Optimization and Applications of Large-Scale Biomedical Event Networks

The overwhelming amount and unprecedented speed of publication in the biomedical domain make it difficult for life science researchers to acquire and maintain a broad view of the field and gather all information that would be relevant for their research. As a response to this problem, the BioNLP (Biomedical Natural Language Processing) community of researches has emerged and strives to assist life science researchers by developing modern natural language processing (NLP), information extraction (IE) and information retrieval (IR) methods that can be applied at large-scale, to scan the whole publicly available biomedical literature and extract and aggregate the information found within, while automatically normalizing the variability of natural language statements. Among different tasks, biomedical event extraction has received much attention within BioNLP community recently. Biomedical event extraction constitutes the identification of biological processes and interactions described in biomedical literature, and their representation as a set of recursive event structures. The 2009–2013 series of BioNLP Shared Tasks on Event Extraction have given raise to a number of event extraction systems, several of which have been applied at a large scale (the full set of PubMed abstracts and PubMed Central Open Access full text articles), leading to creation of massive biomedical event databases, each of which containing millions of events. Sinece top-ranking event extraction systems are based on machine-learning approach and are trained on the narrow-domain, carefully selected Shared Task training data, their performance drops when being faced with the topically highly varied PubMed and PubMed Central documents. Specifically, false-positive predictions by these systems lead to generation of incorrect biomolecular events which are spotted by the end-users. This thesis proposes a novel post-processing approach, utilizing a combination of supervised and unsupervised learning techniques, that can automatically identify and filter out a considerable proportion of incorrect events from large-scale event databases, thus increasing the general credibility of those databases. The second part of this thesis is dedicated to a system we developed for hypothesis generation from large-scale event databases, which is able to discover novel biomolecular interactions among genes/gene-products. We cast the hypothesis generation problem as a supervised network topology prediction, i.e predicting new edges in the network, as well as types and directions for these edges, utilizing a set of features that can be extracted from large biomedical event networks. Routine machine learning evaluation results, as well as manual evaluation results suggest that the problem is indeed learnable. This work won the Best Paper Award in The 5th International Symposium on Languages in Biology and Medicine (LBM 2013).

Environments of Acitive Galaxies

This dissertation presents studies on the environments of active galaxies. Paper I is a case study of a cluster of galaxies containing BL Lac object RGB 1745+398. We measured the velocity dispersion, mass, and richness of the cluster. This was one of the most thorough studies of the environments of a BL Lac object. Methods used in the paper could be used in the future for studying other clusters as well. In Paper II we studied the environments of nearby quasars in the Sloan Digital Sky Survey (SDSS). We found that quasars have less neighboring galaxies than luminous inactive galaxies. In the large-scale structure, quasars are usually located at the edges of superclusters or even in void regions. We concluded that these low-redshift quasars may have become active only recently because the galaxies in low-density environments evolve later to the phase where quasar activity can be triggered. In Paper III we extended the analysis of Paper II to other types of AGN besides quasars. We found that different types of AGN have different large-scale environments. Radio galaxies are more concentrated in superclusters, while quasars and Seyfert galaxies prefer low-density environments. Different environments indicate that AGN have different roles in galaxy evolution. Our results suggest that activity of galaxies may depend on their environment on the large scale. Our results in Paper III raised questions of the cause of the environment-dependency in the evolution of galaxies. Because high-density large-scale environments contain richer groups and clusters than the underdense environments, our results could reflect smaller-scale effects. In Paper IV we addressed this problem by studying the group and supercluster scale environments of galaxies together. We compared the galaxy populations in groups of different richnesses in different large-scale environments. We found that the large-scale environment affects the galaxies independently of the group richness. Galaxies in low-density environments on the large scale are more likely to be star-forming than those in superclusters even if they are in groups with the same richness. Based on these studies, the conclusion of this dissertation is that the large-scale environment affects the evolution of galaxies. This may be caused by different “speed” of galaxy evolution in low and high-density environments: galaxies in dense environments reach certain phases of evolution earlier than galaxies in underdense environments. As a result, the low-density regions at low redshifts are populated by galaxies in earlier phases of evolution than galaxies in high-density regions.

