Otimização multi-objetivo em aprendizado de máquina

Orientador: Fernando José Von ZubenTese (doutorado) - Universidade Estadual de Campinas, Faculdade de Engenharia Elétrica e de ComputaçãoResumo: Regressão logística multinomial regularizada, classificação multi-rótulo e aprendizado multi-tarefa são exemplos de problemas de aprendizado de máquina em que objetivos conflitantes, como funções de perda e penalidades que promovem regularização, devem ser simultaneamente minimizadas. Portanto, a perspectiva simplista de procurar o modelo de aprendizado com o melhor desempenho deve ser substituída pela proposição e subsequente exploração de múltiplos modelos de aprendizado eficientes, cada um caracterizado por um compromisso (trade-off) distinto entre os objetivos conflitantes. Comitês de máquinas e preferências a posteriori do tomador de decisão podem ser implementadas visando explorar adequadamente este conjunto diverso de modelos de aprendizado eficientes, em busca de melhoria de desempenho. A estrutura conceitual multi-objetivo para aprendizado de máquina é suportada por três etapas: (1) Modelagem multi-objetivo de cada problema de aprendizado, destacando explicitamente os objetivos conflitantes envolvidos; (2) Dada a formulação multi-objetivo do problema de aprendizado, por exemplo, considerando funções de perda e termos de penalização como objetivos conflitantes, soluções eficientes e bem distribuídas ao longo da fronteira de Pareto são obtidas por um solver determinístico e exato denominado NISE (do inglês Non-Inferior Set Estimation); (3) Esses modelos de aprendizado eficientes são então submetidos a um processo de seleção de modelos que opera com preferências a posteriori, ou a filtragem e agregação para a síntese de ensembles. Como o NISE é restrito a problemas de dois objetivos, uma extensão do NISE capaz de lidar com mais de dois objetivos, denominada MONISE (do inglês Many-Objective NISE), também é proposta aqui, sendo uma contribuição adicional que expande a aplicabilidade da estrutura conceitual proposta. Para atestar adequadamente o mérito da nossa abordagem multi-objetivo, foram realizadas investigações mais específicas, restritas à aprendizagem de modelos lineares regularizados: (1) Qual é o mérito relativo da seleção a posteriori de um único modelo de aprendizado, entre os produzidos pela nossa proposta, quando comparado com outras abordagens de modelo único na literatura? (2) O nível de diversidade dos modelos de aprendizado produzidos pela nossa proposta é superior àquele alcançado por abordagens alternativas dedicadas à geração de múltiplos modelos de aprendizado? (3) E quanto à qualidade de predição da filtragem e agregação dos modelos de aprendizado produzidos pela nossa proposta quando aplicados a: (i) classificação multi-classe, (ii) classificação desbalanceada, (iii) classificação multi-rótulo, (iv) aprendizado multi-tarefa, (v) aprendizado com multiplos conjuntos de atributos? A natureza determinística de NISE e MONISE, sua capacidade de lidar adequadamente com a forma da fronteira de Pareto em cada problema de aprendizado, e a garantia de sempre obter modelos de aprendizado eficientes são aqui pleiteados como responsáveis pelos resultados promissores alcançados em todas essas três frentes de investigação específicasAbstract: Regularized multinomial logistic regression, multi-label classification, and multi-task learning are examples of machine learning problems in which conflicting objectives, such as losses and regularization penalties, should be simultaneously minimized. Therefore, the narrow perspective of looking for the learning model with the best performance should be replaced by the proposition and further exploration of multiple efficient learning models, each one characterized by a distinct trade-off among the conflicting objectives. Committee machines and a posteriori preferences of the decision-maker may be implemented to properly explore this diverse set of efficient learning models toward performance improvement. The whole multi-objective framework for machine learning is supported by three stages: (1) The multi-objective modelling of each learning problem, explicitly highlighting the conflicting objectives involved; (2) Given the multi-objective formulation of the learning problem, for instance, considering loss functions and penalty terms as conflicting objective functions, efficient solutions well-distributed along the Pareto front are obtained by a deterministic and exact solver named NISE (Non-Inferior Set Estimation); (3) Those efficient learning models are then subject to a posteriori model selection, or to ensemble filtering and aggregation. Given that NISE is restricted to two objective functions, an extension for many objectives, named MONISE (Many Objective NISE), is also proposed here, being an additional contribution and expanding the applicability of the proposed framework. To properly access the merit of our multi-objective approach, more specific investigations were conducted, restricted to regularized linear learning models: (1) What is the relative merit of the a posteriori selection of a single learning model, among the ones produced by our proposal, when compared with other single-model approaches in the literature? (2) Is the diversity level of the learning models produced by our proposal higher than the diversity level achieved by alternative approaches devoted to generating multiple learning models? (3) What about the prediction quality of ensemble filtering and aggregation of the learning models produced by our proposal on: (i) multi-class classification, (ii) unbalanced classification, (iii) multi-label classification, (iv) multi-task learning, (v) multi-view learning? The deterministic nature of NISE and MONISE, their ability to properly deal with the shape of the Pareto front in each learning problem, and the guarantee of always obtaining efficient learning models are advocated here as being responsible for the promising results achieved in all those three specific investigationsDoutoradoEngenharia de ComputaçãoDoutor em Engenharia Elétrica2014/13533-0FAPES

Deep diversification of an AAV capsid protein by machine learning.

