BOSS: Bayesian Optimization over String Spaces

This article develops a Bayesian optimization (BO) method which acts directly over raw strings, proposing the first uses of string kernels and genetic algorithms within BO loops. Recent applications of BO over strings have been hindered by the need to map inputs into a smooth and unconstrained latent space. Learning this projection is computationally and data-intensive. Our approach instead builds a powerful Gaussian process surrogate model based on string kernels, naturally supporting variable length inputs, and performs efficient acquisition function maximization for spaces with syntactical constraints. Experiments demonstrate considerably improved optimization over existing approaches across a broad range of constraints, including the popular setting where syntax is governed by a context-free grammar

Motif kernel generated by genetic programming improves remote homology and fold detection

BACKGROUND: Protein remote homology detection is a central problem in computational biology. Most recent methods train support vector machines to discriminate between related and unrelated sequences and these studies have introduced several types of kernels. One successful approach is to base a kernel on shared occurrences of discrete sequence motifs. Still, many protein sequences fail to be classified correctly for a lack of a suitable set of motifs for these sequences. RESULTS: We introduce the GPkernel, which is a motif kernel based on discrete sequence motifs where the motifs are evolved using genetic programming. All proteins can be grouped according to evolutionary relations and structure, and the method uses this inherent structure to create groups of motifs that discriminate between different families of evolutionary origin. When tested on two SCOP benchmarks, the superfamily and fold recognition problems, the GPkernel gives significantly better results compared to related methods of remote homology detection. CONCLUSION: The GPkernel gives particularly good results on the more difficult fold recognition problem compared to the other methods. This is mainly because the method creates motif sets that describe similarities among subgroups of both the related and unrelated proteins. This rich set of motifs give a better description of the similarities and differences between different folds than do previous motif-based methods

A Hyper-Solution Framework for SVM Classification: Application for Predicting Destabilizations in Chronic Heart Failure Patients

Support Vector Machines (SVMs) represent a powerful learning paradigm able to provide accurate and reliable decision functions in several application fields. In particular, they are really attractive for application in medical domain, where often a lack of knowledge exists. Kernel trick, on which SVMs are based, allows to map non-linearly separable data into potentially linearly separable one, according to the kernel function and its internal parameters value. During recent years non-parametric approaches have also been proposed for learning the most appropriate kernel, such as linear combination of basic kernels. Thus, SVMs classifiers may have several parameters to be tuned and their optimal values are usually difficult to be identified a-priori. Furthermore, combining different classifiers may reduce risk to perform errors on new unseen data. For such reasons, we present an hyper-solution framework for SVM classification, based on meta-heuristics, that searches for the most reliable hyper-classifier (SVM with a basic kernel, SVM with a combination of kernel, and ensemble of SVMs), and for its optimal configuration. We have applied the proposed framework on a critical and quite complex issue for the management of Chronic Heart Failure patient: the early detection of decompensation conditions. In fact, predicting new destabilizations in advance may reduce the burden of heart failure on the healthcare systems while improving quality of life of affected patients. Promising reliability has been obtained on 10-fold cross validation, proving our approach to be efficient and effective for an high-level analysis of clinical data

