Uma ferramenta unificada para projeto, desenvolvimento, execução e recomendação de experimentos de aprendizado de máquina

Orientadores: Ricardo da Silva Torres, Anderson de Rezende RochaDissertação (mestrado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Devido ao grande crescimento do uso de tecnologias para a aquisição de dados, temos que lidar com grandes e complexos conjuntos de dados a fim de extrair conhecimento que possa auxiliar o processo de tomada de decisão em diversos domínios de aplicação. Uma solução típica para abordar esta questão se baseia na utilização de métodos de aprendizado de máquina, que são métodos computacionais que extraem conhecimento útil a partir de experiências para melhorar o desempenho de aplicações-alvo. Existem diversas bibliotecas e arcabouços na literatura que oferecem apoio à execução de experimentos de aprendizado de máquina, no entanto, alguns não são flexíveis o suficiente para poderem ser estendidos com novos métodos, além de não oferecerem mecanismos que permitam o reuso de soluções de sucesso concebidos em experimentos anteriores na ferramenta. Neste trabalho, propomos um arcabouço para automatizar experimentos de aprendizado de máquina, oferecendo um ambiente padronizado baseado em workflow, tornando mais fácil a tarefa de avaliar diferentes descritores de características, classificadores e abordagens de fusão em uma ampla gama de tarefas. Também propomos o uso de medidas de similaridade e métodos de learning-to-rank em um cenário de recomendação, para que usuários possam ter acesso a soluções alternativas envolvendo experimentos de aprendizado de máquina. Nós realizamos experimentos com quatro medidas de similaridade (Jaccard, Sorensen, Jaro-Winkler e baseada em TF-IDF) e um método de learning-to-rank (LRAR) na tarefa de recomendar workflows modelados como uma sequência de atividades. Os resultados dos experimentos mostram que a medida Jaro-Winkler obteve o melhor desempenho, com resultados comparáveis aos observados para o método LRAR. Em ambos os casos, as recomendações realizadas são promissoras, e podem ajudar usuários reais em diferentes tarefas de aprendizado de máquinaAbstract: Due to the large growth of the use of technologies for data acquisition, we have to handle large and complex data sets in order to extract knowledge that can support the decision-making process in several domains. A typical solution for addressing this issue relies on the use of machine learning methods, which are computational methods that extract useful knowledge from experience to improve performance of target applications. There are several libraries and frameworks in the literature that support the execution of machine learning experiments. However, some of them are not flexible enough for being extended with novel methods and they do not support reusing of successful solutions devised in previous experiments made in the framework. In this work, we propose a framework for automating machine learning experiments that provides a workflow-based standardized environment and makes it easy to evaluate different feature descriptors, classifiers, and fusion approaches in a wide range of tasks. We also propose the use of similarity measures and learning-to-rank methods in a recommendation scenario, in which users may have access to alternative machine learning experiments. We performed experiments with four similarity measures (Jaccard, Sorensen, Jaro-Winkler, and a TF-IDF-based measure) and one learning-to-rank method (LRAR) in the task of recommending workflows modeled as a sequence of activities. Experimental results show that Jaro-Winkler yields the highest effectiveness performance with comparable results to those observed for LRAR. In both cases, the recommendations performed are very promising and might help real-world users in different daily machine learning tasksMestradoCiência da ComputaçãoMestre em Ciência da Computaçã

