On Undecidable Dynamical Properties of Reversible One-Dimensional Cellular Automata

Cellular automata are models for massively parallel computation. A cellular automaton consists of cells which are arranged in some kind of regular lattice and a local update rule which updates the state of each cell according to the states of the cell's neighbors on each step of the computation. This work focuses on reversible one-dimensional cellular automata in which the cells are arranged in a two-way in_nite line and the computation is reversible, that is, the previous states of the cells can be derived from the current ones. In this work it is shown that several properties of reversible one-dimensional cellular automata are algorithmically undecidable, that is, there exists no algorithm that would tell whether a given cellular automaton has the property or not. It is shown that the tiling problem of Wang tiles remains undecidable even in some very restricted special cases. It follows that it is undecidable whether some given states will always appear in computations by the given cellular automaton. It also follows that a weaker form of expansivity, which is a concept of dynamical systems, is an undecidable property for reversible one-dimensional cellular automata. It is shown that several properties of dynamical systems are undecidable for reversible one-dimensional cellular automata. It shown that sensitivity to initial conditions and topological mixing are undecidable properties. Furthermore, non-sensitive and mixing cellular automata are recursively inseparable. It follows that also chaotic behavior is an undecidable property for reversible one-dimensional cellular automata.

Promoting Programming Learning. Engagement, Automatic Assessment with Immediate Feedback in Visualizations

The skill of programming is a key asset for every computer science student. Many studies have shown that this is a hard skill to learn and the outcomes of programming courses have often been substandard. Thus, a range of methods and tools have been developed to assist students’ learning processes. One of the biggest fields in computer science education is the use of visualizations as a learning aid and many visualization based tools have been developed to aid the learning process during last few decades. Studies conducted in this thesis focus on two different visualizationbased tools TRAKLA2 and ViLLE. This thesis includes results from multiple empirical studies about what kind of effects the introduction and usage of these tools have on students’ opinions and performance, and what kind of implications there are from a teacher’s point of view. The results from studies in this thesis show that students preferred to do web-based exercises, and felt that those exercises contributed to their learning. The usage of the tool motivated students to work harder during their course, which was shown in overall course performance and drop-out statistics. We have also shown that visualization-based tools can be used to enhance the learning process, and one of the key factors is the higher and active level of engagement (see. Engagement Taxonomy by Naps et al., 2002). The automatic grading accompanied with immediate feedback helps students to overcome obstacles during the learning process, and to grasp the key element in the learning task. These kinds of tools can help us to cope with the fact that many programming courses are overcrowded with limited teaching resources. These tools allows us to tackle this problem by utilizing automatic assessment in exercises that are most suitable to be done in the web (like tracing and simulation) since its supports students’ independent learning regardless of time and place. In summary, we can use our course’s resources more efficiently to increase the quality of the learning experience of the students and the teaching experience of the teacher, and even increase performance of the students. There are also methodological results from this thesis which contribute to developing insight into the conduct of empirical evaluations of new tools or techniques. When we evaluate a new tool, especially one accompanied with visualization, we need to give a proper introduction to it and to the graphical notation used by tool. The standard procedure should also include capturing the screen with audio to confirm that the participants of the experiment are doing what they are supposed to do. By taken such measures in the study of the learning impact of visualization support for learning, we can avoid drawing false conclusion from our experiments. As computer science educators, we face two important challenges. Firstly, we need to start to deliver the message in our own institution and all over the world about the new – scientifically proven – innovations in teaching like TRAKLA2 and ViLLE. Secondly, we have the relevant experience of conducting teaching related experiment, and thus we can support our colleagues to learn essential know-how of the research based improvement of their teaching. This change can transform academic teaching into publications and by utilizing this approach we can significantly increase the adoption of the new tools and techniques, and overall increase the knowledge of best-practices. In future, we need to combine our forces and tackle these universal and common problems together by creating multi-national and multiinstitutional research projects. We need to create a community and a platform in which we can share these best practices and at the same time conduct multi-national research projects easily.

