Scheme Versioning in the Semantic Web

This paper describes a conceptual framework and meth- odology for managing scheme versioning for the Semantic Web. The first part of the paper introduces the concept of vocabulary encoding schemes, distinguished from metadata schemas, and discusses the characteristics of changes in schemes. The paper then presents a proposal to use a value record–similar to a term record in thesaurus management techniques–to manage scheme versioning challenges for the Semantic Web. The con-clusion identifies future research directions.

Using a Dialogue Manager to Improve Semantic Web Search

Question Answering systems that resort to the Semantic Web as a knowledge base can go well beyond the usual matching words in documents and, preferably, find a precise answer, without requiring user help to interpret the documents returned. In this paper, the authors introduce a Dialogue Manager that, through the analysis of the question and the type of expected answer, provides accurate answers to the questions posed in Natural Language. The Dialogue Manager not only represents the semantics of the questions, but also represents the structure of the discourse, including the user intentions and the questions context, adding the ability to deal with multiple answers and providing justified answers. The authors’ system performance is evaluated by comparing with similar question answering systems. Although the test suite is slight dimension, the results obtained are very promising.

Representing image captions as concept graphs using semantic information

Conceptual interpretation of languages has gathered peak interest in the world of artificial intelligence. The challenge in modeling various complications involved in a language is the main motivation behind our work. Our main focus in this work is to develop conceptual graphical representation for image captions. We have used discourse representation structure to gain semantic information which is further modeled into a graphical structure. The effectiveness of the model is evaluated by a caption based image retrieval system. The image retrieval is performed by computing subgraph based similarity measures. Best retrievals were given an average rating of . ± . out of 4 by a group of 25 human judges. The experiments were performed on a subset of the SBU Captioned Photo Dataset. This purpose of this work is to establish the cognitive sensibility of the approach to caption representations

Using syntactic and semantic features for classifying mo- dal values in the portuguese language

This paper presents a study made in a field poorly explored in the Portuguese language – modality and its automatic tagging. Our main goal was to find a set of attributes for the creation of automatic tag- gers with improved performance over the bag-of-words (bow) approach. The performance was measured using precision, recall and F1. Because it is a relatively unexplored field, the study covers the creation of the corpus (composed by eleven verbs), the use of a parser to extract syntac- tic and semantic information from the sentences and a machine learning approach to identify modality values. Based on three different sets of attributes – from trigger itself and the trigger’s path (from the parse tree) and context – the system creates a tagger for each verb achiev- ing (in almost every verb) an improvement in F1 when compared to the traditional bow approach.

Representing image captions as concept graphs using semantic information

Conceptual interpretation of languages has gathered peak interest in the world of artificial intelligence. The challenge in modeling various complications involved in a language is the main motivation behind our work. Our main focus in this work is to develop conceptual graphical representation for image captions. We have used discourse representation structure to gain semantic information which is further modeled into a graphical structure. The effectiveness of the model is evaluated by a caption based image retrieval system. The image retrieval is performed by computing subgraph based similarity measures. Best retrievals were given an average rating of . ± . out of 4 by a group of 25 human judges. The experiments were performed on a subset of the SBU Captioned Photo Dataset. This purpose of this work is to establish the cognitive sensibility of the approach to caption representations.

HBIM methodology for structural preservation of historical buildings: the semantic modeling of the San Felice sul Panaro fortress

Building Information Modelling is changing the design and construction field ever since it entered the market. It took just some time to show its capabilities, it takes some time to be mastered before it could be used expressing all its best features. Since it was conceived to be adopted from the earliest stage of design to get the maximum from the decisional project, it still struggles to adapt to existing buildings. In fact, there is a branch of this methodology that is dedicated to what has been already made that is called Historic BIM or HBIM. This study aims to make clear what are BIM and HBIM, both from a theoretical point of view and in practice, applying from scratch the state of the art to a case study. It had been chosen the fortress of San Felice sul Panaro, a marvellous building with a thousand years of history in its bricks, that suffered violent earthquakes, but it is still standing. By means of this example, it will be shown which are the limits that could be encountered when applying BIM methodology to existing heritage, moreover will be pointed out all the new features that a simple 2D design could not achieve.

