Unsupervised Graph-based Rank Aggregation for Improved Retrieval

This paper presents a robust and comprehensive graph-based rank aggregation approach, used to combine results of isolated ranker models in retrieval tasks. The method follows an unsupervised scheme, which is independent of how the isolated ranks are formulated. Our approach is able to combine arbitrary models, defined in terms of different ranking criteria, such as those based on textual, image or hybrid content representations. We reformulate the ad-hoc retrieval problem as a document retrieval based on fusion graphs, which we propose as a new unified representation model capable of merging multiple ranks and expressing inter-relationships of retrieval results automatically. By doing so, we claim that the retrieval system can benefit from learning the manifold structure of datasets, thus leading to more effective results. Another contribution is that our graph-based aggregation formulation, unlike existing approaches, allows for encapsulating contextual information encoded from multiple ranks, which can be directly used for ranking, without further computations and post-processing steps over the graphs. Based on the graphs, a novel similarity retrieval score is formulated using an efficient computation of minimum common subgraphs. Finally, another benefit over existing approaches is the absence of hyperparameters. A comprehensive experimental evaluation was conducted considering diverse well-known public datasets, composed of textual, image, and multimodal documents. Performed experiments demonstrate that our method reaches top performance, yielding better effectiveness scores than state-of-the-art baseline methods and promoting large gains over the rankers being fused, thus demonstrating the successful capability of the proposal in representing queries based on a unified graph-based model of rank fusions

Agregação de ranks baseada em grafos

Orientador: Ricardo da Silva TorresTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: Neste trabalho, apresentamos uma abordagem robusta de agregação de listas baseada em grafos, capaz de combinar resultados de modelos de recuperação isolados. O método segue um esquema não supervisionado, que é independente de como as listas isoladas são geradas. Nossa abordagem é capaz de incorporar modelos heterogêneos, de diferentes critérios de recuperação, tal como baseados em conteúdo textual, de imagem ou híbridos. Reformulamos o problema de recuperação ad-hoc como uma recuperação baseada em fusion graphs, que propomos como um novo modelo de representação unificada capaz de mesclar várias listas e expressar automaticamente inter-relações de resultados de recuperação. Assim, mostramos que o sistema de recuperação se beneficia do aprendizado da estrutura intrínseca das coleções, levando a melhores resultados de busca. Nossa formulação de agregação baseada em grafos, diferentemente das abordagens existentes, permite encapsular informação contextual oriunda de múltiplas listas, que podem ser usadas diretamente para ranqueamento. Experimentos realizados demonstram que o método apresenta alto desempenho, produzindo melhores eficácias que métodos recentes da literatura e promovendo ganhos expressivos sobre os métodos de recuperação fundidos. Outra contribuição é a extensão da proposta de grafo de fusão visando consulta eficiente. Trabalhos anteriores são promissores quanto à eficácia, mas geralmente ignoram questões de eficiência. Propomos uma função inovadora de agregação de consulta, não supervisionada, intrinsecamente multimodal almejando recuperação eficiente e eficaz. Introduzimos os conceitos de projeção e indexação de modelos de representação de agregação de consulta com base em grafos, e a sua aplicação em tarefas de busca. Formulações de projeção são propostas para representações de consulta baseadas em grafos. Introduzimos os fusion vectors, uma representação de fusão tardia de objetos com base em listas, a partir da qual é definido um modelo de recuperação baseado intrinsecamente em agregação. A seguir, apresentamos uma abordagem para consulta rápida baseada nos vetores de fusão, promovendo agregação de consultas eficiente. O método apresentou alta eficácia quanto ao estado da arte, além de trazer uma perspectiva de eficiência pouco abordada. Ganhos consistentes de eficiência são alcançadas em relação aos trabalhos recentes. Também propomos modelos de representação baseados em consulta para problemas gerais de predição. Os conceitos de grafos de fusão e vetores de fusão são estendidos para cenários de predição, nos quais podem ser usados para construir um modelo de estimador para determinar se um objeto de avaliação (ainda que multimodal) se refere a uma classe ou não. Experimentos em tarefas de classificação multimodal, tal como detecção de inundação, mostraram que a solução é altamente eficaz para diferentes cenários de predição que envolvam dados textuais, visuais e multimodais, produzindo resultados melhores que vários métodos recentes. Por fim, investigamos a adoção de abordagens de aprendizagem para ajudar a otimizar a criação de modelos de representação baseados em consultas, a fim de maximizar seus aspectos de capacidade discriminativa e eficiência em tarefas de predição e de buscaAbstract: In this work, we introduce a robust graph-based rank aggregation approach, capable of combining results of isolated ranker models in retrieval tasks. The method follows an unsupervised scheme, which is independent of how the isolated ranks are formulated. Our approach is able to incorporate heterogeneous models, defined in terms of different ranking criteria, such as those based on textual, image, or hybrid content representations. We reformulate the ad-hoc retrieval problem as a graph-based retrieval based on {\em fusion graphs}, which we propose as a new unified representation model capable of merging multiple ranks and expressing inter-relationships of retrieval results automatically. By doing so, we show that the retrieval system can benefit from learning the manifold structure of datasets, thus leading to more effective results. Our graph-based aggregation formulation, unlike existing approaches, allows for encapsulating contextual information encoded from multiple ranks, which can be directly used for ranking. Performed experiments demonstrate that our method reaches top performance, yielding better effectiveness scores than state-of-the-art baseline methods and promoting large gains over the rankers being fused. Another contribution refers to the extension of the fusion graph solution for efficient rank aggregation. Although previous works are promising with respect to effectiveness, they usually overlook efficiency aspects. We propose an innovative rank aggregation function that it is unsupervised, intrinsically multimodal, and targeted for fast retrieval and top effectiveness performance. We introduce the concepts of embedding and indexing graph-based rank-aggregation representation models, and their application for search tasks. Embedding formulations are also proposed for graph-based rank representations. We introduce the concept of {\em fusion vectors}, a late-fusion representation of objects based on ranks, from which an intrinsically rank-aggregation retrieval model is defined. Next, we present an approach for fast retrieval based on fusion vectors, thus promoting an efficient rank aggregation system. Our method presents top effectiveness performance among state-of-the-art related work, while promoting an efficiency perspective not yet covered. Consistent speedups are achieved against the recent baselines in all datasets considered. Derived from the fusion graphs and fusion vectors, we propose rank-based representation models for general prediction problems. The concepts of fusion graphs and fusion vectors are extended to prediction scenarios, where they can be used to build an estimator model to determine whether an input (even multimodal) object refers to a class or not. Performed experiments in the context of multimodal classification tasks, such as flood detection, show that the proposed solution is highly effective for different detection scenarios involving textual, visual, and multimodal features, yielding better detection results than several state-of-the-art methods. Finally, we investigate the adoption of learning approaches to help optimize the creation of rank-based representation models, in order to maximize their discriminative power and efficiency aspects in prediction and search tasksDoutoradoCiência da ComputaçãoDoutor em Ciência da Computaçã