Verbal learning in mild cognitive impairment and alzheimer's disease : behavioural and neural approaches

The main focus of the present thesis was at verbal episodic memory processes that are particularly vulnerable to preclinical and clinical Alzheimer’s disease (AD). Here these processes were studied by a word learning paradigm, cutting across the domains of memory and language learning studies. Moreover, the differentiation between normal aging, mild cognitive impairment (MCI) and AD was studied by the cognitive screening test CERAD. In study I, the aim was to examine how patients with amnestic MCI differ from healthy controls in the different CERAD subtests. Also, the sensitivity and specificity of the CERAD screening test to MCI and AD was examined, as previous studies on the sensitivity and specificity of the CERAD have not included MCI patients. The results indicated that MCI is characterized by an encoding deficit, as shown by the overall worse performance on the CERAD Wordlist learning test compared with controls. As a screening test, CERAD was not very sensitive to MCI. In study II, verbal learning and forgetting in amnestic MCI, AD and healthy elderly controls was investigated with an experimental word learning paradigm, where names of 40 unfamiliar objects (mainly archaic tools) were trained with or without semantic support. The object names were trained during a 4-day long period and a follow-up was conducted one week, 4 weeks and 8 weeks after the training period. Manipulation of semantic support was included in the paradigm because it was hypothesized that semantic support might have some beneficial effects in the present learning task especially for the MCI group, as semantic memory is quite well preserved in MCI in contrast to episodic memory. We found that word learning was significantly impaired in MCI and AD patients, whereas forgetting patterns were similar across groups. Semantic support showed a beneficial effect on object name retrieval in the MCI group 8 weeks after training, indicating that the MCI patients’ preserved semantic memory abilities compensated for their impaired episodic memory. The MCI group performed equally well as the controls in the tasks tapping incidental learning and recognition memory, whereas the AD group showed impairment. Both the MCI and the AD group benefited less from phonological cueing than the controls. Our findings indicate that acquisition is compromised in both MCI and AD, whereas long13 term retention is not affected to the same extent. Incidental learning and recognition memory seem to be well preserved in MCI. In studies III and IV, the neural correlates of naming newly learned objects were examined in healthy elderly subjects and in amnestic MCI patients by means of positron emission tomography (PET) right after the training period. The naming of newly learned objects by healthy elderly subjects recruited a left-lateralized network, including frontotemporal regions and the cerebellum, which was more extensive than the one related to the naming of familiar objects (study III). Semantic support showed no effects on the PET results for the healthy subjects. The observed activation increases may reflect lexicalsemantic and lexical-phonological retrieval, as well as more general associative memory mechanisms. In study IV, compared to the controls, the MCI patients showed increased anterior cingulate activation when naming newly learned objects that had been learned without semantic support. This suggests a recruitment of additional executive and attentional resources in the MCI group.

Neural correlates of language learning in adults

The human language-learning ability persists throughout life, indicating considerable flexibility at the cognitive and neural level. This ability spans from expanding the vocabulary in the mother tongue to acquisition of a new language with its lexicon and grammar. The present thesis consists of five studies that tap both of these aspects of adult language learning by using magnetoencephalography (MEG) and functional magnetic resonance imaging (fMRI) during language processing and language learning tasks. The thesis shows that learning novel phonological word forms, either in the native tongue or when exposed to a foreign phonology, activates the brain in similar ways. The results also show that novel native words readily become integrated in the mental lexicon. Several studies in the thesis highlight the left temporal cortex as an important brain region in learning and accessing phonological forms. Incidental learning of foreign phonological word forms was reflected in functionally distinct temporal lobe areas that, respectively, reflected short-term memory processes and more stable learning that persisted to the next day. In a study where explicitly trained items were tracked for ten months, it was found that enhanced naming-related temporal and frontal activation one week after learning was predictive of good long-term memory. The results suggest that memory maintenance is an active process that depends on mechanisms of reconsolidation, and that these process vary considerably between individuals. The thesis put special emphasis on studying language learning in the context of language production. The neural foundation of language production has been studied considerably less than that of perceptive language, especially on the sentence level. A well-known paradigm in language production studies is picture naming, also used as a clinical tool in neuropsychology. This thesis shows that accessing the meaning and phonological form of a depicted object are subserved by different neural implementations. Moreover, a comparison between action and object naming from identical images indicated that the grammatical class of the retrieved word (verb, noun) is less important than the visual content of the image. In the present thesis, the picture naming was further modified into a novel paradigm in order to probe sentence-level speech production in a newly learned miniature language. Neural activity related to grammatical processing did not differ between the novel language and the mother tongue, but stronger neural activation for the novel language was observed during the planning of the upcoming output, likely related to more demanding lexical retrieval and short-term memory. In sum, the thesis aimed at examining language learning by combining different linguistic domains, such as phonology, semantics, and grammar, in a dynamic description of language processing in the human brain.