Deep Semantic Learning Machine: A Convolutional Network Construction Algorithm

Dissertation presented as the partial requirement for obtaining a Master's degree in Data Science and Advanced AnalyticsThe Semantic Learning Machine (SLM), an algorithm that evolves the topology of feed-forward neural networks (NN), has shown remarkable results in generalization and computing time. It has the benefits of searching the space of different NN architectures under a unimodal fitness landscape in any supervised learning problem. Recent research used the SLM at the end of a Convolutional Neural Network (CNN) instead of fully connected layers outperforming stateof- the-art CNNs. It was proposed to extend the SLM to explore the possibility of optimizing the convolution layers - evolving the full CNN topology. This thesis introduces an operator to optimize the convolution layers, extending the SLM to the Deep Semantic Learning Machine. Initial results, computed using the mnist dataset, show that the algorithm does work but are of limited interpretability. Real-life practicability remains to be improved due to high memory and computational requirements.Semantic Learning Machine (SLM), um algoritmo que evolui a topologia de redes neurais feed-forward (NN), tem mostrado resultados notáveis em generalização e tempo de computação. Tem benefícios de pesquisar o espaço de diferentes arquiteturas NN sob um cenário de aptidão unimodal em qualquer problema de aprendizagem supervisionada. Investigação recente recorre ao uso deSLMno final de uma redes neurais convolucional (CNN) em vez de camadas totalmente conectadas, superando CNNs de última geração. Foi proposto estender o SLM para explorar a possibilidade de otimizar as camadas de convolução - evoluindo a totalmente a topologia CNN. A presente tese apresenta um operador para otimizar as camadas de convolução, estendendo o SLM para a Deep Semantic Learning Machine. Os resultados iniciais, calculados usando o conjunto de dados mnist, mostram que o algoritmo funciona, mas revelam uma interpretabilidade limitada. A aplicabilidade em cenários reais precisa ainda de melhorias devido aos altos requisitos de memória e computação

