A Long Skip Connection for Enhanced Color Selectivity in CNN Architectures.

Some recent studies show that filters in convolutional neural networks (CNNs) have low color selectivity in datasets of natural scenes such as Imagenet. CNNs, bio-inspired by the visual cortex, are characterized by their hierarchical learning structure which appears to gradually transform the representation space. Inspired by the direct connection between the LGN and V4, which allows V4 to handle low-level information closer to the trichromatic input in addition to processed information that comes from V2/V3, we propose the addition of a long skip connection (LSC) between the first and last blocks of the feature extraction stage to allow deeper parts of the network to receive information from shallower layers. This type of connection improves classification accuracy by combining simple-visual and complex-abstract features to create more color-selective ones. We have applied this strategy to classic CNN architectures and quantitatively and qualitatively analyzed the improvement in accuracy while focusing on color selectivity. The results show that, in general, skip connections improve accuracy, but LSC improves it even more and enhances the color selectivity of the original CNN architectures. As a side result, we propose a new color representation procedure for organizing and filtering feature maps, making their visualization more manageable for qualitative color selectivity analysis.

An overview of graph databases and their applications in the biomedical domain.

Over the past couple of decades, the explosion of densely interconnected data has stimulated the research, development and adoption of graph database technologies. From early graph models to more recent native graph databases, the landscape of implementations has evolved to cover enterprise-ready requirements. Because of the interconnected nature of its data, the biomedical domain has been one of the early adopters of graph databases, enabling more natural representation models and better data integration workflows, exploration and analysis facilities. In this work, we survey the literature to explore the evolution, performance and how the most recent graph database solutions are applied in the biomedical domain, compiling a great variety of use cases. With this evidence, we conclude that the available graph database management systems are fit to support data-intensive, integrative applications, targeted at both basic research and exploratory tasks closer to the clinic.

Integrative Base Ontology for the Research Analysis of Alzheimer's Disease-Related Mild Cognitive Impairment.

Early detection of mild cognitive impairment (MCI) has become a priority in Alzheimer's disease (AD) research, as it is a transitional phase between normal aging and dementia. However, information on MCI and AD is scattered across different formats and standards generated by different technologies, making it difficult to work with them manually. Ontologies have emerged as a solution to this problem due to their capacity for homogenization and consensus in the representation and reuse of data. In this context, an ontology that integrates the four main domains of neurodegenerative diseases, diagnostic tests, cognitive functions, and brain areas will be of great use in research. Here, we introduce the first approach to this ontology, the Neurocognitive Integrated Ontology (NIO), which integrates the knowledge regarding neuropsychological tests (NT), AD, cognitive functions, and brain areas. This ontology enables interoperability and facilitates access to data by integrating dispersed knowledge across different disciplines, rendering it useful for other research groups. To ensure the stability and reusability of NIO, the ontology was developed following the ontology-building life cycle, integrating and expanding terms from four different reference ontologies. The usefulness of this ontology was validated through use-case scenarios.

Extending XNAT Platform with an Incremental Semantic Framework.

Informatics increases the yield from neuroscience due to improved data. Data sharing and accessibility enable joint efforts between different research groups, as well as replication studies, pivotal for progress in the field. Research data archiving solutions are evolving rapidly to address these necessities, however, distributed data integration is still difficult because of the need of explicit agreements for disparate data models. To address these problems, ontologies are widely used in biomedical research to obtain common vocabularies and logical descriptions, but its application may suffer from scalability issues, domain bias, and loss of low-level data access. With the aim of improving the application of semantic models in biobanking systems, an incremental semantic framework that takes advantage of the latest advances in biomedical ontologies and the XNAT platform is designed and implemented. We follow a layered architecture that allows the alignment of multi-domain biomedical ontologies to manage data at different levels of abstraction. To illustrate this approach, the development is integrated in the JPND (EU Joint Program for Neurodegenerative Disease) APGeM project, focused on finding early biomarkers for Alzheimer's and other dementia related diseases.

Hippocampal complex atrophy in poststroke and mild cognitive impairment.

To investigate putative interacting or distinct pathways for hippocampal complex substructure (HCS) atrophy and cognitive affection in early-stage Alzheimer's disease (AD) and cerebrovascular disease (CVD), we recruited healthy controls, patients with mild cognitive impairment (MCI) and poststroke patients. HCSs were segmented, and quantitative white-matter hyperintensity (WMH) load and cerebrospinal fluid (CSF) amyloid-ß concentrations were determined. The WMH load was higher poststroke. All examined HCSs were smaller in amyloid-positive MCI than in controls, and the subicular regions were smaller poststroke. Memory was reduced in amyloid-positive MCI, and psychomotor speed and executive function were reduced in poststroke and amyloid-positive MCI. Size of several HCS correlated with WMH load poststroke and with CSF amyloid-ß concentrations in MCI. In poststroke and amyloid-positive MCI, neuropsychological function correlated with WMH load and hippocampal volume. There are similar patterns of HCS atrophy in CVD and early-stage AD, but different HCS associations with WMH and CSF biomarkers. WMHs add to hippocampal atrophy and the archetypal AD deficit delayed recall. In line with mounting evidence of a mechanistic link between primary AD pathology and CVD, these additive effects suggest interacting pathologic processes.

Identification of the optic nerve head with genetic algorithms.

OBJECTIVE: This work proposes creating an automatic system to locate and segment the optic nerve head (ONH) in eye fundus photographic images using genetic algorithms. METHODS AND MATERIAL: Domain knowledge is used to create a set of heuristics that guide the various steps involved in the process. Initially, using an eye fundus colour image as input, a set of hypothesis points was obtained that exhibited geometric properties and intensity levels similar to the ONH contour pixels. Next, a genetic algorithm was used to find an ellipse containing the maximum number of hypothesis points in an offset of its perimeter, considering some constraints. The ellipse thus obtained is the approximation to the ONH. The segmentation method is tested in a sample of 110 eye fundus images, belonging to 55 patients with glaucoma (23.1%) and eye hypertension (76.9%) and random selected from an eye fundus image base belonging to the Ophthalmology Service at Miguel Servet Hospital, Saragossa (Spain). RESULTS AND CONCLUSIONS: The results obtained are competitive with those in the literature. The method's generalization capability is reinforced when it is applied to a different image base from the one used in our study and a discrepancy curve is obtained very similar to the one obtained in our image base. In addition, the robustness of the method proposed can be seen in the high percentage of images obtained with a discrepancy delta<5 (96% and 99% in our and a different image base, respectively). The results also confirm the hypothesis that the ONH contour can be properly approached with a non-deformable ellipse. Another important aspect of the method is that it directly provides the parameters characterising the shape of the papilla: lengths of its major and minor axes, its centre of location and its orientation with regard to the horizontal position.