Information retrieval in multimedia databases using relevance feedback algorithms. Applying logistic regression to relevance feedback in image retrieval systems

This master tesis deals with the problem of image retrieval from large image databases. A particularly interesting problem is the retrieval of all images which are similar to one in the user's mind, taking into account his/her feedback which is expressed as positive or negative preferences for the images that the system progressively shows during the search. Here, a novel algorithm is presented for the incorporation of user preferences in an image retrieval system based exclusively on the visual content of the image, which is stored as a vector of low-level features. The algorithm considers the probability of an image belonging to the set of those sought by the user, and models the logit of this probability as the output of a linear model whose inputs are the low level image features. The image database is ranked by the output of the model and shown to the user, who selects a few positive and negative samples, repeating the process in an iterative way until he/she is satisfied. The problem of the small sample size with respect to the number of features is solved by adjusting several partial linear models and combining their relevance probabilities by means of an ordered weighted averaged (OWA) operator. Experiments were made with 40 users and they exhibited good performance in finding a target image (4 iterations on average) in a database of about 4700 imagesZuccarello, PD. (2007). Information retrieval in multimedia databases using relevance feedback algorithms. Applying logistic regression to relevance feedback in image retrieval systems. http://hdl.handle.net/10251/12196Archivo delegad

Shape based classification and functional forecast of traffic flow profiles

This dissertation proposes a methodology for traffic flow pattern analysis, its validation, and forecasting. The shape of the daily traffic flows are directly related to the commuter’s traffic behavior which merit analysis based on their shape characteristics. As a departure from the traditional approaches, this research proposed a methodology based on shape for traffic flow analysis. Specifically, Granulometric Size Distributions (GSDs) were used to achieve classification of daily traffic flow patterns. A mathematical morphology method was used that allows the clustering of shapes. The proposed methodology leads to discovery of interesting daily traffic phenomena such as five normal daily traffic shapes beside abnormal shapes representing accidents, congestion behavior, peak time fluctuations, and malfunctioning sensors. To ascertain the significance of shape in traffic analysis, the proposed methodology was validated through a comparative classification analysis of the original data and GSD transformed data using the Back Prorogation Neural Network (BPNN). Results demonstrated that through shape based clustering more appropriate grouping can be accomplished that can result in better estimates of model parameters. Lastly, a functional time series approach was proposed to forecast traffic flow for short and medium-term horizons. It is based on functional principal components decomposition to forecast three different traffic scenarios. Real-time forecast scenarios of partially observed traffic profiles through Penalized Least squares (PLS) technique were also demonstrated. Functional methods outperform the conventional ARIMA model in both short and medium-term forecast horizons. In addition, performance of functional methods in forecasting beyond one hour was also found to be robust and consistent. --Abstract, page iii

Discrete Morphological Neural Networks

A classical approach to designing binary image operators is Mathematical Morphology (MM). We propose the Discrete Morphological Neural Networks (DMNN) for binary image analysis to represent W-operators and estimate them via machine learning. A DMNN architecture, which is represented by a Morphological Computational Graph, is designed as in the classical heuristic design of morphological operators, in which the designer should combine a set of MM operators and Boolean operations based on prior information and theoretical knowledge. Then, once the architecture is fixed, instead of adjusting its parameters (i.e., structural elements or maximal intervals) by hand, we propose a lattice gradient descent algorithm (LGDA) to train these parameters based on a sample of input and output images under the usual machine learning approach. We also propose a stochastic version of the LGDA that is more efficient, is scalable and can obtain small error in practical problems. The class represented by a DMNN can be quite general or specialized according to expected properties of the target operator, i.e., prior information, and the semantic expressed by algebraic properties of classes of operators is a differential relative to other methods. The main contribution of this paper is the merger of the two main paradigms for designing morphological operators: classical heuristic design and automatic design via machine learning. Thus, conciliating classical heuristic morphological operator design with machine learning. We apply the DMNN to recognize the boundary of digits with noise, and we discuss many topics for future research