Tools for improving performance portability in heterogeneous environments

Programa Oficial de Doutoramento en Investigación en Tecnoloxías da Información. 524V01[Abstract] Parallel computing is currently partially dominated by the availability of heterogeneous devices. These devices differ from each other in aspects such as the instruction set they execute, the number and the type of computing devices that they offer or the structure of their memory systems. In the last years, langnages, libraries and extensions have appeared to allow to write a parallel code once aud run it in a wide variety of devices, OpenCL being the most widespread solution of this kind. However, functional portability does not imply performance portability. This way, one of the probletns that is still open in this field is to achieve automatic performance portability. That is, the ability to automatically tune a given code for any device where it will be execnted so that it ill obtain a good performance. This thesis develops three different solutions to tackle this problem. The three of them are based on typical source-to-sonrce optimizations for heterogeneous devices. Both the set of optimizations to apply and the way they are applied depend on different optimization parameters, whose values have to be tuned for each specific device. The first solution is OCLoptimizer, a source-to-source optimizer that can optimize annotated OpenCL kemels with the help of configuration files that guide the optimization process. The tool optimizes kernels for a specific device, and it is also able to automate the generation of functional host codes when only a single kernel is optimized. The two remaining solutions are built on top of the Heterogeneous Programming Library (HPL), a C++ framework that provides an easy and portable way to exploit heterogeneous computing systexns. The first of these solutions uses the run-time code generation capabilities of HPL to generate a self-optimizing version of a matrix multiplication that can optimize itself at run-time for an spedfic device. The last solutíon is the development of a built-in just-in-time optirnizer for HPL, that can optirnize, at run-tirne, a HPL code for an specific device. While the first two solutions use search processes to find the best values for the optimization parameters, this Iast alternative relies on heuristics bMed on general optirnization strategies.[Resumen] Actualmente la computación paralela se encuentra dominada parcialmente por los múltiples dispositivos heterogéneos disponibles. Estos dispositivos difieren entre sí en características tales como el conjunto de instrucciones que ejecutan, el número y tipo de unidades de computación que incluyen o la estructura de sus sistemas de memoria. Durante los últimos años han aparecido lenguajes, librerías y extensiones que permiten escribir una única vez la versión paralela de un código y ejecutarla en un amplio abanico de dispositivos, siendo de entre todos ellos OpenCL la solución más extendida. Sin embargo, la portabilidad funcional no implica portabilidad de rendimiento. Así, uno de los grandes problemas que sigue abierto en este campo es la automatización de la portabilidad de rendimiento, es decir, la capacidad de adaptar automáticamente un código dado para su ejecución en cualquier dispositivo y obtener un buen rendimiento. Esta tesis aborda este problema planteando tres soluciones diferentes al mismo. Las tres se basan en la aplicación de optimizaciones de código a código usadas habitualmente en dispositivos heterogéneos. Tanto el conjunto de optimizaciones a aplicar como la forma de aplicarlas dependen de varios parámetros de optimización, cuyos valores han de ser ajustados para cada dispositivo concreto. La primera solución planteada es OCLoptirnizer, un optimizador de código a código que a partir de kernels OpenCL anotados y ficheros de configuración como apoyo, obtiene versiones optimizada de dichos kernels para un dispositivo concreto. Además, cuando el kernel a optimizar es único, automatiza la generación de un código de host funcional para ese kernel. Las otras dos soluciones han sido implementadas utilizando Heterogeneous Prograrnming LibranJ (HPL), una librería C++ que permite programar sistemas heterogéneos de forma fácil y portable. La primera de estas soluciones explota las capacidades de generación de código en tiempo de ejecución de HPL para generar versiones de un producto de matrices que se adaptan automáticamente en tiempo de ejecución a las características de un dispositivo concreto. La última solución consiste en el desarrollo e incorporación a HPL de un optimizador al vuelo, de fonna que se puedan obtener en tiempo de ejecución versiones optimizadas de un código HPL para un dispositivo dado. Mientras las dos primeras soluciones usan procesos de búsqueda para encontrar los mejores valores para los parámetros de optimización, esta última altemativa se basa para ello en heurísticas definidas a partir de recomendaciones generales de optimización.[Resumo] Actualmente a computación paralela atópase dominada parcialmente polos múltiples dispositivos heteroxéneos dispoñibles. Estes dispositivos difiren entre si en características tales como o conxunto de instruccións que executan, o número e tipo de unidades de computación que inclúen ou a estrutura dos seus sistemas de mem~ ría. Nos últimos anos apareceron linguaxes, bibliotecas e extensións que permiten escribir unha soa vez a versión paralela dun código e executala nun amplio abano de dispositivos, senda de entre todos eles OpenCL a solución máis extendida. Porén, a portabilidade funcional non implica portabilidade de rendemento. Deste xeito, uns dos grandes problemas que segue aberto neste campo é a automatización da portabilidade de rendemento, isto é, a capacidade de adaptar automaticamente un código dado para a súa execución en calquera dispositivo e obter un bo rendemento. Esta tese aborda este problema propondo tres solucións diferentes. As tres están baseadas na aplicación de optimizacións de código a código usadas habitualmente en disp~ sitivos heteroxéneos. Tanto o conxunto de optimizacións a aplicar como a forma de aplicalas dependen de varios parámetros de optimización para os que é preciso fixar determinados valores en función do dispositivo concreto. A primeira solución pro posta é OCLoptirnizer, un optimizador de código a código que partindo de kemels OpenCL anotados e ficheiros de configuración de apoio, obtén versións optimizadas dos devanditos kernels para un dispositivo concreto. Amais, cando o kernel a optimizaré único, tarnén automatiza a xeración dun código de host funcional para ese kernel. As outras dúas solucións foron implementadas utilizando Heterogeneous Programming Library (HPL), unha biblioteca C++ que permite programar sistemas heteroxéneos de xeito fácil e portable. A primeira destas solucións explota as capacidades de xeración de código en tempo de execución de HPL para xerar versións dun produto de matrices que se adaptan automaticamente ás características dun dispositivo concreto. A última solución consiste no deseuvolvemento e incorporación a HPL dun optimizador capaz de obter en tiempo de execución versións optimizada<; dun código HPL para un dispositivo dado. Mentres as dúas primeiras solucións usan procesos de procura para atopar os mellares valores para os parámetros de optimización, esta última alternativa baséase para iso en heurísticas definidas a partir de recomendacións xerais de optimización

