Machine Learning and Clinical Text. Supporting Health Information Flow

Fluent health information flow is critical for clinical decision-making. However, a considerable part of this information is free-form text and inabilities to utilize it create risks to patient safety and cost-­effective hospital administration. Methods for automated processing of clinical text are emerging. The aim in this doctoral dissertation is to study machine learning and clinical text in order to support health information flow.First, by analyzing the content of authentic patient records, the aim is to specify clinical needs in order to guide the development of machine learning applications.The contributions are a model of the ideal information flow,a model of the problems and challenges in reality, and a road map for the technology development. Second, by developing applications for practical cases,the aim is to concretize ways to support health information flow. Altogether five machine learning applications for three practical cases are described: The first two applications are binary classification and regression related to the practical case of topic labeling and relevance ranking.The third and fourth application are supervised and unsupervised multi-class classification for the practical case of topic segmentation and labeling.These four applications are tested with Finnish intensive care patient records.The fifth application is multi-label classification for the practical task of diagnosis coding. It is tested with English radiology reports.The performance of all these applications is promising. Third, the aim is to study how the quality of machine learning applications can be reliably evaluated.The associations between performance evaluation measures and methods are addressed,and a new hold-out method is introduced.This method contributes not only to processing time but also to the evaluation diversity and quality. The main conclusion is that developing machine learning applications for text requires interdisciplinary, international collaboration. Practical cases are very different, and hence the development must begin from genuine user needs and domain expertise. The technological expertise must cover linguistics,machine learning, and information systems. Finally, the methods must be evaluated both statistically and through authentic user-feedback.

Knowledge Sharing in a Virtual Learning Community

The focus of this Master’s Thesis is on knowledge sharing in a virtual Learning community. The theoretical part of this study aims at presenting the theory of knowledge sharing, competence development and learning in virtual teams. The features of successful learning organizations as well as enablers of effective knowledge sharing in virtual communities are also introduced to the reader in the theoretical framework. The empirical research for this study was realized in a global ICT company, specifically in its Human Resources business unit. The research consisted of two rounds of online questionnaires, which were conducted among all the members of the virtual Learning community. The research aim was to find shared opinions concerning the features of a successful virtual Learning community. The analysis of the data in this study was conducted using a qualitative research methodology. The empirical research showed that the main important features of a successful virtual Learning community are members’ passion towards the community way of working as well as the relevance of the content in the virtual community. In general, it was found that knowledge sharing and competence development are important matters in dynamic organizations as well as virtual communities as method and tool for sharing knowledge and hence increasing both individual and organizational knowledge. This is proved by theoretical and by empirical research in this study.

Conditions for EFL learning and professional development : Finland-Swedish learner and teacher perspectives

Engelskans dominerande roll som internationellt språk och andra globaliseringstrender påverkar också Svenskfinland. Dessa trender påverkar i sin tur förutsättningarna för lärande och undervisning i engelska som främmande språk, det vill säga undervisningsmålen, de förväntade elev- och lärarroller, materialens ändamålsenlighet, lärares och elevers initiala erfarenheter av engelska och engelskspråkiga länder. Denna studie undersöker förutsättningarna för lärande och professionell utveckling i det svenskspråkiga nybörjarklassrummet i engelska som främmande språk. Utgångsläget för 351 nybörjare i engelska som främmande språk och 19 av deras lärare beskrivs och analyseras. Resultaten tyder på att engelska håller på att bli ett andraspråk snarare än ett traditionellt främmande språk för många unga elever. Dessa elever har också goda förutsättningar att lära sig engelska utanför skolan. Sådan var dock inte situationen för alla elever, vilket tyder på att det finns en anmärkningsvärd heterogenitet och även regional variation i det finlandssvenska klassrummet i engelska som främmande språk. Lärarresultaten tyder på att vissa lärare har klarat av att på ett konstruktivt sätt att tackla de förutsättningar de möter. Andra lärare uttrycker frustration över sin arbetssituation, läroplanen, undervisningsmaterialen och andra aktörer som kommer är av betydelse för skolmiljön. Studien påvisar att förutsättningarna för lärande och undervisning i engelska som främmande språk varierar i Svenskfinland. För att stöda elevers och lärares utveckling föreslås att dialogen mellan aktörer på olika nivå i samhället bör förbättras och systematiseras.