Image Analysis Algorithms for Single-Cell Study in Systems Biology

With the contiguous shift of biology from a qualitative toward a quantitative field of research, digital microscopy and image-based measurements are drawing increased interest. Several methods have been developed for acquiring images of cells and intracellular organelles. Traditionally, acquired images are analyzed manually through visual inspection. The increasing volume of data is challenging the scope of manual analysis, and there is a need to develop methods for automated analysis. This thesis examines the development and application of computational methods for acquisition and analysis of images from single-cell assays. The thesis proceeds with three different aspects.First, a study evaluates several methods for focusing microscopes and proposes a novel strategy to perform focusing in time-lapse imaging. The method relies on the nature of the focus-drift and its predictability. The study shows that focus-drift is a dynamical system with a small randomness. Therefore, a prediction-based method is employed to track the focus-drift overtime. A prototype implementation of the proposed method is created by extending the Nikon EZ-C1 Version 3.30 (Tokyo, Japan) imaging platform for acquiring images with a Nikon Eclipse (TE2000-U, Nikon, Japan) microscope.Second, a novel method is formulated to segment individual cells from a dense cluster. The method incorporates multi-resolution analysis with maximum-likelihood estimation (MAMLE) for cell detection. The MAMLE performs cell segmentation in two phases. The initial phase relies on a cutting-edge filter, edge detection in multi-resolution with a morphological operator, and threshold decomposition for adaptive thresholding. It estimates morphological features from the initial results. In the next phase, the final segmentation is constructed by boosting the initial results with the estimated parameters. The MAMLE method is evaluated with de novo data sets as well as with benchmark data from public databases. An empirical evaluation of the MAMLE method confirms its accuracy.Third, a comparative study is carried out on performance evaluation of state-ofthe-art methods for the detection of subcellular organelles. This study includes eleven algorithms developed in different fields for segmentation. The evaluation procedure encompasses a broad set of samples, ranging from benchmark data to synthetic images. The result from this study suggests that there is no particular method which performs superior to others in the test samples. Next, the effect of tetracycline on transcription dynamics of tetA promoter in Escherichia coli (E. coli ) cells is studied. This study measures expressions of RNA by tagging the MS2d-GFP vector with a target gene. The RNAs are observed as intracellular spots in confocal images. The kernel density estimation (KDE) method for detecting the intracellular spots is employed to quantify the individual RNA molecules.The thesis summarizes the results from five publications. Most of the publications are associated with different methods for imaging and analysis of microscopy. Confocal images with E. coli cells are targeted as the primary area of application. However, potential applications beyond the primary target are also made evident. The findings of the research are confirmed empirically

Three-dimensional hydrodynamic models coupled with GIS-based neuro-fuzzy classification for assessing environmental vulnerability of marine cage aquaculture

There is considerable opportunity to develop new modelling techniques within a Geographic Information Systems (GIS) framework for the development of sustainable marine cage culture. However, the spatial data sets are often uncertain and incomplete, therefore new spatial models employing “soft computing” methods such as fuzzy logic may be more suitable. The aim of this study is to develop a model using Neuro-fuzzy techniques in a 3D GIS (Arc View 3.2) to predict coastal environmental vulnerability for Atlantic salmon cage aquaculture. A 3D hydrodynamic model (3DMOHID) coupled to a particle-tracking model is applied to study the circulation patterns, dispersion processes and residence time in Mulroy Bay, Co. Donegal Ireland, an Irish fjard (shallow fjordic system), an area of restricted exchange, geometrically complicated with important aquaculture activities. The hydrodynamic model was calibrated and validated by comparison with sea surface and water flow measurements. The model provided spatial and temporal information on circulation, renewal time, helping to determine the influence of winds on circulation patterns and in particular the assessment of the hydrographic conditions with a strong influence on the management of fish cage culture. The particle-tracking model was used to study the transport and flushing processes. Instantaneous massive releases of particles from key boxes are modelled to analyse the ocean-fjord exchange characteristics and, by emulating discharge from finfish cages, to show the behaviour of waste in terms of water circulation and water exchange. In this study the results from the hydrodynamic model have been incorporated into GIS to provide an easy-to-use graphical user interface for 2D (maps), 3D and temporal visualization (animations), for interrogation of results. v Data on the physical environment and aquaculture suitability were derived from a 3- dimensional hydrodynamic model and GIS for incorporation into the final model framework and included mean and maximum current velocities, current flow quiescence time, water column stratification, sediment granulometry, particulate waste dispersion distance, oxygen depletion, water depth, coastal protection zones, and slope. The Neuro-fuzzy classification model NEFCLASS–J, was used to develop learning algorithms to create the structure (rule base) and the parameters (fuzzy sets) of a fuzzy classifier from a set of classified training data. A total of 42 training sites were sampled using stratified random sampling from the GIS raster data layers, and the vulnerability categories for each were manually classified into four categories based on the opinions of experts with field experience and specific knowledge of the environmental problems investigated. The final products, GIS/based Neuro Fuzzy maps were achieved by combining modeled and real environmental parameters relevant to marine fin fish Aquaculture. Environmental vulnerability models, based on Neuro-fuzzy techniques, showed sensitivity to the membership shapes of the fuzzy sets, the nature of the weightings applied to the model rules, and validation techniques used during the learning and validation process. The accuracy of the final classifier selected was R=85.71%, (estimated error value of ±16.5% from Cross Validation, N=10) with a Kappa coefficient of agreement of 81%. Unclassified cells in the whole spatial domain (of 1623 GIS cells) ranged from 0% to 24.18 %. A statistical comparison between vulnerability scores and a significant product of aquaculture waste (nitrogen concentrations in sediment under the salmon cages) showed that the final model gave a good correlation between predicted environmental vi vulnerability and sediment nitrogen levels, highlighting a number of areas with variable sensitivity to aquaculture. Further evaluation and analysis of the quality of the classification was achieved and the applicability of separability indexes was also studied. The inter-class separability estimations were performed on two different training data sets to assess the difficulty of the class separation problem under investigation. The Neuro-fuzzy classifier for a supervised and hard classification of coastal environmental vulnerability has demonstrated an ability to derive an accurate and reliable classification into areas of different levels of environmental vulnerability using a minimal number of training sets. The output will be an environmental spatial model for application in coastal areas intended to facilitate policy decision and to allow input into wider ranging spatial modelling projects, such as coastal zone management systems and effective environmental management of fish cage aquaculture