Modern experimental technologies can assay large numbers of biological sequences, but engineered protein libraries rarely exceed the sequence diversity of natural protein families. Machine learning (ML) models trained directly on experimental data without biophysical modeling provide one route to accessing the full potential diversity of engineered proteins. Here we apply deep learning to design highly diverse adeno-associated virus 2 (AAV2) capsid protein variants that remain viable for packaging of a DNA payload. Focusing on a 28-amino acid segment, we generated 201,426 variants of the AAV2 wild-type (WT) sequence yielding 110,689 viable engineered capsids, 57,348 of which surpass the average diversity of natural AAV serotype sequences, with 12-29 mutations across this region. Even when trained on limited data, deep neural network models accurately predict capsid viability across diverse variants. This approach unlocks vast areas of functional but previously unreachable sequence space, with many potential applications for the generation of improved viral vectors and protein therapeutics

Dynamic optimization of classification systems for adaptive incremental learning.

Tese de Doutorado, defendida na Université Du Québec, Canadian. 2010An incremental learning system updates itself in response to incoming data without reexamining all the old data. Since classification systems capable of incrementally storing, filtering, and classifying data are economical, in terms of both space and time, which makes them immensely useful for industrial, military, and commercial purposes, interest in designing them is growing. However, the challenge with incremental learning is that classification tasks can no longer be seen as unvarying, since they can actually change with the evolution of the data. These changes in turn cause dynamic changes to occur in the classification system’s parameters If such variations are neglected, the overall performance of these systems will be compromised in the future. In this thesis, on the development of a system capable of incrementally accommodating new data and dynamically tracking new optimum system parameters for self-adaptation, we first address the optimum selection of classifiers over time. We propose a framework which combines the power of Swarm Intelligence Theory and the conventional grid-search method to progressively identify potential solutions for gradually updating training datasets. The key here is to consider the adjustment of classifier parameters as a dynamic optimization problem that depends on the data available. Specifically, it has been shown that, if the intention is to build efficient Support Vector Machine (SVM) classifiers from sources that provide data gradually and serially, then the best way to do this is to consider model selection as a dynamic process which can evolve and change over time. This means that a number of solutions are required, depending on the knowledge available about the problem and uncertainties in the data. We also investigate measures for evaluating and selecting classifier ensembles composed of SVM classifiers. The measures employed are based on two different theories (diversity and margin) commonly used to understand the success of ensembles. This study has given us valuable insights and helped us to establish confidence-based measures as a tool for the selection of classifier ensembles. The main contribution of this thesis is a dynamic optimization approach that performs incremental learning in an adaptive fashion by tracking, evolving, and combining optimum hypotheses over time. The approach incorporates various theories, such as dynamic Particle Swarm Optimization, incremental Support Vector Machine classifiers, change detection, and dynamic ensemble selection based on classifier confidence levels. Experiments carried out on synthetic and real-world databases demonstrate that the proposed approach outperforms the classification methods often used in incremental learning scenarios

Holistic Learning for Multi-Target and Network Monitoring Problems

abstract: Technological advances have enabled the generation and collection of various data from complex systems, thus, creating ample opportunity to integrate knowledge in many decision making applications. This dissertation introduces holistic learning as the integration of a comprehensive set of relationships that are used towards the learning objective. The holistic view of the problem allows for richer learning from data and, thereby, improves decision making. The first topic of this dissertation is the prediction of several target attributes using a common set of predictor attributes. In a holistic learning approach, the relationships between target attributes are embedded into the learning algorithm created in this dissertation. Specifically, a novel tree based ensemble that leverages the relationships between target attributes towards constructing a diverse, yet strong, model is proposed. The method is justified through its connection to existing methods and experimental evaluations on synthetic and real data. The second topic pertains to monitoring complex systems that are modeled as networks. Such systems present a rich set of attributes and relationships for which holistic learning is important. In social networks, for example, in addition to friendship ties, various attributes concerning the users' gender, age, topic of messages, time of messages, etc. are collected. A restricted form of monitoring fails to take the relationships of multiple attributes into account, whereas the holistic view embeds such relationships in the monitoring methods. The focus is on the difficult task to detect a change that might only impact a small subset of the network and only occur in a sub-region of the high-dimensional space of the network attributes. One contribution is a monitoring algorithm based on a network statistical model. Another contribution is a transactional model that transforms the task into an expedient structure for machine learning, along with a generalizable algorithm to monitor the attributed network. A learning step in this algorithm adapts to changes that may only be local to sub-regions (with a broader potential for other learning tasks). Diagnostic tools to interpret the change are provided. This robust, generalizable, holistic monitoring method is elaborated on synthetic and real networks.Dissertation/ThesisDoctoral Dissertation Industrial Engineering 201

