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.

Customer driven business model – connecting customer value to firm resources in ICT value networks

The objective of this thesis is to provide a business model framework that connects customer value to firm resources and explains the change logic of the business model. Strategic supply management and especially dynamic value network management as its scope, the dissertation is based on basic economic theories, transaction cost economics and the resource-based view. The main research question is how the changing customer values should be taken into account when planning business in a networked environment. The main question is divided into questions that form the basic research problems for the separate case studies presented in the five Publications. This research adopts the case study strategy, and the constructive research approach within it. The material consists of data from several Delphi panels and expert workshops, software pilot documents, company financial statements and information on investor relations on the companies’ web sites. The cases used in this study are a mobile multi-player game value network, smart phone and “Skype mobile” services, the business models of AOL, eBay, Google, Amazon and a telecom operator, a virtual city portal business system and a multi-play offering. The main contribution of this dissertation is bridging the gap between firm resources and customer value. This has been done by theorizing the business model concept and connecting it to both the resource-based view and customer value. This thesis contributes to the resource-based view, which deals with customer value and firm resources needed to deliver the value but has a gap in explaining how the customer value changes should be connected to the changes in key resources. This dissertation also provides tools and processes for analyzing the customer value preferences of ICT services, constructing and analyzing business models and business concept innovation and conducting resource analysis.

Asiakkuuksien strateginen arvottaminen ja luokittelu

Tämän tutkimuksen kohdeorganisaatio on suuren teollisuusyrityksen sisäinen raaka-aineen hankkija ja toimittaja. Tutkimuksessa selvitetään, mistä kohdeorganisaation hankinta-asiakkuuksien arvo muodostuu ja kuinka olemassa olevan liiketoimintadatan perusteella voidaan tutkia, arvioida ja luokitella kauppojen ja asiakkuuksien arvokkuutta aikaan sitomatta, objektiivisesti ja luotettavasti. Tutkimuksen teoriaosiossa esitellään lähestymistapoja ja menetelmiä, joiden avulla voidaan jalostaa olemassa olevasta datasta uutta sidosryhmätietämystä liiketoiminnan käyttöön, sekä tarkastellaan asiakaskannattavuusanalyysin, portfolioanalyysin, sekä asiakassegmentoinnin perusteita ja malleja. Näiden teorioiden ja mallien pohjalta rakennetaan kohdeorganisaatiolle räätälöity, indeksoituihin hinta-, määrä- ja kauppojen toistuvuus-muuttujiin perustuva, asiakkuuksien arvottamis- ja luokittelumalli. Arvottamis- ja luokittelumalli testataan vuosien 2003–2007 liiketoimintadatasta muodostetulla 389 336 kaupparivin otoksella, joka sisältää 42 186 arvioitavaa asiakkuussuhdetta. Merkittävin esille nouseva havainto on noin 5 000:n keskimääräistä selkeästi kalliimman asiakkuuden ryhmä. Aineisto ja sen poikkeavuudet testataan tilastollisin menetelmin, jotta saadaan selville asiakkuuden arvoon vaikuttavat ja arvoa selittävät tekijät. Lopuksi pohditaan arvottamismallin merkitystä analyyttisemman ostotoiminnan ja asiakkuudenhallinnan välineenä, sekä esitetään muutamia parannusehdotuksia.

Business intelligence –järjestelmä integraation tukena kansainvälisessä yrityksessä

Business intelligencellä tarkoitetaan liiketoimintatiedon hallintaan liittyviä prosesseja ja tekniikoita. Se pitää sisällään tiedon keräämiseen, tallentamiseen, analysointiin ja jakamiseen käytettyt tuotteet, tekniikat ja prosessit, joiden tavoitteena on auttaa yrityksen työntekijöitä liiketoimintaan liittyvässä päätöksenteossa. Tutkimuksen tavoitteena on tutkia uuden yritysryhmän laajuisen BI-tietojärjestelmän suunnitteluun ja käyttöönotoon liittyviä seikkoja ja luoda valmiudet BI-tietojärjestelmän kehitys- ja käyttöönottoprojektin kohdeyrityksessä, jonka toimiala on kansainvälinen terveydenhoitoalan tukkuliiketoiminta. Uuden BI-järjestelmän halutaan tukeva yritysryhmän yritysten välistä integraatiota ja tehostavan tiedonhakuun ja analysointiin liittyviä prosesseja. Tutkimus toteutettiin konstruktiivisena tutkimuksena, joka kattaa kohdeyrityksen IT-arkkitehtuurin, tietosisällön, prosessit ja organisaation raportoinnin kannalta. Lisäksi työssä suoritettiin ohjelmistovertailu kahden markkinoilla toimivan merkittävän ohjelmistotalon BI-tuotteiden välillä. Työssä havaittiin, että BI-projekti on laaja-alainen ja suuri hanke, joka ulottuu läpi koko organisaation. BI-ohjelmiston tehokas hyödyntäminen asettaa vaatimuksia erityisesti taustajärjestelmien tiedon huolelliseen mallintamiseen liittyen. Työssä saatiin pilotoinnin kautta käytännön kokemuksia uudesta järjestelmästä ja sen tarjoamista mahdollisuuksista kohdeyrityksessä.