Handbook of Mathematical Geosciences

This Open Access handbook published at the IAMG's 50th anniversary, presents a compilation of invited path-breaking research contributions by award-winning geoscientists who have been instrumental in shaping the IAMG. It contains 45 chapters that are categorized broadly into five parts (i) theory, (ii) general applications, (iii) exploration and resource estimation, (iv) reviews, and (v) reminiscences covering related topics like mathematical geosciences, mathematical morphology, geostatistics, fractals and multifractals, spatial statistics, multipoint geostatistics, compositional data analysis, informatics, geocomputation, numerical methods, and chaos theory in the geosciences

Modelling of Harbour and Coastal Structures

As the most heavily populated areas in the world, coastal zones host the majority and some of the most important human settlements, infrastructures and economic activities. Harbour and coastal structures are essential to the above, facilitating the transport of people and goods through ports, and protecting low-lying areas against flooding and erosion. While these structures were previously based on relatively rigid concepts about service life, at present, the design—or the upgrading—of these structures should effectively proof them against future pressures, enhancing their resilience and long-term sustainability. This Special Issue brings together a versatile collection of articles on the modelling of harbour and coastal structures, covering a wide array of topics on the design of such structures through a study of their interactions with waves and coastal morphology, as well as their role in coastal protection and harbour design in present and future climates

Distance-based methods for detecting associations in structured data with applications in bioinformatics

In bioinformatics applications samples of biological variables of interest can take a variety of structures. For instance, in this thesis we consider vector-valued observations of multiple gene expression and genetic markers, curve-valued gene expression time courses, and graph-valued functional connectivity networks within the brain. This thesis considers three problems routinely encountered when dealing with such variables: detecting differences between populations, detecting predictive relationships between variables, and detecting association between variables. Distance-based approaches to these problems are considered, offering great flexibility over alternative approaches, such as traditional multivariate approaches which may be inappropriate. The notion of distance has been widely adopted in recent years to quantify the dissimilarity between samples, and suitable distance measures can be applied depending on the nature of the data and on the specific objectives of the study. For instance, for gene expression time courses modeled as time-dependent curves, distance measures can be specified to capture biologically meaningful aspects of these curves which may differ. On obtaining a distance matrix containing all pairwise distances between the samples of a given variable, many distance-based testing procedures can then be applied. The main inhibitor of their effective use in bioinformatics is that p-values are typically estimated by using Monte Carlo permutations. Thousands or even millions of tests need to be performed simultaneously, and time/computational constraints lead to a low number of permutations being enumerated for each test. The contributions of this thesis include the proposal of two new distance-based statistics, the DBF statistic for the problem of detecting differences between populations, and the GRV coefficient for the problem of detecting association between variables. In each case approximate null distributions are derived, allowing estimation of p-values with reduced computational cost, and through simulation these are shown to work well for a range of distances and data types. The tests are also demonstrated to be competitive with existing approaches. For the problem of detecting predictive relationships between variables, the approximate null distribution is derived for the routinely used distance-based pseudo F test, and through simulation this is shown to work well for a range of distances and data types. All tests are applied to real datasets, including a longitudinal human immune cell M. tuberculosis dataset, an Alzheimer’s disease dataset, and an ovarian cancer dataset.Open Acces

Sustainable Environmental Solutions

This book collects research activities focused on the development of new processes to replace obsolete practices that are often highly invasive, unsustainable, and socially unacceptable.Taking inspiration from real problems and the need to face real cases of contamination or prevent potentially harmful situations, the development and optimization of ‘smart’ solutions, i.e., sustainable not only from an environmental point of view but also economically, are discussed in order to encourage, as much as possible, their actual implementation