Aurinkokeräimien käyttö turpeen kenttäkuivauksessa

Tämä tutkimus tehtiin osana Vapo Oy:n uuden turvetuotantotekniikan kehitystä. Kihniön Aitonevalle on rakennettu uuden turvetuotantotekniikan tutkimusalue, johon kuuluu muun muassa yksi lämmittämätön kuivatuskenttä sekä yksi aurinkolämmöllä lämmitetty kuivatuskenttä aurinkokeräimineen ja putkistoineen. Työn tavoitteena oli selvittää aurinkolämmöllä lämmitetyn kuivatuskentän tuotannon teho verrattuna lämmittämättömään kenttään. Toinen tavoite oli selvittää Aitonevan tutkimusalueella käytössä olevista aurinkokeräimistä turpeen kuivaustarkoitukseen parhaiten soveltuva keräin. Tuotantoa uudella menetelmällä tehtiin vuoden 2005 kesän ajan. Tuotantotehon ero pyrittiin selvittämään seuraamalla yksittäisten turvetuotantoerien eli satokiertojen kuivumista kosteusnäyttein ja toisaalta vertaamalla koko kesän aikana saatua tuotantoa. Aurinkokeräimien vertailu toteutettiin energiamäärä- ja hyötysuhdemittauksin. Lisäksi kuivatuskenttien lämpötiloja mitattiin kentässä tapahtuvan lämmönsiirron selvittämiseksi. Mittausten perusteella havaittiin, ettälämmitetyn ja lämmittämättömän kentän välillä on tutkimuksen aikaisella kenttärakenteella 6-8 % ero satokierron aikana haihdutetussa vesimäärässä. Tätä voidaanpitää odotuksia pienempänä. Kenttien lämpötilamittausten perusteella osoittautui, että kentän pintarakenne tulisi eristää maaperästä, koska kentän alle siirrettyä lämpöä siirtyy häviöinä kylmään pohjamaahan. Käytössä olleista aurinkokeräimistä parhaaksi osoittautui katettu kumimattokeräin niin hyötysuhteen kuin tehokkuudenkin puolesta. Työn aikana todettiin, että tutkimusta keräimien ja varsinkinkenttärakenteen suhteen tulee jatkaa tulevaisuudessa ennen aurinkokeräinkentän laajamittaisen käytön aloittamista.

Piikarbidipuolijohdekomponentit tehoelektroniikassa

Piikarbidi (SiC) on tunnettu korkealuokkaisena hioma-aineena ja hiekkapaperin pin-noitteena yli 100 vuoden ajan. Nykyisin ainetta käytetään pääasiassa puolijohteiden raaka-aineena. Piikarbidi on puolijohteena ylivoimainen tavanomaiseen piihin (Si) verrattuna lähes joka suhteessa johtuen sen kiderakenteesta, mutta sen valmistus on osoittautunut erittäin monimutkaiseksi johtuen pääasiassa vaikeudesta kasvattaa riittävän suuria ja laadukkaita SiC-kiteitä. Siksi tehoelektroniikan SiC-puolijohdekomponenttien laajamittaista käyttöä joudutaan yhä odottamaan. Tässä diplomityössä tehdään perusteellinen selvitys, miten piikarbidin valmistuspro-sessit eroavat normaaleista piin valmistusprosesseista, mitä etuja piikarbidin käytöllä saavutetaan ja vastaavasti mitä varjopuolia sillä on. Työssä selvitetään tällä hetkellä markkinoilla olevien SiC-tehopuolijohdekomponenttien ominaisuuksia, ketkä ovat teh-neet tutkimusta alalla, sekä esitetään arvioita SiC-tekniikan tulevaisuuden näkymistä.

A study of combustion phenomena in circulating fluidized beds by developing and applying experimental and modelling methods for laboratory-scale reactors