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Automatic annotation for weakly supervised learning of detectors

PhDObject detection in images and action detection in videos are among the most widely studied computer vision problems, with applications in consumer photography, surveillance, and automatic media tagging. Typically, these standard detectors are fully supervised, that is they require a large body of training data where the locations of the objects/actions in images/videos have been manually annotated. With the emergence of digital media, and the rise of high-speed internet, raw images and video are available for little to no cost. However, the manual annotation of object and action locations remains tedious, slow, and expensive. As a result there has been a great interest in training detectors with weak supervision where only the presence or absence of object/action in image/video is needed, not the location. This thesis presents approaches for weakly supervised learning of object/action detectors with a focus on automatically annotating object and action locations in images/videos using only binary weak labels indicating the presence or absence of object/action in images/videos. First, a framework for weakly supervised learning of object detectors in images is presented. In the proposed approach, a variation of multiple instance learning (MIL) technique for automatically annotating object locations in weakly labelled data is presented which, unlike existing approaches, uses inter-class and intra-class cue fusion to obtain the initial annotation. The initial annotation is then used to start an iterative process in which standard object detectors are used to refine the location annotation. Finally, to ensure that the iterative training of detectors do not drift from the object of interest, a scheme for detecting model drift is also presented. Furthermore, unlike most other methods, our weakly supervised approach is evaluated on data without manual pose (object orientation) annotation. Second, an analysis of the initial annotation of objects, using inter-class and intra-class cues, is carried out. From the analysis, a new method based on negative mining (NegMine) is presented for the initial annotation of both object and action data. The NegMine based approach is a much simpler formulation using only inter-class measure and requires no complex combinatorial optimisation but can still meet or outperform existing approaches including the previously pre3 sented inter-intra class cue fusion approach. Furthermore, NegMine can be fused with existing approaches to boost their performance. Finally, the thesis will take a step back and look at the use of generic object detectors as prior knowledge in weakly supervised learning of object detectors. These generic object detectors are typically based on sampling saliency maps that indicate if a pixel belongs to the background or foreground. A new approach to generating saliency maps is presented that, unlike existing approaches, looks beyond the current image of interest and into images similar to the current image. We show that our generic object proposal method can be used by itself to annotate the weakly labelled object data with surprisingly high accuracy

