Abstract: This work addresses the detection of Helicobacter pylori a bacterium classified since 1994 as class 1 carcinogen to humans. By its highest specificity and sensitivity, the preferred diagnosis technique is the analysis of histological images with immunohistochemical staining, a process in which certain stained antibodies bind to antigens of the biological element of interest. This analysis is a time demanding task, which is currently done by an expert pathologist that visually inspects the digitized samples.
We propose to use autoencoders to learn latent patterns of healthy tissue and detect H. pylori as an anomaly in image staining. Unlike existing classification approaches, an autoencoder is able to learn patterns in an unsupervised manner (without the need of image annotations) with high performance. In particular, our model has an overall 91% of accuracy with 86\% sensitivity, 96% specificity and 0.97 AUC in the detection of H. pylori.

Abstract: From its early stages, the community of Pattern Recognition and Computer Vision has considered the importance of leveraging the structural information when understanding images. Usually, graphs have been proposed as a suitable model to represent this kind of information due to their flexibility and representational power able to codify both, the components, objects, or entities and their pairwise relationship. Even though graphs have been successfully applied to a huge variety of tasks, as a result of their symbolic and relational nature, graphs have always suffered from some limitations compared to statistical approaches. Indeed, some trivial mathematical operations do not have an equivalence in the graph domain. For instance, in the core of many pattern recognition applications, there is a need to compare two objects. This operation, which is trivial when considering feature vectors defined in \(\mathbb{R}^n\), is not properly defined for graphs.

In this thesis, we have investigated the importance of the structural information from two perspectives, the traditional graph-based methods and the new advances on Geometric Deep Learning. On the one hand, we explore the problem of defining a graph representation and how to deal with it on a large scale and noisy scenario. On the other hand, Graph Neural Networks are proposed to first redefine a Graph Edit Distance methodologies as a metric learning problem, and second, to apply them in a real use case scenario for the detection of repetitive patterns which define tables in invoice documents. As experimental framework, we have validated the different methodological contributions in the domain of Document Image Analysis and Recognition.

Abstract: It is very common to find different versions of the same music work in archives of Opera Theaters. These differences correspond to modifications and annotations from the musicians. From the musicologist point of view, these variations are very interesting and deserve study. This paper explores the alignment of music scores as a tool for automatically detecting the passages that contain such differences. Given the difficulties in the recognition of handwritten music scores, our goal is to align the music scores and at the same time, avoid the recognition of music elements as much as possible. After removing the staff lines, braces and ties, the bar lines are detected. Then, the bar units are described as a whole using the Blurred Shape Model. The bar units alignment is performed by using Dynamic Time Warping. The analysis of the alignment path is used to detect the variations in the music scores. The method has been evaluated on a subset of the CVC-MUSCIMA dataset, showing encouraging results.

Abstract: Graph representations have been widely used in pattern recognition thanks to their powerful representation formalism and rich theoretical background. A number of error-tolerant graph matching algorithms such as graph edit distance have been proposed for computing a distance between two labelled graphs. However, they typically suffer from a high
computational complexity, which makes it difficult to apply
these matching algorithms in a real scenario. In this paper, we propose an efficient graph distance based on the emerging field of geometric deep learning. Our method employs a message passing neural network to capture the graph structure and learns a metric with a siamese network approach. The performance of the proposed graph distance is validated in two application cases, graph classification and graph retrieval of handwritten words, and shows a promising performance when compared with
(approximate) graph edit distance benchmarks.

Abstract: The emergence of geometric deep learning as a novel framework to deal with graph-based representations has faded away traditional approaches in favor of completely new methodologies. In this paper, we propose a new framework able to combine the advances on deep metric learning with traditional approximations of the graph edit distance. Hence, we propose an efficient graph distance based on the novel field of geometric deep learning. Our method employs a message passing neural network to capture the graph structure, and thus, leveraging this information for its use on a distance computation. The performance of the proposed graph distance is validated on two different scenarios. On the one hand, in a graph retrieval of handwritten words i.e. keyword spotting, showing its superior performance when compared with (approximate) graph edit distance benchmarks. On the other hand, demonstrating competitive results for graph similarity learning when compared with the current state-of-the-art on a recent benchmark dataset.

Abstract: Information Retrieval (IR) is the activity of obtaining information resources relevant to a questioned information. It usually retrieves a set of objects ranked according to the relevancy to the needed fact. In document analysis, information retrieval receives a lot of attention in terms of symbol and word spotting. However, through decades the community mostly focused either on printed or on single writer scenario, where the
state-of-the-art results have achieved reasonable performance on the available datasets. Nevertheless, the existing algorithms do not perform accordingly on multiwriter scenario. A graph representing relations between a set of objects is a structure where each node delineates an individual element and the similarity between them is represented as a weight on the connecting edge. In this paper, we explore different analytics of graphs constructed from words or graphical symbols, such as diffusion, shortest path, etc. to improve the performance of information retrieval methods in multiwriter scenario

Abstract: This paper presents a prototype system running on portable devices for browsing and word searching through historical handwritten document collections. The platform adapts the paradigm of eBook reading, where the narrative is not necessarily sequential, but centered on the user actions. The novelty is to replace digitally born books by digitized historical manuscripts of marriage licenses, so document analysis tasks are required in the browser. With an active reading paradigm, the user can cast queries of people names, so he/she can implicitly follow genealogical links. In addition, the system allows combined searches: the user can refine a search by adding more words to search. As a second contribution, the retrieval functionality involves as a core technology a word spotting module with an unified approach, which allows combined query searches, and also two input modalities: query-by-example, and query-by-string.