Medical image modality classification using discrete Bayesian Networks

In this paper we propose a complete pipeline for medical image modality classification focused on the application of discrete Bayesian network classifiers. Modality refers to the categorization of biomedical images from the literature according to a previously defined set of image types, such as X-ray, graph or gene sequence. We describe an extensive pipeline starting with feature extraction from images, data combination, pre-processing and a range of different classification techniques and models. We study the expressive power of several image descriptors along with supervised discretization and feature selection to show the performance of discrete Bayesian networks compared to the usual deterministic classifiers used in image classification. We perform an exhaustive experimentation by using the ImageCLEFmed 2013 collection. This problem presents a high number of classes so we propose several hierarchical approaches. In a first set of experiments we evaluate a wide range of parameters for our pipeline along with several classification models. Finally, we perform a comparison by setting up the competition environment between our selected approaches and the best ones of the original competition. Results show that the Bayesian Network classifiers obtain very competitive results. Furthermore, the proposed approach is stable and it can be applied to other problems that present inherent hierarchical structures of classes

Analysis of Dynamic Magnetic Resonance Breast Images

Dynamic Magnetic Resonance Imaging is a non-invasive technique that provides an image sequence based on dynamic information for locating lesions and investigating their structures. In this thesis we develop new methodology for analysing dynamic Magnetic Resonance image sequences of the breast. This methodology comprises an image restoration step that reduces random distortions affecting the data and an image classification step that identifies normal, benign or malignant tumoral tissues. In the first part of this thesis we present a non-parametric and a parametric approach for image restoration and classification. Both methods are developed within the Bayesian framework. A prior distribution modelling both spatial homogeneity and temporal continuity between neighbouring image pixels is employed. Statistical inference is performed by means of a Metropolis-Hastings algorithm with a specially chosen proposal distribution that out-performs other algorithms of the same family. We also provide novel procedures for estimating the hyper-parameters of the prior models and the normalizing constant so making the Bayesian methodology automatic. In the second part of this thesis we present new methodology for image classification based on deformable templates of a prototype shape. Our approach uses higher level knowledge about the tumour structure than the spatio-temporal prior distribution of our Bayesian methodology. The prototype shape is deformed to identify the structure of the malignant tumoral tissue by minimizing a novel objective function over the parameters of a set of non-affine transformations. Since these transformations can destroy the connectivity of the shape, we develop a new filter that restores connectivity without smoothing the shape. The restoration and classification results obtained from a small sample of image sequences are very encouraging. In order to validate these results on a larger sample, in the last part of the thesis we present a user friendly software package that implements our methodology

Conditional Graphical Lasso for Multi-label Image Classification

© 2016 IEEE. Multi-label image classification aims to predict multiple labels for a single image which contains diverse content. By utilizing label correlations, various techniques have been developed to improve classification performance. However, current existing methods either neglect image features when exploiting label correlations or lack the ability to learn image-dependent conditional label structures. In this paper, we develop conditional graphical Lasso (CGL) to handle these challenges. CGL provides a unified Bayesian framework for structure and parameter learning conditioned on image features. We formulate the multi-label prediction as CGL inference problem, which is solved by a mean field variational approach. Meanwhile, CGL learning is efficient due to a tailored proximal gradient procedure by applying the maximum a posterior (MAP) methodology. CGL performs competitively for multi-label image classification on benchmark datasets MULAN scene, PASCAL VOC 2007 and PASCAL VOC 2012, compared with the state-of-the-art multi-label classification algorithms

Adaptive Markov random fields for joint unmixing and segmentation of hyperspectral image

Linear spectral unmixing is a challenging problem in hyperspectral imaging that consists of decomposing an observed pixel into a linear combination of pure spectra (or endmembers) with their corresponding proportions (or abundances). Endmember extraction algorithms can be employed for recovering the spectral signatures while abundances are estimated using an inversion step. Recent works have shown that exploiting spatial dependencies between image pixels can improve spectral unmixing. Markov random fields (MRF) are classically used to model these spatial correlations and partition the image into multiple classes with homogeneous abundances. This paper proposes to define the MRF sites using similarity regions. These regions are built using a self-complementary area filter that stems from the morphological theory. This kind of filter divides the original image into flat zones where the underlying pixels have the same spectral values. Once the MRF has been clearly established, a hierarchical Bayesian algorithm is proposed to estimate the abundances, the class labels, the noise variance, and the corresponding hyperparameters. A hybrid Gibbs sampler is constructed to generate samples according to the corresponding posterior distribution of the unknown parameters and hyperparameters. Simulations conducted on synthetic and real AVIRIS data demonstrate the good performance of the algorithm

A very simple safe-Bayesian random forest

Random forests works by averaging several predictions of de-correlated trees. We show a conceptually radical approach to generate a random forest: random sampling of many trees from a prior distribution, and subsequently performing a weighted ensemble of predictive probabilities. Our approach uses priors that allow sampling of decision trees even before looking at the data, and a power likelihood that explores the space spanned by combination of decision trees. While each tree performs Bayesian inference to compute its predictions, our aggregation procedure uses the power likelihood rather than the likelihood and is therefore strictly speaking not Bayesian. Nonetheless, we refer to it as a Bayesian random forest but with a built-in safety. The safeness comes as it has good predictive performance even if the underlying probabilistic model is wrong. We demonstrate empirically that our Safe-Bayesian random forest outperforms MCMC or SMC based Bayesian decision trees in term of speed and accuracy, and achieves competitive performance to entropy or Gini optimised random forest, yet is very simple to construct

A hybrid algorithm for Bayesian network structure learning with application to multi-label learning

We present a novel hybrid algorithm for Bayesian network structure learning, called H2PC. It first reconstructs the skeleton of a Bayesian network and then performs a Bayesian-scoring greedy hill-climbing search to orient the edges. The algorithm is based on divide-and-conquer constraint-based subroutines to learn the local structure around a target variable. We conduct two series of experimental comparisons of H2PC against Max-Min Hill-Climbing (MMHC), which is currently the most powerful state-of-the-art algorithm for Bayesian network structure learning. First, we use eight well-known Bayesian network benchmarks with various data sizes to assess the quality of the learned structure returned by the algorithms. Our extensive experiments show that H2PC outperforms MMHC in terms of goodness of fit to new data and quality of the network structure with respect to the true dependence structure of the data. Second, we investigate H2PC's ability to solve the multi-label learning problem. We provide theoretical results to characterize and identify graphically the so-called minimal label powersets that appear as irreducible factors in the joint distribution under the faithfulness condition. The multi-label learning problem is then decomposed into a series of multi-class classification problems, where each multi-class variable encodes a label powerset. H2PC is shown to compare favorably to MMHC in terms of global classification accuracy over ten multi-label data sets covering different application domains. Overall, our experiments support the conclusions that local structural learning with H2PC in the form of local neighborhood induction is a theoretically well-motivated and empirically effective learning framework that is well suited to multi-label learning. The source code (in R) of H2PC as well as all data sets used for the empirical tests are publicly available.Comment: arXiv admin note: text overlap with arXiv:1101.5184 by other author