Implementing Widely-used Vocabularies to Produce Linked Open Data in the Context of Open Repositories

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.

Becoming Locals in a Borderland of Exiles. Sense of Place in the Stories of Lithuania Minor Dwellers

This thesis deals with sense of place, the relation that we construct with our dwelling and the surrounding environment. The topic belongs to the field of human geography. Sense of place is deeply intertwined with the ideas of feeling at home and having a place where to return. I argue that narratives of life experience help us relate to the places we inhabit, go through, leave. My analysis concerns Lithuania Minor, the Lithuanian region lying by the border with Kaliningrad, and focuses in particular on Vilkyškiai, a village in the municipality of Pagėgiai. Most of the area’s original population disappeared in the war. After 1945, people from all over the country and the USSR settled here. This raised the prickly question of who belongs to the borderland. Refugees, migrants and settlers allow us to observe closely the development of sense of place and its main constituents. Through this analysis, I challenge the idea of people’s natural rights to places and shows how time, engagement in local-based cultural activities and recollection help foreigners become locals. To grasp the locals’ sense of place, I collected open, light-structured interviews and applied some elements of semantic analysis to interpret the materials. From my research, it emerges that the cultivation of the region’s cultural heritage and the practice of storytelling were crucial in making the respondents feel at home. Leaving aside all legalistic claims concerning the issue, I suggest that people belong to the land they dwell. I believe that their sense of place deserves consideration from the State and the other actors seeing them as migrants.

Connections that work – Linked Open Data demystified

Esitys Kirjastoverkkopäivillä 22.10.2014 Helsingissä – Presentation of Jakob Voß at the Library Network Days, October 22, 2014 in Helsinki.

A systematic mapping study of web services discovery mechanisms

Context: Web services have been gaining popularity due to the success of service oriented architecture and cloud computing. Web services offer tremendous opportunity for service developers to publish their services and applications over the boundaries of the organization or company. However, to fully exploit these opportunities it is necessary to find efficient discovery mechanism thus, Web services discovering mechanism has attracted a considerable attention in Semantic Web research, however, there have been no literature surveys that systematically map the present research result thus overall impact of these research efforts and level of maturity of their results are still unclear. This thesis aims at providing an overview of the current state of research into Web services discovering mechanism using systematic mapping. The work is based on the papers published 2004 to 2013, and attempts to elaborate various aspects of the analyzed literature including classifying them in terms of the architecture, frameworks and methods used for web services discovery mechanism. Objective: The objective if this work is to summarize the current knowledge that is available as regards to Web service discovery mechanisms as well as to systematically identify and analyze the current published research works in order to identify different approaches presented. Method: A systematic mapping study has been employed to assess the various Web Services discovery approaches presented in the literature. Systematic mapping studies are useful for categorizing and summarizing the level of maturity research area. Results: The result indicates that there are numerous approaches that are consistently being researched and published in this field. In terms of where these researches are published, conferences are major contributing publishing arena as 48% of the selected papers were conference published papers illustrating the level of maturity of the research topic. Additionally selected 52 papers are categorized into two broad segments namely functional and non-functional based approaches taking into consideration architectural aspects and information retrieval approaches, semantic matching, syntactic matching, behavior based matching as well as QOS and other constraints.

Rigorous development of safety-critical systems

Nowadays, computer-based systems tend to become more complex and control increasingly critical functions affecting different areas of human activities. Failures of such systems might result in loss of human lives as well as significant damage to the environment. Therefore, their safety needs to be ensured. However, the development of safety-critical systems is not a trivial exercise. Hence, to preclude design faults and guarantee the desired behaviour, different industrial standards prescribe the use of rigorous techniques for development and verification of such systems. The more critical the system is, the more rigorous approach should be undertaken. To ensure safety of a critical computer-based system, satisfaction of the safety requirements imposed on this system should be demonstrated. This task involves a number of activities. In particular, a set of the safety requirements is usually derived by conducting various safety analysis techniques. Strong assurance that the system satisfies the safety requirements can be provided by formal methods, i.e., mathematically-based techniques. At the same time, the evidence that the system under consideration meets the imposed safety requirements might be demonstrated by constructing safety cases. However, the overall safety assurance process of critical computerbased systems remains insufficiently defined due to the following reasons. Firstly, there are semantic differences between safety requirements and formal models. Informally represented safety requirements should be translated into the underlying formal language to enable further veri cation. Secondly, the development of formal models of complex systems can be labour-intensive and time consuming. Thirdly, there are only a few well-defined methods for integration of formal verification results into safety cases. This thesis proposes an integrated approach to the rigorous development and verification of safety-critical systems that (1) facilitates elicitation of safety requirements and their incorporation into formal models, (2) simplifies formal modelling and verification by proposing specification and refinement patterns, and (3) assists in the construction of safety cases from the artefacts generated by formal reasoning. Our chosen formal framework is Event-B. It allows us to tackle the complexity of safety-critical systems as well as to structure safety requirements by applying abstraction and stepwise refinement. The Rodin platform, a tool supporting Event-B, assists in automatic model transformations and proof-based verification of the desired system properties. The proposed approach has been validated by several case studies from different application domains.

