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.
Leiden University Medical Center（莱顿大学医学中心）；Centrum Wiskunde & Informatica（荷兰国家数学与计算机科学研究所）
Dimensionality reduction (DR) is an important technique for data exploration and knowledge discovery. However, most of the main DR methods are either linear (e.g., PCA), do not provide an explicit mapping between the original data and its lower-dimensional representation (e.g., MDS, t-SNE, isomap), or produce mappings that cannot be easily interpreted (e.g., kernel PCA, neural-based autoencoder). Recently, genetic programming (GP) has been used to evolve interpretable DR mappings in the form of symbolic expressions. There exists a number of ways in which GP can be used to this end and no study…
For classification problems, feature extraction is a crucial process which aims to find a suitable data representation that increases the performance of the machine learning algorithm. According to the curse of dimensionality theorem, the number of samples needed for a classification task increases exponentially as the number of dimensions (variables, features) increases. On the other hand, it is costly to collect, store and process data. Moreover, irrelevant and redundant features might hinder classifier performance. In exploratory analysis settings, high dimensionality prevents the users fro…
Genetic programming is an often-used technique for symbolic regression: finding symbolic expressions that match data from an unknown function. To make the symbolic regression more efficient, one can also use dimensionally-aware genetic programming that constrains the physical units of the equation. Nevertheless, there is no formal analysis of how much dimensionality awareness helps in the regression process. In this paper, we conduct a fitness landscape analysis of dimensionallyaware genetic programming search spaces on a subset of equations from Richard Feynmans well-known lectures. We define…
When seeking a predictive model in biomedical data, one often has more than a single objective in mind, e.g., attaining both high accuracy and low complexity (to promote interpretability). We investigate herein whether multiple objectives can be dynamically tuned by our recently proposed coevolutionary algorithm, SAFE (Solution And Fitness Evolution). We find that SAFE is able to automatically tune accuracy and complexity with no performance loss, as compared with a standard evolutionary algorithm, over complex simulated genetics datasets produced by the GAMETES tool.
AutoQML: Automatic Generation and Training of Robust Quantum-Inspired Classifiers by Using Genetic Algorithms on Grayscale Images
Consejo Superior de Investigaciones Científicas（西班牙国家研究委员会）；Centre for Automation and Robotics（自动化与机器人中心）；Universidad Politécnica de Madrid（马德里理工大学）；Instituto de Física Fundamental（基础物理研究所）
Biomarkers which predict patient's survival can play an important role in medical diagnosis and treatment. How to select the significant biomarkers from hundreds of protein markers is a key step in survival analysis. In this paper a novel method is proposed to detect the prognostic biomarkers of survival in colorectal cancer patients using wavelet analysis, genetic algorithm, and Bayes classifier. One dimensional discrete wavelet transform (DWT) is normally used to reduce the dimensionality of biomedical data. In this study one dimensional continuous wavelet transform (CWT) was proposed to ext…
Genetic Programming for Explainable Manifold Learning
Centre for Data Science and Artificial Intelligence（数据科学与人工智能中心）；School of Engineering and Computer Science（工程与计算机科学学院）；Victoria University of Wellington（威灵顿维多利亚大学）
Random sample consensus (RANSAC) is a successful algorithm in model fitting applications. It is vital to have strong exploration phase when there are an enormous amount of outliers within the dataset. Achieving a proper model is guaranteed by pure exploration strategy of RANSAC. However, finding the optimum result requires exploitation. GASAC is an evolutionary paradigm to add exploitation capability to the algorithm. Although GASAC improves the results of RANSAC, it has a fixed strategy for balancing between exploration and exploitation. In this paper, a new paradigm is proposed based on gene…
The world is connected through the Internet. As the abundance of Internet users connected into the Web and the popularity of cloud computing research, the need of Artificial Intelligence (AI) is demanding. In this research, Genetic Algorithm (GA) as AI optimization method through natural selection and genetic evolution is utilized. There are many applications of GA such as web mining, load balancing, routing, and scheduling or web service selection. Hence, it is a challenging task to discover whether the code mainly server side and web based language technology affects the performance of GA. T…