Lightweight Adaptation of Classifiers to Users and Contexts: Trends of the Emerging Domain

Intelligent computer applications need to adapt their behaviour to contexts and users, but conventional classifier adaptation methods require long data collection and/or training times. Therefore classifier adaptation is often performed as follows: at design time application developers define typical usage contexts and provide reasoning models for each of these contexts, and then at runtime an appropriate model is selected from available ones. Typically, definition of usage contexts and reasoning models heavily relies on domain knowledge. However, in practice many applications are used in so diverse situations that no developer can predict them all and collect for each situation adequate training and test databases. Such applications have to adapt to a new user or unknown context at runtime just from interaction with the user, preferably in fairly lightweight ways, that is, requiring limited user effort to collect training data and limited time of performing the adaptation. This paper analyses adaptation trends in several emerging domains and outlines promising ideas, proposed for making multimodal classifiers user-specific and context-specific without significant user efforts, detailed domain knowledge, and/or complete retraining of the classifiers. Based on this analysis, this paper identifies important application characteristics and presents guidelines to consider these characteristics in adaptation design

Biomedical information extraction for matching patients to clinical trials

Digital Medical information had an astonishing growth on the last decades, driven by an unprecedented number of medical writers, which lead to a complete revolution in what and how much information is available to the health professionals. The problem with this wave of information is that performing a precise selection of the information retrieved by medical information repositories is very exhaustive and time consuming for physicians. This is one of the biggest challenges for physicians with the new digital era: how to reduce the time spent finding the perfect matching document for a patient (e.g. intervention articles, clinical trial, prescriptions). Precision Medicine (PM) 2017 is the track by the Text REtrieval Conference (TREC), that is focused on this type of challenges exclusively for oncology. Using a dataset with a large amount of clinical trials, this track is a good real life example on how information retrieval solutions can be used to solve this types of problems. This track can be a very good starting point for applying information extraction and retrieval methods, in a very complex domain. The purpose of this thesis is to improve a system designed by the NovaSearch team for TREC PM 2017 Clinical Trials task, which got ranked on the top-5 systems of 2017. The NovaSearch team also participated on the 2018 track and got a 15% increase on precision compared to the 2017 one. It was used multiple IR techniques for information extraction and processing of data, including rank fusion, query expansion (e.g. Pseudo relevance feedback, Mesh terms expansion) and experiments with Learning to Rank (LETOR) algorithms. Our goal is to retrieve the best possible set of trials for a given patient, using precise documents filters to exclude the unwanted clinical trials. This work can open doors in what can be done for searching and perceiving the criteria to exclude or include the trials, helping physicians even on the more complex and difficult information retrieval tasks

Improving Feature Selection Techniques for Machine Learning

As a commonly used technique in data preprocessing for machine learning, feature selection identifies important features and removes irrelevant, redundant or noise features to reduce the dimensionality of feature space. It improves efficiency, accuracy and comprehensibility of the models built by learning algorithms. Feature selection techniques have been widely employed in a variety of applications, such as genomic analysis, information retrieval, and text categorization. Researchers have introduced many feature selection algorithms with different selection criteria. However, it has been discovered that no single criterion is best for all applications. We proposed a hybrid feature selection framework called based on genetic algorithms (GAs) that employs a target learning algorithm to evaluate features, a wrapper method. We call it hybrid genetic feature selection (HGFS) framework. The advantages of this approach include the ability to accommodate multiple feature selection criteria and find small subsets of features that perform well for the target algorithm. The experiments on genomic data demonstrate that ours is a robust and effective approach that can find subsets of features with higher classification accuracy and/or smaller size compared to each individual feature selection algorithm. A common characteristic of text categorization tasks is multi-label classification with a great number of features, which makes wrapper methods time-consuming and impractical. We proposed a simple filter (non-wrapper) approach called Relation Strength and Frequency Variance (RSFV) measure. The basic idea is that informative features are those that are highly correlated with the class and distribute most differently among all classes. The approach is compared with two well-known feature selection methods in the experiments on two standard text corpora. The experiments show that RSFV generate equal or better performance than the others in many cases