Mathematical methods to analyze and interpret calcium signals of astrocytes

Astrocytes are the most numerous glial cell type in the mammalian brain and permeate the entire CNS interacting with neurons, vasculature, and other glial cells. Astrocytes display intracellular calcium signals that encode information about local synaptic function, distributed network activity, and high-level cognitive functions. Several studies have investigated the calcium dynamics of astrocytes in sensory areas and have shown that these cells can encode sensory stimuli. Nevertheless, only recently the neuro-scientific community has focused its attention on the role and functions of astrocytes in associative areas such as the hippocampus. In our first study, we used the information theory formalism to show that astrocytes in the CA1 area of the hippocampus recorded with 2-photon fluorescence microscopy during spatial navigation encode spatial information that is complementary and synergistic to information encoded by nearby "place cell" neurons. In our second study, we investigated various computational aspects of applying the information theory formalism to astrocytic calcium data. For this reason, we generated realistic simulations of calcium signals in astrocytes to determine optimal hyperparameters and procedures of information measures and applied them to real astrocytic calcium imaging data. Calcium signals of astrocytes are characterized by complex spatiotemporal dynamics occurring in subcellular parcels of the astrocytic domain which makes studying these cells in 2-photon calcium imaging recordings difficult. However, current analytical tools which identify the astrocytic subcellular regions are time consuming and extensively rely on user-defined parameters. Here, we present Rapid Astrocytic calcium Spatio-Temporal Analysis (RASTA), a novel machine learning algorithm for spatiotemporal semantic segmentation of 2-photon calcium imaging recordings of astrocytes which operates without human intervention. We found that RASTA provided fast and accurate identification of astrocytic cell somata, processes, and cellular domains, extracting calcium signals from identified regions of interest across individual cells and populations of hundreds of astrocytes recorded in awake mice.

High-resolution stratigraphy and seismic site characterization of late Quaternary paleovalley systems (Adriatic coastal plain, Italy)

In highly urbanized coastal lowlands, effective site characterization is crucial for assessing seismic risk. It requires a comprehensive stratigraphic analysis of the shallow subsurface, coupled with the precise assessment of the geophysical properties of buried deposits. In this context, late Quaternary paleovalley systems, shallowly buried fluvial incisions formed during the Late Pleistocene sea-level fall and filled during the Holocene sea-level rise, are crucial for understanding seismic amplification due to their soft sediment infill and sharp lithologic contrasts. In this research, we conducted high-resolution stratigraphic analyses of two regions, the Pescara and Manfredonia areas along the Adriatic coastline of Italy, to delineate the geometries and facies architecture of two paleovalley systems. Furthermore, we carried out geophysical investigations to characterize the study areas and perform seismic response analyses. We tested the microtremor-based horizontal-to-vertical spectral ratio as a mapping tool to reconstruct the buried paleovalley geometries. We evaluated the relationship between geological and geophysical data and identified the stratigraphic surfaces responsible for the observed resonances. To perform seismic response analysis of the Pescara paleovalley system, we integrated the stratigraphic framework with microtremor and shear wave velocity measurements. The seismic response analysis highlights strong seismic amplifications in frequency ranges that can interact with a wide variety of building types. Additionally, we explored the applicability of artificial intelligence in performing facies analysis from borehole images. We used a robust dataset of high-resolution digital images from continuous sediment cores of Holocene age to outline a novel, deep-learning-based approach for performing automatic semantic segmentation directly on core images, leveraging the power of convolutional neural networks. We propose an automated model to rapidly characterize sediment cores, reproducing the sedimentologist's interpretation, and providing guidance for stratigraphic correlation and subsurface reconstructions.

Metodologie di Corrispondenza Stereo Basate su Deep Learning per Superfici Altamente Riflettenti e Trasparenti: Dataset e Architettura