Learning through role-playing games: an approach for active learning and teaching

This study evaluates the use of role-playing games (RPGs) as a methodological approach for teaching cellular biology, assessing student satisfaction, learning outcomes, and retention of acquired knowledge. First-year undergraduate medical students at two Brazilian public universities attended either an RPG-based class (RPG group) or a lecture (lecture-based group) on topics related to cellular biology. Pre- and post-RPG-based class questionnaires were compared to scores in regular exams and in an unannounced test one year later to assess students' attitudes and learning. From the 230 students that attended the RPG classes, 78.4% responded that the RPG-based classes were an effective tool for learning; 55.4% thought that such classes were better than lectures but did not replace them; and 81% responded that they would use this method. The lecture-based group achieved a higher grade in 1 of 14 regular exam questions. In the medium-term evaluation (one year later), the RPG group scored higher in 2 of 12 questions. RPG classes are thus quantitatively as effective as formal lectures, are well accepted by students, and may serve as educational tools, giving students the chance to learn actively and potentially retain the acquired knowledge more efficiently.

The development and evaluation of a distance learning system in ophthalmology

INTRODUCTION: Web-based e-learning is a teaching tool increasingly used in many medical schools and specialist fields, including ophthalmology. AIMS: this pilot study aimed to develop internet-based course-based clinical cases and to evaluate the effectiveness of this method within a graduate medical education group. METHODS: this was an interventional randomized study. First, a website was built using a distance learning platform. Sixteen first-year ophthalmology residents were then divided into two randomized groups: one experimental group, which was submitted to the intervention (use of the e-learning site) and another control group, which was not submitted to the intervention. The students answered a printed clinical case and their scores were compared. RESULTS: there was no statistically significant difference between the groups. CONCLUSION: We were able to successfully develop the e-learning site and the respective clinical cases. Despite the fact that there was no statistically significant difference between the access and the non access group, the study was a pioneer in our department, since a clinical case online program had never previously been developed.

Organizational learning from customer interaction

In the fierce competition of today‟s business world an organization‟s capacity to learn maybe its only competitive advantage. This research aims at increasing the understanding on how organizational learning from the customer happens in technology companies. In doing so it provides a synthesized definition of organizational learning and investigates processes of organizational learning within technology companies. A qualitative research method and in-depth interviews with different sized high technology companies, as applied here, enables in-depth study of the learning processes. Research contributes to the understanding of what type of knowledge firms acquire, how new knowledge is transferred and used in a learning firm‟s routines and processes. Research findings show that SMEs and large size companies also, depending on their position in the software value chain, consider different knowledge types as most important and that they use different learning methods to acquire knowledge from their customers.

Learning Robot Environment through Simulation

Traditionally simulators have been used extensively in robotics to develop robotic systems without the need to build expensive hardware. However, simulators can be also be used as a “memory”for a robot. This allows the robot to try out actions in simulation before executing them for real. The key obstacle to this approach is an uncertainty of knowledge about the environment. The goal of the Master’s Thesis work was to develop a method, which allows updating the simulation model based on actual measurements to achieve a success of the planned task. OpenRAVE was chosen as an experimental simulation environment on planning,trial and update stages. Steepest Descent algorithm in conjunction with Golden Section search procedure form the principle part of optimization process. During experiments, the properties of the proposed method, such as sensitivity to different parameters, including gradient and error function, were examined. The limitations of the approach were established, based on analyzing the regions of convergence.

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.