Genetic programming applied to morphological image processing

This thesis presents three approaches to the automatic design of algorithms for the processing of binary images based on the Genetic Programming (GP) paradigm. In the first approach the algorithms are designed using the basic Mathematical Morphology (MM) operators, i.e. erosion and dilation, with a variety of Structuring Elements (SEs). GP is used to design algorithms to convert a binary image into another containing just a particular characteristic of interest. In the study we have tested two similarity fitness functions, training sets with different numbers of elements and different sizes of the training images over three different objectives. The results of the first approach showed some success in the evolution of MM algorithms but also identifed problems with the amount of computational resources the method required. The second approach uses Sub-Machine-Code GP (SMCGP) and bitwise operators as an attempt to speed-up the evolution of the algorithms and to make them both feasible and effective. The SMCGP approach was successful in the speeding up of the computation but it was not successful in improving the quality of the obtained algorithms. The third approach presents the combination of logical and morphological operators in an attempt to improve the quality of the automatically designed algorithms. The results obtained provide empirical evidence showing that the evolution of high quality MM algorithms using GP is possible and that this technique has a broad potential that should be explored further. This thesis includes an analysis of the potential of GP and other Machine Learning techniques for solving the general problem of Signal Understanding by means of exploring Mathematical Morphology

Evolutionary design of deep neural networks

Mención Internacional en el título de doctorFor three decades, neuroevolution has applied evolutionary computation to the optimization of the topology of artificial neural networks, with most works focusing on very simple architectures. However, times have changed, and nowadays convolutional neural networks are the industry and academia standard for solving a variety of problems, many of which remained unsolved before the discovery of this kind of networks. Convolutional neural networks involve complex topologies, and the manual design of these topologies for solving a problem at hand is expensive and inefficient. In this thesis, our aim is to use neuroevolution in order to evolve the architecture of convolutional neural networks. To do so, we have decided to try two different techniques: genetic algorithms and grammatical evolution. We have implemented a niching scheme for preserving the genetic diversity, in order to ease the construction of ensembles of neural networks. These techniques have been validated against the MNIST database for handwritten digit recognition, achieving a test error rate of 0.28%, and the OPPORTUNITY data set for human activity recognition, attaining an F1 score of 0.9275. Both results have proven very competitive when compared with the state of the art. Also, in all cases, ensembles have proven to perform better than individual models. Later, the topologies learned for MNIST were tested on EMNIST, a database recently introduced in 2017, which includes more samples and a set of letters for character recognition. Results have shown that the topologies optimized for MNIST perform well on EMNIST, proving that architectures can be reused across domains with similar characteristics. In summary, neuroevolution is an effective approach for automatically designing topologies for convolutional neural networks. However, it still remains as an unexplored field due to hardware limitations. Current advances, however, should constitute the fuel that empowers the emergence of this field, and further research should start as of today.This Ph.D. dissertation has been partially supported by the Spanish Ministry of Education, Culture and Sports under FPU fellowship with identifier FPU13/03917. This research stay has been partially co-funded by the Spanish Ministry of Education, Culture and Sports under FPU short stay grant with identifier EST15/00260.Programa Oficial de Doctorado en Ciencia y Tecnología InformáticaPresidente: María Araceli Sanchís de Miguel.- Secretario: Francisco Javier Segovia Pérez.- Vocal: Simon Luca

Automatic CNN channel selection and effective detection on face and rotated aerial objects

