A Field Guide to Genetic Programming

xiv, 233 p. : il. ; 23 cm.Libro ElectrónicoA Field Guide to Genetic Programming (ISBN 978-1-4092-0073-4) is an introduction to genetic programming (GP). GP is a systematic, domain-independent method for getting computers to solve problems automatically starting from a high-level statement of what needs to be done. Using ideas from natural evolution, GP starts from an ooze of random computer programs, and progressively refines them through processes of mutation and sexual recombination, until solutions emerge. All this without the user having to know or specify the form or structure of solutions in advance. GP has generated a plethora of human-competitive results and applications, including novel scientific discoveries and patentable inventions. The authorsIntroduction -- Representation, initialisation and operators in Tree-based GP -- Getting ready to run genetic programming -- Example genetic programming run -- Alternative initialisations and operators in Tree-based GP -- Modular, grammatical and developmental Tree-based GP -- Linear and graph genetic programming -- Probalistic genetic programming -- Multi-objective genetic programming -- Fast and distributed genetic programming -- GP theory and its applications -- Applications -- Troubleshooting GP -- Conclusions.Contents xi 1 Introduction 1.1 Genetic Programming in a Nutshell 1.2 Getting Started 1.3 Prerequisites 1.4 Overview of this Field Guide I Basics 2 Representation, Initialisation and GP 2.1 Representation 2.2 Initialising the Population 2.3 Selection 2.4 Recombination and Mutation Operators in Tree-based 3 Getting Ready to Run Genetic Programming 19 3.1 Step 1: Terminal Set 19 3.2 Step 2: Function Set 20 3.2.1 Closure 21 3.2.2 Sufficiency 23 3.2.3 Evolving Structures other than Programs 23 3.3 Step 3: Fitness Function 24 3.4 Step 4: GP Parameters 26 3.5 Step 5: Termination and solution designation 27 4 Example Genetic Programming Run 4.1 Preparatory Steps 29 4.2 Step-by-Step Sample Run 31 4.2.1 Initialisation 31 4.2.2 Fitness Evaluation Selection, Crossover and Mutation Termination and Solution Designation Advanced Genetic Programming 5 Alternative Initialisations and Operators in 5.1 Constructing the Initial Population 5.1.1 Uniform Initialisation 5.1.2 Initialisation may Affect Bloat 5.1.3 Seeding 5.2 GP Mutation 5.2.1 Is Mutation Necessary? 5.2.2 Mutation Cookbook 5.3 GP Crossover 5.4 Other Techniques 32 5.5 Tree-based GP 39 6 Modular, Grammatical and Developmental Tree-based GP 47 6.1 Evolving Modular and Hierarchical Structures 47 6.1.1 Automatically Defined Functions 48 6.1.2 Program Architecture and Architecture-Altering 50 6.2 Constraining Structures 51 6.2.1 Enforcing Particular Structures 52 6.2.2 Strongly Typed GP 52 6.2.3 Grammar-based Constraints 53 6.2.4 Constraints and Bias 55 6.3 Developmental Genetic Programming 57 6.4 Strongly Typed Autoconstructive GP with PushGP 59 7 Linear and Graph Genetic Programming 61 7.1 Linear Genetic Programming 61 7.1.1 Motivations 61 7.1.2 Linear GP Representations 62 7.1.3 Linear GP Operators 64 7.2 Graph-Based Genetic Programming 65 7.2.1 Parallel Distributed GP (PDGP) 65 7.2.2 PADO 67 7.2.3 Cartesian GP 67 7.2.4 Evolving Parallel Programs using Indirect Encodings 68 8 Probabilistic Genetic Programming 8.1 Estimation of Distribution Algorithms 69 8.2 Pure EDA GP 71 8.3 Mixing Grammars and Probabilities 74 9 Multi-objective Genetic Programming 75 9.1 Combining Multiple Objectives into a Scalar Fitness Function 75 9.2 Keeping the Objectives Separate 76 9.2.1 Multi-objective Bloat and Complexity Control 77 9.2.2 Other Objectives 78 9.2.3 Non-Pareto Criteria 80 9.3 Multiple Objectives via Dynamic and Staged Fitness Functions 80 9.4 Multi-objective Optimisation via Operator Bias 81 10 Fast and Distributed Genetic Programming 83 10.1 Reducing Fitness Evaluations/Increasing their Effectiveness 83 10.2 Reducing Cost of Fitness with Caches 86 10.3 Parallel and Distributed GP are Not Equivalent 88 10.4 Running GP on Parallel Hardware 89 10.4.1 Master–slave GP 89 10.4.2 GP Running on GPUs 90 10.4.3 GP on FPGAs 92 10.4.4 Sub-machine-code GP 93 10.5 Geographically Distributed GP 93 11 GP Theory and its Applications 97 11.1 Mathematical Models 98 11.2 Search Spaces 99 11.3 Bloat 101 11.3.1 Bloat in Theory 101 11.3.2 Bloat Control in Practice 104 III Practical Genetic Programming 12 Applications 12.1 Where GP has Done Well 12.2 Curve Fitting, Data Modelling and Symbolic Regression 12.3 Human Competitive Results – the Humies 12.4 Image and Signal Processing 12.5 Financial Trading, Time Series, and Economic Modelling 12.6 Industrial Process Control 12.7 Medicine, Biology and Bioinformatics 12.8 GP to Create Searchers and Solvers – Hyper-heuristics xiii 12.9 Entertainment and Computer Games 127 12.10The Arts 127 12.11Compression 128 13 Troubleshooting GP 13.1 Is there a Bug in the Code? 13.2 Can you Trust your Results? 13.3 There are No Silver Bullets 13.4 Small Changes can have Big Effects 13.5 Big Changes can have No Effect 13.6 Study your Populations 13.7 Encourage Diversity 13.8 Embrace Approximation 13.9 Control Bloat 13.10 Checkpoint Results 13.11 Report Well 13.12 Convince your Customers 14 Conclusions Tricks of the Trade A Resources A.1 Key Books A.2 Key Journals A.3 Key International Meetings A.4 GP Implementations A.5 On-Line Resources 145 B TinyGP 151 B.1 Overview of TinyGP 151 B.2 Input Data Files for TinyGP 153 B.3 Source Code 154 B.4 Compiling and Running TinyGP 162 Bibliography 167 Inde