Application of social media and ICT-tools in new and small business ventures.

The current research emphasizes on various questions raised and deliberated upon by different entrepreneurs. It provides a valuable contribution to comprehend the importance of social media and ICT-applications. Furthermore, it demonstrates how to support and implement the management consulting and business coaching start-ups with the help of social media and ICT-tools. The thesis presents a literary review from different information systems science, SME and e-business journals, web articles, as well as, survey analysis reports on social media applications. The methodology incorporated into a qualitative research method in which social anthropological approaches were used to oversee the case study activities in order to collect data. The collaborative social research approach was used to shelter the action research method. The research discovered that new business start-ups, as well as small businesses do not use social media and ICT-tools, unlike most of the large corporations use. At present, the current open-source ICT-technologies and social media applications are equally available for new and small businesses as they are available for larger companies. Successful implementation of social media and ICT-applications can easily enhance start-up performance and overcome business hassles. The thesis sheds some light on effective and innovative implementation of social media and ICT-applications for new business risk takers and small business birds. Key words

From network pictures to network insight in solution business – the role of internal communication

Operating in business-to-business markets requires an in-depth understanding on business networks. Actions and reactions made to compete in markets are fundamentally based on managers‘ subjective perceptions of the network. However, an amalgamation of these individual perceptions, termed a network picture, to a common company level shared understanding on that network, known as network insight, is found to be a substantial challenge for companies. A company‘s capability to enhance common network insight is even argued to lead competitive advantage. Especially companies with value creating logics that require wide comprehension of and collaborating in networks, such as solution business, are necessitated to develop advanced network insight. According to the extant literature, dispersed pieces of atomized network pictures can be unified to a common network insight through a process of amalgamation that comprises barriers/drivers of multilateral exchange, manifold rationality, and recursive time. However, the extant body of literature appears to lack an understanding on the role of internal communication in the development of network insight. Nonetheless, the extant understanding on the amalgamation process indicates that internal communication plays a substantial role in the development of company level network insight. The purpose of the present thesis is to enhance understanding on internal communication in the amalgamation of network pictures to develop network insight in the solution business setting, which was chosen to represent business-to-business value creating logic that emphasizes the capability to understand and utilize networks. Thus, in solution business the role of succeeding in the amalgamation process is expected to emphasize. The study combines qualitative and quantitative research by means of various analytical methods including multiple case analysis, simulation, and social network analysis. Approaching the nascent research topic with differing perspectives and means provides a broader insight on the phenomenon. The study provides empirical evidence from Finnish business-to-business companies which operate globally. The empirical data comprise interviews (n=28) with managers of three case companies. In addition the data includes a questionnaire (n=23) collected mainly for the purpose of social network analysis. In addition, the thesis includes a simulation study more specifically achieved by means of agent based modeling. The findings of the thesis shed light on the role of internal communication in the amalgamation process, contributing to the emergent discussion of network insights and thus to the industrial marketing research. In addition, the thesis increases understanding on internal communication in the change process to solution business, a supplier‘s internal communication in its matrix organization structure during a project sales process, key barriers and drivers that influence internal communication in project sales networks, perceived power within industrial project sales, and the revisioning of network pictures. According to the findings, internal communication is found to play a substantial role in the amalgamation process. First, it is suggested that internal communication is a base of multilateral exchange. Second, it is suggested that internal communication intensifies and maintains manifold rationality. Third, internal communication is needed to explicate the usually differing time perspectives of others and thus it is suggested that internal communication has role as the explicator of recursive time. Furthermore, the role of an efficient amalgamation process is found to be emphasized in solutions business as it requires a more advanced network insight for cross-functional collaboration. Finally, the thesis offers several managerial implications for industrial suppliers to enhance the amalgamation process when operating in solution business.