The results shown in this thesis are based on selected publications of the 2000s decade. The work was carried out in several national and EC funded public research projects and in close cooperation with industrial partners. The main objective of the thesis was to study and quantify the most important phenomena of circulating fluidized bed combustors by developing and applying proper experimental and modelling methods using laboratory scale equipments. An understanding of the phenomena plays an essential role in the development of combustion and emission performance, and the availability and controls of CFB boilers. Experimental procedures to study fuel combustion behaviour under CFB conditions are presented in the thesis. Steady state and dynamic measurements under well controlled conditions were carried out to produce the data needed for the development of high efficiency, utility scale CFB technology. The importance of combustion control and furnace dynamics is emphasized when CFB boilers are scaled up with a once through steam cycle. Qualitative information on fuel combustion characteristics was obtained directly by comparing flue gas oxygen responses during the impulse change experiments with fuel feed. A one-dimensional, time dependent model was developed to analyse the measurement data Emission formation was studied combined with fuel combustion behaviour. Correlations were developed for NO, N2O, CO and char loading, as a function of temperature and oxygen concentration in the bed area. An online method to characterize char loading under CFB conditions was developed and validated with the pilot scale CFB tests. Finally, a new method to control air and fuel feeds in CFB combustion was introduced. The method is based on models and an analysis of the fluctuation of the flue gas oxygen concentration. The effect of high oxygen concentrations on fuel combustion behaviour was also studied to evaluate the potential of CFB boilers to apply oxygenfiring technology to CCS. In future studies, it will be necessary to go through the whole scale up chain from laboratory phenomena devices through pilot scale test rigs to large scale, commercial boilers in order to validate the applicability and scalability of the, results. This thesis shows the chain between the laboratory scale phenomena test rig (bench scale) and the CFB process test rig (pilot). CFB technology has been scaled up successfully from an industrial scale to a utility scale during the last decade. The work shown in the thesis, for its part, has supported the development by producing new detailed information on combustion under CFB conditions.

Tool-supported invariant-based programming

The development of correct programs is a core problem in computer science. Although formal verification methods for establishing correctness with mathematical rigor are available, programmers often find these difficult to put into practice. One hurdle is deriving the loop invariants and proving that the code maintains them. So called correct-by-construction methods aim to alleviate this issue by integrating verification into the programming workflow. Invariant-based programming is a practical correct-by-construction method in which the programmer first establishes the invariant structure, and then incrementally extends the program in steps of adding code and proving after each addition that the code is consistent with the invariants. In this way, the program is kept internally consistent throughout its development, and the construction of the correctness arguments (proofs) becomes an integral part of the programming workflow. A characteristic of the approach is that programs are described as invariant diagrams, a graphical notation similar to the state charts familiar to programmers. Invariant-based programming is a new method that has not been evaluated in large scale studies yet. The most important prerequisite for feasibility on a larger scale is a high degree of automation. The goal of the Socos project has been to build tools to assist the construction and verification of programs using the method. This thesis describes the implementation and evaluation of a prototype tool in the context of the Socos project. The tool supports the drawing of the diagrams, automatic derivation and discharging of verification conditions, and interactive proofs. It is used to develop programs that are correct by construction. The tool consists of a diagrammatic environment connected to a verification condition generator and an existing state-of-the-art theorem prover. Its core is a semantics for translating diagrams into verification conditions, which are sent to the underlying theorem prover. We describe a concrete method for 1) deriving sufficient conditions for total correctness of an invariant diagram; 2) sending the conditions to the theorem prover for simplification; and 3) reporting the results of the simplification to the programmer in a way that is consistent with the invariantbased programming workflow and that allows errors in the program specification to be efficiently detected. The tool uses an efficient automatic proof strategy to prove as many conditions as possible automatically and lets the remaining conditions be proved interactively. The tool is based on the verification system PVS and i uses the SMT (Satisfiability Modulo Theories) solver Yices as a catch-all decision procedure. Conditions that were not discharged automatically may be proved interactively using the PVS proof assistant. The programming workflow is very similar to the process by which a mathematical theory is developed inside a computer supported theorem prover environment such as PVS. The programmer reduces a large verification problem with the aid of the tool into a set of smaller problems (lemmas), and he can substantially improve the degree of proof automation by developing specialized background theories and proof strategies to support the specification and verification of a specific class of programs. We demonstrate this workflow by describing in detail the construction of a verified sorting algorithm. Tool-supported verification often has little to no presence in computer science (CS) curricula. Furthermore, program verification is frequently introduced as an advanced and purely theoretical topic that is not connected to the workflow taught in the early and practically oriented programming courses. Our hypothesis is that verification could be introduced early in the CS education, and that verification tools could be used in the classroom to support the teaching of formal methods. A prototype of Socos has been used in a course at Åbo Akademi University targeted at first and second year undergraduate students. We evaluate the use of Socos in the course as part of a case study carried out in 2007.

