arXiv subjects

Mengjie Zhang

Publications and source records attributed to Mengjie Zhang.

At least 127 records · Page 7Linked to original sources

arXiv2020

Multi-Objective Genetic Programming for Manifold Learning: Balancing Quality and Dimensionality

Manifold learning techniques have become increasingly valuable as data continues to grow in size. By discovering a lower-dimensional representation (embedding) of the structure of a dataset, manifold learning algorithms can substantially reduce the dimensionality of a dataset while preserving as much information as possible. However, state-of-the-art manifold learning algorithms are opaque in how they perform this transformation. Understanding the way in which the embedding relates to the original high-dimensional space is critical in exploratory data analysis. We previously proposed a Genetic Programming method that performed manifold learning by evolving mappings that are transparent and interpretable. This method required the dimensionality of the embedding to be known a priori, which makes it hard to use when little is known about a dataset. In this paper, we substantially extend our previous work, by introducing a multi-objective approach that automatically balances the competing objectives of manifold quality and dimensionality. Our proposed approach is competitive with a range of baseline and state-of-the-art manifold learning methods, while also providing a range (front) of solutions that give different trade-offs between quality and dimensionality. Furthermore, the learned models are shown to often be simple and efficient, utilising only a small number of features in an interpretable manner.

cs.NE↗

arXiv2019

Extremal functions for a class of trace Trudinger-Moser inequalities

In this paper, we concern trace Trudinger-Moser inequalities on a compact Riemann surface with smooth boundary. This kind of inequalities were extensively studied by Osgood-Phillips-Sarnak [24], Liu [20], Li-Liu [17], Yang [31, 32] and others. We establish several trace Trudinger-Moser inequalities and obtain the corresponding extremals via the method of blow-up analysis. The results in the current paper generalize those of Li-Liu [17] and Yang [32, 33].

math.AP↗

arXiv2019

Genetic Programming Hyper-Heuristics with Vehicle Collaboration for Uncertain Capacitated Arc Routing Problems

Due to its direct relevance to post-disaster operations, meter reading and civil refuse collection, the Uncertain Capacitated Arc Routing Problem (UCARP) is an important optimisation problem. Stochastic models are critical to study as they more accurately represent the real-world than their deterministic counterparts. Although there have been extensive studies in solving routing problems under uncertainty, very few have considered UCARP, and none consider collaboration between vehicles to handle the negative effects of uncertainty. This paper proposes a novel Solution Construction Procedure (SCP) that generates solutions to UCARP within a collaborative, multi-vehicle framework. It consists of two types of collaborative activities: one when a vehicle unexpectedly expends capacity (\emph{route failure}), and the other during the refill process. Then, we propose a Genetic Programming Hyper-Heuristic (GPHH) algorithm to evolve the routing policy used within the collaborative framework. The experimental studies show that the new heuristic with vehicle collaboration and GP-evolved routing policy significantly outperforms the compared state-of-the-art algorithms on commonly studied test problems. This is shown to be especially true on instances with larger numbers of tasks and vehicles. This clearly shows the advantage of vehicle collaboration in handling the uncertain environment, and the effectiveness of the newly proposed algorithm.

cs.NE↗

arXiv2019

A Trudinger-Moser inequality involving L^p -norm on a closed Riemann surface

In this paper, using the method of blow-up analysis, we obtained a Trudinger-Moser inequality involving L p -norm on a closed Riemann surface and proved the existence of an extremal function for the corresponding Trudinger-Moser functional. This extends an early result of Yang [27]. Similar result in the Euclidean space was also established by Lu-Yang [17].

math.AP↗

arXiv2019

Genetic Programming for Evolving Similarity Functions for Clustering: Representations and Analysis

Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to decide which instances to assign to the same cluster. These similarity measures are generally pre-defined and cannot be easily tailored to the properties of a particular dataset, which leads to limitations in the quality and the interpretability of the clusters produced. In this paper, we propose a new approach to automatically evolving similarity functions for a given clustering algorithm by using genetic programming. We introduce a new genetic programming-based method which automatically selects a small subset of features (feature selection) and then combines them using a variety of functions (feature construction) to produce dynamic and flexible similarity functions that are specifically designed for a given dataset. We demonstrate how the evolved similarity functions can be used to perform clustering using a graph-based representation. The results of a variety of experiments across a range of large, high-dimensional datasets show that the proposed approach can achieve higher and more consistent performance than the benchmark methods. We further extend the proposed approach to automatically produce multiple complementary similarity functions by using a multi-tree approach, which gives further performance improvements. We also analyse the interpretability and structure of the automatically evolved similarity functions to provide insight into how and why they are superior to standard distance metrics.

cs.NE↗

arXiv2019

Genetic Programming and Gradient Descent: A Memetic Approach to Binary Image Classification