Category fluency test: effects of age, gender and education on total scores, clustering and switching in Brazilian Portuguese-speaking subjects

Verbal fluency tests are used as a measure of executive functions and language, and can also be used to evaluate semantic memory. We analyzed the influence of education, gender and age on scores in a verbal fluency test using the animal category, and on number of categories, clustering and switching. We examined 257 healthy participants (152 females and 105 males) with a mean age of 49.42 years (SD = 15.75) and having a mean educational level of 5.58 (SD = 4.25) years. We asked them to name as many animals as they could. Analysis of variance was performed to determine the effect of demographic variables. No significant effect of gender was observed for any of the measures. However, age seemed to influence the number of category changes, as expected for a sensitive frontal measure, after being controlled for the effect of education. Educational level had a statistically significant effect on all measures, except for clustering. Subject performance (mean number of animals named) according to schooling was: illiterates, 12.1; 1 to 4 years, 12.3; 5 to 8 years, 14.0; 9 to 11 years, 16.7, and more than 11 years, 17.8. We observed a decrease in performance in these five educational groups over time (more items recalled during the first 15 s, followed by a progressive reduction until the fourth interval). We conclude that education had the greatest effect on the category fluency test in this Brazilian sample. Therefore, we must take care in evaluating performance in lower educational subjects.

Novel word learning ability in chronic post-stroke aphasia : variability and modality effects

Novel word learning has been rarely studied in people with aphasia (PWA), although it can provide a relatively pure measure of their learning potential, and thereby contribute to the development of effective aphasia treatment methods. The main aim of the present thesis was to explore the capacity of PWA for associative learning of word–referent pairings and cognitive-linguistic factors related to it. More specifically, the thesis examined learning and long-term maintenance of the learned pairings, the role of lexical-semantic abilities in learning as well as acquisition of phonological versus semantic information in associative novel word learning. Furthermore, the effect of modality on associative novel word learning and the neural underpinnings of successful learning were explored. The learning experiments utilized the Ancient Farming Equipment (AFE) paradigm that employs drawings of unfamiliar referents and their unfamiliar names. Case studies of Finnishand English-speaking people with chronic aphasia (n = 6) were conducted in the investigation. The learning results of PWA were compared to those of healthy control participants, and active production of the novel words and their semantic definitions was used as learning outcome measures. PWA learned novel word–novel referent pairings, but the variation between individuals was very wide, from more modest outcomes (Studies I–II) up to levels on a par with healthy individuals (Studies III–IV). In incidental learning of semantic definitions, none of the PWA reached the performance level of the healthy control participants. Some PWA maintained part of the learning outcomes up to months post-training, and one individual showed full maintenance of the novel words at six months post-training (Study IV). Intact lexical-semantic processing skills promoted learning in PWA (Studies I–II) but poor phonological short-term memory capacities did not rule out novel word learning. In two PWA with successful learning and long-term maintenance of novel word–novel referent pairings, learning relied on orthographic input while auditory input led to significantly inferior learning outcomes (Studies III–IV). In one of these individuals, this previously undetected modalityspecific learning ability was successfully translated into training with familiar but inaccessible everyday words (Study IV). Functional magnetic resonance imaging revealed that this individual had a disconnected dorsal speech processing pathway in the left hemisphere, but a right-hemispheric neural network mediated successful novel word learning via reading. Finally, the results of Study III suggested that the cognitive-linguistic profile may not always predict the optimal learning channel for an individual with aphasia. Small-scale learning probes seem therefore useful in revealing functional learning channels in post-stroke aphasia.