Tiedolla johtaminen henkilöstöhallinnossa - Empiirinen tutkimus

Yritysten syvällinen ymmärrys työntekijöistä vaatii yrityksiltä monipuolista panostusta tiedonhallintaan. Tämän yhdistäminen ennakoivaan analytiikkaan ja tiedonlouhintaan mahdollistaa yrityksille uudenlaisen ulottuvuuden kehittää henkilöstöhallinnon toimintoja niin työntekijöiden kuin yrityksen etujen mukaisesti. Tutkielman tavoitteena oli selvittää tiedonlouhinnan hyödyntämistä henkilöstöhallinnossa. Tutkielma toteutettiin konstruktiivistä menetelmää hyödyntäen. Teoreettinen viitekehys keskittyi ennakoivan analytiikan ja tiedonlouhinnan konseptin ymmärtämiseen. Tutkielman empiriaosuus rakentui kvalitatiiviseen ja kvantitatiiviseen osiin. Kvalitatiivinen osa koostui tutkielman esitutkimuksesta, jossa käsiteltiin ennakoivan analytiikan ja tiedonlouhinnan hyödyntämistä. Kvantitatiivinen osa rakentui tiedonlouhintaprojektiin, joka toteutettiin henkilöstöhallintoon tutkien henkilöstövaihtuvuutta. Esitutkimuksen tuloksena tiedonlouhinnan hyödyntämisen haasteiksi ilmeni muun muassa tiedon omistajuus, osaaminen ja ymmärrys mahdollisuuksista. Tiedonlouhintaprojektin tuloksena voidaan todeta, että tutkimuksessa sovelletuista korrelaatioiden tutkimisista ja logistisesta regressioanalyysistä oli havaittavissa tilastollisia riippuvuuksia vapaaehtoisesti poistuvien työntekijöiden osalta.

A platform for assessing the current state of data repositories in Korea, Japan and China

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

On advancing business intelligence in the electricity retail market

In recent decades, business intelligence (BI) has gained momentum in real-world practice. At the same time, business intelligence has evolved as an important research subject of Information Systems (IS) within the decision support domain. Today’s growing competitive pressure in business has led to increased needs for real-time analytics, i.e., so called real-time BI or operational BI. This is especially true with respect to the electricity production, transmission, distribution, and retail business since the law of physics determines that electricity as a commodity is nearly impossible to be stored economically, and therefore demand-supply needs to be constantly in balance. The current power sector is subject to complex changes, innovation opportunities, and technical and regulatory constraints. These range from low carbon transition, renewable energy sources (RES) development, market design to new technologies (e.g., smart metering, smart grids, electric vehicles, etc.), and new independent power producers (e.g., commercial buildings or households with rooftop solar panel installments, a.k.a. Distributed Generation). Among them, the ongoing deployment of Advanced Metering Infrastructure (AMI) has profound impacts on the electricity retail market. From the view point of BI research, the AMI is enabling real-time or near real-time analytics in the electricity retail business. Following Design Science Research (DSR) paradigm in the IS field, this research presents four aspects of BI for efficient pricing in a competitive electricity retail market: (i) visual data-mining based descriptive analytics, namely electricity consumption profiling, for pricing decision-making support; (ii) real-time BI enterprise architecture for enhancing management’s capacity on real-time decision-making; (iii) prescriptive analytics through agent-based modeling for price-responsive demand simulation; (iv) visual data-mining application for electricity distribution benchmarking. Even though this study is from the perspective of the European electricity industry, particularly focused on Finland and Estonia, the BI approaches investigated can: (i) provide managerial implications to support the utility’s pricing decision-making; (ii) add empirical knowledge to the landscape of BI research; (iii) be transferred to a wide body of practice in the power sector and BI research community.