Nell’ambito della Stereo Vision, settore della Computer Vision, partendo da coppie di immagini RGB, si cerca di ricostruire la profondità della scena. La maggior parte degli algoritmi utilizzati per questo compito ipotizzano che tutte le superfici presenti nella scena siano lambertiane. Quando sono presenti superfici non lambertiane (riflettenti o trasparenti), gli algoritmi stereo esistenti sbagliano la predizione della profondità. Per risolvere questo problema, durante l’esperienza di tirocinio, si è realizzato un dataset contenente oggetti trasparenti e riflettenti che sono la base per l’allenamento della rete. Agli oggetti presenti nelle scene sono associate annotazioni 3D usate per allenare la rete. Invece, nel seguente lavoro di tesi, utilizzando l’algoritmo RAFT-Stereo [1], rete allo stato dell’arte per la stereo vision, si analizza come la rete modifica le sue prestazioni (predizione della disparità) se al suo interno viene inserito un modulo per la segmentazione semantica degli oggetti. Si introduce questo layer aggiuntivo perché, trovare la corrispondenza tra due punti appartenenti a superfici lambertiane, risulta essere molto complesso per una normale rete. Si vuole utilizzare l’informazione semantica per riconoscere questi tipi di superfici e così migliorarne la disparità. È stata scelta questa architettura neurale in quanto, durante l’esperienza di tirocinio riguardante la creazione del dataset Booster [2], è risultata la migliore su questo dataset. L’obiettivo ultimo di questo lavoro è vedere se il riconoscimento di superfici non lambertiane, da parte del modulo semantico, influenza la predizione della disparità migliorandola. Nell’ambito della stereo vision, gli elementi riflettenti e trasparenti risultano estremamente complessi da analizzare, ma restano tuttora oggetto di studio dati gli svariati settori di applicazione come la guida autonoma e la robotica.

Deep learning based style transfer for low altitude aerial imagery

Unmanned Aerial Vehicle (UAVs) equipped with cameras have been fast deployed to a wide range of applications, such as smart cities, agriculture or search and rescue applications. Even though UAV datasets exist, the amount of open and quality UAV datasets is limited. So far, we want to overcome this lack of high quality annotation data by developing a simulation framework for a parametric generation of synthetic data. The framework accepts input via a serializable format. The input specifies which environment preset is used, the objects to be placed in the environment along with their position and orientation as well as additional information such as object color and size. The result is an environment that is able to produce UAV typical data: RGB image from the UAVs camera, altitude, roll, pitch and yawn of the UAV. Beyond the image generation process, we improve the resulting image data photorealism by using Synthetic-To-Real transfer learning methods. Transfer learning focuses on storing knowledge gained while solving one problem and applying it to a different - although related - problem. This approach has been widely researched in other affine fields and results demonstrate it to be an interesing area to investigate. Since simulated images are easy to create and synthetic-to-real translation has shown good quality results, we are able to generate pseudo-realistic images. Furthermore, object labels are inherently given, so we are capable of extending the already existing UAV datasets with realistic quality images and high resolution meta-data. During the development of this thesis we have been able to produce a result of 68.4% on UAVid. This can be considered a new state-of-art result on this dataset.

Deep convolutional neural networks for semantic video object segmentation

In this thesis, we propose to infer pixel-level labelling in video by utilising only object category information, exploiting the intrinsic structure of video data. Our motivation is the observation that image-level labels are much more easily to be acquired than pixel-level labels, and it is natural to find a link between the image level recognition and pixel level classification in video data, which would transfer learned recognition models from one domain to the other one. To this end, this thesis proposes two domain adaptation approaches to adapt the deep convolutional neural network (CNN) image recognition model trained from labelled image data to the target domain exploiting both semantic evidence learned from CNN, and the intrinsic structures of unlabelled video data. Our proposed approaches explicitly model and compensate for the domain adaptation from the source domain to the target domain which in turn underpins a robust semantic object segmentation method for natural videos. We demonstrate the superior performance of our methods by presenting extensive evaluations on challenging datasets comparing with the state-of-the-art methods.

Image segmentation through combined methods: watershed transform, unsupervised distance learning and normalized cut

Research on image processing has shown that combining segmentation methods may lead to a solid approach to extract semantic information from different sort of images. Within this context, the Normalized Cut (NCut) is usually used as a final partitioning tool for graphs modeled in some chosen method. This work explores the Watershed Transform as a modeling tool, using different criteria of the hierarchical Watershed to convert an image into an adjacency graph. The Watershed is combined with an unsupervised distance learning step that redistributes the graph weights and redefines the Similarity matrix, before the final segmentation step using NCut. Adopting the Berkeley Segmentation Data Set and Benchmark as a background, our goal is to compare the results obtained for this method with previous work to validate its performance.

