Pudonneet corpora nigrat?

Mielenkiintoinen tapaus

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.

OCR Correction Tool for Linguistic Corpora

We introduce a new tool for correcting OCR errors of materials in a repository of cultural materials. The poster is aimed to all who are interested in digital humanities and who might find our tool useful. The poster will focus on the OCR correction tool and on the background processes. We have started a project on materials published in Finno-Ugric languages in the Soviet Union in the 1920s and 1930s. The materials are digitised in Russia. As they arrive, we publish them in DSpace (fennougrica.kansalliskirjasto.fi). For research purposes, the results of the OCR must be corrected manually. For this we have built a new tool. Although similar tools exist, we found in-house development necessary in order to serve the researchers' needs. The tool enables exporting the corrected text as required by the researchers. It makes it possible to distribute the correction tasks and their supervision. After a supervisor has approved a text as finalised, the new version of the work will replace the old one in DSpace. The project has - benefitted the small language communities, - opened channels for cooperation in Russia. - increased our capabilities in digital humanities. The OCR correction tool will be available to others.

OCR Correction Tool for Linguistic Corpora

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Ilmanvaihtokoneen ohjauksen taloudellisuusvaikutukset

Tämän insinöörityön tarkoituksena oli luoda Insinööritoimisto Olof Granlund Oy:lle malliprojekti ilmanvaihtokoneen ohjauksen mahdollisesta sähköenergian säästöpotentiaalista. Insinöörityötä voidaan myöhemmin käyttää referenssinä tarjottaessa yrityksen palvelua asiakkaille energiakatselmointityössä kiinteistöihin, joissa on suuria ilmanvaihtokone-yksiköitä. Ensin työssä esitellään käytössä olevat, tutkittavat ilmanvaihtokoneet ja niiden toiminta. Sitten selvitetään ilmanvaihtolaitteiden ja niiden ohjauksen eri osien toiminta, sekä ohjausinformaatio, joka välittyy eri laitteiden välillä. Seuraavaksi työssä tutkitaan rakennusautomaation osuutta, sen hyötyä ja rakennetta kiinteistössä. Tämän jälkeen selvitetään hankkeen viranomaismääräykset. Sitten selvitetään, mistä koostuvat kustannukset ilmanvaihtokoneen ohjauksen uusimisessa. Lopuksi vielä tutkitaan, kuinka pitkä on tehtävän investoinnin takaisinmaksuaika, sekä mitkä ovat saneerauksen hiilidioksidi-päästövaikutukset. insinöörityön Lopputuloksena syntyi yrityksen sisäinen kansio. Kansion esimerkkilaskelmia ja laskentamenetelmiä on tarkoitus käyttää jatkossa referenssinä kiinteistönpito-osastolla sähkö- ja lvi-ryhmissä, niiden henkilöiden käytössä, jotka ovat tekemisissä energiakatselmointien kanssa.