Multifrequency VLBI Observations of Selected Active Galactic Nuclei

In this dissertation, active galactic nuclei (AGN) are discussed, as they are seen with the high-resolution radio-astronomical technique called Very Long Baseline Interferometry (VLBI). This observational technique provides very high angular resolution (_ 10−300 = 1 milliarcsecond). VLBI observations, performed at different radio frequencies (multi-frequency VLBI), allow to penetrate deep into the core of an AGN to reveal an otherwise obscured inner part of the jet and the vicinity of the AGN’s central engine. Multi-frequency VLBI data are used to scrutinize the structure and evolution of the jet, as well as the distribution of the polarized emission. These data can help to derive the properties of the plasma and the magnetic field, and to provide constraints to the jet composition and the parameters of emission mechanisms. Also VLBI data can be used for testing the possible physical processes in the jet by comparing observational results with results of numerical simulations. The work presented in this thesis contributes to different aspects of AGN physics studies, as well as to the methodology of VLBI data reduction. In particular, Paper I reports evidence of optical and radio emission of AGN coming from the same region in the inner jet. This result was obtained via simultaneous observations of linear polarization in the optical and in radio using VLBI technique of a sample of AGN. Papers II and III describe, in detail, the jet kinematics of the blazar 0716+714, based on multi-frequency data, and reveal a peculiar kinematic pattern: plasma in the inner jet appears to move substantially faster that that in the large-scale jet. This peculiarity is explained by the jet bending, in Paper III. Also, Paper III presents a test of the new imaging technique for VLBI data, the Generalized Maximum Entropy Method (GMEM), with the observed (not simulated) data and compares its results with the conventional imaging. Papers IV and V report the results of observations of the circularly polarized (CP) emission in AGN at small spatial scales. In particular, Paper IV presents values of the core CP for 41 AGN at 15, 22 and 43 GHz, obtained with the help of the standard Gain transfer (GT) method, which was previously developed by D. Homan and J.Wardle for the calibration of multi-source VLBI observations. This method was developed for long multi-source observations, when many AGN are observed in a single VLBI run. In contrast, in Paper V, an attempt is made to apply the GT method to single-source VLBI observations. In such observations, the object list would include only a few sources: a target source and two or three calibrators, and it lasts much shorter than the multi-source experiment. For the CP calibration of a single-source observation, it is necessary to have a source with zero or known CP as one of the calibrators. If the archival observations included such a source to the list of calibrators, the GT could also be used for the archival data, increasing a list of known AGN with the CP at small spatial scale. Paper V contains also calculation of contributions of different sourced of errors to the uncertainty of the final result, and presents the first results for the blazar 0716+714.

Challenges in transferring the hydropower control centre

Euroopan sähkömarkkinat ovat viime vuosikymmeninä olleet suurien muutoksien kohteena näiden yhtenäistämisprojektin seurauksena. Fortum, yksi Euroopan johtavista energia-alan yrityksistä valmistautuu tähän muutokseen toteuttamalla omia yrityksen sisäisiä muutoksia, tavoitteenaan yksinkertaistaa organisaatiorakennettaan ja parantaa tehokkuuttaan. Yksi suuri muutos tähän liittyen on vesivoimavalvomojen lokalisaatioprojekti. Vesivoimavalvomojen uudelleenlokalisaation ja vesivoiman käytönvalvojien ikääntymisen myötä nähtiin tarpeelliseksi tehdä tutkimus käytönvalvojien hiljaisesta tiedosta. Näin ollen, tässä diplomityössä perehdyttiin Fortumin vesivoiman käytönvalvojien kompetensseihin ja näiden hiljaiseen tietoon. Tutkimusaiheena oli selvittää minkälaista hiljaista tietoa käytönvalvojat omaavat, ja mikä osa tästä tiedosta muodostaa sen kriittisen osaamisen, jota halutaan säilyttää ja kehittää. Tutkimustyypiksi muodostui kvalitatiivinen, jonka päämetodi oli puoli-avoin haastattelu. Tutkimus koostui seuraavista vaiheista: tarkkailu, tekstianalyysi, haastattelu, transkriptio ja data analyysi. Haastatteluja tehtiin kahdeksan, joista kerääntyi yli 24 tuntia haastattelumateriaalia. Tästä materiaalista muodostettiin analyysien avulla taulukko, jonka avulla tunnistettiin ne osa-alueet, joihin käytönvalvojan tärkeimmät kompetenssit liittyvät. Tuloksilla saatiin myös kerättyä lista korjaus- ja kehityskohteista, sekä tarkemmat määritykset jatkotutkimukselle.