The effectiveness of short-term literacy skills intervention on children at risk of reading and writing difficulties in Tanzania : a study of grade one children with dynamic assessment approach

The aim of the study was to create and evaluate an intervention programme for Tanzanian children from a low-income area who are at risk of reading and writing difficulties. The learning difficulties, including reading and writing difficulties, are likely to be behind many of the common school problems in Tanzania, but they are not well understood, and research is needed. The design of the study included an identification and intervention phase with follow-up. A group based dynamic assessment approach was used in identifying children at risk of difficulties in reading and writing. The same approach was used in the intervention. The study was a randomized experiment with one experimental and two control groups. For the experimental and the control groups, a total of 96 (46 girls and 50 boys) children from grade one were screened out of 301 children from two schools in a low income urban area of Dar-es-Salaam. One third of the children, the experimental group, participated in an intensive training programme in literacy skills for five weeks, six hours per week, aimed at promoting reading and writing ability, while the children in the control groups had a mathematics and art programme. Follow-up was performed five months after the intervention. The intervention programme and the tests were based on the Zambian BASAT (Basic Skill Assessment Tool, Ketonen & Mulenga, 2003), but the content was drawn from the Kiswahili school curriculum in Tanzania. The main components of the training and testing programme were the same, only differing in content. The training process was different from traditional training in Tanzanian schools in that principles of teaching and training in dynamic assessment were followed. Feedback was the cornerstone of the training and the focus was on supporting the children in exploring knowledge and strategies in performing the tasks. The experimental group improved significantly more (p = .000) than the control groups during the intervention from pre-test to follow-up (repeated measures ANOVA). No differences between the control groups were noticed. The effect was significant on all the measures: phonological awareness, reading skills, writing skills and overall literacy skills. A transfer effect on school marks in Kiswahili and English was found. Following a discussion of the results, suggestions for further research and adaptation of the programme are presented.

Towards adoption of eLearning technologies at Lappeenranta University of Technology: Understanding Teachers‟ Adoption of Blackboard Learning System

The electronic learning has become crucial in higher education with increased usage of learning management systems as a key source of integration on distance learning. The objective of this study is to understand how university teachers are influenced to use and adopt web-based learning management systems. Blackboard, as one of the systems used internationally by various universities is applied as a case. Semi-structured interviews were made with professors and lecturers who are using Blackboard at Lappeenranta University of Technology. The data collected were categorized under constructs adapted from Unified Theory of Acceptance and Use of Technology (UTAUT) and interpretation and discussion were based on reviewed literature. The findings suggest that adoption of learning management systems by LUT teachers is highly influenced by perceived usefulness, facilitating conditions and gained experience. The findings also suggest that easiness of using the system and social influence appear as medium influence of adoption for teachers at LUT.

Future revenue models: Transformation from textbooks to digital solutions in the educational publishing industry, Case Sanoma Learning

This study was conducted in order to learn how companies’ revenue models will be transformed due to the digitalisation of its products and processes. Because there is still only a limited number of researches focusing solely on revenue models, and particularly on the revenue model change caused by the changes at the business environment, the topic was initially approached through the business model concept, which organises the different value creating operations and resources at a company in order to create profitable revenue streams. This was used as the base for constructing the theoretical framework for this study, used to collect and analyse the information. The empirical section is based on a qualitative study approach and multiple-case analysis of companies operating in learning materials publishing industry. Their operations are compared with companies operating in other industries, which have undergone comparable transformation, in order to recognise either similarities or contrasts between the cases. The sources of evidence are a literature review to find the essential dimensions researched earlier, and interviews 29 of managers and executives at 17 organisations representing six industries. Based onto the earlier literature and the empirical findings of this study, the change of the revenue model is linked with the change of the other dimen-sions of the business model. When one dimension will be altered, as well the other should be adjusted accordingly. At the case companies the transformation is observed as the utilisation of several revenue models simultaneously and the revenue creation processes becoming more complex.