Location intelligence strategisen päätöksenteon tukena

Kilpailuetua tavoittelevan yrityksen pitää kyetä jalostamaan tietoa ja tunnistamaan sen avulla uusia tulevaisuuden mahdollisuuksia. Tulevaisuuden mielikuvien luomiseksi yrityksen on tunnettava toimintaympäristönsä ja olla herkkänä havaitsemaan muutostrendit ja muut toimintaympäristön signaalit. Ympäristön elintärkeät signaalit liittyvät kilpailijoihin, teknologian kehittymiseen, arvomaailman muutoksiin, globaaleihin väestötrendeihin tai jopa ympäristön muutoksiin. Spatiaaliset suhteet ovat peruspilareita käsitteellistää maailmaamme. Pitney (2015) on arvioinut, että 80 % kaikesta bisnesdatasta sisältää jollakin tavoin viittauksia paikkatietoon. Siitä huolimatta paikkatietoa on vielä huonosti hyödynnetty yritysten strategisten päätösten tukena. Teknologioiden kehittyminen, tiedon nopea siirto ja paikannustekniikoiden integroiminen eri laitteisiin ovat mahdollistaneet sen, että paikkatietoa hyödyntäviä palveluja ja ratkaisuja tullaan yhä enemmän näkemään yrityskentässä. Tutkimuksen tavoitteena oli selvittää voiko location intelligence toimia strategisen päätöksenteon tukena ja jos voi, niin miten. Työ toteutettiin konstruktiivista tutkimusmenetelmää käyttäen, jolla pyritään ratkaisemaan jokin relevantti ongelma. Konstruktiivinen tutkimus tehtiin tiiviissä yhteistyössä kolmen pk-yrityksen kanssa ja siihen haastateltiin kuutta eri strategiasta vastaavaa henkilöä. Tutkimuksen tuloksena löydettiin, että location intelligenceä voidaan hyödyntää strategisen päätöksenteon tukena usealla eri tasolla. Yksinkertaisimmassa karttaratkaisussa halutut tiedot tuodaan kartalle ja luodaan visuaalinen esitys, jonka avulla johtopäätöksien tekeminen helpottuu. Toisen tason karttaratkaisu pitää sisällään sekä sijainti- että ominaisuustietoa, jota on yhdistetty eri lähteistä. Tämä toisen tason karttaratkaisu on usein kuvailevaa analytiikkaa, joka mahdollistaa erilaisten ilmiöiden analysoinnin. Kolmannen eli ylimmän tason karttaratkaisu tarjoaa ennakoivaa analytiikkaa ja malleja tulevaisuudesta. Tällöin ohjelmaan koodataan älykkyyttä, jossa informaation keskinäisiä suhteita on määritelty joko tiedon louhintaa tai tilastollisia analyysejä hyödyntäen. Tutkimuksen johtopäätöksenä voidaan todeta, että location intelligence pystyy tarjoamaan lisäarvoa strategisen päätöksenteon tueksi, mikäli yritykselle on hyödyllistä ymmärtää eri ilmiöiden, asiakastarpeiden, kilpailijoiden ja markkinamuutoksien maantieteellisiä eroavaisuuksia. Parhaimmillaan location intelligence -ratkaisu tarjoaa luotettavan analyysin, jossa tieto välittyy muuttumattomana päätöksentekijältä toiselle ja johtopäätökseen johtaneita syitä on mahdollista palata tarkastelemaan tarvittaessa uudelleen.

Opportunity meets uncertainty. Towards sustainable business in the Arctic region

The Arctic region is experiencing a significant change in terms of climate change and a growing economic interest towards its natural resources and emerging business opportunities. The purpose of this study is to explore how can Finnish companies create sustainable business in the Arctic. This is done by examining the arctic business environment, identifying sectors with growth potential, addressing challenges related to operating in the Arctic and suggesting how to ensure sustainability and succeed in the globally competed arctic market. The theoretical framework is based on theories of sustainable development, corporate social responsibility and the role of strategy in creating sustainable business. Empirical data was collected by using qualitative research methods: first, background knowledge was formed based on written documents and, secondly, six expert interviews were conducted in early 2014. The interviewees represented the viewpoints of companies, political decision makers and NGO’s. The analysis of the data was conducted using thematic categorization. The empirical findings of the study suggest that in order to create sustainable business in the Arctic companies should adopt a long-term perspective, embrace a holistic approach to sustainability, understand interdependencies between the dimensions of sustainability and aim at high-level engagement in responsible behavior. To succeed in the arctic market core competencies, customer needs, multivendor cooperation and long-term presence need to be invested in on a company level. In addition, to promote and advance arctic development on a national level support is needed in terms of investments in infrastructure, funding research and design, creating a regulative framework and removing barriers of trade.

