Exploiting Semantics from Widely Available Ontologies to Aid the Model Building Process

This dissertation attempts to address the changing needs of data science and analytics: making it easier to produce accurate models opening up opportunities and perspectives for novices to make sense of existing data. This work aims to incorporate semantics of data in addressing classical machine learning problems, which is one way to tame the deluge of data. The increased availability of data and the existence of easy-to-use procedures for regression and classification in commodity software allows anyone to search for correlations amongst a large set of variables with scant regard of their meaning. Consequently, people tend to use data indiscriminately, leading to the practice of data dredging. It is easy to use sophisticated tools to produce specious models, which generalize poorly and may lead to wrong conclusions. Despite much effort having been placed on advancing learning algorithms, current tools do little to shield people from using data in a semantically lax fashion. By examining the entire model building process and supplying semantic information derived from high-level knowledge in the form of an ontology, the machine can assist in exercising discretion to help the model builder avoid the pitfalls of data dredging. This work introduces a metric, called conceptual distance, to incorporate semantic information into the model building process. The conceptual distance is shown to be practically computed from large-scale existing ontologies. This metric is exploited in feature selection to enable a machine to take semantics of features into consideration when choosing them to build a model. Experiments with ontologies and real world datasets show the comparable performance of this metric in selecting a feature subset to the traditional data-driven measurements, in spite of using only labels of features, not the associated measures. Further, a new end-to-end model building process is developed by using the conceptual distance as a guideline to explore an ontological structure and retrieve relevant features automatically, making it convenient for a novice to build a semantically pertinent model. Experiments show that the proposed model building process can help a user to produce a model with performance comparable to that built by a domain expert. This work offers a tool to help the common man battle the hazard of data dredging that comes from the indiscriminate use of data. The tool results in models with improved generalization and easy to interpret, leading to better decisions or implications

A Learning Health System for Radiation Oncology

The proposed research aims to address the challenges faced by clinical data science researchers in radiation oncology accessing, integrating, and analyzing heterogeneous data from various sources. The research presents a scalable intelligent infrastructure, called the Health Information Gateway and Exchange (HINGE), which captures and structures data from multiple sources into a knowledge base with semantically interlinked entities. This infrastructure enables researchers to mine novel associations and gather relevant knowledge for personalized clinical outcomes. The dissertation discusses the design framework and implementation of HINGE, which abstracts structured data from treatment planning systems, treatment management systems, and electronic health records. It utilizes disease-specific smart templates for capturing clinical information in a discrete manner. HINGE performs data extraction, aggregation, and quality and outcome assessment functions automatically, connecting seamlessly with local IT/medical infrastructure. Furthermore, the research presents a knowledge graph-based approach to map radiotherapy data to an ontology-based data repository using FAIR (Findable, Accessible, Interoperable, Reusable) concepts. This approach ensures that the data is easily discoverable and accessible for clinical decision support systems. The dissertation explores the ETL (Extract, Transform, Load) process, data model frameworks, ontologies, and provides a real-world clinical use case for this data mapping. To improve the efficiency of retrieving information from large clinical datasets, a search engine based on ontology-based keyword searching and synonym-based term matching tool was developed. The hierarchical nature of ontologies is leveraged to retrieve patient records based on parent and children classes. Additionally, patient similarity analysis is conducted using vector embedding models (Word2Vec, Doc2Vec, GloVe, and FastText) to identify similar patients based on text corpus creation methods. Results from the analysis using these models are presented. The implementation of a learning health system for predicting radiation pneumonitis following stereotactic body radiotherapy is also discussed. 3D convolutional neural networks (CNNs) are utilized with radiographic and dosimetric datasets to predict the likelihood of radiation pneumonitis. DenseNet-121 and ResNet-50 models are employed for this study, along with integrated gradient techniques to identify salient regions within the input 3D image dataset. The predictive performance of the 3D CNN models is evaluated based on clinical outcomes. Overall, the proposed Learning Health System provides a comprehensive solution for capturing, integrating, and analyzing heterogeneous data in a knowledge base. It offers researchers the ability to extract valuable insights and associations from diverse sources, ultimately leading to improved clinical outcomes. This work can serve as a model for implementing LHS in other medical specialties, advancing personalized and data-driven medicine