A survey on learning from imbalanced data streams: taxonomy, challenges, empirical study, and reproducible experimental framework

Class imbalance poses new challenges when it comes to classifying data streams. Many algorithms recently proposed in the literature tackle this problem using a variety of data-level, algorithm-level, and ensemble approaches. However, there is a lack of standardized and agreed-upon procedures on how to evaluate these algorithms. This work presents a taxonomy of algorithms for imbalanced data streams and proposes a standardized, exhaustive, and informative experimental testbed to evaluate algorithms in a collection of diverse and challenging imbalanced data stream scenarios. The experimental study evaluates 24 state-of-the-art data streams algorithms on 515 imbalanced data streams that combine static and dynamic class imbalance ratios, instance-level difficulties, concept drift, real-world and semi-synthetic datasets in binary and multi-class scenarios. This leads to the largest experimental study conducted so far in the data stream mining domain. We discuss the advantages and disadvantages of state-of-the-art classifiers in each of these scenarios and we provide general recommendations to end-users for selecting the best algorithms for imbalanced data streams. Additionally, we formulate open challenges and future directions for this domain. Our experimental testbed is fully reproducible and easy to extend with new methods. This way we propose the first standardized approach to conducting experiments in imbalanced data streams that can be used by other researchers to create trustworthy and fair evaluation of newly proposed methods. Our experimental framework can be downloaded from https://github.com/canoalberto/imbalanced-streams

A Novel Data Augmentation Technique for Out-of-Distribution Sample Detection using Compounded Corruptions

Modern deep neural network models are known to erroneously classify out-of-distribution (OOD) test data into one of the in-distribution (ID) training classes with high confidence. This can have disastrous consequences for safety-critical applications. A popular mitigation strategy is to train a separate classifier that can detect such OOD samples at the test time. In most practical settings OOD examples are not known at the train time, and hence a key question is: how to augment the ID data with synthetic OOD samples for training such an OOD detector? In this paper, we propose a novel Compounded Corruption technique for the OOD data augmentation termed CnC. One of the major advantages of CnC is that it does not require any hold-out data apart from the training set. Further, unlike current state-of-the-art (SOTA) techniques, CnC does not require backpropagation or ensembling at the test time, making our method much faster at inference. Our extensive comparison with 20 methods from the major conferences in last 4 years show that a model trained using CnC based data augmentation, significantly outperforms SOTA, both in terms of OOD detection accuracy as well as inference time. We include a detailed post-hoc analysis to investigate the reasons for the success of our method and identify higher relative entropy and diversity of CnC samples as probable causes. We also provide theoretical insights via a piece-wise decomposition analysis on a two-dimensional dataset to reveal (visually and quantitatively) that our approach leads to a tighter boundary around ID classes, leading to better detection of OOD samples. Source code link: https://github.com/cnc-oodComment: 16 pages of the main text, and supplemental material. Accepted in Research Track ECML'22. Project webpage: https://cnc-ood.github.io

Learning from Multi-Class Imbalanced Big Data with Apache Spark

With data becoming a new form of currency, its analysis has become a top priority in both academia and industry, furthering advancements in high-performance computing and machine learning. However, these large, real-world datasets come with additional complications such as noise and class overlap. Problems are magnified when with multi-class data is presented, especially since many of the popular algorithms were originally designed for binary data. Another challenge arises when the number of examples are not evenly distributed across all classes in a dataset. This often causes classifiers to favor the majority class over the minority classes, leading to undesirable results as learning from the rare cases may be the primary goal. Many of the classic machine learning algorithms were not designed for multi-class, imbalanced data or parallelism, and so their effectiveness has been hindered. This dissertation addresses some of these challenges with in-depth experimentation using novel implementations of machine learning algorithms using Apache Spark, a distributed computing framework based on the MapReduce model designed to handle very large datasets. Experimentation showed that many of the traditional classifier algorithms do not translate well to a distributed computing environment, indicating the need for a new generation of algorithms targeting modern high-performance computing. A collection of popular oversampling methods, originally designed for small binary class datasets, have been implemented using Apache Spark for the first time to improve parallelism and add multi-class support. An extensive study on how instance level difficulty affects the learning from large datasets was also performed