Kernel-Based Ranking. Methods for Learning and Performance Estimation

Machine learning provides tools for automated construction of predictive models in data intensive areas of engineering and science. The family of regularized kernel methods have in the recent years become one of the mainstream approaches to machine learning, due to a number of advantages the methods share. The approach provides theoretically well-founded solutions to the problems of under- and overfitting, allows learning from structured data, and has been empirically demonstrated to yield high predictive performance on a wide range of application domains. Historically, the problems of classification and regression have gained the majority of attention in the field. In this thesis we focus on another type of learning problem, that of learning to rank. In learning to rank, the aim is from a set of past observations to learn a ranking function that can order new objects according to how well they match some underlying criterion of goodness. As an important special case of the setting, we can recover the bipartite ranking problem, corresponding to maximizing the area under the ROC curve (AUC) in binary classification. Ranking applications appear in a large variety of settings, examples encountered in this thesis include document retrieval in web search, recommender systems, information extraction and automated parsing of natural language. We consider the pairwise approach to learning to rank, where ranking models are learned by minimizing the expected probability of ranking any two randomly drawn test examples incorrectly. The development of computationally efficient kernel methods, based on this approach, has in the past proven to be challenging. Moreover, it is not clear what techniques for estimating the predictive performance of learned models are the most reliable in the ranking setting, and how the techniques can be implemented efficiently. The contributions of this thesis are as follows. First, we develop RankRLS, a computationally efficient kernel method for learning to rank, that is based on minimizing a regularized pairwise least-squares loss. In addition to training methods, we introduce a variety of algorithms for tasks such as model selection, multi-output learning, and cross-validation, based on computational shortcuts from matrix algebra. Second, we improve the fastest known training method for the linear version of the RankSVM algorithm, which is one of the most well established methods for learning to rank. Third, we study the combination of the empirical kernel map and reduced set approximation, which allows the large-scale training of kernel machines using linear solvers, and propose computationally efficient solutions to cross-validation when using the approach. Next, we explore the problem of reliable cross-validation when using AUC as a performance criterion, through an extensive simulation study. We demonstrate that the proposed leave-pair-out cross-validation approach leads to more reliable performance estimation than commonly used alternative approaches. Finally, we present a case study on applying machine learning to information extraction from biomedical literature, which combines several of the approaches considered in the thesis. The thesis is divided into two parts. Part I provides the background for the research work and summarizes the most central results, Part II consists of the five original research articles that are the main contribution of this thesis.

Playing to Learn: Business Simulation Games as Leadership Learning Environments

The aim of this dissertation is to investigate if participation in business simulation gaming sessions can make different leadership styles visible and provide students with experiences beneficial for the development of leadership skills. Particularly, the focus is to describe the development of leadership styles when leading virtual teams in computer-­supported collaborative game settings and to identify the outcomes of using computer simulation games as leadership training tools. To answer to the objectives of the study, three empirical experiments were conducted to explore if participation in business simulation gaming sessions (Study I and II), which integrate face-­to-­face and virtual communication (Study III and IV), can make different leadership styles visible and provide students with experiences beneficial for the development of leadership skills. In the first experiment, a group of multicultural graduate business students (N=41) participated in gaming sessions with a computerized business simulation game (Study III). In the second experiment, a group of graduate students (N=9) participated in the training with a ‘real estate’ computer game (Study I and II). In the third experiment, a business simulation gaming session was organized for graduate students group (N=26) and the participants played the simulation game in virtual teams, which were organizationally and geographically dispersed but connected via technology (Study IV). Each team in all experiments had three to four students and students were between 22 and 25 years old. The business computer games used for the empirical experiments presented an enormous number of complex operations in which a team leader needed to make the final decisions involved in leading the team to win the game. These gaming environments were interactive;; participants interacted by solving the given tasks in the game. Thus, strategy and appropriate leadership were needed to be successful. The training was competition-­based and required implementation of leadership skills. The data of these studies consist of observations, participants’ reflective essays written after the gaming sessions, pre-­ and post-­tests questionnaires and participants’ answers to open-­ ended questions. Participants’ interactions and collaboration were observed when they played the computer games. The transcripts of notes from observations and students dialogs were coded in terms of transactional, transformational, heroic and post-­heroic leadership styles. For the data analysis of the transcribed notes from observations, content analysis and discourse analysis was implemented. The Multifactor Leadership Questionnaire (MLQ) was also utilized in the study to measure transformational and transactional leadership styles;; in addition, quantitative (one-­way repeated measures ANOVA) and qualitative data analyses have been performed. The results of this study indicate that in the business simulation gaming environment, certain leadership characteristics emerged spontaneously. Experiences about leadership varied between the teams and were dependent on the role individual students had in their team. These four studies showed that simulation gaming environment has the potential to be used in higher education to exercise the leadership styles relevant in real-­world work contexts. Further, the study indicated that given debriefing sessions, the simulation game context has much potential to benefit learning. The participants who showed interest in leadership roles were given the opportunity of developing leadership skills in practice. The study also provides evidence of unpredictable situations that participants can experience and learn from during the gaming sessions. The study illustrates the complex nature of experiences from the gaming environments and the need for the team leader and role divisions during the gaming sessions. It could be concluded that the experience of simulation game training illustrated the complexity of real life situations and provided participants with the challenges of virtual leadership experiences and the difficulties of using leadership styles in practice. As a result, the study offers playing computer simulation games in small teams as one way to exercise leadership styles in practice.

