Large-Scale Multiobjective Evolutionary Algorithm Guided by Low-Dimensional Surrogates of Scalarization Functions.

Recently, computationally intensive multiobjective optimization problems have been efficiently solved by surrogate-assisted multiobjective evolutionary algorithms. However, most of those algorithms can only handle no more than 200 decision variables. As the number of decision variables increases further, unreliable surrogate models will result in a dramatic deterioration of their performance, which makes large-scale expensive multiobjective optimization challenging. To address this challenge, we develop a large-scale multiobjective evolutionary algorithm guided by low-dimensional surrogate models of scalarization functions. The proposed algorithm (termed LDS-AF) reduces the dimension of the original decision space based on principal component analysis, and then directly approximates the scalarization functions in a decompositionbased multiobjective evolutionary algorithm. With the help of a two-stage modeling strategy and convergence control strategy, LDS-AF can keep a good balance between convergence and diversity, and achieve a promising performance without being trapped in a local optimum prematurely. The experimental results on a set of test instances have demonstrated its superiority over eight state-of-the-art algorithms on multiobjective optimization problems with up to 1000 decision variables using only 500 real function evaluations.

Systematic evaluation of machine learning methods for identifying human-pathogen protein-protein interactions.

In recent years, high-throughput experimental techniques have significantly enhanced the accuracy and coverage of protein-protein interaction identification, including human-pathogen protein-protein interactions (HP-PPIs). Despite this progress, experimental methods are, in general, expensive in terms of both time and labour costs, especially considering that there are enormous amounts of potential protein-interacting partners. Developing computational methods to predict interactions between human and bacteria pathogen has thus become critical and meaningful, in both facilitating the detection of interactions and mining incomplete interaction maps. In this paper, we present a systematic evaluation of machine learning-based computational methods for human-bacterium protein-protein interactions (HB-PPIs). We first reviewed a vast number of publicly available databases of HP-PPIs and then critically evaluate the availability of these databases. Benefitting from its well-structured nature, we subsequently preprocess the data and identified six bacterium pathogens that could be used to study bacterium subjects in which a human was the host. Additionally, we thoroughly reviewed the literature on 'host-pathogen interactions' whereby existing models were summarized that we used to jointly study the impact of different feature representation algorithms and evaluate the performance of existing machine learning computational models. Owing to the abundance of sequence information and the limited scale of other protein-related information, we adopted the primary protocol from the literature and dedicated our analysis to a comprehensive assessment of sequence information and machine learning models. A systematic evaluation of machine learning models and a wide range of feature representation algorithms based on sequence information are presented as a comparison survey towards the prediction performance evaluation of HB-PPIs.

A Data Stream Ensemble Assisted Multifactorial Evolutionary Algorithm for Offline Data-Driven Dynamic Optimization.

Existing work on offline data-driven optimization mainly focuses on problems in static environments, and little attention has been paid to problems in dynamic environments. Offline data-driven optimization in dynamic environments is a challenging problem because the distribution of collected data varies over time, requiring surrogate models and optimal solutions tracking with time. This paper proposes a knowledge-transfer-based data-driven optimization algorithm to address these issues. First, an ensemble learning method is adopted to train surrogate models to leverage the knowledge of data in historical environments as well as adapt to new environments. Specifically, given data in a new environment, a model is constructed with the new data, and the preserved models of historical environments are further trained with the new data. Then, these models are considered to be base learners and combined as an ensemble surrogate model. After that, all base learners and the ensemble surrogate model are simultaneously optimized in a multitask environment for finding optimal solutions for real fitness functions. In this way, the optimization tasks in the previous environments can be used to accelerate the tracking of the optimum in the current environment. Since the ensemble model is the most accurate surrogate, we assign more individuals to the ensemble surrogate than its base learners. Empirical results on six dynamic optimization benchmark problems demonstrate the effectiveness of the proposed algorithm compared with four state-of-the-art offline data-driven optimization algorithms. Code is available at https://github.com/Peacefulyang/DSE_MFS.git.

Transfer Learning Based Co-Surrogate Assisted Evolutionary Bi-Objective Optimization for Objectives with Non-Uniform Evaluation Times.

