Abstract: Despite the “paperless office” ideal that started in the decade of the seventies, businesses still strive against an increasing amount of paper documentation. Companies still receive huge amounts of paper documentation that need to be analyzed and processed, mostly in a manual way. A solution for this task consists in, first, automatically scanning the incoming documents. Then, document images can be analyzed and information can be extracted from the data. Documents can also be automatically dispatched to the appropriate workflows, used to retrieve similar documents in the dataset to transfer information, etc.
Due to the nature of this “digital mailroom”, we need document representation methods to be general, i.e., able to cope with very different types of documents. We need the methods to be sound, i.e., able to cope with unexpected types of documents, noise, etc. And, we need to methods to be scalable, i.e., able to cope with thousands or millions of documents that need to be processed, stored, and consulted. Unfortunately, current techniques of document representation, classification and retrieval are not apt for this digital mailroom framework, since they do not fulfill some or all of these requirements.
Through this thesis we focus on the problem of document representation aimed at classification and retrieval tasks under this digital mailroom framework. We first propose a novel document representation based on runlength histograms, and extend it to cope with more complex documents such as multiple-page documents, or documents that contain more sources of information such as extracted OCR text. Then we focus on the scalability requirements and propose a novel binarization method which we dubbed PCAE, as well as two general asymmetric distances between binary embeddings that can significantly improve the retrieval results at a minimal extra computational cost. Finally, we note the importance of supervised learning when performing large-scale retrieval, and study several approaches that can significantly boost the results at no extra cost at query time.

Abstract: Restricted Boltzmann Machines (RBMs) are generative neural networks that have received much attention recently. In particular, choosing the appropriate number of hidden units is important as it might hinder their representative power. According to the literature, RBM require numerous hidden units to approximate any distribution properly. In this paper, we present an experiment to determine whether such amount of hidden units is required in a classification context. We then propose an incremental algorithm that trains RBM reusing the previously trained parameters using a trade-off measure to determine the appropriate number of hidden units. Results on the MNIST and OCR letters databases show that using a number of hidden units, which is one order of magnitude smaller than the literature estimate, suffices to achieve similar performance. Moreover, the proposed algorithm allows to estimate the required number of hidden units without the need of training many RBM from scratch.

Abstract: Aggregates of misfolded proteins are a hallmark of many age-related diseases. Recently, they have been linked to aging of Escherichia coli (E. coli) where protein aggregates accumulate at the old pole region of the aging bacterium. Because of the potential of E. coli as a model organism, elucidating aging and protein aggregation in this bacterium may pave the way to significant advances in our global understanding of aging. A first obstacle along this path is to decipher the mechanisms by which protein aggregates are targeted to specific intercellular locations. Here, using an integrated approach based on individual-based modeling, time-lapse fluorescence microscopy and automated image analysis, we show that the movement of aging-related protein aggregates in E. coli is purely diffusive (Brownian). Using single-particle tracking of protein aggregates in live E. coli cells, we estimated the average size and diffusion constant of the aggregates. Our results provide evidence that the aggregates passively diffuse within the cell, with diffusion constants that depend on their size in agreement with the Stokes-Einstein law. However, the aggregate displacements along the cell long axis are confined to a region that roughly corresponds to the nucleoid-free space in the cell pole, thus confirming the importance of increased macromolecular crowding in the nucleoids. We thus used 3D individual-based modeling to show that these three ingredients (diffusion, aggregation and diffusion hindrance in the nucleoids) are sufficient and necessary to reproduce the available experimental data on aggregate localization in the cells. Taken together, our results strongly support the hypothesis that the localization of aging-related protein aggregates in the poles of E. coli results from the coupling of passive diffusion-aggregation with spatially non-homogeneous macromolecular crowding. They further support the importance of “soft” intracellular structuring (based on macromolecular crowding) in diffusion-based protein localization in E. coli.