Mobile learning and video experience in delivering digital content

In recent years, the worldwide distribution of smartphone devices has been growing rapidly. Mobile technologies are evolving fast, a situation which provides new possibilities for mobile learning applications. Along with new delivery methods, this development enables new concepts for learning. This study focuses on the effectiveness and experience of a mobile learning video promoting the key features of a specific device. Through relevant learning theories, mobile technologies and empirical findings, the thesis presents the key elements for a mobile learning video that are essential for effective learning. This study also explores how previous experience with mobile services and knowledge of a mobile handset relate to final learning results. Moreover, this study discusses the optimal delivery mechanisms for a mobile video. The target group for the study consists of twenty employees of a Sanoma Company. The main findings show that the individual experience of learning and the actual learning results may differ and that the design for certain video elements, such as sound and the presentation of technical features, can have an impact on the experience and effectiveness of a mobile learning video. Moreover, a video delivery method based on cloud technologies and HTML5 is suggested to be used in parallel with standalone applications.

Learning Grasp Affordances from Vision

Monimutkaisissa ja muuttuvissa ympäristöissä työskentelevät robotit tarvitsevat kykyä manipuloida ja tarttua esineisiin. Tämä työ tutkii robottitarttumisen ja robottitartuntapis-teiden koneoppimisen aiempaa tutkimusta ja nykytilaa. Nykyaikaiset menetelmät käydään läpi, ja Le:n koneoppimiseen pohjautuva luokitin toteutetaan, koska se tarjoaa parhaan onnistumisprosentin tutkituista menetelmistä ja on muokattavissa sopivaksi käytettävissä olevalle robotille. Toteutettu menetelmä käyttää intensititeettikuvaan ja syvyyskuvaan po-hjautuvia ominaisuuksi luokitellakseen potentiaaliset tartuntapisteet. Tämän toteutuksen tulokset esitellään.

Learning to Understand the Retailers - The New Approach of a Paperboard Manufacturer

The aim of the study is to expand networking between a packaging material manufacturer and retailers in order to develop products which appeal to brand owners and their customers. The in-built targets are to understand the retailer’s role in the value chain, clarify who makes packaging decision of private label products, and canvass the importance of sustainability. The present value chain of the packaging material manufacturer is reviewed first. It is assumed that sustainability could be a common interest, and The Consumer Goods Forum’s “A Global Language for Packaging and Sustainability” report is shortly discussed. The presentation of the most common packaging materials is based on a guide called “Packaging in the Sustainability Agenda: A Guide for Corporate Decision Makers”. The terms manufacturer’s brand and private label are defined. A retail value chain with emphasis on the role of customers as partners is introduced. The study area is the Nordic countries, and the information about Nordic retailers was provided first by desk research. The interviews were made in Finland, Sweden, Norway and Denmark. The study method is qualitative: the intention was to get initial insights, ideas and understandings. The results are compiled under the headings: sustainability, private labels, cooperation and packaging development. Also the reasons for good profitability of private labels are explained. Sustainability or responsibility is a key driver for innovation in the retail sector. Private labels have become brands. The ways of cooperation between a packaging material manufacturer and a retailer could be education and training. Packaging development is of great interest to retailers and they are willing to contribute.

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.

Learning information technology business in a changing industry landscape. Introducing Team Entrepreneurship in Renewing Bachelor Education in Renewing Bachelor Education in Information

