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

Recasting Residual-based Local Descriptors as Convolutional Neural Networks: an Application to Image Forgery Detection

Local descriptors based on the image noise residual have proven extremely effective for a number of forensic applications, like forgery detection and localization. Nonetheless, motivated by promising results in computer vision, the focus of the research community is now shifting on deep learning. In this paper we show that a class of residual-based descriptors can be actually regarded as a simple constrained convolutional neural network (CNN). Then, by relaxing the constraints, and fine-tuning the net on a relatively small training set, we obtain a significant performance improvement with respect to the conventional detector

Automatic detection, tracking and counting of birds in marine video content

Robust automatic detection of moving objects in a marine context is a multi-faceted problem due to the complexity of the observed scene. The dynamic nature of the sea caused by waves, boat wakes, and weather conditions poses huge challenges for the development of a stable background model. Moreover, camera motion, reflections, lightning and illumination changes may contribute to false detections. Dynamic background subtraction (DBGS) is widely considered as a solution to tackle this issue in the scope of vessel detection for maritime traffic analysis. In this paper, the DBGS techniques suggested for ships are investigated and optimized for the monitoring and tracking of birds in marine video content. In addition to background subtraction, foreground candidates are filtered by a classifier based on their feature descriptors in order to remove non-bird objects. Different types of classifiers have been evaluated and results on a ground truth labeled dataset of challenging video fragments show similar levels of precision and recall of about 95% for the best performing classifier. The remaining foreground items are counted and birds are tracked along the video sequence using spatio-temporal motion prediction. This allows marine scientists to study the presence and behavior of birds

Image Forgery Localization Based on Multi-Scale Convolutional Neural Networks

In this paper, we propose to utilize Convolutional Neural Networks (CNNs) and the segmentation-based multi-scale analysis to locate tampered areas in digital images. First, to deal with color input sliding windows of different scales, a unified CNN architecture is designed. Then, we elaborately design the training procedures of CNNs on sampled training patches. With a set of robust multi-scale tampering detectors based on CNNs, complementary tampering possibility maps can be generated. Last but not least, a segmentation-based method is proposed to fuse the maps and generate the final decision map. By exploiting the benefits of both the small-scale and large-scale analyses, the segmentation-based multi-scale analysis can lead to a performance leap in forgery localization of CNNs. Numerous experiments are conducted to demonstrate the effectiveness and efficiency of our method.Comment: 7 pages, 6 figure

Joint segmentation and classification of retinal arteries/veins from fundus images

Objective Automatic artery/vein (A/V) segmentation from fundus images is required to track blood vessel changes occurring with many pathologies including retinopathy and cardiovascular pathologies. One of the clinical measures that quantifies vessel changes is the arterio-venous ratio (AVR) which represents the ratio between artery and vein diameters. This measure significantly depends on the accuracy of vessel segmentation and classification into arteries and veins. This paper proposes a fast, novel method for semantic A/V segmentation combining deep learning and graph propagation. Methods A convolutional neural network (CNN) is proposed to jointly segment and classify vessels into arteries and veins. The initial CNN labeling is propagated through a graph representation of the retinal vasculature, whose nodes are defined as the vessel branches and edges are weighted by the cost of linking pairs of branches. To efficiently propagate the labels, the graph is simplified into its minimum spanning tree. Results The method achieves an accuracy of 94.8% for vessels segmentation. The A/V classification achieves a specificity of 92.9% with a sensitivity of 93.7% on the CT-DRIVE database compared to the state-of-the-art-specificity and sensitivity, both of 91.7%. Conclusion The results show that our method outperforms the leading previous works on a public dataset for A/V classification and is by far the fastest. Significance The proposed global AVR calculated on the whole fundus image using our automatic A/V segmentation method can better track vessel changes associated to diabetic retinopathy than the standard local AVR calculated only around the optic disc.Comment: Preprint accepted in Artificial Intelligence in Medicin

Explainable and Advisable Learning for Self-driving Vehicles

Deep neural perception and control networks are likely to be a key component of self-driving vehicles. These models need to be explainable - they should provide easy-to-interpret rationales for their behavior - so that passengers, insurance companies, law enforcement, developers, etc., can understand what triggered a particular behavior. Explanations may be triggered by the neural controller, namely introspective explanations, or informed by the neural controller's output, namely rationalizations. Our work has focused on the challenge of generating introspective explanations of deep models for self-driving vehicles. In Chapter 3, we begin by exploring the use of visual explanations. These explanations take the form of real-time highlighted regions of an image that causally influence the network's output (steering control). In the first stage, we use a visual attention model to train a convolution network end-to-end from images to steering angle. The attention model highlights image regions that potentially influence the network's output. Some of these are true influences, but some are spurious. We then apply a causal filtering step to determine which input regions actually influence the output. This produces more succinct visual explanations and more accurately exposes the network's behavior. In Chapter 4, we add an attention-based video-to-text model to produce textual explanations of model actions, e.g. "the car slows down because the road is wet". The attention maps of controller and explanation model are aligned so that explanations are grounded in the parts of the scene that mattered to the controller. We explore two approaches to attention alignment, strong- and weak-alignment. These explainable systems represent an externalization of tacit knowledge. The network's opaque reasoning is simplified to a situation-specific dependence on a visible object in the image. This makes them brittle and potentially unsafe in situations that do not match training data. In Chapter 5, we propose to address this issue by augmenting training data with natural language advice from a human. Advice includes guidance about what to do and where to attend. We present the first step toward advice-giving, where we train an end-to-end vehicle controller that accepts advice. The controller adapts the way it attends to the scene (visual attention) and the control (steering and speed). Further, in Chapter 6, we propose a new approach that learns vehicle control with the help of long-term (global) human advice. Specifically, our system learns to summarize its visual observations in natural language, predict an appropriate action response (e.g. "I see a pedestrian crossing, so I stop"), and predict the controls, accordingly