Organisational learning and knowledge acquisition. A case study of internationalising manufacturers of wood-based prefabricated buildings

The study investigates organisational learning and knowledge acquisition of wood-based prefabricated building manufacturers. This certain group of case companies was chosen, because their management and their employees generally have a strong manufacturing and engineering background, while the housing sector is characterised by national norms, regulations, as well as local building styles. Considering this setting, it was investigated, how the case companies develop organisational learning capabilities, acquire and transfer knowledge for their internationalisation. The theoretical framework of this study constitutes the knowledge-based conceptualisation of internationalisation, which combines the traditional internationalisation process, as well as the international new venture perspective based on their commonalities in the knowledge-based view of the firm. Different theories of internationalisation, including the network-perspective, were outlined and a framework on organisational learning and knowledge acquisition was established. The empirical research followed a qualitative approach, deploying a multiple-case study with five case companies from Austria, Finland and Germany. In the study, the development of the wood-based prefabricated building industry and of the case companies are described, and the motives, facilitators and challenges for foreign expansion, as well as the companies’ internationalisation approaches are compared. Different methods of how companies facilitate the knowledge-exchange or learn about new markets are also outlined. Experience, market knowledge and personal contacts are considered essential for the internationalisation process. The major finding of the study is that it is not necessary to acquire the market knowledge internally in a slow process as proposed by the Uppsala model. In four cases companies engaged knowledge in symbiotic relations with local business partners. Thereby, the building manufacturers contribute their design and production capabilities, and in return, their local partners provide them with knowledge about the market and local regulations; while they manage the sales and construction operations. Thus, the study provides strong evidence for the propositions of network perspective. One case company developed the knowledge internally in a gradual process: it entered the market sequentially with several business lines, showing an increasing level of complexity. In both of the observed strategies, single-loop and double-loop learning processes occurred.

The nature of communication structures of university students in an international web-based computer-supported collaborative learning (CSCL) course

Communication, the flow of ideas and information between individuals in a social context, is the heart of educational experience. Constructivism and constructivist theories form the foundation for the collaborative learning processes of creating and sharing meaning in online educational contexts. The Learning and Collaboration in Technology-enhanced Contexts (LeCoTec) course comprised of 66 participants drawn from four European universities (Oulu, Turku, Ghent and Ramon Llull). These participants were split into 15 groups with the express aim of learning about computer-supported collaborative learning (CSCL). The Community of Inquiry model (social, cognitive and teaching presences) provided the content and tools for learning and researching the collaborative interactions in this environment. The sampled comments from the collaborative phase were collected and analyzed at chain-level and group-level, with the aim of identifying the various message types that sustained high learning outcomes. Furthermore, the Social Network Analysis helped to view the density of whole group interactions, as well as the popular and active members within the highly collaborating groups. It was observed that long chains occur in groups having high quality outcomes. These chains were also characterized by Social, Interactivity, Administrative and Content comment-types. In addition, high outcomes were realized from the high interactive cases and high-density groups. In low interactive groups, commenting patterned around the one or two central group members. In conclusion, future online environments should support high-order learning and develop greater metacognition and self-regulation. Moreover, such an environment, with a wide variety of problem solving tools, would enhance interactivity.