Balancing accuracy and computational cost is a challenging task in computer vision. This is especially true for convolutional neural networks (CNNs), which required far larger scale of processing power than traditional learning algorithms. This thesis is aimed at the development of new CNN structures and loss functions to tackle the unbalanced accuracy-effciency issue in image classification and object detection, which are two fundamental yet challenging tasks of computer vision. For a CNN based object detector, the main computational cost is caused by the feature extractor (backbone), which has been originally applied to image classification.;Optimising the structure of CNN applied to image classification will bring benefits when it is applied to object detection. Although the outputs of detectors may vary across detection tasks, the challenges and the design principles among detectors are similar. Therefore, this thesis will start with face detection (i.e. a single object detection task), which is a significant branch of objection detection and has been widely used in real life. After that, object detection on aerial image will be investigated, which is a more challenging detection task.;Specifically, the objectives of this thesis are: 1. Optimising the CNN structures for image classification; 2. Developing a face detector which enables a trade-off between computational cost and accuracy; and 3. Proposing an object detector for aerial images, which suppresses the background noise without damaging the inference efficiency.;For the first target, this thesis aims to automatically optimise the topology of CNNs to generate the structure of fixed-length models, in which unnecessary convolutional kernels are removed. Experimental results have demonstrated that the optimised model can achieve comparable accuracy to the state-of-the-art models, across a broad range of datasets, whilst significantly reducing the number of parameters.;To tackle the unbalanced accuracy-effciency challenge in face detection, a novel context enhanced approach is proposed which improves the performance of the face detector in terms of both loss function and structure. For loss function optimisation, a hierarchical loss, referred to as 'triple loss' in this thesis, is introduced to optimise the feature pyramid network (FPN) based face detector. For structural optimisation, this thesis proposes a context-sensitive structure to increase the capacity of the network prediction. Experimental results indicate that the proposed method achieves a good balance between the accuracy and computational cost of face detection.;To suppress the background noise in aerial image object detection, this thesis presents a two-stage detector, named as 'SAFDet'. To be more specific, a rotation anchor-free-branch (RAFB) is proposed to regress the precise rectangle boundary. Asthe RAFB is anchor free, the computational cost is negligible during training. Meanwhile,a centre prediction module (CPM) is introduced to enhance the capabilities oftarget localisation and noise suppression from the background. As the CPM is only deployed during training, it does not increase the computational cost of inference. Experimental results indicate that the proposed method achieves a good balance between the accuracy and computational cost, and it effectively suppresses the background noise at the same time.Balancing accuracy and computational cost is a challenging task in computer vision. This is especially true for convolutional neural networks (CNNs), which required far larger scale of processing power than traditional learning algorithms. This thesis is aimed at the development of new CNN structures and loss functions to tackle the unbalanced accuracy-effciency issue in image classification and object detection, which are two fundamental yet challenging tasks of computer vision. For a CNN based object detector, the main computational cost is caused by the feature extractor (backbone), which has been originally applied to image classification.;Optimising the structure of CNN applied to image classification will bring benefits when it is applied to object detection. Although the outputs of detectors may vary across detection tasks, the challenges and the design principles among detectors are similar. Therefore, this thesis will start with face detection (i.e. a single object detection task), which is a significant branch of objection detection and has been widely used in real life. After that, object detection on aerial image will be investigated, which is a more challenging detection task.;Specifically, the objectives of this thesis are: 1. Optimising the CNN structures for image classification; 2. Developing a face detector which enables a trade-off between computational cost and accuracy; and 3. Proposing an object detector for aerial images, which suppresses the background noise without damaging the inference efficiency.;For the first target, this thesis aims to automatically optimise the topology of CNNs to generate the structure of fixed-length models, in which unnecessary convolutional kernels are removed. Experimental results have demonstrated that the optimised model can achieve comparable accuracy to the state-of-the-art models, across a broad range of datasets, whilst significantly reducing the number of parameters.;To tackle the unbalanced accuracy-effciency challenge in face detection, a novel context enhanced approach is proposed which improves the performance of the face detector in terms of both loss function and structure. For loss function optimisation, a hierarchical loss, referred to as 'triple loss' in this thesis, is introduced to optimise the feature pyramid network (FPN) based face detector. For structural optimisation, this thesis proposes a context-sensitive structure to increase the capacity of the network prediction. Experimental results indicate that the proposed method achieves a good balance between the accuracy and computational cost of face detection.;To suppress the background noise in aerial image object detection, this thesis presents a two-stage detector, named as 'SAFDet'. To be more specific, a rotation anchor-free-branch (RAFB) is proposed to regress the precise rectangle boundary. Asthe RAFB is anchor free, the computational cost is negligible during training. Meanwhile,a centre prediction module (CPM) is introduced to enhance the capabilities oftarget localisation and noise suppression from the background. As the CPM is only deployed during training, it does not increase the computational cost of inference. Experimental results indicate that the proposed method achieves a good balance between the accuracy and computational cost, and it effectively suppresses the background noise at the same time