sets) for practical hydrological forecasting in the study area. The entropy-based method has been proved that it is effective to analyze and evaluate the performance of different combinations of objective functions and can provide more comprehensive and impersonal decision support for hydrological forecasting.

scholarly journals Lipschitz and differentiable dependence of solutions on a parameter in a scalarization method

1987 ◽  
Vol 42 (3) ◽  
pp. 353-364 ◽  
Author(s):  
Alicia Sterna-Karwat
Keyword(s):  
Vector Optimization ◽  
Normed Space ◽  
Convex Cone ◽  
Optimization Problem ◽  
Vector Optimization Problem ◽  
Optimal Solutions ◽  
Scalar Problem ◽  
Lipschitz Continuous ◽  
Scalarization Method ◽  
Convexity Assumptions

AbstractThis paper is concerned with a vector optimization problem set in a normed space where optimality is defined through a convex cone. The vector problem can be solved using a parametrized scalar problem. Under some convexity assumptions, it is shown that dependence of optimal solutions on the parameter is Lipschitz continuous. Hence differentiable dependence on the solutions on the parameter is derived.

scholarly journals Control Force Recalculation for Balancing Problems

2019 ◽  
Vol 19 (05) ◽  
pp. 1941010
Author(s):  
Bálint Bodor ◽  
László Bencsik ◽  
Tamás Insperger
Keyword(s):  
Optimization Problem ◽  
Control Mechanism ◽  
Numerical Differentiation ◽  
Open Loop ◽  
Second Step ◽  
Control Force ◽  
New Approach ◽  
Numerical Errors ◽  
Linearized System ◽  
Control Forces

Understanding the mechanism of human balancing is a scientifically challenging task. In order to describe the nature of the underlying control mechanism, the control force has to be determined experimentally. A main feature of balancing tasks is that the open-loop system is unstable. Therefore, reconstruction of the trajectories using the measured control force is difficult, since measurement inaccuracies, noise and numerical errors increase exponentially with time. In order to overcome this problem, a new approach is proposed in this paper. In the presented technique, first the solution of the linearized system is used. As a second step, an optimization problem is solved which is based on a variational principle. A main advantage of the method is that there is no need for the numerical differentiation of the measured data for the calculation of the control forces, which is the main source of the numerical errors. The method is demonstrated in case of a human stick balancing.

scholarly journals Location histogram privacy by Sensitive Location Hiding and Target Histogram Avoidance/Resemblance

2019 ◽  
Vol 62 (7) ◽  
pp. 2613-2651
Author(s):  
Grigorios Loukides ◽  
George Theodorakopoulos
Keyword(s):  
Price Discrimination ◽  
Optimization Problem ◽  
Optimal Algorithm ◽  
Search Space ◽  
Greedy Heuristic ◽  
Optimal Solutions ◽  
Area Of Interest ◽  
Minority Member ◽  
Specific Search

AbstractA location histogram is comprised of the number of times a user has visited locations as they move in an area of interest, and it is often obtained from the user in the context of applications such as recommendation and advertising. However, a location histogram that leaves a user’s computer or device may threaten privacy when it contains visits to locations that the user does not want to disclose (sensitive locations), or when it can be used to profile the user in a way that leads to price discrimination and unsolicited advertising (e.g., as “wealthy” or “minority member”). Our work introduces two privacy notions to protect a location histogram from these threats: Sensitive Location Hiding, which aims at concealing all visits to sensitive locations, and Target Avoidance/Resemblance, which aims at concealing the similarity/dissimilarity of the user’s histogram to a target histogram that corresponds to an undesired/desired profile. We formulate an optimization problem around each notion: Sensitive Location Hiding ($${ SLH}$$SLH), which seeks to construct a histogram that is as similar as possible to the user’s histogram but associates all visits with nonsensitive locations, and Target Avoidance/Resemblance ($${ TA}$$TA/$${ TR}$$TR), which seeks to construct a histogram that is as dissimilar/similar as possible to a given target histogram but remains useful for getting a good response from the application that analyzes the histogram. We develop an optimal algorithm for each notion, which operates on a notion-specific search space graph and finds a shortest or longest path in the graph that corresponds to a solution histogram. In addition, we develop a greedy heuristic for the $${ TA}$$TA/$${ TR}$$TR problem, which operates directly on a user’s histogram. Our experiments demonstrate that all algorithms are effective at preserving the distribution of locations in a histogram and the quality of location recommendation. They also demonstrate that the heuristic produces near-optimal solutions while being orders of magnitude faster than the optimal algorithm for $${ TA}$$TA/$${ TR}$$TR.

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