Hammashihnajohdeakseleiden liikkeiden synkronointi

Nykyisessä valmistusteollisuudessa erilaisten robottien ja automatisoitujen tuotantovaiheiden rooli on erittäin merkittävä. Tarkasti suunnitellut liikkeet ja toimintavaiheet voidaan nykyisillä järjestelmillä ajoittaa tarkasti toisiinsa nähden, jolloin erilaisten virhetilanteidenkin sattuessa järjestelmä pystyy toimimaan tilanteen edellyttämällä tavalla. Automatisoinnin etuna on myös tuotannon muokkaaminen erilaisten tuotteiden valmistamiseen pienillä muutoksilla, jolloin tuotantokustannukset pysyvät matalina myös pienten valmistuserien tapauksissa. Usean akselin laitteissa eli niin sanotuissa moniakselikäytöissä laitteen toimintatarkkuus riippuu jokaisen liikeakselin tarkkuudesta. Liikkeenohjauksessa on perinteisesti ollut käytössä myötäkytketty paikkakaskadi, jonka virityksessä otetaan huomioon akselilla olevat erilaiset dynaamiset tilat ja käytettävät referenssit. Monissa nykyisissä hajautetuissa järjestelmissä eli moniakselikäytöissä, joissa jokaiselle akselille on oma ohjauslaite, ei yksittäisen akselin paikkavirhettä huomioida muiden akseleiden ohjauksessa. Työssä tutkitaan erilaisia moniakselijärjestelmien ohjausmenetelmiä ja myötäkytketyn paikkakaskadin toimintaa moniakselikäytössä pyritään parantamaan tuomalla paikkasäätimen rinnalle toinen säädin, jonka tulona on akseleiden välinen paikkaero.

Memristive Computing

Memristive computing refers to the utilization of the memristor, the fourth fundamental passive circuit element, in computational tasks. The existence of the memristor was theoretically predicted in 1971 by Leon O. Chua, but experimentally validated only in 2008 by HP Labs. A memristor is essentially a nonvolatile nanoscale programmable resistor — indeed, memory resistor — whose resistance, or memristance to be precise, is changed by applying a voltage across, or current through, the device. Memristive computing is a new area of research, and many of its fundamental questions still remain open. For example, it is yet unclear which applications would benefit the most from the inherent nonlinear dynamics of memristors. In any case, these dynamics should be exploited to allow memristors to perform computation in a natural way instead of attempting to emulate existing technologies such as CMOS logic. Examples of such methods of computation presented in this thesis are memristive stateful logic operations, memristive multiplication based on the translinear principle, and the exploitation of nonlinear dynamics to construct chaotic memristive circuits. This thesis considers memristive computing at various levels of abstraction. The first part of the thesis analyses the physical properties and the current-voltage behaviour of a single device. The middle part presents memristor programming methods, and describes microcircuits for logic and analog operations. The final chapters discuss memristive computing in largescale applications. In particular, cellular neural networks, and associative memory architectures are proposed as applications that significantly benefit from memristive implementation. The work presents several new results on memristor modeling and programming, memristive logic, analog arithmetic operations on memristors, and applications of memristors. The main conclusion of this thesis is that memristive computing will be advantageous in large-scale, highly parallel mixed-mode processing architectures. This can be justified by the following two arguments. First, since processing can be performed directly within memristive memory architectures, the required circuitry, processing time, and possibly also power consumption can be reduced compared to a conventional CMOS implementation. Second, intrachip communication can be naturally implemented by a memristive crossbar structure.

Interpreting marine benthic ecosystem functioning in coastal waters: validating the biological trait concept