Most existing multiobjective evolutionary algorithms (MOEAs) implicitly assume that each objective function can be evaluated within the same period of time. Typically. this is untenable in many real-world optimization scenarios where evaluation of different objectives involves different computer simulations or physical experiments with distinct time complexity. To address this issue, a transfer learning scheme based on surrogate-assisted evolutionary algorithms (SAEAs) is proposed, in which a co-surrogate is adopted to model the functional relationship between the fast and slow objective functions and a transferable instance selection method is introduced to acquire useful knowledge from the search process of the fast objective. Our experimental results on DTLZ and UF test suites demonstrate that the proposed algorithm is competitive for solving bi-objective optimization where objectives have non-uniform evaluation times.

A Self-Adaptive Response Strategy for Dynamic Multiobjective Evolutionary Optimization Based on Objective Space Decomposition.

Dynamic multiobjective optimization deals with simultaneous optimization of multiple conflicting objectives that change over time. Several response strategies for dynamic optimization have been proposed, which do not work well for all types of environmental changes. In this article, we propose a new dynamic multiobjective evolutionary algorithm based on objective space decomposition, in which the maxi-min fitness function is adopted for selection and a self-adaptive response strategy integrating a number of different response strategies is designed to handle unknown environmental changes. The self-adaptive response strategy can adaptively select one of the strategies according to their contributions to the tracking performance in the previous environments. Experimental results indicate that the proposed algorithm is competitive and promising for solving different DMOPs in the presence of unknown environmental changes. Meanwhile, the proposed algorithm is applied to solve the parameter tuning problem of a proportional integral derivative (PID) controller of a dynamic system, obtaining better control effect.

On the Effectiveness of Sampling for Evolutionary Optimization in Noisy Environments.

In real-world optimization tasks, the objective (i.e., fitness) function evaluation is often disturbed by noise due to a wide range of uncertainties. Evolutionary algorithms are often employed in noisy optimization, where reducing the negative effect of noise is a crucial issue. Sampling is a popular strategy for dealing with noise: to estimate the fitness of a solution, it evaluates the fitness multiple ([Formula: see text]) times independently and then uses the sample average to approximate the true fitness. Obviously, sampling can make the fitness estimation closer to the true value, but also increases the estimation cost. Previous studies mainly focused on empirical analysis and design of efficient sampling strategies, while the impact of sampling is unclear from a theoretical viewpoint. In this article, we show that sampling can speed up noisy evolutionary optimization exponentially via rigorous running time analysis. For the (1[Formula: see text]1)-EA solving the OneMax and the LeadingOnes problems under prior (e.g., one-bit) or posterior (e.g., additive Gaussian) noise, we prove that, under a high noise level, the running time can be reduced from exponential to polynomial by sampling. The analysis also shows that a gap of one on the value of [Formula: see text] for sampling can lead to an exponential difference on the expected running time, cautioning for a careful selection of [Formula: see text]. We further prove by using two illustrative examples that sampling can be more effective for noise handling than parent populations and threshold selection, two strategies that have shown to be robust to noise. Finally, we also show that sampling can be ineffective when noise does not bring a negative impact.

A time series driven decomposed evolutionary optimization approach for reconstructing large-scale gene regulatory networks based on fuzzy cognitive maps.

BACKGROUND: Reconstructing gene regulatory networks (GRNs) from expression data plays an important role in understanding the fundamental cellular processes and revealing the underlying relations among genes. Although many algorithms have been proposed to reconstruct GRNs, more rapid and efficient methods which can handle large-scale problems still need to be developed. The process of reconstructing GRNs can be formulated as an optimization problem, which is actually reconstructing GRNs from time series data, and the reconstructed GRNs have good ability to simulate the observed time series. This is a typical big optimization problem, since the number of variables needs to be optimized increases quadratically with the scale of GRNs, resulting an exponential increase in the number of candidate solutions. Thus, there is a legitimate need to devise methods capable of automatically reconstructing large-scale GRNs. RESULTS: In this paper, we use fuzzy cognitive maps (FCMs) to model GRNs, in which each node of FCMs represent a single gene. However, most of the current training algorithms for FCMs are only able to train FCMs with dozens of nodes. Here, a new evolutionary algorithm is proposed to train FCMs, which combines a dynamical multi-agent genetic algorithm (dMAGA) with the decomposition-based model, and termed as dMAGA-FCMD, which is able to deal with large-scale FCMs with up to 500 nodes. Both large-scale synthetic FCMs and the benchmark DREAM4 for reconstructing biological GRNs are used in the experiments to validate the performance of dMAGA-FCMD. CONCLUSIONS: The dMAGA-FCMD is compared with the other four algorithms which are all state-of-the-art FCM training algorithms, and the results show that the dMAGA-FCMD performs the best. In addition, the experimental results on FCMs with 500 nodes and DREAM4 project demonstrate that dMAGA-FCMD is capable of effectively and computationally efficiently training large-scale FCMs and GRNs.