Advanced machine learning methods for oncological image analysis

Cancer is a major public health problem, accounting for an estimated 10 million deaths worldwide in 2020 alone. Rapid advances in the field of image acquisition and hardware development over the past three decades have resulted in the development of modern medical imaging modalities that can capture high-resolution anatomical, physiological, functional, and metabolic quantitative information from cancerous organs. Therefore, the applications of medical imaging have become increasingly crucial in the clinical routines of oncology, providing screening, diagnosis, treatment monitoring, and non/minimally- invasive evaluation of disease prognosis. The essential need for medical images, however, has resulted in the acquisition of a tremendous number of imaging scans. Considering the growing role of medical imaging data on one side and the challenges of manually examining such an abundance of data on the other side, the development of computerized tools to automatically or semi-automatically examine the image data has attracted considerable interest. Hence, a variety of machine learning tools have been developed for oncological image analysis, aiming to assist clinicians with repetitive tasks in their workflow. This thesis aims to contribute to the field of oncological image analysis by proposing new ways of quantifying tumor characteristics from medical image data. Specifically, this thesis consists of six studies, the first two of which focus on introducing novel methods for tumor segmentation. The last four studies aim to develop quantitative imaging biomarkers for cancer diagnosis and prognosis. The main objective of Study I is to develop a deep learning pipeline capable of capturing the appearance of lung pathologies, including lung tumors, and integrating this pipeline into the segmentation networks to leverage the segmentation accuracy. The proposed pipeline was tested on several comprehensive datasets, and the numerical quantifications show the superiority of the proposed prior-aware DL framework compared to the state of the art. Study II aims to address a crucial challenge faced by supervised segmentation models: dependency on the large-scale labeled dataset. In this study, an unsupervised segmentation approach is proposed based on the concept of image inpainting to segment lung and head- neck tumors in images from single and multiple modalities. The proposed autoinpainting pipeline shows great potential in synthesizing high-quality tumor-free images and outperforms a family of well-established unsupervised models in terms of segmentation accuracy. Studies III and IV aim to automatically discriminate the benign from the malignant pulmonary nodules by analyzing the low-dose computed tomography (LDCT) scans. In Study III, a dual-pathway deep classification framework is proposed to simultaneously take into account the local intra-nodule heterogeneities and the global contextual information. Study IV seeks to compare the discriminative power of a series of carefully selected conventional radiomics methods, end-to-end Deep Learning (DL) models, and deep features-based radiomics analysis on the same dataset. The numerical analyses show the potential of fusing the learned deep features into radiomic features for boosting the classification power. Study V focuses on the early assessment of lung tumor response to the applied treatments by proposing a novel feature set that can be interpreted physiologically. This feature set was employed to quantify the changes in the tumor characteristics from longitudinal PET-CT scans in order to predict the overall survival status of the patients two years after the last session of treatments. The discriminative power of the introduced imaging biomarkers was compared against the conventional radiomics, and the quantitative evaluations verified the superiority of the proposed feature set. Whereas Study V focuses on a binary survival prediction task, Study VI addresses the prediction of survival rate in patients diagnosed with lung and head-neck cancer by investigating the potential of spherical convolutional neural networks and comparing their performance against other types of features, including radiomics. While comparable results were achieved in intra- dataset analyses, the proposed spherical-based features show more predictive power in inter-dataset analyses. In summary, the six studies incorporate different imaging modalities and a wide range of image processing and machine-learning techniques in the methods developed for the quantitative assessment of tumor characteristics and contribute to the essential procedures of cancer diagnosis and prognosis

