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.

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.

Particle Swarm Optimisation for Evolving Deep Neural Networks for Image Classification by Evolving and Stacking Transferable Blocks

Deep Convolutional Neural Networks (CNNs) have been widely used in image classification tasks, but the process of designing CNN architectures is very complex, so Neural Architecture Search (NAS), automatically searching for optimal CNN architectures, has attracted more and more research interests. However, the computational cost of NAS is often too high to apply NAS on real-life applications. In this paper, an efficient particle swarm optimisation method named EPSOCNN is proposed to evolve CNN architectures inspired by the idea of transfer learning. EPSOCNN successfully reduces the computation cost by minimising the search space to a single block and utilising a small subset of the training set to evaluate CNNs during evolutionary process. Meanwhile, EPSOCNN also keeps very competitive classification accuracy by stacking the evolved block multiple times to fit the whole dataset. The proposed EPSOCNN algorithm is evaluated on CIFAR-10 dataset and compared with 13 peer competitors comprised of deep CNNs crafted by hand, learned by reinforcement learning methods and evolved by evolutionary computation approaches, which shows very promising results by outperforming all of the peer competitors with regard to the classification accuracy, number of parameters and the computational cost.

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.

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.

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.

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.

Automatically Designing CNN Architectures Using Genetic Algorithm for Image Classification

Convolutional Neural Networks (CNNs) have gained a remarkable success on many real-world problems in recent years. However, the performance of CNNs is highly relied on their architectures. For some state-of-the-art CNNs, their architectures are hand-crafted with expertise in both CNNs and the investigated problems. To this end, it is difficult for researchers, who have no extended expertise in CNNs, to explore CNNs for their own problems of interest. In this paper, we propose an automatic architecture design method for CNNs by using genetic algorithms, which is capable of discovering a promising architecture of a CNN on handling image classification tasks. The proposed algorithm does not need any pre-processing before it works, nor any post-processing on the discovered CNN, which means it is completely automatic. The proposed algorithm is validated on widely used benchmark datasets, by comparing to the state-of-the-art peer competitors covering eight manually designed CNNs, four semi-automatically designed CNNs and additional four automatically designed CNNs. The experimental results indicate that the proposed algorithm achieves the best classification accuracy consistently among manually and automatically designed CNNs. Furthermore, the proposed algorithm also shows the competitive classification accuracy to the semi-automatic peer competitors, while reducing 10 times of the parameters. In addition, on the average the proposed algorithm takes only one percentage of computational resource compared to that of all the other architecture discovering algorithms.

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.

Evolving Deep Convolutional Neural Networks by Variable-length Particle Swarm Optimization for Image Classification

Convolutional neural networks (CNNs) are one of the most effective deep learning methods to solve image classification problems, but the best architecture of a CNN to solve a specific problem can be extremely complicated and hard to design. This paper focuses on utilising Particle Swarm Optimisation (PSO) to automatically search for the optimal architecture of CNNs without any manual work involved. In order to achieve the goal, three improvements are made based on traditional PSO. First, a novel encoding strategy inspired by computer networks which empowers particle vectors to easily encode CNN layers is proposed; Second, in order to allow the proposed method to learn variable-length CNN architectures, a Disabled layer is designed to hide some dimensions of the particle vector to achieve variable-length particles; Third, since the learning process on large data is slow, partial datasets are randomly picked for the evaluation to dramatically speed it up. The proposed algorithm is examined and compared with 12 existing algorithms including the state-of-art methods on three widely used image classification benchmark datasets. The experimental results show that the proposed algorithm is a strong competitor to the state-of-art algorithms in terms of classification error. This is the first work using PSO for automatically evolving the architectures of CNNs.