Reduction strategies for hierarchical multi-label classification in protein function prediction.

BACKGROUND: Hierarchical Multi-Label Classification is a classification task where the classes to be predicted are hierarchically organized. Each instance can be assigned to classes belonging to more than one path in the hierarchy. This scenario is typically found in protein function prediction, considering that each protein may perform many functions, which can be further specialized into sub-functions. We present a new hierarchical multi-label classification method based on multiple neural networks for the task of protein function prediction. A set of neural networks are incrementally training, each being responsible for the prediction of the classes belonging to a given level. RESULTS: The method proposed here is an extension of our previous work. Here we use the neural network output of a level to complement the feature vectors used as input to train the neural network in the next level. We experimentally compare this novel method with several other reduction strategies, showing that it obtains the best predictive performance. Empirical results also show that the proposed method achieves better or comparable predictive performance when compared with state-of-the-art methods for hierarchical multi-label classification in the context of protein function prediction. CONCLUSIONS: The experiments showed that using the output in one level as input to the next level contributed to better classification results. We believe the method was able to learn the relationships between the protein functions during training, and this information was useful for classification. We also identified in which functional classes our method performed better.

Evolutionary non-linear modelling for selecting vaccines against antigenically variable viruses.

MOTIVATION: In vitro and in vivo selection of vaccines is time consuming, expensive and the selected vaccines may not be able to provide protection against broad-spectrum viruses because of emerging antigenically novel disease strains. A powerful computational model that incorporates these protein/DNA or RNA level fluctuations can effectively predict antigenically variant strains, and can minimize the amount of resources spent on exclusive serological testing of vaccines and make wide spectrum vaccines possible for many diseases. However, in silico vaccine prediction remains a grand challenge. To address the challenge, we investigate the use of linear and non-linear regression models to predict the antigenic similarity in foot-and-mouth disease virus strains and in influenza strains, where the structure and parameters of the non-linear model are optimized using an evolutionary algorithm (EA). In addition, we examine two different scoring methods for weighting the type of amino acid substitutions in the linear and non-linear models. We also test our models with some unseen data. RESULTS: We achieved the best prediction results on three datasets of SAT2 (Foot-and-Mouth disease), two datasets of serotype A (Foot-and-Mouth disease) and two datasets of influenza when the scoring method based on biochemical properties of amino acids is employed in combination with a non-linear regression model. Models based on substitutions in the antigenic areas performed better than those that took the entire exposed viral capsid proteins. A majority of the non-linear regression models optimi Z: ed with the EA: performed better than the linear and non-linear models whose parameters are estimated using the least-squares method. In addition, for the best models, optimi Z: ed non-linear regression models consist of more terms than their linear counterparts, implying a non-linear nature of influences of amino acid substitutions. Our models were also tested on five recently generated FMDV datasets and the best model was able to achieve an 80% agreement rate.

DRL-Searcher: A Unified Approach to Multirobot Efficient Search for a Moving Target.

This article studies the multirobot efficient search (MuRES) for a nonadversarial moving target problem, whose objective is usually defined as either minimizing the target's expected capture time or maximizing the target's capture probability within a given time budget. Different from canonical MuRES algorithms, which target only one specific objective, our proposed algorithm, named distributional reinforcement learning-based searcher (DRL-Searcher), serves as a unified solution to both MuRES objectives. DRL-Searcher employs distributional reinforcement learning (DRL) to evaluate the full distribution of a given search policy's return, that is, the target's capture time, and thereafter makes improvements with respect to the particularly specified objective. We further adapt DRL-Searcher to the use case without the target's real-time location information, where only the probabilistic target belief (PTB) information is provided. Lastly, the recency reward is designed for implicit coordination among multiple robots. Comparative simulation results in a range of MuRES test environments show the superior performance of DRL-Searcher to state of the arts. Additionally, we deploy DRL-Searcher to a real multirobot system for moving target search in a self-constructed indoor environment with satisfying results.