Enhancing Workflow with a Semantic Description of Scientific Intent

Peer reviewedPreprin

Towards Collaborative Scientific Workflow Management System

The big data explosion phenomenon has impacted several domains, starting from research areas to divergent of business models in recent years. As this intensive amount of data opens up the possibilities of several interesting knowledge discoveries, over the past few years divergent of research domains have undergone the shift of trend towards analyzing those massive amount data. Scientific Workflow Management System (SWfMS) has gained much popularity in recent years in accelerating those data-intensive analyses, visualization, and discoveries of important information. Data-intensive tasks are often significantly time-consuming and complex in nature and hence SWfMSs are designed to efficiently support the specification, modification, execution, failure handling, and monitoring of the tasks in a scientific workflow. As far as the complexity, dimension, and volume of data are concerned, their effective analysis or management often become challenging for an individual and requires collaboration of multiple scientists instead. Hence, the notion of 'Collaborative SWfMS' was coined - which gained significant interest among researchers in recent years as none of the existing SWfMSs directly support real-time collaboration among scientists. In terms of collaborative SWfMSs, consistency management in the face of conflicting concurrent operations of the collaborators is a major challenge for its highly interconnected document structure among the computational modules - where any minor change in a part of the workflow can highly impact the other part of the collaborative workflow for the datalink relation among them. In addition to the consistency management, studies show several other challenges that need to be addressed towards a successful design of collaborative SWfMSs, such as sub-workflow composition and execution by different sub-groups, relationship between scientific workflows and collaboration models, sub-workflow monitoring, seamless integration and access control of the workflow components among collaborators and so on. In this thesis, we propose a locking scheme to facilitate consistency management in collaborative SWfMSs. The proposed method works by locking workflow components at a granular attribute level in addition to supporting locks on a targeted part of the collaborative workflow. We conducted several experiments to analyze the performance of the proposed method in comparison to related existing methods. Our studies show that the proposed method can reduce the average waiting time of a collaborator by up to 36% while increasing the average workflow update rate by up to 15% in comparison to existing descendent modular level locking techniques for collaborative SWfMSs. We also propose a role-based access control technique for the management of collaborative SWfMSs. We leverage the Collaborative Interactive Application Methodology (CIAM) for the investigation of role-based access control in the context of collaborative SWfMSs. We present our proposed method with a use-case of Plant Phenotyping and Genotyping research domain. Recent study shows that the collaborative SWfMSs often different sets of opportunities and challenges. From our investigations on existing research works towards collaborative SWfMSs and findings of our prior two studies, we propose an architecture of collaborative SWfMSs. We propose - SciWorCS - a Collaborative Scientific Workflow Management System as a proof of concept of the proposed architecture; which is the first of its kind to the best of our knowledge. We present several real-world use-cases of scientific workflows using SciWorCS. Finally, we conduct several user studies using SciWorCS comprising different real-world scientific workflows (i.e., from myExperiment) to understand the user behavior and styles of work in the context of collaborative SWfMSs. In addition to evaluating SciWorCS, the user studies reveal several interesting facts which can significantly contribute in the research domain, as none of the existing methods considered such empirical studies, and rather relied only on computer generated simulated studies for evaluation

Recuperação de informação multimodal em repositórios de imagem médica

The proliferation of digital medical imaging modalities in hospitals and other diagnostic facilities has created huge repositories of valuable data, often not fully explored. Moreover, the past few years show a growing trend of data production. As such, studying new ways to index, process and retrieve medical images becomes an important subject to be addressed by the wider community of radiologists, scientists and engineers. Content-based image retrieval, which encompasses various methods, can exploit the visual information of a medical imaging archive, and is known to be beneficial to practitioners and researchers. However, the integration of the latest systems for medical image retrieval into clinical workflows is still rare, and their effectiveness still show room for improvement. This thesis proposes solutions and methods for multimodal information retrieval, in the context of medical imaging repositories. The major contributions are a search engine for medical imaging studies supporting multimodal queries in an extensible archive; a framework for automated labeling of medical images for content discovery; and an assessment and proposal of feature learning techniques for concept detection from medical images, exhibiting greater potential than feature extraction algorithms that were pertinently used in similar tasks. These contributions, each in their own dimension, seek to narrow the scientific and technical gap towards the development and adoption of novel multimodal medical image retrieval systems, to ultimately become part of the workflows of medical practitioners, teachers, and researchers in healthcare.A proliferação de modalidades de imagem médica digital, em hospitais, clínicas e outros centros de diagnóstico, levou à criação de enormes repositórios de dados, frequentemente não explorados na sua totalidade. Além disso, os últimos anos revelam, claramente, uma tendência para o crescimento da produção de dados. Portanto, torna-se importante estudar novas maneiras de indexar, processar e recuperar imagens médicas, por parte da comunidade alargada de radiologistas, cientistas e engenheiros. A recuperação de imagens baseada em conteúdo, que envolve uma grande variedade de métodos, permite a exploração da informação visual num arquivo de imagem médica, o que traz benefícios para os médicos e investigadores. Contudo, a integração destas soluções nos fluxos de trabalho é ainda rara e a eficácia dos mais recentes sistemas de recuperação de imagem médica pode ser melhorada. A presente tese propõe soluções e métodos para recuperação de informação multimodal, no contexto de repositórios de imagem médica. As contribuições principais são as seguintes: um motor de pesquisa para estudos de imagem médica com suporte a pesquisas multimodais num arquivo extensível; uma estrutura para a anotação automática de imagens; e uma avaliação e proposta de técnicas de representation learning para deteção automática de conceitos em imagens médicas, exibindo maior potencial do que as técnicas de extração de features visuais outrora pertinentes em tarefas semelhantes. Estas contribuições procuram reduzir as dificuldades técnicas e científicas para o desenvolvimento e adoção de sistemas modernos de recuperação de imagem médica multimodal, de modo a que estes façam finalmente parte das ferramentas típicas dos profissionais, professores e investigadores da área da saúde.Programa Doutoral em Informátic

