Bio-Inspired Computer Vision: Towards a Synergistic Approach of Artificial and Biological Vision

To appear in CVIUStudies in biological vision have always been a great source of inspiration for design of computer vision algorithms. In the past, several successful methods were designed with varying degrees of correspondence with biological vision studies, ranging from purely functional inspiration to methods that utilise models that were primarily developed for explaining biological observations. Even though it seems well recognised that computational models of biological vision can help in design of computer vision algorithms, it is a non-trivial exercise for a computer vision researcher to mine relevant information from biological vision literature as very few studies in biology are organised at a task level. In this paper we aim to bridge this gap by providing a computer vision task centric presentation of models primarily originating in biological vision studies. Not only do we revisit some of the main features of biological vision and discuss the foundations of existing computational studies modelling biological vision, but also we consider three classical computer vision tasks from a biological perspective: image sensing, segmentation and optical flow. Using this task-centric approach, we discuss well-known biological functional principles and compare them with approaches taken by computer vision. Based on this comparative analysis of computer and biological vision, we present some recent models in biological vision and highlight a few models that we think are promising for future investigations in computer vision. To this extent, this paper provides new insights and a starting point for investigators interested in the design of biology-based computer vision algorithms and pave a way for much needed interaction between the two communities leading to the development of synergistic models of artificial and biological vision

Creativity and the Brain

Neurocognitive approach to higher cognitive functions that bridges the gap between psychological and neural level of description is introduced. Relevant facts about the brain, working memory and representation of symbols in the brain are summarized. Putative brain processes responsible for problem solving, intuition, skill learning and automatization are described. The role of non-dominant brain hemisphere in solving problems requiring insight is conjectured. Two factors seem to be essential for creativity: imagination constrained by experience, and filtering that selects most interesting solutions. Experiments with paired words association are analyzed in details and evidence for stochastic resonance effects is found. Brain activity in the process of invention of novel words is proposed as the simplest way to understand creativity using experimental and computational means. Perspectives on computational models of creativity are discussed

Defining an epidemiological landscape that connects movement ecology to pathogen transmission and pace-of-life

Pathogen transmission depends on host density, mobility and contact. These components emerge from host and pathogen movements that themselves arise through interactions with the surrounding environment. The environment, the emergent host and pathogen movements, and the subsequent patterns of density, mobility and contact form an ‘epidemiological landscape’ connecting the environment to specific locations where transmissions occur. Conventionally, the epidemiological landscape has been described in terms of the geographical coordinates where hosts or pathogens are located. We advocate for an alternative approach that relates those locations to attributes of the local environment. Environmental descriptions can strengthen epidemiological forecasts by allowing for predictions even when local geographical data are not available. Environmental predictions are more accessible than ever thanks to new tools from movement ecology, and we introduce a ‘movement-pathogen pace of life’ heuristic to help identify aspects of movement that have the most influence on spatial epidemiology. By linking pathogen transmission directly to the environment, the epidemiological landscape offers an efficient path for using environmental information to inform models describing when and where transmission will occur

French Roadmap for complex Systems 2008-2009

This second issue of the French Complex Systems Roadmap is the outcome of the Entretiens de Cargese 2008, an interdisciplinary brainstorming session organized over one week in 2008, jointly by RNSC, ISC-PIF and IXXI. It capitalizes on the first roadmap and gathers contributions of more than 70 scientists from major French institutions. The aim of this roadmap is to foster the coordination of the complex systems community on focused topics and questions, as well as to present contributions and challenges in the complex systems sciences and complexity science to the public, political and industrial spheres

Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences

Advances in the technologies and informatics used to generate and process large biological data sets (omics data) are promoting a critical shift in the study of biomedical sciences. While genomics, transcriptomics and proteinomics, coupled with bioinformatics and biostatistics, are gaining momentum, they are still, for the most part, assessed individually with distinct approaches generating monothematic rather than integrated knowledge. As other areas of biomedical sciences, including metabolomics, epigenomics and pharmacogenomics, are moving towards the omics scale, we are witnessing the rise of inter-disciplinary data integration strategies to support a better understanding of biological systems and eventually the development of successful precision medicine. This review cuts across the boundaries between genomics, transcriptomics and proteomics, summarizing how omics data are generated, analysed and shared, and provides an overview of the current strengths and weaknesses of this global approach. This work intends to target students and researchers seeking knowledge outside of their field of expertise and fosters a leap from the reductionist to the global-integrative analytical approach in research

High Fidelity Bioelectric Modelling of the Implanted Cochlea

Cochlear implants are medical devices that can restore sound perception in individuals with sensorineural hearing loss (SHL). Since their inception, improvements in performance have largely been driven by advances in signal processing, but progress has plateaued for almost a decade. This suggests that there is a bottleneck at the electrode-tissue interface, which is responsible for enacting the biophysical changes that govern neuronal recruitment. Understanding this interface is difficult because the cochlea is small, intricate, and difficult to access. As such, researchers have turned to modelling techniques to provide new insights. The state-of-the-art involves calculating the electric field using a volume conduction model of the implanted cochlea and coupling it with a neural excitation model to predict the response. However, many models are unable to predict patient outcomes consistently. This thesis aims to improve the reliability of these models by creating high fidelity reconstructions of the inner ear and critically assessing the validity of the underlying and hitherto untested assumptions. Regarding boundary conditions, the evidence suggests that the unmodelled monopolar return path should be accounted for, perhaps by applying a voltage offset at a boundary surface. Regarding vasculature, the models show that large modiolar vessels like the vein of the scala tympani have a strong local effect near the stimulating electrode. Finally, it appears that the oft-cited quasi-static assumption is not valid due to the high permittivity of neural tissue. It is hoped that the study improves the trustworthiness of all bioelectric models of the cochlea, either by validating the claims of existing models, or by prompting improvements in future work. Developing our understanding of the underlying physics will pave the way for advancing future electrode array designs as well as patient-specific simulations, ultimately improving the quality of life for those with SHL