Assessment of Tandem Mass Spectrometry and High Resolution Mass Spectrometry for the Analysis of Bupivacaine in Plasma

Triple quadrupole mass spectrometers coupled with high performance liquid chromatography are workhorses in quantitative bioanalyses. It provides substantial benefits including reproducibility, sensitivity and selectivity for trace analysis. Selected Reaction Monitoring allows targeted assay development but data sets generated contain very limited information. Data mining and analysis of non-targeted high-resolution mass spectrometry profiles of biological samples offer the opportunity to perform more exhaustive assessments, including quantitative and qualitative analysis. The objectives of this study was to test method precision and accuracy, statistically compare bupivacaine drug concentration in real study samples and verify if high resolution and accurate mass data collected in scan mode can actually permit retrospective data analysis, more specifically, extract metabolite related information. The precision and accuracy data presented using both instruments provided equivalent results. Overall, the accuracy was ranging from 106.2 to 113.2% and the precision observed was from 1.0 to 3.7%. Statistical comparisons using a linear regression between both methods reveal a coefficient of determination (R2) of 0.9996 and a slope of 1.02 demonstrating a very strong correlation between both methods. Individual sample comparison showed differences from -4.5% to 1.6% well within the accepted analytical error. Moreover, post acquisition extracted ion chromatograms at m/z 233.1648 ± 5 ppm (M-56) and m/z 305.2224 ± 5 ppm (M+16) revealed the presence of desbutyl-bupivacaine and three distinct hydroxylated bupivacaine metabolites. Post acquisition analysis allowed us to produce semiquantitative evaluations of the concentration-time profiles for bupicavaine metabolites.

“Reconstruction of Gene Regulatory Network from Expression Profile of Plasma RNA Data of Colorectal Cancer Patients using Soft Computing Techniques”

Microarray data analysis is one of data mining tool which is used to extract meaningful information hidden in biological data. One of the major focuses on microarray data analysis is the reconstruction of gene regulatory network that may be used to provide a broader understanding on the functioning of complex cellular systems. Since cancer is a genetic disease arising from the abnormal gene function, the identification of cancerous genes and the regulatory pathways they control will provide a better platform for understanding the tumor formation and development. The major focus of this thesis is to understand the regulation of genes responsible for the development of cancer, particularly colorectal cancer by analyzing the microarray expression data. In this thesis, four computational algorithms namely fuzzy logic algorithm, modified genetic algorithm, dynamic neural fuzzy network and Takagi Sugeno Kang-type recurrent neural fuzzy network are used to extract cancer specific gene regulatory network from plasma RNA dataset of colorectal cancer patients. Plasma RNA is highly attractive for cancer analysis since it requires a collection of small amount of blood and it can be obtained at any time in repetitive fashion allowing the analysis of disease progression and treatment response.

Statistical Models for Co-occurrence Data

Modeling and predicting co-occurrences of events is a fundamental problem of unsupervised learning. In this contribution we develop a statistical framework for analyzing co-occurrence data in a general setting where elementary observations are joint occurrences of pairs of abstract objects from two finite sets. The main challenge for statistical models in this context is to overcome the inherent data sparseness and to estimate the probabilities for pairs which were rarely observed or even unobserved in a given sample set. Moreover, it is often of considerable interest to extract grouping structure or to find a hierarchical data organization. A novel family of mixture models is proposed which explain the observed data by a finite number of shared aspects or clusters. This provides a common framework for statistical inference and structure discovery and also includes several recently proposed models as special cases. Adopting the maximum likelihood principle, EM algorithms are derived to fit the model parameters. We develop improved versions of EM which largely avoid overfitting problems and overcome the inherent locality of EM--based optimization. Among the broad variety of possible applications, e.g., in information retrieval, natural language processing, data mining, and computer vision, we have chosen document retrieval, the statistical analysis of noun/adjective co-occurrence and the unsupervised segmentation of textured images to test and evaluate the proposed algorithms.

Data collection and analysis

A presentation on the collection and analysis of data taken from SOES 6018. This module aims to ensure that MSc Oceanography, MSc Marine Science, Policy & Law and MSc Marine Resource Management students are equipped with the skills they need to function as professional marine scientists, in addition to / in conjuction with the skills training in other MSc modules. The module covers training in fieldwork techniques, communication & research skills, IT & data analysis and professional development.