Neuropsychological dysfunction related to earlier occupational exposure to mercury vapor

We assessed the neuropsychological test performances of 26 patients (mean age = 41.5 ± 6.1 years; mean years of education = 9.8 ± 1.8; 20 males) diagnosed with chronic occupational mercurialism who were former workers at a fluorescent lamp factory. They had been exposed to elemental mercury for an average of 10.2 ± 3.8 years and had been away from this work for 6 ± 4.7 years. Mean urinary mercury concentrations 1 year after cessation of work were 1.8 ± 0.9 µg/g creatinine. Twenty control subjects matched for age, gender, and education (18 males) were used for comparison. Neuropsychological assessment included attention, inhibitory control, verbal and visual memory, verbal fluency, manual dexterity, visual-spatial function, executive function, and semantic knowledge tests. The Beck Depression Inventory and the State and Trait Inventory were used to assess depression and anxiety symptoms, respectively. The raw score for the group exposed to mercury indicated slower information processing speed, inferior performance in psychomotor speed, verbal spontaneous recall memory, and manual dexterity of the dominant hand and non-dominant hand (P < 0.05). In addition, the patients showed increased depression and anxiety symptoms (P < 0.001). A statistically significant correlation (Pearson) was demonstrable between mean urinary mercury and anxiety trait (r = 0.75, P = 0.03). The neuropsychological performances of the former workers suggest that occupational exposure to elemental mercury has long-term effects on information processing and psychomotor function, with increased depression and anxiety also possibly reflecting the psychosocial context.

Lauseen aspektin ilmaiseminen suomen kielessä. Tutkimus olla-, tehdä- ja tulla-verbillisistä tekstilauseista käyttökonteksteissaan

Tutkimuksessa tarkastellaan lauseen aspektin ilmaisemista suomen kielessä. Aspektia käsitellään merkityskategoriana, joka osoittaa lauseen kuvaaman asiaintilan ajallisen keston, ja perustavanlaatuisena aspektuaalisena erontekona pidetään rajattuuden ja rajaamattomuuden vastakohtaisuutta. Tutkimuksessa selvitetään, millä perusteella lauseet saavat joko rajatun tai rajaamattoman aspektitulkinnan ja miten konteksti vaikuttaa tähän tulkintaan. Lauseen kontekstina käsitellään kielellistä kontekstia eli tekstiä. Työ on aineistopohjainen tutkimus kirjoitetusta nykysuomesta, ja tarkastelun kohteena on sanomalehtiteksteistä koottu lauseaineisto. Lauseiden pääverbit ovat olla, tehdä ja tulla. Aineistosta on mahdollista esittää sekä kvalitatiivisia että kvantitatiivisia huomioita. Tutkimuksen teoreettisen ja metodologisen taustan muodostavat eräiden kognitiivisen kielitieteen suuntausten kuvauskäsitteet ja -metodit sekä fennistinen aspektin kuvaamisen perinne. Tutkimuksessa tarkastellaan kahta fennistiikassa esitettyä tapaa määritellä lauseen aspektimerkitys ja osoitetaan, että ne ovat toisiaan täydentäviä. Molemmat lähestymistavat huomioon ottamalla on siis mahdollista kuvata lauseen aspektimerkityksen määräytyminen täsmällisemmin kuin vain yhteen kuvaustapaan keskittymällä. Lisäksi osoitetaan, että keskeisinä aspektin ilmaisemisen keinoina pidetyt keston ja toistuvuuden adverbiaalit jäävät aineistossa marginaalisiksi. Ajankohdan adverbiaaleja puolestaan käsitellään aiemmasta tutkimuksesta poiketen rajattuina tarkastelunäkökulmina kuvattuun asiaintilaan, ja ne toimivat tässä tehtävässä liittyessään aspektiltaan rajaamattomiin lauseisiin. Lisäksi tutkimus osoittaa, että aspektin ilmaisemisen kerroksellisuutta voidaan aspektin ilmaisemiseen osallistuvien lauseenjäsenten kerrostumisen ohella tarkastella lausekokonaisuuden eri semanttisten tasojen kerrostumisena. Lausetta laajemman kontekstin vaikutusta aspektitulkintaan ei ole aiemmin tutkittu suomen kielessä. Tutkimus osoittaa, että aspektiltaan monitulkintaisten lauseiden konteksti voi selventää tulkinnan tai mahdollistaa samanaikaisesti vaihtoehtoiset tulkinnat. Lisäksi erilaisten lauseenulkoisten rajan ilmausten avulla on mahdollista osoittaa lauseen aspektin rajattuutta siinä tapauksessa, että lause muutoin ymmärrettäisiin aspektiltaan rajaamattomaksi.

