A feedback model of visual attention

Feedback connections are a prominent feature of cortical anatomy and are likely to have significant functional role in neural information processing. We present a neural network model of cortical feedback that successfully simulates neurophysiological data associated with attention. In this domain our model can be considered a more detailed, and biologically plausible, implementation of the biased competition model of attention. However, our model is more general as it can also explain a variety of other top-down processes in vision, such as figure/ground segmentation and contextual cueing. This model thus suggests that a common mechanism, involving cortical feedback pathways, is responsible for a range of phenomena and provides a unified account of currently disparate areas of research

A kernel-based framework for medical big-data analytics

The recent trend towards standardization of Electronic Health Records (EHRs) represents a significant opportunity and challenge for medical big-data analytics. The challenge typically arises from the nature of the data which may be heterogeneous, sparse, very high-dimensional, incomplete and inaccurate. Of these, standard pattern recognition methods can typically address issues of high-dimensionality, sparsity and inaccuracy. The remaining issues of incompleteness and heterogeneity however are problematic; data can be as diverse as handwritten notes, blood-pressure readings and MR scans, and typically very little of this data will be co-present for each patient at any given time interval. We therefore advocate a kernel-based framework as being most appropriate for handling these issues, using the neutral point substitution method to accommodate missing inter-modal data. For pre-processing of image-based MR data we advocate a Deep Learning solution for contextual areal segmentation, with edit-distance based kernel measurement then used to characterize relevant morphology

Symbolic and Deep Learning Based Data Representation Methods for Activity Recognition and Image Understanding at Pixel Level

Efficient representation of large amount of data particularly images and video helps in the analysis, processing and overall understanding of the data. In this work, we present two frameworks that encapsulate the information present in such data. At first, we present an automated symbolic framework to recognize particular activities in real time from videos. The framework uses regular expressions for symbolically representing (possibly infinite) sets of motion characteristics obtained from a video. It is a uniform framework that handles trajectory-based and periodic articulated activities and provides polynomial time graph algorithms for fast recognition. The regular expressions representing motion characteristics can either be provided manually or learnt automatically from positive and negative examples of strings (that describe dynamic behavior) using offline automata learning frameworks. Confidence measures are associated with recognitions using Levenshtein distance between a string representing a motion signature and the regular expression describing an activity. We have used our framework to recognize trajectory-based activities like vehicle turns (U-turns, left and right turns, and K-turns), vehicle start and stop, person running and walking, and periodic articulated activities like digging, waving, boxing, and clapping in videos from the VIRAT public dataset, the KTH dataset, and a set of videos obtained from YouTube. Next, we present a core sampling framework that is able to use activation maps from several layers of a Convolutional Neural Network (CNN) as features to another neural network using transfer learning to provide an understanding of an input image. The intermediate map responses of a Convolutional Neural Network (CNN) contain information about an image that can be used to extract contextual knowledge about it. Our framework creates a representation that combines features from the test data and the contextual knowledge gained from the responses of a pretrained network, processes it and feeds it to a separate Deep Belief Network. We use this representation to extract more information from an image at the pixel level, hence gaining understanding of the whole image. We experimentally demonstrate the usefulness of our framework using a pretrained VGG-16 model to perform segmentation on the BAERI dataset of Synthetic Aperture Radar (SAR) imagery and the CAMVID dataset. Using this framework, we also reconstruct images by removing noise from noisy character images. The reconstructed images are encoded using Quadtrees. Quadtrees can be an efficient representation in learning from sparse features. When we are dealing with handwritten character images, they are quite susceptible to noise. Hence, preprocessing stages to make the raw data cleaner can improve the efficacy of their use. We improve upon the efficiency of probabilistic quadtrees by using a pixel level classifier to extract the character pixels and remove noise from the images. The pixel level denoiser uses a pretrained CNN trained on a large image dataset and uses transfer learning to aid the reconstruction of characters. In this work, we primarily deal with classification of noisy characters and create the noisy versions of handwritten Bangla Numeral and Basic Character datasets and use them and the Noisy MNIST dataset to demonstrate the usefulness of our approach

A survey of visual preprocessing and shape representation techniques

Many recent theories and methods proposed for visual preprocessing and shape representation are summarized. The survey brings together research from the fields of biology, psychology, computer science, electrical engineering, and most recently, neural networks. It was motivated by the need to preprocess images for a sparse distributed memory (SDM), but the techniques presented may also prove useful for applying other associative memories to visual pattern recognition. The material of this survey is divided into three sections: an overview of biological visual processing; methods of preprocessing (extracting parts of shape, texture, motion, and depth); and shape representation and recognition (form invariance, primitives and structural descriptions, and theories of attention)

How to describe a cell: a path to automated versatile characterization of cells in imaging data