Content Recommendation Through Linked Data

Nowadays, people can easily obtain a huge amount of information from the Web, but often they have no criteria to discern it. This issue is known as information overload. Recommender systems are software tools to suggest interesting items to users and can help them to deal with a vast amount of information. Linked Data is a set of best practices to publish data on the Web, and it is the basis of the Web of Data, an interconnected global dataspace. This thesis discusses how to discover information useful for the user from the vast amount of structured data, and notably Linked Data available on the Web. The work addresses this issue by considering three research questions: how to exploit existing relationships between resources published on the Web to provide recommendations to users; how to represent the user and his context to generate better recommendations for the current situation; and how to effectively visualize the recommended resources and their relationships. To address the first question, the thesis proposes a new algorithm based on Linked Data which exploits existing relationships between resources to recommend related resources. The algorithm was integrated into a framework to deploy and evaluate Linked Data based recommendation algorithms. In fact, a related problem is how to compare them and how to evaluate their performance when applied to a given dataset. The user evaluation showed that our algorithm improves the rate of new recommendations, while maintaining a satisfying prediction accuracy. To represent the user and their context, this thesis presents the Recommender System Context ontology, which is exploited in a new context-aware approach that can be used with existing recommendation algorithms. The evaluation showed that this method can significantly improve the prediction accuracy. As regards the problem of effectively visualizing the recommended resources and their relationships, this thesis proposes a visualization framework for DBpedia (the Linked Data version of Wikipedia) and mobile devices, which is designed to be extended to other datasets. In summary, this thesis shows how it is possible to exploit structured data available on the Web to recommend useful resources to users. Linked Data were successfully exploited in recommender systems. Various proposed approaches were implemented and applied to use cases of Telecom Italia

An Ontology-Driven Methodology To Derive Cases From Structured And Unstructured Sources

The problem-solving capability of a Case-Based Reasoning (CBR) system largely depends on the richness of its knowledge stored in the form of cases, i.e. the CaseBase (CB). Populating and subsequently maintaining a critical mass of cases in a CB is a tedious manual activity demanding vast human and operational resources. The need for human involvement in populating a CB can be drastically reduced as case-like knowledge already exists in the form of databases and documents and harnessed and transformed into cases that can be operationalized. Nevertheless, the transformation process poses many hurdles due to the disparate structure and the heterogeneous coding standards used. The featured work aims to address knowledge creation from heterogeneous sources and structures. To meet this end, this thesis presents a Multi-Source Case Acquisition and Transformation Info-Structure (MUSCATI). MUSCATI has been implemented as a multi-layer architecture using state-of-the-practice tools and can be perceived as a functional extension to traditional CBR-systems. In principle, MUSCATI can be applied in any domain but in this thesis healthcare was chosen. Thus, Electronic Medical Records (EMRs) were used as the source to generate the knowledge. The results from the experiments showed that the volume and diversity of cases improves the reasoning outcome of the CBR engine. The experiments showed that knowledge found in medical records (regardless of structure) can be leveraged and standardized to enhance the (medical) knowledge of traditional medical CBR systems. Subsequently, the Google search engine proved to be very critical in “fixing” and enriching the domain ontology on-the-fly

Mining Meaning from Text by Harvesting Frequent and Diverse Semantic Itemsets

Abstract. In this paper, we present a novel and completely-unsupervised approach to unravel meanings (or senses) from linguistic constructions found in large corpora by introducing the concept of semantic vector. A semantic vector is a space-transformed vector where features repre-sent fine-grained semantic information units, instead of values of co-occurrences within a collection of texts. More in detail, instead of seeing words as vectors of frequency values, we propose to first explode words into a multitude of tiny semantic information retrieved from existing re-sources like WordNet and ConceptNet, and then clustering them into frequent and diverse patterns. This way, on the one hand, we are able to model linguistic data with a larger but much more dense and informa-tive semantic feature space. On the other hand, being the model based on basic and conceptual information, we are also able to generate new data by querying the above-mentioned semantic resources with the fea-tures contained in the extracted patterns. We experimented the idea on a dataset of 640 millions of triples subject-verb-object to automatically inducing senses for specific input verbs, demonstrating the validity and the potential of the presented approach in modeling and understanding natural language