Hälsa i vårdande gemenskap : gemenskapens betydelse för äldre

The aim of the study and research questions: The aim of this study is to illuminate how caring communion can aid in promoting health as becoming in elderly people in the context of natural caring. The target group of the study consists of elderly citizens living at home. The focus of this thesis is on the concept of communion and how caring communion can affect the inner health resources in a patient’s inner health domain, as well as how caring communion can support health as becoming and inner health resources in the elderly. The main research questions of this study are the following: 1) what does communion mean? 2) what does caring communion mean? 3) what is the connection between caring communion and health? Theoretical perspective: The theoretical perspective of this qualitative study relies on the caritative caring theory as developed by scholars of caring sciences at the Åbo Academi University’s Vasa unit. The caritas motive is based on an ethos built on a consideration of togetherness, i.e. caring communion, a place where one feels at home and where one can be the person one was meant to be. Methodology: A hermeneutic research approach based on Gadamer (1997) permeates the study. This entails that understanding and interpretation become central. The study conducted in the thesis is divided into three sub-studies. Sub-study one and two are based on ontological determination whereas the third sub-study is carried out by contextual determination. The first sub-study is conducted by etymological and semantic analysis of the concept of communion (gemenskap) based on Koort (1975) and the second sub-study by determining the basic epistemological category of the concept based on Eriksson (2010b). Sub-study three is conducted through content analysis of 18 multidisciplinary and 13 caring science articles and dissertations based on Kvale (2009). The aim in the third sub-study is to define caring communions in various contexts of meaning based on Eriksson´s model of conceptual determination (2010b). All studies are interpreted through hermeneutic interpretation where the continuous movement from a part of a whole, to the whole, to part again, leads to new understanding. Finally, the findings from all the three sub-studies are compared to the concepts of pre-understanding and the inner-health-domain model of Wärnås (2002). Results: The results of the study offer a description of the dimensions of caring communion and a model that illuminates how caring communion can further health as becoming. The fundamentals of caring communion rest on the idea of a human being’s absolute right to dignity as a base for communion. The concept of communion contains a moral, an ethical, and a spiritual component. In communion, there exists a moral and ethical responsibility and a willingness to commit oneself. The individual is part of a connection or relation and knows the aim and course for the communion. A caring connection, a caring culture, a caring atmosphere and caring listening are characteristics of caring communion. In caring communion, the elderly feel trusting and see themselves as unique, powerful, and valuable. The model demonstrates that when the elderly are able to rest in caring communion, the virtues of courage and faith become strong and desire for life awaken within the elderly and health as becoming becomes possible. Conclusions: The outcome of the study is that all communion is not necessarily caring communion. In order for communion to be caring and for the elderly to achieve health as becoming, there are certain criteria that must be met. This is especially important when designing activities for the elderly in the context of natural caring.

A systematic mapping study on open data

This thesis presented the overview of Open Data research area, quantity of evidence and establishes the research evidence based on the Systematic Mapping Study (SMS). There are 621 such publications were identified published between years 2005 and 2014, but only 243 were selected in the review process. This thesis highlights the implications of Open Data principals’ proliferation in the emerging era of the accessibility, reusability and sustainability of data transparency. The findings of mapping study are described in quantitative and qualitative measurement based on the organization affiliation, countries, year of publications, research method, star rating and units of analysis identified. Furthermore, units of analysis were categorized by development lifecycle, linked open data, type of data, technical platforms, organizations, ontology and semantic, adoption and awareness, intermediaries, security and privacy and supply of data which are important component to provide a quality open data applications and services. The results of the mapping study help the organizations (such as academia, government and industries), re-searchers and software developers to understand the existing trend of open data, latest research development and the demand of future research. In addition, the proposed conceptual framework of Open Data research can be adopted and expanded to strengthen and improved current open data applications.