Methods and Techniques for Segmentation of Consumers in Social Media

Los medios sociales han revolucionado la manera en la que los consumidores se relacionan entre sí y con las marcas. Las opiniones publicadas en dichos medios tienen un poder de influencia en las decisiones de compra tan importante como las campañas de publicidad. En consecuencia, los profesionales del marketing cada vez dedican mayores esfuerzos e inversión a la obtención de indicadores que permitan medir el estado de salud de las marcas a partir de los contenidos digitales generados por sus consumidores. Dada la naturaleza no estructurada de los contenidos publicados en los medios sociales, la tecnología usada para procesar dichos contenidos ha menudo implementa técnicas de Inteligencia Artificial, tales como algoritmos de procesamiento de lenguaje natural, aprendizaje automático y análisis semántico. Esta tesis, contribuye al estado de la cuestión, con un modelo que permite estructurar e integrar la información publicada en medios sociales, y una serie de técnicas cuyos objetivos son la identificación de consumidores, así como la segmentación psicográfica y sociodemográfica de los mismos. La técnica de identificación de consumidores se basa en la huella digital de los dispositivos que utilizan para navegar por la Web y es tolerante a los cambios que se producen con frecuencia en dicha huella digital. Las técnicas de segmentación psicográfica descritas obtienen la posición en el embudo de compra de los consumidores y permiten clasificar las opiniones en función de una serie de atributos de marketing. Finalmente, las técnicas de segmentación sociodemográfica permiten obtener el lugar de residencia y el género de los consumidores. ABSTRACT Social media has revolutionised the way in which consumers relate to each other and with brands. The opinions published in social media have a power of influencing purchase decisions as important as advertising campaigns. Consequently, marketers are increasing efforts and investments for obtaining indicators to measure brand health from the digital content generated by consumers. Given the unstructured nature of social media contents, the technology used for processing such contents often implements Artificial Intelligence techniques, such as natural language processing, machine learning and semantic analysis algorithms. This thesis contributes to the State of the Art, with a model for structuring and integrating the information posted on social media, and a number of techniques whose objectives are the identification of consumers, as well as their socio-demographic and psychographic segmentation. The consumer identification technique is based on the fingerprint of the devices they use to surf the Web and is tolerant to the changes that occur frequently in such fingerprint. The psychographic profiling techniques described infer the position of consumer in the purchase funnel, and allow to classify the opinions based on a series of marketing attributes. Finally, the socio-demographic profiling techniques allow to obtain the residence and gender of consumers.

Topic Segmentation: How Much Can We Do by Counting Words and Sequences of Words

In this paper, we present an innovative topic segmentation system based on a new informative similarity measure that takes into account word co-occurrence in order to avoid the accessibility to existing linguistic resources such as electronic dictionaries or lexico-semantic databases such as thesauri or ontology. Topic segmentation is the task of breaking documents into topically coherent multi-paragraph subparts. Topic segmentation has extensively been used in information retrieval and text summarization. In particular, our architecture proposes a language-independent topic segmentation system that solves three main problems evidenced by previous research: systems based uniquely on lexical repetition that show reliability problems, systems based on lexical cohesion using existing linguistic resources that are usually available only for dominating languages and as a consequence do not apply to less favored languages and finally systems that need previously existing harvesting training data. For that purpose, we only use statistics on words and sequences of words based on a set of texts. This solution provides a flexible solution that may narrow the gap between dominating languages and less favored languages thus allowing equivalent access to information.

The Use of Latent Semantic Indexing to Mitigate OCR Effects of Related Document Images

Due to both the widespread and multipurpose use of document images and the current availability of a high number of document images repositories, robust information retrieval mechanisms and systems have been increasingly demanded. This paper presents an approach to support the automatic generation of relationships among document images by exploiting Latent Semantic Indexing (LSI) and Optical Character Recognition (OCR). We developed the LinkDI (Linking of Document Images) service, which extracts and indexes document images content, computes its latent semantics, and defines relationships among images as hyperlinks. LinkDI was experimented with document images repositories, and its performance was evaluated by comparing the quality of the relationships created among textual documents as well as among their respective document images. Considering those same document images, we ran further experiments in order to compare the performance of LinkDI when it exploits or not the LSI technique. Experimental results showed that LSI can mitigate the effects of usual OCR misrecognition, which reinforces the feasibility of LinkDI relating OCR output with high degradation.

Effects of meal size and proximal-distal segmentation on gastric activity

AIM: To evaluate the effects of meal size and three segmentations on intragastric distribution of the meal and gastric motility, by scintigraphy. METHODS: Twelve healthy volunteers were randomly assessed, twice, by scintigraphy. The test meal consisted of 60 or 180 mL of yogurt labeled with 64 MBq (99m)Tc-tin colloid. Anterior and posterior dynamic frames were simultaneously acquired for 18 min and all data were analyzed in MatLab. Three proximal-distal segmentations using regions of interest were adopted for both meals. RESULTS: Intragastric distribution of the meal between the proximal and distal compartments was strongly influenced by the way in which the stomach was divided, showing greater proximal retention after the 180 mL. An important finding was that both dominant frequencies (1 and 3 cpm) were simultaneously recorded in the proximal and distal stomach; however, the power ratio of those dominant frequencies varied in agreement with the segmentation adopted and was independent of the meal size. CONCLUSION: It was possible to simultaneously evaluate the static intragastric distribution and phasic contractility from the same recording using our scintigraphic approach. (C) 2010 Baishideng. All rights reserved.

