Bayesian Learning with Dependency Structures via Latent Factors, Mixtures, and Copulas

Bayesian methods offer a flexible and convenient probabilistic learning framework to extract interpretable knowledge from complex and structured data. Such methods can characterize dependencies among multiple levels of hidden variables and share statistical strength across heterogeneous sources. In the first part of this dissertation, we develop two dependent variational inference methods for full posterior approximation in non-conjugate Bayesian models through hierarchical mixture- and copula-based variational proposals, respectively. The proposed methods move beyond the widely used factorized approximation to the posterior and provide generic applicability to a broad class of probabilistic models with minimal model-specific derivations. In the second part of this dissertation, we design probabilistic graphical models to accommodate multimodal data, describe dynamical behaviors and account for task heterogeneity. In particular, the sparse latent factor model is able to reveal common low-dimensional structures from high-dimensional data. We demonstrate the effectiveness of the proposed statistical learning methods on both synthetic and real-world data.

Étude de quelques populations structurées : processus de coalescence et abondance d’une stratégie

Le fichiers qui accompagnent mon document ont été réalisés avec le logiciel Mathematica

Processing of hierarchical syntactic strusture in music

Hierarchical structure with nested nonlocal dependencies is a key feature of human language and can be identified theoretically in most pieces of tonal music. However, previous studies have argued against the perception of such structures in music. Here, we show processing of nonlocal dependencies in music. We presented chorales by J. S. Bach and modified versions inwhich the hierarchical structure was rendered irregular whereas the local structure was kept intact. Brain electric responses differed between regular and irregular hierarchical structures, in both musicians and nonmusicians. This finding indicates that, when listening to music, humans apply cognitive processes that are capable of dealing with longdistance dependencies resulting from hierarchically organized syntactic structures. Our results reveal that a brain mechanism fundamental for syntactic processing is engaged during the perception of music, indicating that processing of hierarchical structure with nested nonlocal dependencies is not just a key component of human language, but a multidomain capacity of human cognition.

Processing of hierarchical syntactic strusture in music

Hierarchical structure with nested nonlocal dependencies is a key feature of human language and can be identified theoretically in most pieces of tonal music. However, previous studies have argued against the perception of such structures in music. Here, we show processing of nonlocal dependencies in music. We presented chorales by J. S. Bach and modified versions inwhich the hierarchical structure was rendered irregular whereas the local structure was kept intact. Brain electric responses differed between regular and irregular hierarchical structures, in both musicians and nonmusicians. This finding indicates that, when listening to music, humans apply cognitive processes that are capable of dealing with longdistance dependencies resulting from hierarchically organized syntactic structures. Our results reveal that a brain mechanism fundamental for syntactic processing is engaged during the perception of music, indicating that processing of hierarchical structure with nested nonlocal dependencies is not just a key component of human language, but a multidomain capacity of human cognition.

A flexible bio-inspired hierarchical model for analyzing musical timbre

A flexible and multipurpose bio-inspired hierarchical model for analyzing musical timbre is presented in this paper. Inspired by findings in the fields of neuroscience, computational neuroscience, and psychoacoustics, not only does the model extract spectral and temporal characteristics of a signal, but it also analyzes amplitude modulations on different timescales. It uses a cochlear filter bank to resolve the spectral components of a sound, lateral inhibition to enhance spectral resolution, and a modulation filter bank to extract the global temporal envelope and roughness of the sound from amplitude modulations. The model was evaluated in three applications. First, it was used to simulate subjective data from two roughness experiments. Second, it was used for musical instrument classification using the k-NN algorithm and a Bayesian network. Third, it was applied to find the features that characterize sounds whose timbres were labeled in an audiovisual experiment. The successful application of the proposed model in these diverse tasks revealed its potential in capturing timbral information.

Étude de quelques populations structurées : processus de coalescence et abondance d’une stratégie

Le fichiers qui accompagnent mon document ont été réalisés avec le logiciel Mathematica

ENGINEERING HIERARCHICAL MESO-/MICROPOROUS LAMELLAR ZEOLITES WITH VARIABLE TEXTURAL AND CATALYTIC PROPERTIES

Meso-/microporous zeolites combine the charactersitics of well-defined micropores of zeolite with efficient mass transfer consequences of mesopores to increase the efficiency of the catalysts in reactions involving bulky molecules. Different methods such as demetallation and templating have been explored for the synthesis of meso-/microporous zeolites. However, they all have limitations in production of meso-/microporous zeolites with tunable textural and catalytic properties using few synthesis steps. To address this challenge, a simple one-step dual template synthesis approach has been developed in this work to engineer lamellar meso-/microporous zeolites structures with tunable textural and catalytic properties. First, one-step dual template synthesis of meso-/microporous mordenite framework inverted (MFI) zeolite structures was investigated. Tetrapropyl ammonium hydroxide (TPAOH) and diquaternary ammonium surfactant ([C22H45-N+(CH3)2-C6H12-N+(CH3)2-C6H13]Br2, C22-6-6) were used as templates to produce micropores and mesopores, respectively. The variation in concentration ratios of dual templates and hydrothermal synthesis conditions resulted in production of multi-lamellar MFI and the hybrid lamellar-bulk MFI (HLBM) zeolite structures. The relationship between the morphology, porosity, acidity, and catalytic properties of these catalysts was systematically studied. Then, the validity of the proposed synthesis approach for production of other types of zeolites composites was examined by creating a meso-/microporous bulk polymorph A (BEA)-lamellar MFI (BBLM) composite. The resulted composite samples showed higher catalytic stability compared to their single component zeolites. The studies demonstrated the high potential of the one-step dual template synthesis procedure for engineering the textural and catalytic properties of the synthesized zeolites.

