A multi-view approach to cDNA micro-array analysis

The official published version can be obtained from the link below.Microarray has emerged as a powerful technology that enables biologists to study thousands of genes simultaneously, therefore, to obtain a better understanding of the gene interaction and regulation mechanisms. This paper is concerned with improving the processes involved in the analysis of microarray image data. The main focus is to clarify an image's feature space in an unsupervised manner. In this paper, the Image Transformation Engine (ITE), combined with different filters, is investigated. The proposed methods are applied to a set of real-world cDNA images. The MatCNN toolbox is used during the segmentation process. Quantitative comparisons between different filters are carried out. It is shown that the CLD filter is the best one to be applied with the ITE.This work was supported in part by the Engineering and Physical Sciences Research Council (EPSRC) of the UK under Grant GR/S27658/01, the National Science Foundation of China under Innovative Grant 70621001, Chinese Academy of Sciences under Innovative Group Overseas Partnership Grant, the BHP Billiton Cooperation of Australia Grant, the International Science and Technology Cooperation Project of China under Grant 2009DFA32050 and the Alexander von Humboldt Foundation of Germany

Probabilistic framework for image understanding applications using Bayesian Networks

Machine learning algorithms have been successfully utilized in various systems/devices. They have the ability to improve the usability/quality of such systems in terms of intelligent user interface, fast performance, and more importantly, high accuracy. In this research, machine learning techniques are used in the field of image understanding, which is a common research area between image analysis and computer vision, to involve higher processing level of a target image to make sense of the scene captured in it. A general probabilistic framework for image understanding where topics associated with (i) collection of images to generate a comprehensive and valid database, (ii) generation of an unbiased ground-truth for the aforesaid database, (iii) selection of classification features and elimination of the redundant ones, and (iv) usage of such information to test a new sample set, are discussed. Two research projects have been developed as examples of the general image understanding framework; identification of region(s) of interest, and image segmentation evaluation. These techniques, in addition to others, are combined in an object-oriented rendering system for printing applications. The discussion included in this doctoral dissertation explores the means for developing such a system from an image understanding/ processing aspect. It is worth noticing that this work does not aim to develop a printing system. It is only proposed to add some essential features for current printing pipelines to achieve better visual quality while printing images/photos. Hence, we assume that image regions have been successfully extracted from the printed document. These images are used as input to the proposed object-oriented rendering algorithm where methodologies for color image segmentation, region-of-interest identification and semantic features extraction are employed. Probabilistic approaches based on Bayesian statistics have been utilized to develop the proposed image understanding techniques

Context Based Visual Content Verification

In this paper the intermediary visual content verification method based on multi-level co-occurrences is studied. The co-occurrence statistics are in general used to determine relational properties between objects based on information collected from data. As such these measures are heavily subject to relative number of occurrences and give only limited amount of accuracy when predicting objects in real world. In order to improve the accuracy of this method in the verification task, we include the context information such as location, type of environment etc. In order to train our model we provide new annotated dataset the Advanced Attribute VOC (AAVOC) that contains additional properties of the image. We show that the usage of context greatly improve the accuracy of verification with up to 16% improvement.Comment: 6 pages, 6 Figures, Published in Proceedings of the Information and Digital Technology Conference, 201

Relational Reasoning Network (RRN) for Anatomical Landmarking

Accurately identifying anatomical landmarks is a crucial step in deformation analysis and surgical planning for craniomaxillofacial (CMF) bones. Available methods require segmentation of the object of interest for precise landmarking. Unlike those, our purpose in this study is to perform anatomical landmarking using the inherent relation of CMF bones without explicitly segmenting them. We propose a new deep network architecture, called relational reasoning network (RRN), to accurately learn the local and the global relations of the landmarks. Specifically, we are interested in learning landmarks in CMF region: mandible, maxilla, and nasal bones. The proposed RRN works in an end-to-end manner, utilizing learned relations of the landmarks based on dense-block units and without the need for segmentation. For a given a few landmarks as input, the proposed system accurately and efficiently localizes the remaining landmarks on the aforementioned bones. For a comprehensive evaluation of RRN, we used cone-beam computed tomography (CBCT) scans of 250 patients. The proposed system identifies the landmark locations very accurately even when there are severe pathologies or deformations in the bones. The proposed RRN has also revealed unique relationships among the landmarks that help us infer several reasoning about informativeness of the landmark points. RRN is invariant to order of landmarks and it allowed us to discover the optimal configurations (number and location) for landmarks to be localized within the object of interest (mandible) or nearby objects (maxilla and nasal). To the best of our knowledge, this is the first of its kind algorithm finding anatomical relations of the objects using deep learning.Comment: 10 pages, 6 Figures, 3 Table