Mining Biomedical Texts to Generate Semantic Annotations

This report focuses on text mining in the biomedical domain for the generation of semantic annotations based on a formal model which is ontology. We start by exposing the generic methodology for the generation of annotations from texts. Then, we present a state of the art on different knowledge extraction techniques used on biomedical texts. We propose our approach based on Semantic Web Technologies and Natural Language Processing (NLP): it relies on formal ontologies to generate semantic annotations on scientific articles and on other knowledge sources (databases, experiment sheets). This approach can be extended to other do-mains requiring experiments and massive data analyses. Finally, we conclude with a discussion about our work and we present some learnt lessons

Mining Biomedical Texts to Generate Semantic Annotations

This report focuses on text mining in the biomedical domain for the generation of semantic annotations based on a formal model which is ontology. We start by exposing the generic methodology for the generation of annotations from texts. Then, we present a state of the art on different knowledge extraction techniques used on biomedical texts. We propose our approach based on Semantic Web Technologies and Natural Language Processing (NLP): it relies on formal ontologies to generate semantic annotations on scientific articles and on other knowledge sources (databases, experiment sheets). This approach can be extended to other do-mains requiring experiments and massive data analyses. Finally, we conclude with a discussion about our work and we present some learnt lessons

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Agile in-litero experiments:how can semi-automated information extraction from neuroscientific literature help neuroscience model building?

In neuroscience, as in many other scientific domains, the primary form of knowledge dissemination is through published articles in peer-reviewed journals. One challenge for modern neuroinformatics is to design methods to make the knowledge from the tremendous backlog of publications accessible for search, analysis and its integration into computational models. In this thesis, we introduce novel natural language processing (NLP) models and systems to mine the neuroscientific literature. In addition to in vivo, in vitro or in silico experiments, we coin the NLP methods developed in this thesis as in litero experiments, aiming at analyzing and making accessible the extended body of neuroscientific literature. In particular, we focus on two important neuroscientific entities: brain regions and neural cells. An integrated NLP model is designed to automatically extract brain region connectivity statements from very large corpora. This system is applied to a large corpus of 25M PubMed abstracts and 600K full-text articles. Central to this system is the creation of a searchable database of brain region connectivity statements, allowing neuroscientists to gain an overview of all brain regions connected to a given region of interest. More importantly, the database enables researcher to provide feedback on connectivity results and links back to the original article sentence to provide the relevant context. The database is evaluated by neuroanatomists on real connectomics tasks (targets of Nucleus Accumbens) and results in significant effort reduction in comparison to previous manual methods (from 1 week to 2h). Subsequently, we introduce neuroNER to identify, normalize and compare instances of identify neuronsneurons in the scientific literature. Our method relies on identifying and analyzing each of the domain features used to annotate a specific neuron mention, like the morphological term 'basket' or brain region 'hippocampus'. We apply our method to the same corpus of 25M PubMed abstracts and 600K full-text articles and find over 500K unique neuron type mentions. To demonstrate the utility of our approach, we also apply our method towards cross-comparing the NeuroLex and Human Brain Project (HBP) cell type ontologies. By decoupling a neuron mention's identity into its specific compositional features, our method can successfully identify specific neuron types even if they are not explicitly listed within a predefined neuron type lexicon, thus greatly facilitating cross-laboratory studies. In order to build such large databases, several tools and infrastructureslarge-scale NLP were developed: a robust pipeline to preprocess full-text PDF articles, as well as bluima, an NLP processing pipeline specialized on neuroscience to perform text-mining at PubMed scale. During the development of those two NLP systems, we acknowledged the need for novel NLP approaches to rapidly develop custom text mining solutions. This led to the formalization of the agile text miningagile text-mining methodology to improve the communication and collaboration between subject matter experts and text miners. Agile text mining is characterized by short development cycles, frequent tasks redefinition and continuous performance monitoring through integration tests. To support our approach, we developed Sherlok, an NLP framework designed for the development of agile text mining applications

Designing a Library of Components for Textual Scholarship

Il presente lavoro affronta e descrive temi legati all'applicazione di nuove tecnologie, di metodologie informatiche e di progettazione software volti allo sviluppo di strumenti innovativi per le Digital Humanities (DH), un’area di studio caratterizzata da una forte interdisciplinarità e da una continua evoluzione. In particolare, questo contributo definisce alcuni specifici requisiti relativi al dominio del Literary Computing e al settore del Digital Textual Scholarship. Conseguentemente, il contesto principale di elaborazione tratta documenti scritti in latino, greco e arabo, nonché testi in lingue moderne contenenti temi storici e filologici. L'attività di ricerca si concentra sulla progettazione di una libreria modulare (TSLib) in grado di operare su fonti ad elevato valore culturale, al fine di editarle, elaborarle, confrontarle, analizzarle, visualizzarle e ricercarle. La tesi si articola in cinque capitoli. Il capitolo 1 riassume il contesto del dominio applicativo e fornisce un quadro generale degli obiettivi e dei benefici della ricerca. Il capitolo 2 illustra alcuni importanti lavori e iniziative analoghe, insieme a una breve panoramica dei risultati più significativi ottenuti nel settore delle DH. Il capitolo 3 ripercorre accuratamente e motiva il processo di progettazione messo a punto. Esso inizia con la descrizione dei principi tecnici adottati e mostra come essi vengono applicati al dominio d'interesse. Il capitolo continua definendo i requisiti, l'architettura e il modello del metodo proposto. Sono così evidenziati e discussi gli aspetti concernenti i design patterns e la progettazione delle Application Programming Interfaces (APIs). La parte finale del lavoro (capitolo 4) illustra i risultati ottenuti da concreti progetti di ricerca che, da un lato, hanno contribuito alla progettazione della libreria e, dall'altro, hanno avuto modo di sfruttarne gli sviluppi. Sono stati quindi discussi diversi temi: (a) l'acquisizione e la codifica del testo, (b) l'allineamento e la gestione delle varianti testuali, (c) le annotazioni multilivello. La tesi si conclude con alcune riflessioni e considerazioni indicando anche possibili percorsi d'indagine futuri (capitolo 5)

Empirical studies on word representations

One of the most fundamental tasks in natural language processing is representing words with mathematical objects (such as vectors). The word representations, which are most often estimated from data, allow capturing the meaning of words. They enable comparing words according to their semantic similarity, and have been shown to work extremely well when included in complex real-world applications. A large part of our work deals with ways of estimating word representations directly from large quantities of text. Our methods exploit the idea that words which occur in similar contexts have a similar meaning. How we define the context is an important focus of our thesis. The context can consist of a number of words to the left and to the right of the word in question, but, as we show, obtaining context words via syntactic links (such as the link between the verb and its subject) often works better. We furthermore investigate word representations that accurately capture multiple meanings of a single word. We show that translation of a word in context contains information that can be used to disambiguate the meaning of that word