Learning cell representations in temporal and 3D contexts

Cell morphology and its changes under different circumstances is one of the primary ways by which we can understand biology. Computational tools for characterization and analysis, therefore, play a critical role in advancing studies involving cell morphology. In this thesis, I explored the use of representation learning and self-supervised methods to analyze nuclear texture in fluorescence imaging across different contexts and scales. To analyze the cell cycle using 2D temporal imaging data, as well as DNA damage in 3D imaging data, I employed a simple model based on the VAE-GAN architecture. Through the VAE-GAN model, I constructed manifolds in which the latent representations of the data can be grouped and clustered based on textural similarities without the need for exhaustive training annotations. I used these representations, as well as manually engineered features, to perform various analyses both at the single cell and tissue levels. The application on the cell cycle data revealed that common tasks such as cell cycle staging and cell cycle time estimation can be done even with minimal fluorescence information and user annotation. On the other hand, the texture classes derived to characterize DNA damage in 3D histology images unveiled differences between control and treated tissue regions. Lastly, by aggregating cell-level information to characterize local cell neighborhoods, interactions between DNA-damaged cells and immune cells can be quantified and some tissue microstructures can be identified. The results presented in this thesis demonstrated the utility of the representations learned through my approach in supporting biological inquiries involving temporal and 3D spatial data. The quantitative measurements computed using the presented methods have the potential to aid not only similar experiments on the cell cycle and DNA damage but also in exploratory studies in 3D histology

Artificial ontogenesis: a connectionist model of development

This thesis suggests that ontogenetic adaptive processes are important for generating intelligent beha- viour. It is thus proposed that such processes, as they occur in nature, need to be modelled and that such a model could be used for generating artificial intelligence, and specifically robotic intelligence. Hence, this thesis focuses on how mechanisms of intelligence are specified.A major problem in robotics is the need to predefine the behaviour to be followed by the robot. This makes design intractable for all but the simplest tasks and results in controllers that are specific to that particular task and are brittle when faced with unforeseen circumstances. These problems can be resolved by providing the robot with the ability to adapt the rules it follows and to autonomously create new rules for controlling behaviour. This solution thus depends on the predefinition of how rules to control behaviour are to be learnt rather than the predefinition of rules for behaviour themselves.Learning new rules for behaviour occurs during the developmental process in biology. Changes in the structure of the cerebral 'cortex underly behavioural and cognitive development throughout infancy and beyond. The uniformity of the neocortex suggests that there is significant computational uniformity across the cortex resulting from uniform mechanisms of development, and holds out the possibility of a general model of development. Development is an interactive process between genetic predefinition and environmental influences. This interactive process is constructive: qualitatively new behaviours are learnt by using simple abilities as a basis for learning more complex ones. The progressive increase in competence, provided by development, may be essential to make tractable the process of acquiring higher -level abilities.While simple behaviours can be triggered by direct sensory cues, more complex behaviours require the use of more abstract representations. There is thus a need to find representations at the correct level of abstraction appropriate to controlling each ability. In addition, finding the correct level of abstrac- tion makes tractable the task of associating sensory representations with motor actions. Hence, finding appropriate representations is important both for learning behaviours and for controlling behaviours. Representations can be found by recording regularities in the world or by discovering re- occurring pat- terns through repeated sensory -motor interactions. By recording regularities within the representations thus formed, more abstract representations can be found. Simple, non -abstract, representations thus provide the basis for learning more complex, abstract, representations.A modular neural network architecture is presented as a basis for a model of development. The pat- tern of activity of the neurons in an individual network constitutes a representation of the input to that network. This representation is formed through a novel, unsupervised, learning algorithm which adjusts the synaptic weights to improve the representation of the input data. Representations are formed by neurons learning to respond to correlated sets of inputs. Neurons thus became feature detectors or pat- tern recognisers. Because the nodes respond to patterns of inputs they encode more abstract features of the input than are explicitly encoded in the input data itself. In this way simple representations provide the basis for learning more complex representations. The algorithm allows both more abstract represent- ations to be formed by associating correlated, coincident, features together, and invariant representations to be formed by associating correlated, sequential, features together.The algorithm robustly learns accurate and stable representations, in a format most appropriate to the structure of the input data received: it can represent both single and multiple input features in both the discrete and continuous domains, using either topologically or non -topologically organised nodes. The output of one neural network is used to provide inputs for other networks. The robustness of the algorithm enables each neural network to be implemented using an identical algorithm. This allows a modular `assembly' of neural networks to be used for learning more complex abilities: the output activations of a network can be used as the input to other networks which can then find representations of more abstract information within the same input data; and, by defining the output activations of neurons in certain networks to have behavioural consequences it is possible to learn sensory -motor associations, to enable sensory representations to be used to control behaviour