Exploratory search in time-oriented primary data

In a variety of research fields, primary data that describes scientific phenomena in an original condition is obtained. Time-oriented primary data, in particular, is an indispensable data type, derived from complex measurements depending on time. Today, time-oriented primary data is collected at rates that exceed the domain experts’ abilities to seek valuable information undiscovered in the data. It is widely accepted that the magnitudes of uninvestigated data will disclose tremendous knowledge in data-driven research, provided that domain experts are able to gain insight into the data. Domain experts involved in data-driven research urgently require analytical capabilities. In scientific practice, predominant activities are the generation and validation of hypotheses. In analytical terms, these activities are often expressed in confirmatory and exploratory data analysis. Ideally, analytical support would combine the strengths of both types of activities. Exploratory search (ES) is a concept that seamlessly includes information-seeking behaviors ranging from search to exploration. ES supports domain experts in both gaining an understanding of huge and potentially unknown data collections and the drill-down to relevant subsets, e.g., to validate hypotheses. As such, ES combines predominant tasks of domain experts applied to data-driven research. For the design of useful and usable ES systems (ESS), data scientists have to incorporate different sources of knowledge and technology. Of particular importance is the state-of-the-art in interactive data visualization and data analysis. Research in these factors is at heart of Information Visualization (IV) and Visual Analytics (VA). Approaches in IV and VA provide meaningful visualization and interaction designs, allowing domain experts to perform the information-seeking process in an effective and efficient way. Today, bestpractice ESS almost exclusively exist for textual data content, e.g., put into practice in digital libraries to facilitate the reuse of digital documents. For time-oriented primary data, ES mainly remains at a theoretical state. Motivation and Problem Statement. This thesis is motivated by two main assumptions. First, we expect that ES will have a tremendous impact on data-driven research for many research fields. In this thesis, we focus on time-oriented primary data, as a complex and important data type for data-driven research. Second, we assume that research conducted to IV and VA will particularly facilitate ES. For time-oriented primary data, however, novel concepts and techniques are required that enhance the design and the application of ESS. In particular, we observe a lack of methodological research in ESS for time-oriented primary data. In addition, the size, the complexity, and the quality of time-oriented primary data hampers the content-based access, as well as the design of visual interfaces for gaining an overview of the data content. Furthermore, the question arises how ESS can incorporate techniques for seeking relations between data content and metadata to foster data-driven research. Overarching challenges for data scientists are to create usable and useful designs, urgently requiring the involvement of the targeted user group and support techniques for choosing meaningful algorithmic models and model parameters. Throughout this thesis, we will resolve these challenges from conceptual, technical, and systemic perspectives. In turn, domain experts can benefit from novel ESS as a powerful analytical support to conduct data-driven research. Concepts for Exploratory Search Systems (Chapter 3). We postulate concepts for the ES in time-oriented primary data. Based on a survey of analysis tasks supported in IV and VA research, we present a comprehensive selection of tasks and techniques relevant for search and exploration activities. The assembly guides data scientists in the choice of meaningful techniques presented in IV and VA. Furthermore, we present a reference workflow for the design and the application of ESS for time-oriented primary data. The workflow divides the data processing and transformation process into four steps, and thus divides the complexity of the design space into manageable parts. In addition, the reference workflow describes how users can be involved in the design. The reference workflow is the framework for the technical contributions of this thesis. Visual-Interactive Preprocessing of Time-Oriented Primary Data (Chapter 4). We present a visual-interactive system that enables users to construct workflows for preprocessing time-oriented primary data. In this way, we introduce a means of providing content-based access. Based on a rich set of preprocessing routines, users can create individual solutions for data cleansing, normalization, segmentation, and other preprocessing tasks. In addition, the system supports the definition of time series descriptors and time series distance measures. Guidance concepts support users in assessing the workflow generalizability, which is important for large data sets. The execution of the workflows transforms time-oriented primary data into feature vectors, which can subsequently be used for downstream search and exploration techniques. We demonstrate the applicability of the system in usage scenarios and case studies. Content-Based Overviews (Chapter 5). We introduce novel guidelines and techniques for the design of contentbased overviews. The three key factors are the creation of meaningful data aggregates, the visual mapping of these aggregates into the visual space, and the view transformation providing layouts of these aggregates in the display space. For each of these steps, we characterize important visualization and interaction design parameters allowing the involvement of users. We introduce guidelines supporting data scientists in choosing meaningful solutions. In addition, we present novel visual-interactive quality assessment techniques enhancing the choice of algorithmic model and model parameters. Finally, we present visual interfaces enabling users to formulate visual queries of the time-oriented data content. In this way, we provide means of combining content-based exploration with content-based search. Relation Seeking Between Data Content and Metadata (Chapter 6). We present novel visual interfaces enabling domain experts to seek relations between data content and metadata. These interfaces can be integrated into ESS to bridge analytical gaps between the data content and attached metadata. In three different approaches, we focus on different types of relations and define algorithmic support to guide users towards most interesting relations. Furthermore, each of the three approaches comprises individual visualization and interaction designs, enabling users to explore both the data and the relations in an efficient and effective way. We demonstrate the applicability of our interfaces with usage scenarios, each conducted together with domain experts. The results confirm that our techniques are beneficial for seeking relations between data content and metadata, particularly for data-centered research. Case Studies - Exploratory Search Systems (Chapter 7). In two case studies, we put our concepts and techniques into practice. We present two ESS constructed in design studies with real users, and real ES tasks, and real timeoriented primary data collections. The web-based VisInfo ESS is a digital library system facilitating the visual access to time-oriented primary data content. A content-based overview enables users to explore large collections of time series measurements and serves as a baseline for content-based queries by example. In addition, VisInfo provides a visual interface for querying time oriented data content by sketch. A result visualization combines different views of the data content and metadata with faceted search functionality. The MotionExplorer ESS supports domain experts in human motion analysis. Two content-based overviews enhance the exploration of large collections of human motion capture data from two perspectives. MotionExplorer provides a search interface, allowing domain experts to query human motion sequences by example. Retrieval results are depicted in a visual-interactive view enabling the exploration of variations of human motions. Field study evaluations performed for both ESS confirm the applicability of the systems in the environment of the involved user groups. The systems yield a significant improvement of both the effectiveness and the efficiency in the day-to-day work of the domain experts. As such, both ESS demonstrate how large collections of time-oriented primary data can be reused to enhance data-centered research. In essence, our contributions cover the entire time series analysis process starting from accessing raw time-oriented primary data, processing and transforming time series data, to visual-interactive analysis of time series. We present visual search interfaces providing content-based access to time-oriented primary data. In a series of novel explorationsupport techniques, we facilitate both gaining an overview of large and complex time-oriented primary data collections and seeking relations between data content and metadata. Throughout this thesis, we introduce VA as a means of designing effective and efficient visual-interactive systems. Our VA techniques empower data scientists to choose appropriate models and model parameters, as well as to involve users in the design. With both principles, we support the design of usable and useful interfaces which can be included into ESS. In this way, our contributions bridge the gap between search systems requiring exploration support and exploratory data analysis systems requiring visual querying capability. In the ESS presented in two case studies, we prove that our techniques and systems support data-driven research in an efficient and effective way