Comparing children's self-report instruments for health-related quality of life using the International Classification of Functioning, Disability and Health for Children and Youth (ICF-CY)

Children with chronic conditions often experience a long treatment which can be complex and negatively impacts the child's well-being. In planning treatment and interventions for children with chronic conditions, it is important to measure health-related quality of life (HrQoL). HrQoL instruments are considered to be a patient-reported outcome measure (PROM) and should be used in routine practice. Purpose: The aim of this study was to compare the content dimensions of HrQoL instruments for children's self-reports using the framework of ICF-CY. Method: The sample consist of six instruments for health-related quality of life for children 5 to 18 years of age, which was used in the Swedish national quality registries for children and adolescents with chronic conditions. The following instruments were included: CHQ-CF, DCGM-37, EQ-5D-Y, KIDSCREEN-52, Kid-KINDL and PedsQL 4.0. The framework of the ICF-CY was used as the basis for the comparison. Results: There were 290 meaningful concepts identified and linked to 88 categories in the classification ICF-CY with 29 categories of the component body functions, 48 categories of the component activities and participation and 11 categories of the component environmental factors. No concept were linked to the component body structures. The comparison revealed that the items in the HrQoL instruments corresponded primarily with the domains of activities and less with environmental factors. Conclusions: In conclusion, the results confirm that ICF-CY provide a good framework for content comparisons that evaluate similarities and differences to ICF-CY categories. The results of this study revealed the need for greater consensus of content across different HrQoL instruments. To obtain a detailed description of children's HrQoL, DCGM-37 and KIDSCREEN-52 may be appropriate instruments to use that can increase the understanding of young patients' needs.

Measured Time: Imposing a Temporal Metric toClassificatory Structures

Describes three units of time helpful for understanding and evaluating classificatory structures: long time (versions and states of classification schemes), short time (the act of indexing as repeated ritual or form), and micro-time (where stages of the interpretation process of indexing are separated out and inventoried). Concludes with a short discussion of how time and the impermanence of classification also conjures up an artistic conceptualization of indexing, and briefly uses that to question the seemingly dominant understanding of classification practice as outcome of scientific management and assembly line thought.

Experientialist Epistemology and Classification Theory: Embodied and Dimensional Classification

What theoretical framework can help in building, maintaining and evaluating networked knowledge organization resources? Specifically, what theoretical framework makes sense of the semantic prowess of ontologies and peer-to-peer sys- tems, and by extension aids in their building, maintenance, and evaluation? I posit that a theoretical work that weds both for- mal and associative (structural and interpretive) aspects of knowledge organization systems provides that framework. Here I lay out the terms and the intellectual constructs that serve as the foundation for investigative work into experientialist classifi- cation theory, a theoretical framework of embodied, infrastructural, and reified knowledge organization. I build on the inter- pretive work of scholars in information studies, cognitive semantics, sociology, and science studies. With the terms and the framework in place, I then outline classification theory s critiques of classificatory structures. In order to address these cri- tiques with an experientialist approach an experientialist semantics is offered as a design commitment for an example: metadata in peer-to-peer network knowledge organization structures.

Using linear algebra for protein structural comparison and classification.

In this article, we describe a novel methodology to extract semantic characteristics from protein structures using linear algebra in order to compose structural signature vectors which may be used efficiently to compare and classify protein structures into fold families. These signatures are built from the pattern of hydrophobic intrachain interactions using Singular Value Decomposition (SVD) and Latent Semantic Indexing (LSI) techniques. Considering proteins as documents and contacts as terms, we have built a retrieval system which is able to find conserved contacts in samples of myoglobin fold family and to retrieve these proteins among proteins of varied folds with precision of up to 80%. The classifier is a web tool available at our laboratory website. Users can search for similar chains from a specific PDB, view and compare their contact maps and browse their structures using a JMol plug-in.

Phylogenetics, Ancestral State Reconstruction, And A New Infrafamilial Classification Of The Pantropical Ochnaceae (medusagynaceae, Ochnaceae S.str., Quiinaceae) Based On Five Dna Regions.