Utility-Preserving Anonymization of Textual Documents

Cada dia els éssers humans afegim una gran quantitat de dades a Internet, tals com piulades, opinions, fotos i vídeos. Les organitzacions que recullen aquestes dades tan diverses n'extreuen informació per tal de millorar llurs serveis o bé per a propòsits comercials. Tanmateix, si les dades recollides contenen informació personal sensible, hom no les pot compartir amb tercers ni les pot publicar sense el consentiment o una protecció adequada dels subjectes de les dades. Els mecanismes de preservació de la privadesa forneixen maneres de sanejar les dades per tal que no revelin identitats o atributs confidencials. S'ha proposat una gran varietat de mecanismes per anonimitzar bases de dades estructurades amb atributs numèrics i categòrics; en canvi, la protecció automàtica de dades textuals no estructurades ha rebut molta menys atenció. En general, l'anonimització de dades textuals exigeix, primer, detectar trossos del text que poden revelar informació sensible i, després, emmascarar aquests trossos mitjançant supressió o generalització. En aquesta tesi fem servir diverses tecnologies per anonimitzar documents textuals. De primer, millorem les tècniques existents basades en etiquetatge de seqüències. Després, estenem aquestes tècniques per alinear-les millor amb el risc de revelació i amb les exigències de privadesa. Finalment, proposem un marc complet basat en models d'immersió de paraules que captura un concepte més ampli de protecció de dades i que forneix una protecció flexible guiada per les exigències de privadesa. També recorrem a les ontologies per preservar la utilitat del text emmascarat, és a dir, la seva semàntica i la seva llegibilitat. La nostra experimentació extensa i detallada mostra que els nostres mètodes superen els mètodes existents a l'hora de proporcionar anonimització robusta tot preservant raonablement la utilitat del text protegit.Cada día las personas añadimos una gran cantidad de datos a Internet, tales como tweets, opiniones, fotos y vídeos. Las organizaciones que recogen dichos datos los usan para extraer información para mejorar sus servicios o para propósitos comerciales. Sin embargo, si los datos recogidos contienen información personal sensible, no pueden compartirse ni publicarse sin el consentimiento o una protección adecuada de los sujetos de los datos. Los mecanismos de protección de la privacidad proporcionan maneras de sanear los datos de forma que no revelen identidades ni atributos confidenciales. Se ha propuesto una gran variedad de mecanismos para anonimizar bases de datos estructuradas con atributos numéricos y categóricos; en cambio, la protección automática de datos textuales no estructurados ha recibido mucha menos atención. En general, la anonimización de datos textuales requiere, primero, detectar trozos de texto que puedan revelar información sensible, para luego enmascarar dichos trozos mediante supresión o generalización. En este trabajo empleamos varias tecnologías para anonimizar documentos textuales. Primero mejoramos las técnicas existentes basadas en etiquetaje de secuencias. Posteriormente las extendmos para alinearlas mejor con la noción de riesgo de revelación y con los requisitos de privacidad. Finalmente, proponemos un marco completo basado en modelos de inmersión de palabras que captura una noción más amplia de protección de datos y ofrece protección flexible guiada por los requisitos de privacidad. También recurrimos a las ontologías para preservar la utilidad del texto enmascarado, es decir, su semantica y legibilidad. Nuestra experimentación extensa y detallada muestra que nuestros métodos superan a los existentes a la hora de proporcionar una anonimización más robusta al tiempo que se preserva razonablemente la utilidad del texto protegido.Every day, people post a significant amount of data on the Internet, such as tweets, reviews, photos, and videos. Organizations collecting these types of data use them to extract information in order to improve their services or for commercial purposes. Yet, if the collected data contain sensitive personal information, they cannot be shared with third parties or released publicly without consent or adequate protection of the data subjects. Privacy-preserving mechanisms provide ways to sanitize data so that identities and/or confidential attributes are not disclosed. A great variety of mechanisms have been proposed to anonymize structured databases with numerical and categorical attributes; however, automatically protecting unstructured textual data has received much less attention. In general, textual data anonymization requires, first, to detect pieces of text that may disclose sensitive information and, then, to mask those pieces via suppression or generalization. In this work, we leverage several technologies to anonymize textual documents. We first improve state-of-the-art techniques based on sequence labeling. After that, we extend them to make them more aligned with the notion of privacy risk and the privacy requirements. Finally, we propose a complete framework based on word embedding models that captures a broader notion of data protection and provides flexible protection driven by privacy requirements. We also leverage ontologies to preserve the utility of the masked text, that is, its semantics and readability. Extensive experimental results show that our methods outperform the state of the art by providing more robust anonymization while reasonably preserving the utility of the protected outcome

Universal schema for entity type prediction

Categorizing entities by their types is useful in many applications, including knowledge base construction, relation extraction and query intent prediction. Fine-grained entity type ontologies are especially valuable, but typically difficult to design because of unavoidable quandaries about level of detail and boundary cases. Automatically classifying entities by type is challenging as well, usually involving hand-labeling data and training a supervised predictor. This paper presents a universal schema approach to fine-grained entity type prediction. The set of types is taken as the union of textual surface patterns (e.g. appositives) and pre-defined types from available databases (e.g. Freebase) - yielding not tens or hundreds of types, but more than ten thousands of entity types, such as financier, criminologist, and musical trio. We robustly learn mutual implication among this large union by learning latent vector embeddings from probabilistic matrix factorization, thus avoiding the need for hand-labeled data. Experimental results demonstrate more than 30% reduction in error versus a traditional classification approach on predicting fine-grained entities types. © 2013 ACM