Machine learning tools for protein annotation: the cases of transmembrane β-barrel and myristoylated proteins

Biology is now a “Big Data Science” thanks to technological advancements allowing the characterization of the whole macromolecular content of a cell or a collection of cells. This opens interesting perspectives, but only a small portion of this data may be experimentally characterized. From this derives the demand of accurate and efficient computational tools for automatic annotation of biological molecules. This is even more true when dealing with membrane proteins, on which my research project is focused leading to the development of two machine learning-based methods: BetAware-Deep and SVMyr. BetAware-Deep is a tool for the detection and topology prediction of transmembrane beta-barrel proteins found in Gram-negative bacteria. These proteins are involved in many biological processes and primary candidates as drug targets. BetAware-Deep exploits the combination of a deep learning framework (bidirectional long short-term memory) and a probabilistic graphical model (grammatical-restrained hidden conditional random field). Moreover, it introduced a modified formulation of the hydrophobic moment, designed to include the evolutionary information. BetAware-Deep outperformed all the available methods in topology prediction and reported high scores in the detection task. Glycine myristoylation in Eukaryotes is the binding of a myristic acid on an N-terminal glycine. SVMyr is a fast method based on support vector machines designed to predict this modification in dataset of proteomic scale. It uses as input octapeptides and exploits computational scores derived from experimental examples and mean physicochemical features. SVMyr outperformed all the available methods for co-translational myristoylation prediction. In addition, it allows (as a unique feature) the prediction of post-translational myristoylation. Both the tools here described are designed having in mind best practices for the development of machine learning-based tools outlined by the bioinformatics community. Moreover, they are made available via user-friendly web servers. All this make them valuable tools for filling the gap between sequential and annotated data.

Plutarch's chemistry of stones and metals: conceptions and explanations. With an appendix on the TheSu XML annotation scheme

This dissertation presents a systematic and analytic overview of most of the information related to stones, minerals, and stone masonry which is found in the corpus of Plutarch of Chaeronea, combined with most of the information on metals and metalworking which is connected to the former. This survey is intended as a first step in the reconstruction of the full landscape of ‘chemical’ ideas occurring in Plutarch’s writings; accordingly, the exposition of the relevant passages, the assessment of their possible interpretations, the discussion on their implications, and their contextualization in the ancient traditions have been conducted with a special interest in the ‘mineralogical’ and ‘metallurgic’ themes developed in the frame of natural philosophy and meteorology. Although in this perspective physical etiology could have come to acquire central prominence, non-etiological information on Plutarch’s ideas on the nature and behaviour of stones and metals has been treated as equally relevant to reach a fuller understanding of how Plutarch conceptualized and visualized them in general, in- and outside the frame of philosophical explanation. Such extensive outline of Plutarch’s ideas on stones and metals is a prerequisite for an accurate inquiry into his use of the two in analogies, metaphors, and symbols: to predispose this kind of research was another aim of the present survey, and this aim has contributed to shape it; moreover, a special attention has been paid to the analysis of analogical and figurative speaking due to the nature itself of a large part of Plutarch’s references to stones and metals, which are either metaphorical, presented in close association with metaphors, or framed in analogies. Much of the information used for the present overview has been extracted —always with supporting argumentation— from the implications of such metaphors and analogies.

Integrating structural variant calling, annotation and prioritization into whole genome analysis workflows: a practical application in the molecular diagnosis of neurodevelopmental disorders

Background: WGS is increasingly used as a first-line diagnostic test for patients with rare genetic diseases such as neurodevelopmental disorders (NDD). Clinical applications require a robust infrastructure to support processing, storage and analysis of WGS data. The identification and interpretation of SVs from WGS data also needs to be improved. Finally, there is a need for a prioritization system that enables downstream clinical analysis and facilitates data interpretation. Here, we present the results of a clinical application of WGS in a cohort of patients with NDD. Methods: We developed highly portable workflows for processing WGS data, including alignment, quality control, and variant calling of SNVs and SVs. A benchmark analysis of state-of-the-art SV detection tools was performed to select the most accurate combination for SV calling. A gene-based prioritization system was also implemented to support variant interpretation. Results: Using a benchmark analysis, we selected the most accurate combination of tools to improve SV detection from WGS data and build a dedicated pipeline. Our workflows were used to process WGS data from 77 NDD patient-parent families. The prioritization system supported downstream analysis and enabled molecular diagnosis in 32% of patients, 25% of which were SVs and suggested a potential diagnosis in 20% of patients, requiring further investigation to achieve diagnostic certainty. Conclusion: Our data suggest that the integration of SNVs and SVs is a main factor that increases diagnostic yield by WGS and show that the adoption of a dedicated pipeline improves the process of variant detection and interpretation.