Image classification is an essential task in computer vision, which aims to categorise a set of images into different groups based on some visual criteria. Existing methods, such as convolutional neural networks, have been successfully utilised to perform image classification. However, such methods often require human intervention to design a model. Furthermore, such models are difficult to interpret and it is challenging to analyse the patterns of different classes. This paper presents a hybrid (memetic) approach combining genetic programming (GP) and Gradient-based optimisation for image classification to overcome the limitations mentioned. The performance of the proposed method is compared to a baseline version (without local search) on four binary classification image datasets to provide an insight into the usefulness of local search mechanisms for enhancing the performance of GP.

cs.NE↗

arXiv2019

Improving the Results of De novo Peptide Identification via Tandem Mass Spectrometry Using a Genetic Programming-based Scoring Function for Re-ranking Peptide-Spectrum Matches

De novo peptide sequencing algorithms have been widely used in proteomics to analyse tandem mass spectra (MS/MS) and assign them to peptides, but quality-control methods to evaluate the confidence of de novo peptide sequencing are lagging behind. A fundamental part of a quality-control method is the scoring function used to evaluate the quality of peptide-spectrum matches (PSMs). Here, we propose a genetic programming (GP) based method, called GP-PSM, to learn a PSM scoring function for improving the rate of confident peptide identification from MS/MS data. The GP method learns from thousands of MS/MS spectra. Important characteristics about goodness of the matches are extracted from the learning set and incorporated into the GP scoring functions. We compare GP-PSM with two methods including Support Vector Regression (SVR) and Random Forest (RF). The GP method along with RF and SVR, each is used for post-processing the results of peptide identification by PEAKS, a commonly used de novo sequencing method. The results show that GP-PSM outperforms RF and SVR and discriminates accurately between correct and incorrect PSMs. It correctly assigns peptides to 10% more spectra on an evaluation dataset containing 120 MS/MS spectra and decreases the false positive rate (FPR) of peptide identification.

cs.NE↗

arXiv2019

Evolving Deep Neural Networks by Multi-objective Particle Swarm Optimization for Image Classification

In recent years, convolutional neural networks (CNNs) have become deeper in order to achieve better classification accuracy in image classification. However, it is difficult to deploy the state-of-the-art deep CNNs for industrial use due to the difficulty of manually fine-tuning the hyperparameters and the trade-off between classification accuracy and computational cost. This paper proposes a novel multi-objective optimization method for evolving state-of-the-art deep CNNs in real-life applications, which automatically evolves the non-dominant solutions at the Pareto front. Three major contributions are made: Firstly, a new encoding strategy is designed to encode one of the best state-of-the-art CNNs; With the classification accuracy and the number of floating point operations as the two objectives, a multi-objective particle swarm optimization method is developed to evolve the non-dominant solutions; Last but not least, a new infrastructure is designed to boost the experiments by concurrently running the experiments on multiple GPUs across multiple machines, and a Python library is developed and released to manage the infrastructure. The experimental results demonstrate that the non-dominant solutions found by the proposed algorithm form a clear Pareto front, and the proposed infrastructure is able to almost linearly reduce the running time.

cs.NE↗

arXiv2019

Evolving Deep Convolutional Neural Networks for Image Classification

Evolutionary computation methods have been successfully applied to neural networks since two decades ago, while those methods cannot scale well to the modern deep neural networks due to the complicated architectures and large quantities of connection weights. In this paper, we propose a new method using genetic algorithms for evolving the architectures and connection weight initialization values of a deep convolutional neural network to address image classification problems. In the proposed algorithm, an efficient variable-length gene encoding strategy is designed to represent the different building blocks and the unpredictable optimal depth in convolutional neural networks. In addition, a new representation scheme is developed for effectively initializing connection weights of deep convolutional neural networks, which is expected to avoid networks getting stuck into local minima which is typically a major issue in the backward gradient-based optimization. Furthermore, a novel fitness evaluation method is proposed to speed up the heuristic search with substantially less computational resource. The proposed algorithm is examined and compared with 22 existing algorithms on nine widely used image classification tasks, including the state-of-the-art methods. The experimental results demonstrate the remarkable superiority of the proposed algorithm over the state-of-the-art algorithms in terms of classification error rate and the number of parameters (weights).