Mixing Methods: Practical Insights from the Humanities in the Digital Age

The digital transformation is accompanied by two simultaneous processes: digital humanities challenging the humanities, their theories, methodologies and disciplinary identities, and pushing computer science to get involved in new fields. But how can qualitative and quantitative methods be usefully combined in one research project? What are the theoretical and methodological principles across all disciplinary digital approaches? This volume focusses on driving innovation and conceptualising the humanities in the 21st century. Building on the results of 10 research projects, it serves as a useful tool for designing cutting-edge research that goes beyond conventional strategies

Computer Vision and Architectural History at Eye Level:Mixed Methods for Linking Research in the Humanities and in Information Technology

Information on the history of architecture is embedded in our daily surroundings, in vernacular and heritage buildings and in physical objects, photographs and plans. Historians study these tangible and intangible artefacts and the communities that built and used them. Thus valuableinsights are gained into the past and the present as they also provide a foundation for designing the future. Given that our understanding of the past is limited by the inadequate availability of data, the article demonstrates that advanced computer tools can help gain more and well-linked data from the past. Computer vision can make a decisive contribution to the identification of image content in historical photographs. This application is particularly interesting for architectural history, where visual sources play an essential role in understanding the built environment of the past, yet lack of reliable metadata often hinders the use of materials. The automated recognition contributes to making a variety of image sources usable forresearch.<br/