A cell is the basic functional unit of life. Most ulticellular organisms, including animals, are composed of a variety of different cell types that fulfil distinct roles. Within an organism, all cells share the same genome, however, their diverse genetic programs lead them to acquire different molecular and anatomical characteristics. Describing these characteristics is essential for understanding how cellular diversity emerged and how it contributes to the organism function. Probing cellular appearance by microscopy methods is the original way of describing cell types and the main approach to characterise cellular morphology and position in the organism. Present cutting-edge microscopy techniques generate immense amounts of data, requiring efficient automated unbiased methods of analysis. Not only can such methods accelerate the process of scientific discovery, they should also facilitate large-scale systematic reproducible analysis. The necessity of processing big datasets has led to development of intricate image analysis pipelines, however, they are mostly tailored to a particular dataset and a specific research question. In this thesis I aimed to address the problem of creating more general fully-automated ways of describing cells in different imaging modalities, with a specific focus on deep neural networks as a promising solution for extracting rich general-purpose features from the analysed data. I further target the problem of integrating multiple data modalities to generate a detailed description of cells on the whole-organism level. First, on two examples of cell analysis projects, I show how using automated image analysis pipelines and neural networks in particular, can assist characterising cells in microscopy data. In the first project I analyse a movie of drosophila embryo development to elucidate the difference in myosin patterns between two populations of cells with different shape fate. In the second project I develop a pipeline for automatic cell classification in a new imaging modality to show that the quality of the data is sufficient to tell apart cell types in a volume of mouse brain cortex. Next, I present an extensive collaborative effort aimed at generating a whole-body multimodal cell atlas of a three-segmented Platynereis dumerilii worm, combining high resolution morphology and gene expression. To generate a multi-sided description of cells in the atlas I create a pipeline for assigning coherent denoised gene expression profiles, obtained from spatial gene expression maps, to cells segmented in the EM volume. Finally, as the main project of this thesis, I focus on extracting comprehensive unbiased cell morphology features from an EM volume of Platynereis dumerilii. I design a fully unsupervised neural network pipeline for extracting rich morphological representations that enable grouping cells into morphological cell classes with characteristic gene expression. I further show how such descriptors could be used to explore the morphological diversity of cells, tissues and organs in the dataset

Fast unsupervised multiresolution color image segmentation using adaptive gradient thresholding and progressive region growing

In this thesis, we propose a fast unsupervised multiresolution color image segmentation algorithm which takes advantage of gradient information in an adaptive and progressive framework. This gradient-based segmentation method is initialized by a vector gradient calculation on the full resolution input image in the CIE L*a*b* color space. The resultant edge map is used to adaptively generate thresholds for classifying regions of varying gradient densities at different levels of the input image pyramid, obtained through a dyadic wavelet decomposition scheme. At each level, the classification obtained by a progressively thresholded growth procedure is combined with an entropy-based texture model in a statistical merging procedure to obtain an interim segmentation. Utilizing an association of a gradient quantized confidence map and non-linear spatial filtering techniques, regions of high confidence are passed from one level to another until the full resolution segmentation is achieved. Evaluation of our results on several hundred images using the Normalized Probabilistic Rand (NPR) Index shows that our algorithm outperforms state-of the art segmentation techniques and is much more computationally efficient than its single scale counterpart, with comparable segmentation quality

Patch-based semantic labelling of images.

PhDThe work presented in this thesis is focused at associating a semantics to the content of an image, linking the content to high level semantic categories. The process can take place at two levels: either at image level, towards image categorisation, or at pixel level, in se- mantic segmentation or semantic labelling. To this end, an analysis framework is proposed, and the different steps of part (or patch) extraction, description and probabilistic modelling are detailed. Parts of different nature are used, and one of the contributions is a method to complement information associated to them. Context for parts has to be considered at different scales. Short range pixel dependences are accounted by associating pixels to larger patches. A Conditional Random Field, that is, a probabilistic discriminative graphical model, is used to model medium range dependences between neighbouring patches. Another contribution is an efficient method to consider rich neighbourhoods without having loops in the inference graph. To this end, weak neighbours are introduced, that is, neighbours whose label probability distribution is pre-estimated rather than mutable during the inference. Longer range dependences, that tend to make the inference problem intractable, are addressed as well. A novel descriptor based on local histograms of visual words has been proposed, meant to both complement the feature descriptor of the patches and augment the context awareness in the patch labelling process. Finally, an alternative approach to consider multiple scales in a hierarchical framework based on image pyramids is proposed. An image pyramid is a compositional representation of the image based on hierarchical clustering. All the presented contributions are extensively detailed throughout the thesis, and experimental results performed on publicly available datasets are reported to assess their validity. A critical comparison with the state of the art in this research area is also presented, and the advantage in adopting the proposed improvements are clearly highlighted

Adaptive learning in a compartmental model of visual cortex—how feedback enables stable category learning and refinement

The categorization of real world objects is often reflected in the similarity of their visual appearances. Such categories of objects do not necessarily form disjunct sets of objects, neither semantically nor visually. The relationship between categories can often be described in terms of a hierarchical structure. For instance, tigers and leopards build two separate mammalian categories, but both belong to the category of felines. In other words, tigers and leopards are subcategories of the category Felidae. In the last decades, the unsupervised learning of categories of visual input stimuli has been addressed by numerous approaches in machine learning as well as in the computational neurosciences. However, the question of what kind of mechanisms might be involved in the process of subcategory learning, or category refinement, remains a topic of active investigation. We propose a recurrent computational network architecture for the unsupervised learning of categorial and subcategorial visual input representations. During learning, the connection strengths of bottom-up weights from input to higher-level category representations are adapted according to the input activity distribution. In a similar manner, top-down weights learn to encode the characteristics of a specific stimulus category. Feedforward and feedback learning in combination realize an associative memory mechanism, enabling the selective top-down propagation of a category's feedback weight distribution. We suggest that the difference between the expected input encoded in the projective field of a category node and the current input pattern controls the amplification of feedforward-driven representations. Large enough differences trigger the recruitment of new representational resources and the establishment of (sub-) category representations. We demonstrate the temporal evolution of such learning and show how the approach successully establishes category and subcategory representations

Multiresolution Segmentation of Natural Images: From linear to Non-Linear Scale-Space Representations

In this paper, we introduce a framework that merges classical ideas borrowed from scale-space and multi-resolution segmentation with non-linear partial differential equations. A non-linear scale-space stack is constructed by means of an appropriate diffusion equation. This stack is analyzed and a tree of coherent segments is constructed based on relationships between different scale layers. Pruning this tree proves to be a very efficient tool for unsupervised segmentation of different classes of images (e.g. natural, medical ...). This technique is light on the computational point of view and can be extended to non-scalar data in a straightforward manner