Survey of Template-Based Code Generation

L'automatisation de la génération des artefacts textuels à partir des modèles est une étape critique dans l'Ingénierie Dirigée par les Modèles (IDM). C'est une transformation de modèles utile pour générer le code source, sérialiser les modèles dans de stockages persistents, générer les rapports ou encore la documentation. Parmi les différents paradigmes de transformation de modèle-au-texte, la génération de code basée sur les templates (TBCG) est la plus utilisée en IDM. La TBCG est une technique de génération qui produit du code à partir des spécifications de haut niveau appelées templates. Compte tenu de la diversité des outils et des approches, il est nécessaire de classifier et de comparer les techniques de TBCG existantes afin d'apporter un soutien approprié aux développeurs. L'objectif de ce mémoire est de mieux comprendre les caractéristiques des techniques de TBCG, identifier les tendances dans la recherche, et éxaminer l'importance du rôle de l'IDM par rapport à cette approche. J'évalue également l'expressivité, la performance et la mise à l'échelle des outils associés selon une série de modèles. Je propose une étude systématique de cartographie de la littérature qui décrit une intéressante vue d'ensemble de la TBCG et une étude comparitive des outils de la TBCG pour mieux guider les dévloppeurs dans leur choix. Cette étude montre que les outils basés sur les modèles offrent plus d'expressivité tandis que les outils basés sur le code sont les plus performants. Enfin, Xtend2 offre le meilleur compromis entre l'expressivité et la performance.A critical step in model-driven engineering (MDE) is the automatic synthesis of a textual artifact from models. This is a very useful model transformation to generate application code, to serialize the model in persistent storage, generate documentation or reports. Among the various model-to-text transformation paradigms, Template-Based Code Generation (TBCG) is the most popular in MDE. TBCG is a synthesis technique that produces code from high-level specifications, called templates. It is a popular technique in MDE given that they both emphasize abstraction and automation. Given the diversity of tools and approaches, it is necessary to classify and compare existing TBCG techniques to provide appropriate support to developers. The goal of this thesis is to better understand the characteristics of TBCG techniques, identify research trends, and assess the importance of the role of MDE in this code synthesis approach. We also evaluate the expressiveness, performance and scalability of the associated tools based on a range of models that implement critical patterns. To this end, we conduct a systematic mapping study of the literature that paints an interesting overview of TBCG and a comparative study on TBCG tools to better guide developers in their choices. This study shows that model-based tools offer more expressiveness whereas code-based tools performed much faster. Xtend2 offers the best compromise between the expressiveness and the performance

MRI-Based classification of neuropsychiatric systemic lupus erythematosus patients with self-supervised contrastive learning

Introduction/Purpose: Systemic lupus erythematosus (SLE) is a chronic auto-immune disease with a broad spectrum of clinical presentations, including heterogeneous neuropsychiatric (NP) syndromes. Structural brain abnormalities are commonly found in SLE and NPSLE, but their role in diagnosis is limited, and their usefulness in distinguishing between NPSLE patients and patients in which the NP symptoms are not primarily attributed to SLE (non-NPSLE) is non-existent. Self-supervised contrastive learning algorithms proved to be useful in classification tasks in rare diseases with limited number of datasets. Our aim was to apply self-supervised contrastive learning on T1-weighted images acquired from a well-defined cohort of SLE patients, aiming to distinguish between NPSLE and non-NPSLE patients. Subjects and Methods: We used 3T MRI T1-weighted images of 163 patients. The training set comprised 68 non-NPSLE and 34 NPSLE patients. We applied random geometric transformations between iterations to augment our data sets. The ML pipeline consisted of convolutional base encoder and linear projector. To test the classification task, the projector was removed and one linear layer was measured. Validation of the method consisted of 6 repeated random sub-samplings, each using a random selection of a small group of patients of both subtypes. Results: In the 6 trials, between 79% and 83% of the patients were correctly classified as NPSLE or non-NPSLE. For a qualitative evaluation of spatial distribution of the common features found in both groups, Gradient-weighted Class Activation Maps (Grad-CAM) were examined. Thresholded Grad-CAM maps show areas of common features identified for the NPSLE cohort, while no such communality was found for the non-NPSLE group. Discussion/Conclusion: The self-supervised contrastive learning model was effective in capturing common brain MRI features from a limited but well-defined cohort of SLE patients with NP symptoms. The interpretation of the Grad-CAM results is not straightforward, but indicates involvement of the lateral and third ventricles, periventricular white matter and basal cisterns. We believe that the common features found in the NPSLE population in this study indicate a combination of tissue loss, local atrophy and to some extent that of periventricular white matter lesions, which are commonly found in NPSLE patients and appear hypointense on T1-weighted images