Gene Expression Noise in Spatial Patterning: hunchback Promoter Structure Affects Noise Amplitude and Distribution in Drosophila Segmentation

Positional information in developing embryos is specified by spatial gradients of transcriptional regulators. One of the classic systems for studying this is the activation of the hunchback (hb) gene in early fruit fly (Drosophila) segmentation by the maternally-derived gradient of the Bicoid (Bcd) protein. Gene regulation is subject to intrinsic noise which can produce variable expression. This variability must be constrained in the highly reproducible and coordinated events of development. We identify means by which noise is controlled during gene expression by characterizing the dependence of hb mRNA and protein output noise on hb promoter structure and transcriptional dynamics. We use a stochastic model of the hb promoter in which the number and strength of Bcd and Hb (self-regulatory) binding sites can be varied. Model parameters are fit to data from WT embryos, the self-regulation mutant hb(14F), and lacZ reporter constructs using different portions of the hb promoter. We have corroborated model noise predictions experimentally. The results indicate that WT (self-regulatory) Hb output noise is predominantly dependent on the transcription and translation dynamics of its own expression, rather than on Bcd fluctuations. The constructs and mutant, which lack self-regulation, indicate that the multiple Bcd binding sites in the hb promoter (and their strengths) also play a role in buffering noise. The model is robust to the variation in Bcd binding site number across a number of fly species. This study identifies particular ways in which promoter structure and regulatory dynamics reduce hb output noise. Insofar as many of these are common features of genes (e. g. multiple regulatory sites, cooperativity, self-feedback), the current results contribute to the general understanding of the reproducibility and determinacy of spatial patterning in early development.

Improvements on ICA mixture models for image pre-processing and segmentation

Today several different unsupervised classification algorithms are commonly used to cluster similar patterns in a data set based only on its statistical properties. Specially in image data applications, self-organizing methods for unsupervised classification have been successfully applied for clustering pixels or group of pixels in order to perform segmentation tasks. The first important contribution of this paper refers to the development of a self-organizing method for data classification, named Enhanced Independent Component Analysis Mixture Model (EICAMM), which was built by proposing some modifications in the Independent Component Analysis Mixture Model (ICAMM). Such improvements were proposed by considering some of the model limitations as well as by analyzing how it should be improved in order to become more efficient. Moreover, a pre-processing methodology was also proposed, which is based on combining the Sparse Code Shrinkage (SCS) for image denoising and the Sobel edge detector. In the experiments of this work, the EICAMM and other self-organizing models were applied for segmenting images in their original and pre-processed versions. A comparative analysis showed satisfactory and competitive image segmentation results obtained by the proposals presented herein. (C) 2008 Published by Elsevier B.V.

A Procedure for Semantic Querying in the Adaptive Formalism

This paper contains a new proposal for the definition of the fundamental operation of query under the Adaptive Formalism, one capable of locating functional nuclei from descriptions of their semantics. To demonstrate the method`s applicability, an implementation of the query procedure constrained to a specific class of devices is shown, and its asymptotic computational complexity is discussed.

AUTOMATIC CORONARY WALL SEGMENTATION IN INTRAVASCULAR ULTRASOUND IMAGES USING BINARY MORPHOLOGICAL RECONSTRUCTION

Intravascular ultrasound (IVUS) image segmentation can provide more detailed vessel and plaque information, resulting in better diagnostics, evaluation and therapy planning. A novel automatic segmentation proposal is described herein; the method relies on a binary morphological object reconstruction to segment the coronary wall in IVUS images. First, a preprocessing followed by a feature extraction block are performed, allowing for the desired information to be extracted. Afterward, binary versions of the desired objects are reconstructed, and their contours are extracted to segment the image. The effectiveness is demonstrated by segmenting 1300 images, in which the outcomes had a strong correlation to their corresponding gold standard. Moreover, the results were also corroborated statistically by having as high as 92.72% and 91.9% of true positive area fraction for the lumen and media adventitia border, respectively. In addition, this approach can be adapted easily and applied to other related modalities, such as intravascular optical coherence tomography and intravascular magnetic resonance imaging. (E-mail: matheuscardosomg@hotmail.com) (C) 2011 World Federation for Ultrasound in Medicine & Biology.

Semantic molecules

This paper explains and explores the concept of "semantic molecules" in the NSM methodology of semantic analysis. A semantic molecule is a complex lexical meaning which functions as an intermediate unit in the structure of other, more complex concepts. The paper undertakes an overview of different kinds of semantic molecule, showing how they enter into more complex meanings and how they themselves can be explicated. It shows that four levels of "nesting" of molecules within molecules are attested, and it argues that while some molecules such as 'hands' and 'make', may well be language-universal, many others are language-specific.