Learning to Guide Particle Search for Dynamic Multiobjective Optimization.

Dynamic multiobjective optimization problems (DMOPs) are characterized by multiple objectives that change over time in varying environments. More specifically, environmental changes can be described as various dynamics. However, it is difficult for existing dynamic multiobjective algorithms (DMOAs) to handle DMOPs due to their inability to learn in different environments to guide the search. Besides, solving DMOPs is typically an online task, requiring low computational cost of a DMOA. To address the above challenges, we propose a particle search guidance network (PSGN), capable of directing individuals' search actions, including learning target selection and acceleration coefficient control. PSGN can learn the actions that should be taken in each environment through rewarding or punishing the network by reinforcement learning. Thus, PSGN is capable of tackling DMOPs of various dynamics. Additionally, we efficiently adjust PSGN hidden nodes and update the output weights in an incremental learning way, enabling PSGN to direct particle search at a low computational cost. We compare the proposed PSGN with seven state-of-the-art algorithms, and the excellent performance of PSGN verifies that it can handle DMOPs of various dynamics in a computationally very efficient way.

IM-IAD: Industrial Image Anomaly Detection Benchmark in Manufacturing.

Image anomaly detection (IAD) is an emerging and vital computer vision task in industrial manufacturing (IM). Recently, many advanced algorithms have been reported, but their performance deviates considerably with various IM settings. We realize that the lack of a uniform IM benchmark is hindering the development and usage of IAD methods in real-world applications. In addition, it is difficult for researchers to analyze IAD algorithms without a uniform benchmark. To solve this problem, we propose a uniform IM benchmark, for the first time, to assess how well these algorithms perform, which includes various levels of supervision (unsupervised versus fully supervised), learning paradigms (few-shot, continual and noisy label), and efficiency (memory usage and inference speed). Then, we construct a comprehensive IAD benchmark (IM-IAD), which includes 19 algorithms on seven major datasets with a uniform setting. Extensive experiments (17 017 total) on IM-IAD provide in-depth insights into IAD algorithm redesign or selection. Moreover, the proposed IM-IAD benchmark challenges existing algorithms and suggests future research directions. For reproducibility and accessibility, the source code is uploaded to the website: https://github.com/M-3LAB/open-iad.

Evolution by adapting surrogates.

To deal with complex optimization problems plagued with computationally expensive fitness functions, the use of surrogates to replace the original functions within the evolutionary framework is becoming a common practice. However, the appropriate datacentric approximation methodology to use for the construction of surrogate model would depend largely on the nature of the problem of interest, which varies from fitness landscape and state of the evolutionary search, to the characteristics of search algorithm used. This has given rise to the plethora of surrogate-assisted evolutionary frameworks proposed in the literature with ad hoc approximation/surrogate modeling methodologies considered. Since prior knowledge on the suitability of the data centric approximation methodology to use in surrogate-assisted evolutionary optimization is typically unavailable beforehand, this paper presents a novel evolutionary framework with the evolvability learning of surrogates (EvoLS) operating on multiple diverse approximation methodologies in the search. Further, in contrast to the common use of fitness prediction error as a criterion for the selection of surrogates, the concept of evolvability to indicate the productivity or suitability of an approximation methodology that brings about fitness improvement in the evolutionary search is introduced as the basis for adaptation. The backbone of the proposed EvoLS is a statistical learning scheme to determine the evolvability of each approximation methodology while the search progresses online. For each individual solution, the most productive approximation methodology is inferred, that is, the method with highest evolvability measure. Fitness improving surrogates are subsequently constructed for use within a trust-region enabled local search strategy, leading to the self-configuration of a surrogate-assisted memetic algorithm for solving computationally expensive problems. A numerical study of EvoLS on commonly used benchmark problems and a real-world computationally expensive aerodynamic car rear design problem highlights the efficacy of the proposed EvoLS in attaining reliable, high quality, and efficient performance under a limited computational budget.

Adaptive Prototypical Networks With Label Words and Joint Representation Learning for Few-Shot Relation Classification.