A Middleware framework for self-adaptive large scale distributed services

Modern service-oriented applications demand the ability to adapt to changing conditions and unexpected situations while maintaining a required QoS. Existing self-adaptation approaches seem inadequate to address this challenge because many of their assumptions are not met on the large-scale, highly dynamic infrastructures where these applications are generally deployed on. The main motivation of our research is to devise principles that guide the construction of large scale self-adaptive distributed services. We aim to provide sound modeling abstractions based on a clear conceptual background, and their realization as a middleware framework that supports the development of such services. Taking the inspiration from the concepts of decentralized markets in economics, we propose a solution based on three principles: emergent self-organization, utility driven behavior and model-less adaptation. Based on these principles, we designed Collectives, a middleware framework which provides a comprehensive solution for the diverse adaptation concerns that rise in the development of distributed systems. We tested the soundness and comprehensiveness of the Collectives framework by implementing eUDON, a middleware for self-adaptive web services, which we then evaluated extensively by means of a simulation model to analyze its adaptation capabilities in diverse settings. We found that eUDON exhibits the intended properties: it adapts to diverse conditions like peaks in the workload and massive failures, maintaining its QoS and using efficiently the available resources; it is highly scalable and robust; can be implemented on existing services in a non-intrusive way; and do not require any performance model of the services, their workload or the resources they use. We can conclude that our work proposes a solution for the requirements of self-adaptation in demanding usage scenarios without introducing additional complexity. In that sense, we believe we make a significant contribution towards the development of future generation service-oriented applications.Las Aplicaciones Orientadas a Servicios modernas demandan la capacidad de adaptarse a condiciones variables y situaciones inesperadas mientras mantienen un cierto nivel de servio esperado (QoS). Los enfoques de auto-adaptación existentes parecen no ser adacuados debido a sus supuestos no se cumplen en infrastructuras compartidas de gran escala. La principal motivación de nuestra investigación es inerir un conjunto de principios para guiar el desarrollo de servicios auto-adaptativos de gran escala. Nuesto objetivo es proveer abstraciones de modelaje apropiadas, basadas en un marco conceptual claro, y su implemetnacion en un middleware que soporte el desarrollo de estos servicios. Tomando como inspiración conceptos económicos de mercados decentralizados, hemos propuesto una solución basada en tres principios: auto-organización emergente, comportamiento guiado por la utilidad y adaptación sin modelos. Basados en estos principios diseñamos Collectives, un middleware que proveer una solución exhaustiva para los diversos aspectos de adaptación que surgen en el desarrollo de sistemas distribuidos. La adecuación y completitud de Collectives ha sido provada por medio de la implementación de eUDON, un middleware para servicios auto-adaptativos, el ha sido evaluado de manera exhaustiva por medio de un modelo de simulación, analizando sus propiedades de adaptación en diversos escenarios de uso. Hemos encontrado que eUDON exhibe las propiedades esperadas: se adapta a diversas condiciones como picos en la carga de trabajo o fallos masivos, mateniendo su calidad de servicio y haciendo un uso eficiente de los recusos disponibles. Es altamente escalable y robusto; puedeoo ser implementado en servicios existentes de manera no intrusiva; y no requiere la obtención de un modelo de desempeño para los servicios. Podemos concluir que nuestro trabajo nos ha permitido desarrollar una solucion que aborda los requerimientos de auto-adaptacion en escenarios de uso exigentes sin introducir complejidad adicional. En este sentido, consideramos que nuestra propuesta hace una contribución significativa hacia el desarrollo de la futura generación de aplicaciones orientadas a servicios.Postprint (published version