Connecting works of art within the semantic web of symbolic meanings

My doctoral research is about the modelling of symbolism in the cultural heritage domain, and on connecting artworks based on their symbolism through knowledge extraction and representation techniques. In particular, I participated in the design of two ontologies: one models the relationships between a symbol, its symbolic meaning, and the cultural context in which the symbol symbolizes the symbolic meaning; the second models artistic interpretations of a cultural heritage object from an iconographic and iconological (thus also symbolic) perspective. I also converted several sources of unstructured data, a dictionary of symbols and an encyclopaedia of symbolism, and semi-structured data, DBpedia and WordNet, to create HyperReal, the first knowledge graph dedicated to conventional cultural symbolism. By making use of HyperReal's content, I showed how linked open data about cultural symbolism could be utilized to initiate a series of quantitative studies that analyse (i) similarities between cultural contexts based on their symbologies, (ii) broad symbolic associations, (iii) specific case studies of symbolism such as the relationship between symbols, their colours, and their symbolic meanings. Moreover, I developed a system that can infer symbolic, cultural context-dependent interpretations from artworks according to what they depict, envisioning potential use cases for museum curation. I have then re-engineered the iconographic and iconological statements of Wikidata, a widely used general-domain knowledge base, creating ICONdata: an iconographic and iconological knowledge graph. ICONdata was then enriched with automatic symbolic interpretations. Subsequently, I demonstrated the significance of enhancing artwork information through alignment with linked open data related to symbolism, resulting in the discovery of novel connections between artworks. Finally, I contributed to the creation of a software application. This application leverages established connections, allowing users to investigate the symbolic expression of a concept across different cultural contexts through the generation of a three-dimensional exhibition of artefacts symbolising the chosen concept.

One archive, many readings. Personal archives as complex networks in the semantic web

Personal archives are the archives created by individuals for their own purposes. Among these are the library and documentary collections of writers and scholars. It is only recently that archival literature has begun to focus on this category of archives, emphasising how their heterogeneous nature necessitates the conciliation of different approaches to archival description, and calling for a broader understanding of the principle of provenance, recognising that multiple creators, including subsequent researchers, can contribute to shaping personal archives over time by adding new layers of contexts. Despite these advances in the theoretical debate, current architectures for archival representation remain behind. Finding aids privilege a single point of view and do not allow subsequent users to embed their own, potentially conflicting, readings. Using semantic web technologies this study aims to define a conceptual model for writers' archives based on existing and widely adopted models in the cultural heritage and humanities domains. The model developed can be used to represent different types of documents at various levels of analysis, as well as record content and components. It also enables the representation of complex relationships and the incorporation of additional layers of interpretation into the finding aid, transforming it from a static search tool into a dynamic research platform.  The personal archive and library of Giuseppe Raimondi serves as a case study for the creation of an archival knowledge base using the proposed conceptual model. By querying the knowledge graph through SPARQL, the effectiveness of the model is evaluated. The results demonstrate that the model addresses the primary representation challenges identified in archival literature, from both a technological and methodological standpoint. The ultimate goal is to bring the output par excellence of archival science, i.e. the finding aid, more in line with the latest developments in archival thinking.

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.

Sim-xl: A Powerful And User-friendly Tool For Peptide Cross-linking Analysis.

Chemical cross-linking has emerged as a powerful approach for the structural characterization of proteins and protein complexes. However, the correct identification of covalently linked (cross-linked or XL) peptides analyzed by tandem mass spectrometry is still an open challenge. Here we present SIM-XL, a software tool that can analyze data generated through commonly used cross-linkers (e.g., BS3/DSS). Our software introduces a new paradigm for search-space reduction, which ultimately accounts for its increase in speed and sensitivity. Moreover, our search engine is the first to capitalize on reporter ions for selecting tandem mass spectra derived from cross-linked peptides. It also makes available a 2D interaction map and a spectrum-annotation tool unmatched by any of its kind. We show SIM-XL to be more sensitive and faster than a competing tool when analyzing a data set obtained from the human HSP90. The software is freely available for academic use at http://patternlabforproteomics.org/sim-xl. A video demonstrating the tool is available at http://patternlabforproteomics.org/sim-xl/video. SIM-XL is the first tool to support XL data in the mzIdentML format; all data are thus available from the ProteomeXchange consortium (identifier PXD001677).

Intercompreensão de texto escrito por falantes nativos de português e de espanhol

The aim of this paper is to verify the level of text comprehension (reading and translation) in Portuguese, by native speakers of Spanish and vice-versa. The subjects are freshmen, from different fields (300 native speakers of Portuguese and 300 of Spanish), who have never studied the other language neither as a second (L2) nor as a foreign language (FL). The results show that, in each group of subjects, there is a high level of comprehension of the foreign language, which varies from 58% to 94%, depending on the context and on the lexical/semantic similarity (or difference) between the key-words in the texts used in this research.

Estruturas factivas e padrões de extração

This paper investigates the relationship between structural and semantic properties of factive sentences and the pattern of extraction exhibited. It is argued that a classification as weak or strong island is unfeasible for what has been termed Factive Island. The kinds of structures allowed as factive complements are analyzed as well as their corresponding behavior concerning extraction. The common feature these structures show is their presuppositional character, which is derived from a selection requirement. I assume that factive predicates select a [+ specific] complement. The differences showed concerning extraction constitute a spontaneous effect from the structural way each construction may satisfy this requirement.