The amount of data and analysis being published and archived in the biomedical research community is more than can feasibly be sifted through manually, which limits the information an individual or small group can synthesize and integrate into their own research. This presents an opportunity for using automated methods, including Natural Language Processing (NLP), to extract important information from text on various topics. Named Entity Recognition (NER), is one way to automate knowledge extraction of raw text. NER is defined as the task of identifying named entities from text using labels such as people, dates, locations, diseases, and proteins. There are several NLP tools that are designed for entity recognition, but rely on large established corpus for training data. Biomedical research has the potential to guide diagnostic and therapeutic decisions, yet the overwhelming density of publications acts as a barrier to getting these results into a clinical setting. An exceptional example of this is the field of breast cancer biology where over 2 million people are diagnosed worldwide every year and billions of dollars are spent on research. Breast cancer biology literature and research relies on a highly specific domain with unique language and vocabulary, and therefore requires specialized NLP tools which can generate biologically meaningful results. This thesis presents a novel annotation tool, that is optimized for quickly creating training data for spaCy pipelines as well as exploring the viability of said data for analyzing papers with automated processing. Custom pipelines trained on these annotations are shown to be able to recognize custom entities at levels comparable to large corpus based recognition.

Orientador: Antonio Carlos Vitte / Tese (doutorado) - Universidade Estadual de Campinas, Instituto de Geociencias / Made available in DSpace on 2018-08-11T04:40:29Z (GMT). No. of bitstreams: 1 Santos_JoseAparecidodos_D.pdf: 47479724 bytes, checksum: 080379363bf8d494c4e3f290ca1af014 (MD5) Previous issue date: 2008 / Resumo: O estudo procura analisar o processo de degradação ambiental representado pelo voçorocamento, no sítio urbano de Bauru. A degradação provocada por características naturais, que revelam alta fragilidade ambiental e predisposição para erosões, comum em grande parte do Planalto Ocidental Paulista e que em interação com a produção social do espaço urbano levada a cabo por agentes econômicos, políticos e sociais intensificam um processo pré-existente na Natureza. Relaciona-se o agravamento da degradação aliado à característica da urbanização desordenada após a década de 1950 com a produção da renda fundiária urbana. Em decorrência dessa problemática interligada ao processo de segregação sócio-espacial em Bauru, observamos uma crescente mobilização da Sociedade que passa a exigir do poder local a solução dos problemas socioambientais. Objetivou-se, ainda compreender a produção do espaço urbano e suas repercussões no meio ambiente, que, ao ser degradado, desencadeia uma mobilização social que procura uma sustentabilidade ambiental. O estudo, relacionando os aspectos ambientais e sociais permitiu obtenção de alguns resultados: o processo de voçorocamento, a fragmentação da cidade e seu espraiamento, marcado pela presença de vazios urbanos, se converteu em problema social, estabelecido entre características e especificidades da urbanização que combinada com os aspectos físicos nota-se que o processo de voçorocamento deixe de ser comandado somente pelos processos naturais e passa a incorporar uma clara lógica de acumulação / Abstract: The presupposed of this project is to analyze the process of environmental degradation represented by gully in the urban location of Bauru. Such process is the result of natural characteristics that reveals high environmental frailty with a tendency to erosions, common in most part of Paulista Western Plateau, in interaction with the social production of urban space carried out by economical, political and social agents. It¿s related to the aggravation of the degradation provoked after the 1950s attached to the production of urban landed revenue. As a consequence of this issue interconnected to the process of social and spatial segregation in Bauru, we assist to a growing mobilization of the society that starts demanding of the local power the resolution of social environmental problems. It has been objectified to understand the production of urban space and its reverberations in the environment, that, when it is deteriorated, has unchained a social mobilization searching for environmental sustenance. This project relating to the environmental and social aspects granted some results: the gully process, in the same way that, the disintegration of the city and its spreading noticed for the presence of urban unoccupied is a social problem, established between the characteristics and the specification of urbanization that compounded with the physical aspects makes the gully process is not commanded only by natural process and it begins to incorporate a clear logic of accumulation / Doutorado / Análise Ambiental e Dinâmica Territorial / Doutor em Geografia

The amount of data available and consumed by people globally is growing. To reduce mental fatigue and increase the general ability to gain insight into complex texts or documents, we have developed an application to aid in this task. The application allows users to upload documents and ask domain-specific questions about them using our web application. A summarized version of each document is presented to the user, which could further facilitate their understanding of the document and guide them towards what types of questions could be relevant to ask. Our application allows users flexibility with the types of documents that can be processed, it is publicly available, stores no user data, and uses state-of-the-art models for its summaries and answers. The result is an application that yields near human-level intuition for answering questions in certain isolated cases, such as Wikipedia and news articles, as well as some scientific texts. The application shows a decrease in reliability and its prediction as to the complexity of the subject, the number of words in the document, and grammatical inconsistency in the questions increases. These are all aspects that can be improved further if used in production. / Mängden data som är tillgänglig och konsumeras av människor växer globalt. För att minska den mentala trötthet och öka den allmänna förmågan att få insikt i komplexa, massiva texter eller dokument, har vi utvecklat en applikation för att bistå i de uppgifterna. Applikationen tillåter användare att ladda upp dokument och fråga kontextspecifika frågor via vår webbapplikation. En sammanfattad version av varje dokument presenteras till användaren, vilket kan ytterligare förenkla förståelsen av ett dokument och vägleda dem mot vad som kan vara relevanta frågor att ställa. Vår applikation ger användare möjligheten att behandla olika typer av dokument, är tillgänglig för alla, sparar ingen personlig data, och använder de senaste modellerna inom språkbehandling för dess sammanfattningar och svar. Resultatet är en applikation som når en nära mänsklig intuition för vissa domäner och frågor, som exempelvis Wikipedia- och nyhetsartiklar, samt viss vetensaplig text. Noterade undantag för tillämpningen härrör från ämnets komplexitet, grammatiska korrekthet för frågorna och dokumentets längd. Dessa är områden som kan förbättras ytterligare om den används i produktionen.