cs.NE↗

arXiv2019

Automatically Evolving CNN Architectures Based on Blocks

The performance of Convolutional Neural Networks (CNNs) highly relies on their architectures. In order to design a CNN with promising performance, extended expertise in both CNNs and the investigated problem is required, which is not necessarily held by every user interested in CNNs or the problem domain. In this paper, we propose to automatically evolve CNN architectures by using a genetic algorithm based on ResNet blocks and DenseNet blocks. The proposed algorithm is \textbf{completely} automatic in designing CNN architectures, particularly, neither pre-processing before it starts nor post-processing on the designed CNN is needed. Furthermore, the proposed algorithm does not require users with domain knowledge on CNNs, the investigated problem or even genetic algorithms. The proposed algorithm is evaluated on CIFAR10 and CIFAR100 against 18 state-of-the-art peer competitors. Experimental results show that it outperforms state-of-the-art CNNs hand-crafted and CNNs designed by automatic peer competitors in terms of the classification accuracy, and achieves the competitive classification accuracy against semi-automatic peer competitors. In addition, the proposed algorithm consumes much less time than most peer competitors in finding the best CNN architectures.

cs.NE↗

arXiv2019

A Hybrid GA-PSO Method for Evolving Architecture and Short Connections of Deep Convolutional Neural Networks

Image classification is a difficult machine learning task, where Convolutional Neural Networks (CNNs) have been applied for over 20 years in order to solve the problem. In recent years, instead of the traditional way of only connecting the current layer with its next layer, shortcut connections have been proposed to connect the current layer with its forward layers apart from its next layer, which has been proved to be able to facilitate the training process of deep CNNs. However, there are various ways to build the shortcut connections, it is hard to manually design the best shortcut connections when solving a particular problem, especially given the design of the network architecture is already very challenging. In this paper, a hybrid evolutionary computation (EC) method is proposed to \textit{automatically} evolve both the architecture of deep CNNs and the shortcut connections. Three major contributions of this work are: Firstly, a new encoding strategy is proposed to encode a CNN, where the architecture and the shortcut connections are encoded separately; Secondly, a hybrid two-level EC method, which combines particle swarm optimisation and genetic algorithms, is developed to search for the optimal CNNs; Lastly, an adjustable learning rate is introduced for the fitness evaluations, which provides a better learning rate for the training process given a fixed number of epochs. The proposed algorithm is evaluated on three widely used benchmark datasets of image classification and compared with 12 peer Non-EC based competitors and one EC based competitor. The experimental results demonstrate that the proposed method outperforms all of the peer competitors in terms of classification accuracy.

cs.CV↗

arXiv2019

Can Genetic Programming Do Manifold Learning Too?

Exploratory data analysis is a fundamental aspect of knowledge discovery that aims to find the main characteristics of a dataset. Dimensionality reduction, such as manifold learning, is often used to reduce the number of features in a dataset to a manageable level for human interpretation. Despite this, most manifold learning techniques do not explain anything about the original features nor the true characteristics of a dataset. In this paper, we propose a genetic programming approach to manifold learning called GP-MaL which evolves functional mappings from a high-dimensional space to a lower dimensional space through the use of interpretable trees. We show that GP-MaL is competitive with existing manifold learning algorithms, while producing models that can be interpreted and re-used on unseen data. A number of promising future directions of research are found in the process.

cs.NE↗

arXiv2019

GA-Novo: De Novo Peptide Sequencing via Tandem Mass Spectrometry using Genetic Algorithm

Proteomics is the large-scale analysis of the proteins. The common method for identifying proteins and characterising their amino acid sequences is to digest the proteins into peptides, analyse the peptides using mass spectrometry and assign the resulting tandem mass spectra (MS/MS) to peptides using database search tools. However, database search algorithms are highly dependent on a reference protein database and they cannot identify peptides and proteins not included in the database. Therefore, de novo sequencing algorithms are developed to overcome the problem by directly reconstructing the peptide sequence of an MS/MS spectrum without using any protein database. Current de novo sequencing algorithms often fail to construct the completely matched sequences, and produce partial matches. In this study, we propose a genetic algorithm based method, GA-Novo, to solve the complex optimisation task of de novo peptide sequencing, aiming at constructing full length sequences. Given an MS/MS spectrum, GA-Novo optimises the amino acid sequences to best fit the input spectrum. On the testing dataset, GA-Novo outperforms PEAKS, the most commonly used software for this task, by constructing 8% higher number of fully matched peptide sequences, and 4% higher recall at partially matched sequences.

cs.CE↗

arXiv2018

A Particle Swarm Optimization-based Flexible Convolutional Auto-Encoder for Image Classification

Convolutional auto-encoders have shown their remarkable performance in stacking to deep convolutional neural networks for classifying image data during past several years. However, they are unable to construct the state-of-the-art convolutional neural networks due to their intrinsic architectures. In this regard, we propose a flexible convolutional auto-encoder by eliminating the constraints on the numbers of convolutional layers and pooling layers from the traditional convolutional auto-encoder. We also design an architecture discovery method by using particle swarm optimization, which is capable of automatically searching for the optimal architectures of the proposed flexible convolutional auto-encoder with much less computational resource and without any manual intervention. We use the designed architecture optimization algorithm to test the proposed flexible convolutional auto-encoder through utilizing one graphic processing unit card on four extensively used image classification datasets. Experimental results show that our work in this paper significantly outperform the peer competitors including the state-of-the-art algorithm.