Speed, uncertainty and complexity are increasing in the business world all the time. When knowledge and skills become quickly irrelevant, new challenges are set for information technology (IT) education. Meta-learning skills – learning how to learn rapidly - and innovation skills have become more essential than single technologies or other specific issues. The drastic changes in the information and communications technology (ICT) sector have caused a need to reconsider how IT Bachelor education in Universities of Applied Sciences should be organized and employed to cope with the change. The objective of the study was to evaluate how a new approach to IT Bachelor education, the ICT entrepreneurship study path (ICT-ESP) fits IT Bachelor education in a Finnish University of Applied Sciences. This kind of educational arrangement has not been employed elsewhere in the context of IT Bachelor education. The study presents the results of a four-year period during which IT Bachelor education was renewed in a Finnish University of Applied Sciences. The learning environment was organized into an ICT-ESP based on Nonaka’s knowledge theory and Kolb’s experiental learning. The IT students who studied in the ICT-ESP established a cooperative and learned ICT by running their cooperative at the University of Applied Sciences. The students (called team entrepreneurs) studied by reading theory in books and other sources of explicit information, doing projects for their customers, and reflecting in training sessions on what was learnt by doing and by studying the literature. Action research was used as the research strategy in this study. Empirical data was collected via theme-based interviews, direct observation, and participative observation. Grounded theory method was utilized in the data analysis and the theoretical sampling was used to guide the data collection. The context of the University of Applied Sciences provided a good basis for fostering team entrepreneurship. However, the results showed that the employment of the ICT-ESP did not fit into the IT Bachelor education well enough. The ICT-ESP was cognitively too tough for the team entrepreneurs because they had two different set of rules to follow in their studies. The conventional courses engaged lot of energy which should have been spent for professional development in the ICT-ESP. The amount of competencies needed in the ICT-ESP for professional development was greater than those needed for any other ways of studying. The team entrepreneurs needed to develop skills in ICT, leadership and self-leadership, team development and entrepreneurship skills. The entrepreneurship skills included skills on marketing and sales, brand development, productization, and business administration. Considering the three-year time the team entrepreneurs spent in the ICT-ESP, the challenges were remarkable. Changes to the organization of IT Bachelor education are also suggested in the study. At first, it should be admitted that the ICT-ESP produces IT Bachelors with a different set of competencies compared to the conventional way of educating IT Bachelors. Secondly, the number of courses on general topics in mathematics, physics, and languages for team entrepreneurs studying in the ICTESP should be reconsidered and the conventional course-based teaching of the topics should be reorganized to support the team coaching process of the team entrepreneurs with their practiceoriented projects. Third, the upcoming team entrepreneurs should be equipped with relevant information about the ICT-ESP and what it would require in practice to study as a team entrepreneur. Finally, the upcoming team entrepreneurs should be carefully selected before they start in the ICT-ESP to have a possibility to eliminate solo players and those who have a too romantic view of being a team entrepreneur. The results gained in the study provided answers to the original research questions and the objectives of the study were met. Even though the IT degree programme was terminated during the research process, the amount of qualitative data gathered made it possible to justify the interpretations done.

Learning from projects: a qualitative metasummary

The objective of this thesis was to form an understanding about the common gaps in learning from projects, as well as possible approaches to bridging them. In the research focus were the questions on how project teams create knowledge, which fac- tors affect the capture and re-use of this knowledge and how organizations can best capture and utilize this project-based knowledge. The method used was qualitative metasummary, a literature-based research method that has previously been mainly applied in the domains of nursing and health care research. The focus was laid on firms conducting knowledge-intensive business in some form of matrix organization. The research produced a theoretical model of knowledge creation in projects as well as a typology of factors affecting transfer of project-based knowledge. These include experience, culture and leadership, planning and controlling, relationships, project review and documentation. From these factors, suggestions could be derived as to how organizations should conduct projects in order not to lose what has been learned.

Informal learning and competence development during a management trainee program

The purpose of this research was to study how management trainee program participants experienced the program with respect to their learning and competence development. Additionally, the purpose was also to examine what the trainees learned and how the learning occurred. Furthermore, factors affecting learning in the workplace were examined. The theoretical framework of this research was formed utilizing individual competence and informal learning frameworks. Research was conducted as a single case study and data was gathered by thematic interviews. The results of this research indicate that the trainees experienced the program as a good method for learning the overall picture of the organization and its business. Regarding competence development, especially knowledge- and cognitive competence categories were developed during the program. The best learning outcomes were achieved through learning by doing, in co-operation with others, and learning from others. The results indicate that the planning of the program and its structure have a significant effect on learning. Furthermore, a sufficient level of challenge was experienced as being important for the quality of the learning as well.