Ochnaceae s.str. (Malpighiales) are a pantropical family of about 500 species and 27 genera of almost exclusively woody plants. Infrafamilial classification and relationships have been controversial partially due to the lack of a robust phylogenetic framework. Including all genera except Indosinia and Perissocarpa and DNA sequence data for five DNA regions (ITS, matK, ndhF, rbcL, trnL-F), we provide for the first time a nearly complete molecular phylogenetic analysis of Ochnaceae s.l. resolving most of the phylogenetic backbone of the family. Based on this, we present a new classification of Ochnaceae s.l., with Medusagynoideae and Quiinoideae included as subfamilies and the former subfamilies Ochnoideae and Sauvagesioideae recognized at the rank of tribe. Our data support a monophyletic Ochneae, but Sauvagesieae in the traditional circumscription is paraphyletic because Testulea emerges as sister to the rest of Ochnoideae, and the next clade shows Luxemburgia+Philacra as sister group to the remaining Ochnoideae. To avoid paraphyly, we classify Luxemburgieae and Testuleeae as new tribes. The African genus Lophira, which has switched between subfamilies (here tribes) in past classifications, emerges as sister to all other Ochneae. Thus, endosperm-free seeds and ovules with partly to completely united integuments (resulting in an apparently single integument) are characters that unite all members of that tribe. The relationships within its largest clade, Ochnineae (former Ochneae), are poorly resolved, but former Ochninae (Brackenridgea, Ochna) are polyphyletic. Within Sauvagesieae, the genus Sauvagesia in its broad circumscription is polyphyletic as Sauvagesia serrata is sister to a clade of Adenarake, Sauvagesia spp., and three other genera. Within Quiinoideae, in contrast to former phylogenetic hypotheses, Lacunaria and Touroulia form a clade that is sister to Quiina. Bayesian ancestral state reconstructions showed that zygomorphic flowers with adaptations to buzz-pollination (poricidal anthers), a syncarpous gynoecium (a near-apocarpous gynoecium evolved independently in Quiinoideae and Ochninae), numerous ovules, septicidal capsules, and winged seeds with endosperm are the ancestral condition in Ochnoideae. Although in some lineages poricidal anthers were lost secondarily, the evolution of poricidal superstructures secured the maintenance of buzz-pollination in some of these genera, indicating a strong selective pressure on keeping that specialized pollination system.

Advancing Bag-of-visual-words Representations For Lesion Classification In Retinal Images.

Diabetic Retinopathy (DR) is a complication of diabetes that can lead to blindness if not readily discovered. Automated screening algorithms have the potential to improve identification of patients who need further medical attention. However, the identification of lesions must be accurate to be useful for clinical application. The bag-of-visual-words (BoVW) algorithm employs a maximum-margin classifier in a flexible framework that is able to detect the most common DR-related lesions such as microaneurysms, cotton-wool spots and hard exudates. BoVW allows to bypass the need for pre- and post-processing of the retinographic images, as well as the need of specific ad hoc techniques for identification of each type of lesion. An extensive evaluation of the BoVW model, using three large retinograph datasets (DR1, DR2 and Messidor) with different resolution and collected by different healthcare personnel, was performed. The results demonstrate that the BoVW classification approach can identify different lesions within an image without having to utilize different algorithms for each lesion reducing processing time and providing a more flexible diagnostic system. Our BoVW scheme is based on sparse low-level feature detection with a Speeded-Up Robust Features (SURF) local descriptor, and mid-level features based on semi-soft coding with max pooling. The best BoVW representation for retinal image classification was an area under the receiver operating characteristic curve (AUC-ROC) of 97.8% (exudates) and 93.5% (red lesions), applying a cross-dataset validation protocol. To assess the accuracy for detecting cases that require referral within one year, the sparse extraction technique associated with semi-soft coding and max pooling obtained an AUC of 94.2 ± 2.0%, outperforming current methods. Those results indicate that, for retinal image classification tasks in clinical practice, BoVW is equal and, in some instances, surpasses results obtained using dense detection (widely believed to be the best choice in many vision problems) for the low-level descriptors.

Ssr-based Genetic Diversity And Structure Of Garlic Accessions From Brazil.

Garlic is a spice and a medicinal plant; hence, there is an increasing interest in 'developing' new varieties with different culinary properties or with high content of nutraceutical compounds. Phenotypic traits and dominant molecular markers are predominantly used to evaluate the genetic diversity of garlic clones. However, 24 SSR markers (codominant) specific for garlic are available in the literature, fostering germplasm researches. In this study, we genotyped 130 garlic accessions from Brazil and abroad using 17 polymorphic SSR markers to assess the genetic diversity and structure. This is the first attempt to evaluate a large set of accessions maintained by Brazilian institutions. A high level of redundancy was detected in the collection (50 % of the accessions represented eight haplotypes). However, non-redundant accessions presented high genetic diversity. We detected on average five alleles per locus, Shannon index of 1.2, HO of 0.5, and HE of 0.6. A core collection was set with 17 accessions, covering 100 % of the alleles with minimum redundancy. Overall FST and D values indicate a strong genetic structure within accessions. Two major groups identified by both model-based (Bayesian approach) and hierarchical clustering (UPGMA dendrogram) techniques were coherent with the classification of accessions according to maturity time (growth cycle): early-late and midseason accessions. Assessing genetic diversity and structure of garlic collections is the first step towards an efficient management and conservation of accessions in genebanks, as well as to advance future genetic studies and improvement of garlic worldwide.

Hippocampal Dysplasia With Balloon Cells: Case Report And Discussion On Classification.

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