Relation classification (RC) task is one of fundamental tasks of information extraction, aiming to detect the relation information between entity pairs in unstructured natural language text and generate structured data in the form of entity-relation triple. Although distant supervision methods can effectively alleviate the problem of lack of training data in supervised learning, they also introduce noise into the data and still cannot fundamentally solve the long-tail distribution problem of the training instances. In order to enable the neural network to learn new knowledge through few instances such as humans, this work focuses on few-shot relation classification (FSRC), where a classifier should generalize to new classes that have not been seen in the training set, given only a number of samples for each class. To make full use of the existing information and get a better feature representation for each instance, we propose to encode each class prototype in an adaptive way from two aspects. First, based on the prototypical networks, we propose an adaptive mixture mechanism to add label words to the representation of the class prototype, which, to the best of our knowledge, is the first attempt to integrate the label information into features of the support samples of each class so as to get more interactive class prototypes. Second, to more reasonably measure the distances between samples of each category, we introduce a loss function for joint representation learning (JRL) to encode each support instance in an adaptive manner. Extensive experiments have been conducted on FewRel under different few-shot (FS) settings, and the results show that the proposed adaptive prototypical networks with label words and JRL has not only achieved significant improvements in accuracy but also increased the generalization ability of FSRC.

Performance Indicator-Based Adaptive Model Selection for Offline Data-Driven Multiobjective Evolutionary Optimization.

A number of real-world multiobjective optimization problems (MOPs) are driven by the data from experiments or computational simulations. In some cases, no new data can be sampled during the optimization process and only a certain amount of data can be sampled before optimization starts. Such problems are known as offline data-driven MOPs. Although multiple surrogate models approximating each objective function are able to replace the real fitness evaluations in evolutionary algorithms (EAs), their approximation errors are easily accumulated and therefore, mislead the solution ranking. To mitigate this issue, a new surrogate-assisted indicator-based EA for solving offline data-driven multiobjective problems is proposed. The proposed algorithm adopts an indicator-based selection EA as the baseline optimizer due to its selection robustness to the approximation errors of surrogate models. Both the Kriging models and radial basis function networks (RBFNs) are employed as surrogate models. An adaptive model selection mechanism is designed to choose the right type of models according to a maximum acceptable approximation error that is less likely to mislead the indicator-based search. The main idea is that when the uncertainty of the Kriging models exceeds the acceptable error, the proposed algorithm selects RBFNs as the surrogate models. The results comparing with state-of-the-art algorithms on benchmark problems with up to ten objectives indicate that the proposed algorithm is effective on offline data-driven optimization problems with up to 20 and 30 decision variables.

A Generic Self-Supervised Framework of Learning Invariant Discriminative Features.

Self-supervised learning (SSL) has become a popular method for generating invariant representations without the need for human annotations. Nonetheless, the desired invariant representation is achieved by utilizing prior online transformation functions on the input data. As a result, each SSL framework is customized for a particular data type, for example, visual data, and further modifications are required if it is used for other dataset types. On the other hand, autoencoder (AE), which is a generic and widely applicable framework, mainly focuses on dimension reduction and is not suited for learning invariant representation. This article proposes a generic SSL framework based on a constrained self-labeling assignment process that prevents degenerate solutions. Specifically, the prior transformation functions are replaced with a self-transformation mechanism, derived through an unsupervised training process of adversarial training, for imposing invariant representations. Via the self-transformation mechanism, pairs of augmented instances can be generated from the same input data. Finally, a training objective based on contrastive learning is designed by leveraging both the self-labeling assignment and the self-transformation mechanism. Despite the fact that the self-transformation process is very generic, the proposed training strategy outperforms a majority of state-of-the-art representation learning methods based on AE structures. To validate the performance of our method, we conduct experiments on four types of data, namely visual, audio, text, and mass spectrometry data and compare them in terms of four quantitative metrics. Our comparison results demonstrate that the proposed method is effective and robust in identifying patterns within the tested datasets.

Solution Set Augmentation for Knee Identification in Multiobjective Decision Analysis.