Coastal areas harbour high biodiversity, but are simultaneously affected by rapid degradations of species and habitats due to human interactions. Such alterations also affect the functioning of the ecosystem, which is primarily governed by the characteristics or traits expressed by the organisms present. Marine benthic fauna is nvolved in numerous functions such as organic matter transformation and transport, secondary production, oxygen transport as well as nutrient cycling. Approaches utilising the variety of faunal traits to assess benthic community functioning have rapidly increased and shown the need for further development of the concept. In this thesis, I applied biological trait analysis that allows for assessments of a multitude of categorical traits and thus evaluation of multiple functional aspects simultaneously. I determined the functional trait structure, diversity and variability of coastal zoobenthic communities in the Baltic Sea. The measures were related to recruitment processes, habitat heterogeneity, large-scale environmental and taxonomic gradients as well as anthropogenic impacts. The studies comprised spatial scales from metres to thousands of kilometres, and temporal scales spanning one season as well as a decade. The benthic functional structure was found to vary within and between seagrass landscape microhabitats and four different habitats within a coastal bay, in papers I and II respectively. Expressions of trait categories varied within habitats, while the density of individuals was found to drive the functional differences between habitats. The findings in paper III unveiled high trait richness of Finnish coastal benthos (25 traits and 102 cateogries) although this differed between areas high and low in salinity and human pressure. In paper IV, the natural reduction in taxonomic richness across the Baltic Sea led to an overall reduction in function. However, functional richness in terms of number of trait categories remained comparatively high at low taxon richness. Changes in number of taxa within trait categories were also subtle and some individual categories were maintained or even increased. The temporal analysis in papers I and III highlighted generalities in trait expressions and dominant trait categories in a seagrass landscape as well as a “type organism” for the northern Baltic Sea. Some initial findings were made in all four papers on the role of common and rare species and traits for benthic community functioning. The findings show that common and rare species may not always express the same trait categories in relation to each other. Rare species in general did not express unique functional properties. In order to advance the understanding of the approach, I also assessed some issues concerning the limitations of the concept. This was conducted by evaluating the link between trait category and taxonomic richness using especially univariate measures. My results also show the need to collaborate nationally and internationally on safeguarding the utility of taxonomic and trait data. The findings also highlight the importance of including functional trait information into current efforts in marine spatial planning and biomonitoring.

Modeling of Liquid-Solid Flow in Industrial Scale

In the present work, liquid-solid flow in industrial scale is modeled using the commercial software of Computational Fluid Dynamics (CFD) ANSYS Fluent 14.5. In literature, there are few studies on liquid-solid flow in industrial scale, but any information about the particular case with modified geometry cannot be found. The aim of this thesis is to describe the strengths and weaknesses of the multiphase models, when a large-scale application is studied within liquid-solid flow, including the boundary-layer characteristics. The results indicate that the selection of the most appropriate multiphase model depends on the flow regime. Thus, careful estimations of the flow regime are recommended to be done before modeling. The computational tool is developed for this purpose during this thesis. The homogeneous multiphase model is valid only for homogeneous suspension, the discrete phase model (DPM) is recommended for homogeneous and heterogeneous suspension where pipe Froude number is greater than 1.0, while the mixture and Eulerian models are able to predict also flow regimes, where pipe Froude number is smaller than 1.0 and particles tend to settle. With increasing material density ratio and decreasing pipe Froude number, the Eulerian model gives the most accurate results, because it does not include simplifications in Navier-Stokes equations like the other models. In addition, the results indicate that the potential location of erosion in the pipe depends on material density ratio. Possible sedimentation of particles can cause erosion and increase pressure drop as well. In the pipe bend, especially secondary flows, perpendicular to the main flow, affect the location of erosion.

Venäjän sotilasreformi : asevoimien uusi ilme

Tässä työpaperissa Venäjän sotilasreformin tarkastelu painottuu maavoimiin. Muista puolustushaaroista käsitellään lyhyesti meri- ja ilmavoimia. Lisäksi käsitellään koulutus, reservi ja mobilisaatio, johtaminen, toiminnan ulkoistaminen ja sosiaaliset kysymykset sekä asevoimien varustaminen. Julkaisun lähdemateriaali on lähes kokonaan venäjänkielistä. Sen avulla esitetään venäläisten omat niin myönteiset kuin kriittiset näkemykset koskien Venäjän asevoimien sotilasreformia, uutta ilmettä. Venäjänkielisistä termeistä käytetään mahdollisimman vastaavaa tai kuvaavaa suomenkielistä ilmaisua.