What happens in the first 200 ms of word reading : ERP studies on visual word recognition with top-down and bottom-up approaches /

In this thesis, three main questions were addressed using event-related potentials (ERPs): (1) the timing of lexical semantic access, (2) the influence of "top-down" processes on visual word processing, and (3) the influence of "bottom-up" factors on visual word processing. The timing of lexical semantic access was investigated in two studies using different designs. In Study 1,14 participants completed two tasks: a standard lexical decision (LD) task which required a word/nonword decision to each target stimulus, and a semantically primed version (LS) of it using the same category of words (e.g., animal) within each block following which participants made a category judgment. In Study 2, another 12 participants performed a standard semantic priming task, where target stimulus words (e.g., nurse) could be either semantically related or unrelated to their primes (e.g., doctor, tree) but the order of presentation was randomized. We found evidence in both ERP studies that lexical semantic access might occur early within the first 200 ms (at about 170 ms for Study 1 and at about 160 ms for Study 2). Our results were consistent with more recent ERP and eye-tracking studies and are in contrast with the traditional research focus on the N400 component. "Top-down" processes, such as a person's expectation and strategic decisions, were possible in Study 1 because of the blocked design, but they were not for Study 2 with a randomized design. Comparing results from two studies, we found that visual word processing could be affected by a person's expectation and the effect occurred early at a sensory/perceptual stage: a semantic task effect in the PI component at about 100 ms in the ERP was found in Study 1 , but not in Study 2. Furthermore, we found that such "top-down" influence on visual word processing might be mediated through separate mechanisms depending on whether the stimulus was a word or a nonword. "Bottom-up" factors involve inherent characteristics of particular words, such as bigram frequency (the total frequency of two-letter combinations of a word), word frequency (the frequency of the written form of a word), and neighborhood density (the number of words that can be generated by changing one letter of an original word or nonword). A bigram frequency effect was found when comparing the results from Studies 1 and 2, but it was examined more closely in Study 3. Fourteen participants performed a similar standard lexical decision task but the words and nonwords were selected systematically to provide a greater range in the aforementioned factors. As a result, a total of 18 word conditions were created with 18 nonword conditions matched on neighborhood density and neighborhood frequency. Using multiple regression analyses, we foimd that the PI amplitude was significantly related to bigram frequency for both words and nonwords, consistent with results from Studies 1 and 2. In addition, word frequency and neighborhood frequency were also able to influence the PI amplitude separately for words and for nonwords and there appeared to be a spatial dissociation between the two effects: for words, the word frequency effect in PI was found at the left electrode site; for nonwords, the neighborhood frequency effect in PI was fovind at the right elecfrode site. The implications of otir findings are discussed.

The generation effect and word learning: a test of the effect of the language experience approach versus the text approach in the acquisition of new reading vocabulary

A class of twenty-two grade one children was tested to determine their reading levels using the Stanford Diagnostic Reading Achievement Test. Based on these results and teacher input the students were paired according to reading ability. The students ages ranged from six years four months to seven years four months at the commencement of the study. Eleven children were assigned to the language experience group and their partners became the text group. Each member of the language experience group generated a list of eight to be learned words. The treatment consisted of exposing the student to a given word three times per session for ten sessions, over a period of five days. The dependent variables consisted of word identification speed, word identification accuracy, and word recognition accuracy. Each member of the text group followed the same procedure using his/her partner's list of words. Upon completion of this training, the entire process was repeated with members of the text group from the first part becoming members of the language experience group and vice versa. The results suggest that generally speaking language experience words are identified faster than text words but that there is no difference in the rate at which these words are learned. Language experience words may be identified faster because the auditory-semantic information is more readily available in them than in text words. The rate of learning in both types of words, however, may be dictated by the orthography of the to be learned word.

Visual word learning in good and poor readers

Forty students from regular, grade five classes were divided into two groups of twenty, a good reader group and a' poor reader group, on the basis. of their reading scores on Canadian Achievement Tests. .The subjects took. part in four experimental conditions iM which they .learned lists of pronounceable and unprono~nceable pseudowords, some with semantic referents, and responded to questions designed tci test visual perceptu~l learning and lexical ·and semantic association learning. It' was hypothesized "that the good reade~ group would be able to make use of graphemic and phonemic redundancy patterns in order to improv~·visuSl perceptual learning and lexical and semantic association lea~ningto a greater extent. than would .the poor reader gr6up. The data supported this hypothesis, and also indicated that, although the poor readers were less adept at using familiar sound and letter patterns, they were more dependent on· such pa~terns as an aid to visual recognition memory and semantic recall than were the good readers. It wa.s postulated that poor readers are in a double- ~ . bind situatio~ of having to choose between using weak graphemic-semantic associations or gr~pheme-phoneme associations which are also weak and which have hindered them in developing automaticity in. reading.