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…
This paper introduces NSGA-Net -- an evolutionary approach for neural architecture search (NAS). NSGA-Net is designed with three goals in mind: (1) a procedure considering multiple and conflicting objectives, (2) an efficient procedure balancing exploration and exploitation of the space of potential neural network architectures, and (3) a procedure finding a diverse set of trade-off network architectures achieved in a single run. NSGA-Net is a population-based search algorithm that explores a space of potential neural network architectures in three steps, namely, a population initialization st…
Machine learning has been gaining traction in recent years to meet the demand for tools that can efficiently analyze and make sense of the ever-growing databases of biomedical data in health care systems around the world. However, effectively using machine learning methods requires considerable domain expertise, which can be a barrier of entry for bioinformaticians new to computational data science methods. Therefore, off-the-shelf tools that make machine learning more accessible can prove invaluable for bioinformaticians. To this end, we have developed an open source pipeline optimization too…
Adaptive Genetic Selection based Pinning Control with Asymmetric Coupling for Multi-Network Heterogeneous Vehicular Systems
Sino-German College of Applied Sciences, Tongji University（同济大学中德应用技术学院）；School of Transportation, Tongji University（同济大学交通运输工程学院）；Department of Electronics and Information Sciences, Tongji University（同济大学电子与信息科学系）
The analysis of electroencephalogram (EEG) waves is of critical importance for the diagnosis of sleep disorders, such as sleep apnea and insomnia, besides that, seizures, epilepsy, head injuries, dizziness, headaches and brain tumors. In this context, one important task is the identification of visible structures in the EEG signal, such as sleep spindles and K-complexes. The identification of these structures is usually performed by visual inspection from human experts, a process that can be error prone and susceptible to biases. Therefore there is interest in developing technologies for the a…
Genetic Algorithms (GAs) are explored as a tool for probing new physics with high dimensionality. We study the 19-dimensional pMSSM, including experimental constraints from all sources and assessing the consistency of potential signals of new physics. We show that GAs excel at making a fast and accurate diagnosis of the cross-compatibility of a set of experimental constraints in such high dimensional models. In the case of the pMSSM, it is found that only ${\cal O}(10^4)$ model evaluations are required to obtain a best fit point in agreement with much more costly MCMC scans. This efficiency al…
GARA: A novel approach to Improve Genetic Algorithms' Accuracy and Efficiency by Utilizing Relationships among Genes
School of Computer Science and Technology, Beijing Institute of Technology（北京理工大学计算机科学与技术学院）；School of Computer Science and Engineering, University of Aizu（会津大学计算机科学与工程学院）
We have employed a recent implementation of genetic algorithms to study a range of standard benchmark functions for global optimization. It turns out that some of them are not very useful as challenging test functions, since they neither allow for a discrimination between different variants of genetic operators nor exhibit a dimensionality scaling resembling that of real-world problems, for example that of global structure optimization of atomic and molecular clusters. The latter properties seem to be simulated better by two other types of benchmark functions. One type is designed to be decept…
Many mathematical optimization algorithms fail to sufficiently explore the solution space of high-dimensional nonlinear optimization problems due to the curse of dimensionality. This paper proposes generative models as a complement to optimization algorithms to improve performance in problems with high dimensionality. To demonstrate this method, a conditional generative adversarial network (C-GAN) is used to augment the solutions produced by a genetic algorithm (GA) for a 311-dimensional nonconvex multi-objective mixed-integer nonlinear optimization. The C-GAN, composed of two networks with th…
In recent years genetic algorithms have emerged as a useful tool for the heuristic solution of complex discrete optimisation problems. In particular there has been considerable interest in their use in tackling problems arising in the areas of scheduling and timetabling. However, the classical genetic algorithm paradigm is not well equipped to handle constraints and successful implementations usually require some sort of modification to enable the search to exploit problem specific knowledge in order to overcome this shortcoming. This paper is concerned with the development of a family of gene…