Public and private sector cooperative opportunities in the Finnish healthcare internationalization : views from the public sector’s perspective

Traditionally mostly publicly provided Finnish healthcare services are confronted today by the evident challenge of rising healthcare costs as the expenditure on health and social case has exceeded Finland’s national GDP growth significantly since the new millennium. While the opening of the traditional barriers through the EU’s new patient directive resulting in increasing international competition and the free flow of patients within the EU present opportunities for the Finnish healthcare services industry there are also several challenges for the existing healthcare system as proposed by the Ministry of Employment and the Economy in 2011. Due to the structure and nature of the current Finnish healthcare service system the greatest potential for internationalization is seen from a joint cooperation of the public and private sectors in an internationalization network for Finnish healthcare services. As its formation has recently also taken as a strategic initiative to be completed by the Ministry of Employment and the Economy and no earlier research exists on how this is seen in practice by the network actors, the purpose of this study is to examine the proposed solution of forming an internationalization network between the public and private sector actors in Finland in practice from the viewpoint of public sector actors. The research relied heavily on the reports by the Finnish Ministries in understanding the current situation of the Finnish healthcare services internationalization and its potential. Suitable theories were also used to build a more comprehensive view of the matter. The study applied a qualitative research approach on the explorative research problem. The data collection was achieved through expert interviews in two of the largest Finnish public healthcare service providers; the Turku and Helsinki Central University Hospitals. Expert interviews were considered as the most suitable method for data collection in order to create an in-depth understanding of the topic within the limitations of this thesis. In turn, two different public healthcare service providers were chosen to give a broader view of the field instead of focusing on a specific unit and also to allow a possible comparison between the two different organizations. The latter however was shown not to be suitable for the purposes of this study as the opinions of the respondents varied largely also within their own organizations. The conclusion is that while the actors agree on the evident internationalization of Finnish healthcare services, there are several large-scale structural challenges effectively preventing such activities while at the same time the opportunities within Finland vary, as there are several niches but no real large-scale advantages in the highly competitive industry. Interest towards cooperation between the sectors are seen especially in exploiting the advantages offered by the private sector in commercialization and marketization, yet however no clear views exist on how these activities should be governed or structured in the short-term as a larger reform of the entire Finnish healthcare service sector is needed in the long-term.

Biomedical Event Extraction with Machine Learning

Biomedical natural language processing (BioNLP) is a subfield of natural language processing, an area of computational linguistics concerned with developing programs that work with natural language: written texts and speech. Biomedical relation extraction concerns the detection of semantic relations such as protein-protein interactions (PPI) from scientific texts. The aim is to enhance information retrieval by detecting relations between concepts, not just individual concepts as with a keyword search. In recent years, events have been proposed as a more detailed alternative for simple pairwise PPI relations. Events provide a systematic, structural representation for annotating the content of natural language texts. Events are characterized by annotated trigger words, directed and typed arguments and the ability to nest other events. For example, the sentence “Protein A causes protein B to bind protein C” can be annotated with the nested event structure CAUSE(A, BIND(B, C)). Converted to such formal representations, the information of natural language texts can be used by computational applications. Biomedical event annotations were introduced by the BioInfer and GENIA corpora, and event extraction was popularized by the BioNLP'09 Shared Task on Event Extraction. In this thesis we present a method for automated event extraction, implemented as the Turku Event Extraction System (TEES). A unified graph format is defined for representing event annotations and the problem of extracting complex event structures is decomposed into a number of independent classification tasks. These classification tasks are solved using SVM and RLS classifiers, utilizing rich feature representations built from full dependency parsing. Building on earlier work on pairwise relation extraction and using a generalized graph representation, the resulting TEES system is capable of detecting binary relations as well as complex event structures. We show that this event extraction system has good performance, reaching the first place in the BioNLP'09 Shared Task on Event Extraction. Subsequently, TEES has achieved several first ranks in the BioNLP'11 and BioNLP'13 Shared Tasks, as well as shown competitive performance in the binary relation Drug-Drug Interaction Extraction 2011 and 2013 shared tasks. The Turku Event Extraction System is published as a freely available open-source project, documenting the research in detail as well as making the method available for practical applications. In particular, in this thesis we describe the application of the event extraction method to PubMed-scale text mining, showing how the developed approach not only shows good performance, but is generalizable and applicable to large-scale real-world text mining projects. Finally, we discuss related literature, summarize the contributions of the work and present some thoughts on future directions for biomedical event extraction. This thesis includes and builds on six original research publications. The first of these introduces the analysis of dependency parses that leads to development of TEES. The entries in the three BioNLP Shared Tasks, as well as in the DDIExtraction 2011 task are covered in four publications, and the sixth one demonstrates the application of the system to PubMed-scale text mining.