cs.NE↗

arXiv2018

Effective Exploration for Deep Reinforcement Learning via Bootstrapped Q-Ensembles under Tsallis Entropy Regularization

Recently deep reinforcement learning (DRL) has achieved outstanding success on solving many difficult and large-scale RL problems. However the high sample cost required for effective learning often makes DRL unaffordable in resource-limited applications. With the aim of improving sample efficiency and learning performance, we will develop a new DRL algorithm in this paper that seamless integrates entropy-induced and bootstrap-induced techniques for efficient and deep exploration of the learning environment. Specifically, a general form of Tsallis entropy regularizer will be utilized to drive entropy-induced exploration based on efficient approximation of optimal action-selection policies. Different from many existing works that rely on action dithering strategies for exploration, our algorithm is efficient in exploring actions with clear exploration value. Meanwhile, by employing an ensemble of Q-networks under varied Tsallis entropy regularization, the diversity of the ensemble can be further enhanced to enable effective bootstrap-induced exploration. Experiments on Atari game playing tasks clearly demonstrate that our new algorithm can achieve more efficient and effective exploration for DRL, in comparison to recently proposed exploration methods including Bootstrapped Deep Q-Network and UCB Q-Ensemble.

cs.LG↗

arXiv2018

A Hybrid Differential Evolution Approach to Designing Deep Convolutional Neural Networks for Image Classification

Convolutional Neural Networks (CNNs) have demonstrated their superiority in image classification, and evolutionary computation (EC) methods have recently been surging to automatically design the architectures of CNNs to save the tedious work of manually designing CNNs. In this paper, a new hybrid differential evolution (DE) algorithm with a newly added crossover operator is proposed to evolve the architectures of CNNs of any lengths, which is named DECNN. There are three new ideas in the proposed DECNN method. Firstly, an existing effective encoding scheme is refined to cater for variable-length CNN architectures; Secondly, the new mutation and crossover operators are developed for variable-length DE to optimise the hyperparameters of CNNs; Finally, the new second crossover is introduced to evolve the depth of the CNN architectures. The proposed algorithm is tested on six widely-used benchmark datasets and the results are compared to 12 state-of-the-art methods, which shows the proposed method is vigorously competitive to the state-of-the-art algorithms. Furthermore, the proposed method is also compared with a method using particle swarm optimisation with a similar encoding strategy named IPPSO, and the proposed DECNN outperforms IPPSO in terms of the accuracy.

cs.NE↗

arXiv2018

An Adaptive Clipping Approach for Proximal Policy Optimization

Very recently proximal policy optimization (PPO) algorithms have been proposed as first-order optimization methods for effective reinforcement learning. While PPO is inspired by the same learning theory that justifies trust region policy optimization (TRPO), PPO substantially simplifies algorithm design and improves data efficiency by performing multiple epochs of \emph{clipped policy optimization} from sampled data. Although clipping in PPO stands for an important new mechanism for efficient and reliable policy update, it may fail to adaptively improve learning performance in accordance with the importance of each sampled state. To address this issue, a new surrogate learning objective featuring an adaptive clipping mechanism is proposed in this paper, enabling us to develop a new algorithm, known as PPO-$λ$. PPO-$λ$ optimizes policies repeatedly based on a theoretical target for adaptive policy improvement. Meanwhile, destructively large policy update can be effectively prevented through both clipping and adaptive control of a hyperparameter $λ$ in PPO-$λ$, ensuring high learning reliability. PPO-$λ$ enjoys the same simple and efficient design as PPO. Empirically on several Atari game playing tasks and benchmark control tasks, PPO-$λ$ also achieved clearly better performance than PPO.

cs.LG↗

arXiv2018

Generating Redundant Features with Unsupervised Multi-Tree Genetic Programming

Recently, feature selection has become an increasingly important area of research due to the surge in high-dimensional datasets in all areas of modern life. A plethora of feature selection algorithms have been proposed, but it is difficult to truly analyse the quality of a given algorithm. Ideally, an algorithm would be evaluated by measuring how well it removes known bad features. Acquiring datasets with such features is inherently difficult, and so a common technique is to add synthetic bad features to an existing dataset. While adding noisy features is an easy task, it is very difficult to automatically add complex, redundant features. This work proposes one of the first approaches to generating redundant features, using a novel genetic programming approach. Initial experiments show that our proposed method can automatically create difficult, redundant features which have the potential to be used for creating high-quality feature selection benchmark datasets.

cs.NE↗