Building the ‘Digital’ Library: Routes to Managing our Institutional Digital Learning, Teaching and Research Assets Together

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

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.

International Partnering strategy for e-learning provider in emerging economies: Evidence from East Africa learning institutions

International partnership has received growing interest in the literature during the past decades due to globalization, increased technological approaches and rapid changes in competitive environments. The study specifically determines the support provided by international partners on promotion of e-learning in East Africa, assess the motives of partner selection criteria, the determinants of selecting partners, partner models and partner competence of e-learning provider. The study also evaluates obstacles of e-learning partnering strategy in East Africa learning institutions. The research adopts a descriptive survey design. Target population involved East Africa learning institutions with a list of potential institutions generated from the Ministry of Higher Education database. Through a targeted reduction of the initial database, consisting of all learning institutions, both public and private, the study created a target sample base of 200 learning institutions. Structured questionnaires scheduled were used to collect primary data. Study findings showed the approach way East African communities in selecting their e-learning partners depend on international reputation of partners, partner with ability to negotiate with foreign governments, partner with international and local experiences, nationality of foreign partner and partners with local market knowledge.

Employees’ continuous learning and job satisfaction - effects on productivity

In today’s knowledge intense economy the human capital is a source for competitive advantage for organizations. Continuous learning and sharing the knowledge within the organization are important to enhance and utilize this human capital in order to maximize the productivity. The new generation with different views and expectations of work is coming to work life giving its own characteristics on learning and sharing. Work should offer satisfaction so that the new generation employees would commit to organizations. At the same time organizations have to be able to focus on productivity to survive in the competitive market. The objective of this thesis is to construct a theory based framework of productivity, continuous learning and job satisfaction and further examine this framework and its applications in a global organization operating in process industry. Suggestions for future actions are presented for this case organization. The research is a qualitative case study and the empiric material was gathered by personal interviews concluding 15 employee and one supervisor interview. Results showed that more face to face interaction is needed between employees for learning because much of the knowledge of the process is tacit and so difficult to share in other ways. Offering these sharing possibilities can also impact positively to job satisfaction because they will increase the sense of community among employees which was found to be lacking. New employees demand more feedback to improve their learning and confidence. According to the literature continuous learning and job satisfaction have a relative strong relationship on productivity. The employee’s job description in the case organization has moved towards knowledge work due to continuous automation and expansion of the production process. This emphasizes the importance of continuous learning and means that productivity can be seen also from quality perspective. The normal productivity output in the case organization is stable and by focusing on the quality of work by improving continuous learning and job satisfaction the upsets in production can be handled and prevented more effectively. Continuous learning increases also the free human capital input and utilization of it and this can breed output increasing innovations that can increase productivity in long term. Also job satisfaction can increase productivity output in the end because employees will work more efficiently, not doing only the minimum tasks required. Satisfied employees are also found participating more in learning activities.

Individual learner, peer group and teacher roles in fostering autonomous language-learning behaviour

Julkaisumaa: Bulgaria

Long-lasting mnemotropic effect of substance P and its N-terminal fragment (SP1-7) on avoidance learning

We investigated the long-lasting effect of peripheral injection of the neuropeptide substance P (SP) and of some N- or C-terminal SP fragments (SPN and SPC, respectively) on retention test performance of avoidance learning. Male Wistar rats (220 to 280 g) were trained in an inhibitory step-down avoidance task and tested 24 h or 21 days later. Immediately after the training trial rats received an intraperitoneal injection of SP (50 µg/kg), SPN 1-7 (167 µg/kg) or SPC 7-11 (134 µg/kg). Control groups were injected with vehicle or SP 5 h after the training trial. The immediate post-training administration of SP and SPN, but not SPC, facilitated avoidance behavior in rats tested 24 h or 21 days later, i.e., the retention test latencies of the SP and SPN groups were significantly longer (P<0.05, Mann-Whitney U-test) during both training-test intervals. These observations suggest that the memory-enhancing effect of SP is long-lasting and that the amino acid sequence responsible for this effect is encoded by its N-terminal part

Signaled two-way avoidance learning using electrical stimulation of the inferior colliculus as negative reinforcement: effects of visual and auditory cues as warning stimuli

The inferior colliculus is a primary relay for the processing of auditory information in the brainstem. The inferior colliculus is also part of the so-called brain aversion system as animals learn to switch off the electrical stimulation of this structure. The purpose of the present study was to determine whether associative learning occurs between aversion induced by electrical stimulation of the inferior colliculus and visual and auditory warning stimuli. Rats implanted with electrodes into the central nucleus of the inferior colliculus were placed inside an open-field and thresholds for the escape response to electrical stimulation of the inferior colliculus were determined. The rats were then placed inside a shuttle-box and submitted to a two-way avoidance paradigm. Electrical stimulation of the inferior colliculus at the escape threshold (98.12 ± 6.15 (A, peak-to-peak) was used as negative reinforcement and light or tone as the warning stimulus. Each session consisted of 50 trials and was divided into two segments of 25 trials in order to determine the learning rate of the animals during the sessions. The rats learned to avoid the inferior colliculus stimulation when light was used as the warning stimulus (13.25 ± 0.60 s and 8.63 ± 0.93 s for latencies and 12.5 ± 2.04 and 19.62 ± 1.65 for frequencies in the first and second halves of the sessions, respectively, P<0.01 in both cases). No significant changes in latencies (14.75 ± 1.63 and 12.75 ± 1.44 s) or frequencies of responses (8.75 ± 1.20 and 11.25 ± 1.13) were seen when tone was used as the warning stimulus (P>0.05 in both cases). Taken together, the present results suggest that rats learn to avoid the inferior colliculus stimulation when light is used as the warning stimulus. However, this learning process does not occur when the neutral stimulus used is an acoustic one. Electrical stimulation of the inferior colliculus may disturb the signal transmission of the stimulus to be conditioned from the inferior colliculus to higher brain structures such as amygdala

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.

The brain decade in debate: I. Neurobiology of learning and memory

This article is a transcription of an electronic symposium in which some active researchers were invited by the Brazilian Society for Neuroscience and Behavior (SBNeC) to discuss the last decade's advances in neurobiology of learning and memory. The way different parts of the brain are recruited during the storage of different kinds of memory (e.g., short-term vs long-term memory, declarative vs procedural memory) and even the property of these divisions were discussed. It was pointed out that the brain does not really store memories, but stores traces of information that are later used to create memories, not always expressing a completely veridical picture of the past experienced reality. To perform this process different parts of the brain act as important nodes of the neural network that encode, store and retrieve the information that will be used to create memories. Some of the brain regions are recognizably active during the activation of short-term working memory (e.g., prefrontal cortex), or the storage of information retrieved as long-term explicit memories (e.g., hippocampus and related cortical areas) or the modulation of the storage of memories related to emotional events (e.g., amygdala). This does not mean that there is a separate neural structure completely supporting the storage of each kind of memory but means that these memories critically depend on the functioning of these neural structures. The current view is that there is no sense in talking about hippocampus-based or amygdala-based memory since this implies that there is a one-to-one correspondence. The present question to be solved is how systems interact in memory. The pertinence of attributing a critical role to cellular processes like synaptic tagging and protein kinase A activation to explain the memory storage processes at the cellular level was also discussed.