In multiobjective decision making, most knee identification algorithms implicitly assume that the given solutions are well distributed and can provide sufficient information for identifying knee solutions. However, this assumption may fail to hold when the number of objectives is large or when the shape of the Pareto front is complex. To address the above issues, we propose a knee-oriented solution augmentation (KSA) framework that converts the Pareto front into a multimodal auxiliary function whose basins correspond to the knee regions of the Pareto front. The auxiliary function is then approximated using a surrogate and its basins are identified by a peak detection method. Additional solutions are then generated in the detected basins in the objective space and mapped to the decision space with the help of an inverse model. These solutions are evaluated by the original objective functions and added to the given solution set. To assess the quality of the augmented solution set, a measurement is proposed for the verification of knee solutions when the true Pareto front is unknown. The effectiveness of KSA is verified on widely used benchmark problems and successfully applied to a hybrid electric vehicle controller design problem.

Evolutionary Large-Scale Dynamic Optimization Using Bilevel Variable Grouping.

Variable grouping provides an efficient approach to large-scale optimization, and multipopulation strategies are effective for both large-scale optimization and dynamic optimization. However, variable grouping is not well studied in large-scale dynamic optimization when cooperating with multipopulation strategies. Specifically, when the numbers/sizes of the variable subcomponents are large, the performance of the algorithms will be substantially degraded. To address this issue, we propose a bilevel variable grouping (BLVG)-based framework. First, the primary grouping applies a state-of-the-art variable grouping method based on variable interaction analysis to group the variables into subcomponents. Second, the secondary grouping further groups the subcomponents into variable cells, that is, combination variable cells and decomposition variable cells. We then tailor a multipopulation strategy to process the two types of variable cells efficiently in a cooperative coevolutionary (CC) way. As indicated by the empirical study on large-scale dynamic optimization problems (DOPs) of up to 300 dimensions, the proposed framework outperforms several state-of-the-art frameworks for large-scale dynamic optimization.

Efficient Surrogate Modeling Method for Evolutionary Algorithm to Solve Bilevel Optimization Problems.

The purpose of this study was to develop an evolutionary algorithm (EA) with bilevel surrogate modeling, called BL-SAEA, for tackling bilevel optimization problems (BLOPs), in which an upper level problem is to be solved subject to the optimality of a corresponding lower level problem. The motivation of this article is that the extensive lower level optimization required by each upper level solution consumes too many function evaluations, leading to poor optimization performance of EAs. To this end, during the upper level optimization, the BL-SAEA builds an upper level surrogate model to select several promising upper level solutions for the lower level optimization. Because only a small number of upper level solutions require the lower level optimization, the number of function evaluations can be considerably reduced. During the lower level optimization, the BL-SAEA constructs multiple lower level surrogate models to initialize the population of the lower level optimization, thus further decreasing the number of function evaluations. Experimental results on two widely used benchmarks and two real-world BLOPs demonstrate the superiority of our proposed algorithm over six state-of-the-art algorithms in terms of effectiveness and efficiency.

Calcium control of triphasic hippocampal STDP.

Synaptic plasticity is believed to represent the neural correlate of mammalian learning and memory function. It has been demonstrated that changes in synaptic conductance can be induced by approximately synchronous pairings of pre- and post- synaptic action potentials delivered at low frequencies. It has also been established that NMDAr-dependent calcium influx into dendritic spines represents a critical signal for plasticity induction, and can account for this spike-timing dependent plasticity (STDP) as well as experimental data obtained using other stimulation protocols. However, subsequent empirical studies have delineated a more complex relationship between spike-timing, firing rate, stimulus duration and post-synaptic bursting in dictating changes in the conductance of hippocampal excitatory synapses. Here, we present a detailed biophysical model of single dendritic spines on a CA1 pyramidal neuron, describe the NMDAr-dependent calcium influx generated by different stimulation protocols, and construct a parsimonious model of calcium driven kinase and phosphatase dynamics that dictate the probability of stochastic transitions between binary synaptic weight states in a Markov model. We subsequently demonstrate that this approach can account for a range of empirical observations regarding the dynamics of synaptic plasticity induced by different stimulation protocols, under regimes of pharmacological blockade and metaplasticity. Finally, we highlight the strengths and weaknesses of this parsimonious, unified computational synaptic plasticity model, discuss differences between the properties of cortical and hippocampal plasticity highlighted by the experimental literature, and the manner in which further empirical and theoretical research might elucidate the cellular basis of mammalian learning and memory function.