Adult education policy in the European Union during the Lisbon decade : the shift to vocational adult learning and work skills matching

This doctoral dissertation investigates the adult education policy of the European Union (EU) in the framework of the Lisbon agenda 2000–2010, with a particular focus on the changes of policy orientation that occurred during this reference decade. The year 2006 can be considered, in fact, a turning point for the EU policy-making in the adult learning sector: a radical shift from a wide--ranging and comprehensive conception of educating adults towards a vocationally oriented understanding of this field and policy area has been observed, in particular in the second half of the so--called ‘Lisbon decade’. In this light, one of the principal objectives of the mainstream policy set by the Lisbon Strategy, that of fostering all forms of participation of adults in lifelong learning paths, appears to have muted its political background and vision in a very short period of time, reflecting an underlying polarisation and progressive transformation of European policy orientations. Hence, by means of content analysis and process tracing, it is shown that the new target of the EU adult education policy, in this framework, has shifted from citizens to workers, and the competence development model, borrowed from the corporate sector, has been established as the reference for the new policy road maps. This study draws on the theory of governance architectures and applies a post-ontological perspective to discuss whether the above trends are intrinsically due to the nature of the Lisbon Strategy, which encompasses education policies, and to what extent supranational actors and phenomena such as globalisation influence the European governance and decision--making. Moreover, it is shown that the way in which the EU is shaping the upgrading of skills and competences of adult learners is modeled around the needs of the ‘knowledge economy’, thus according a great deal of importance to the ‘new skills for new jobs’ and perhaps not enough to life skills in its broader sense which include, for example, social and civic competences: these are actually often promoted but rarely implemented in depth in the EU policy documents. In this framework, it is conveyed how different EU policy areas are intertwined and interrelated with global phenomena, and it is emphasised how far the building of the EU education systems should play a crucial role in the formation of critical thinking, civic competences and skills for a sustainable democratic citizenship, from which a truly cohesive and inclusive society fundamentally depend, and a model of environmental and cosmopolitan adult education is proposed in order to address the challenges of the new millennium. In conclusion, an appraisal of the EU’s public policy, along with some personal thoughts on how progress might be pursued and actualised, is outlined.

Integration of learning supportive applications into the development of the e-portfolio construction process

The portfolio as a means of demonstrating personal skills has lately been gaining prominence among technology students. This is partially due to the introduction of electronic portfolios, or e-portfolios. As platforms for e-portfolio management with different approaches have been introduced, the learning cycle, traditional portfolio pedagogy, and learner centricity have sometimes been forgotten, and as a result, the tools have been used for the most part as data depositories. The purpose of this thesis is to show how the construction of e-portfolios of IT students can be supported by institutions through the usage of different tools that relate to study advising, teaching, and learning. The construction process is presented as a cycle based on learning theories. Actions related to the various phases of the e-portfolio construction process are supported by the implementation of software applications. To maximize learner-centricity and minimize the intervention of the institution, the evaluated and controlled actions for these practices can be separated from the e-portfolios, leaving the construction of the e-portfolio to students. The main contributions of this thesis are the implemented applications, which can be considered to support the e-portfolio construction by assisting in planning, organizing, and reflecting activities. Eventually, this supports the students in their construction of better and more extensive e-portfolios. The implemented tools include 1) JobSkillSearcher to help students’ recognition of the demands of the ICT industry regarding skills, 2) WebTUTOR to support students’ personal study planning, 3) Learning Styles to determine students' learning styles, and 4) MyPeerReview to provide a platform on which to carry out anonymous peer review processes in courses. The most visible outcome concerning the e-portfolio is its representation, meaning that one can use it to demonstrate personal achievements at the time of seeking a job and gaining employment. Testing the tools and the selected open-source e-portfolio application indicates that the degree of richness of e-portfolio content can be increased by using the implemented applications.

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.