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

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

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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.

Uraohjaus ja urasuunnittelu ammattikorkeakoulussa

Tutkimuksen tarkoituksena oli selvittää, millaista uraohjausta ammattikorkeakoulun tuutoriopettajat antavat ja millaista uraohjausta opiskelijat haluavat. Lisäksi tavoitteena oli selvittää, löytyykö opiskelijoiden koulutusalavalinnan perusteista yhteyttä uran suunnittelutaitoihin ja ohjauksen tarpeeseen, ja tunnistavatko tuutoriopettajat opiskelijoiden erilaiset uraohjauksen tarpeet. Tutkimuksen teoreettisissa rakenteissa hyödynnettiin kolmea postmodernia urateoriaa, jotka olivat Hodkinsonin ja Sparkesin (1997) uranvalinnan päätöksentekoteoria, Mitchellin, Lewinin ja Krumbolzin (1999) suunnitellun sattuman teoria ja Savickasin (2005) uran rakentamisteoria. Tutkimusympäristönä oli Satakunnan ammattikorkeakoulu. Tutkimus oli kaksivaiheinen. Ensimmäisessä vaiheessa kerättiin harkinnanvaraisesti valituilta tuutoriopettajilta (n=14) ja opintojensa eri vaiheissa olevilta opiskelijoilta (n=65) kirjoitettu aineisto. Kvalitatiivinen aineisto analysoitiin sisällönanalyysillä. Aineiston perusteella löydettiin kolmenlaisia urasuunnittelijoita: epävarmat, uteliaat ja tietoiset. Aineiston perusteella laadittiin kyselylomake tutkimuksen toisen vaiheen tiedonkeruuta varten. Tutkimuksen toisessa vaiheessa kerättiin opintojen eri vaiheissa olevilta opiskelijoilta kyselylomakekyselynä kvantitatiivinen aineisto (n=903), joka analysoitiin tilastollisin menetelmin. Koulutusalavalinnan perusteista elämäntilanne, alan mahdollisuudet, oma toive, kutsumus, aktiivinen tiedonhaku ja halu opiskella ammattikorkeakoulussa olivat yhteydessä opiskelijan hyvään urasuunnittelukykyyn. Näillä perusteilla koulutusalansa valinneita tietoisiksi luokiteltuja urasuunnittelijoita oli 72 % vastanneista. Alavalinnan perusteista sattuman, kavereiden, sukulaisten, lukion opinto-ohjauksen ja paikkakunnan perusteella koulutusalansa valinneet luokiteltiin epävarmoiksi urasuunnittelijoiksi, ja heitä oli 28 % vastanneista. Tulokset antavat ohjaajille tukea epävarman ja muita enemmän uraohjausta tarvitsevan opiskelijan tunnistamiseen ja heidän hops-prosessinsa tehostamiseen opintojen alusta asti. Lisäksi tulosten perusteella esitetään seuraavia suosituksia: tuutoriopettajille tulisi asettaa pätevyysvaatimukseksi ohjausalan opintojen suorittaminen; opiskelijoita tulisi ohjata tunnistamaan erilaisia satunnaisesti avautuvia mahdollisuuksia ja tietoisesti hyödyntämään niitä elämässään; uraohjaukseen tulisi kytkeä mukaan työelämäyhteistyö; ohjaajien tulisi tiivistää yhteistyötä toisen asteen ohjaajien kanssa, jotta opiskelijoiden koulutusalavalinnat onnistuisivat paremmin; uraohjausta tulisi antaa tulevaisuuden kvalifikaatioiden ennakoinnin ja elinikäisten oppimisvalmiuksien näkökulmasta.

How to increase brand quality perception with audiovisual content? : Exploring the role of emotions in B2C and B2B contexts

This study discusses how audiovisual content can influence brand quality perceptions. The purpose of this study is to explore how audiovisual content creation can increase brand quality perceptions. This research problem is addressed with three sub questions, which aim at clarifying the role of emotions between content marketing and brand quality perception, explaining how different functions of audiovisual content can increase brand quality perception, and by identifying and comparing the key differences in content creation in business-to-consumer and business-to-businesscontexts. The theoretical background of the study is in brand personality, consumer emotions, consumerbrand relationships, content marketing and B2B branding literature. The empirical research part includes a single-case study. The case company was a Swiss startup that wished to build a highquality brand for both B2C and B2B segments. The empirical data was collected in September 2014. Eight interviews were conducted; seven with target segment representatives and one with an existing customer of the case company. The empirical findings were analyzed with thematic analysis and finally a 5-stage framework was created based on the findings of the research, offering a guideline for high-quality content creation. This study finds that emotions play an important role in brand quality perceptions. Psychological processes, emotion, cognition and conation, influence the engagement process of the target segment which ultimately can lead to activation and electronic word-of-mouth. Brand quality perception is the result of the overall emotion of the brand. The overall emotion derives from brand personality, brand concept, product attributes and utilitarian benefits of the brand. The entertaining and educational functions of the audiovisual content can target and evoke these emotional processes, and result in increased quality perceptions. In the B2B context, emotions are found to play a relatively smaller role in the quality perception processes. However, the significance of emotions cannot be ignored, since they can emphasize the value for the buying organization, and build on the trust and loyalty among the potential customers. The final framework presents five stages of content creation that ultimately improve brand quality perceptions. These stages help marketers to design and implement their content and evoke positive emotions in their target segment as part of a quality-based marketing strategy. Further research is warranted to quantitatively test the generalizability of the framework. Further research is also suggested to make the framework adaptable to different stages of the brand life cycle.

A novel polar-based human face recognition computational model

Motivated by a recently proposed biologically inspired face recognition approach, we investigated the relation between human behavior and a computational model based on Fourier-Bessel (FB) spatial patterns. We measured human recognition performance of FB filtered face images using an 8-alternative forced-choice method. Test stimuli were generated by converting the images from the spatial to the FB domain, filtering the resulting coefficients with a band-pass filter, and finally taking the inverse FB transformation of the filtered coefficients. The performance of the computational models was tested using a simulation of the psychophysical experiment. In the FB model, face images were first filtered by simulated V1- type neurons and later analyzed globally for their content of FB components. In general, there was a higher human contrast sensitivity to radially than to angularly filtered images, but both functions peaked at the 11.3-16 frequency interval. The FB-based model presented similar behavior with regard to peak position and relative sensitivity, but had a wider frequency band width and a narrower response range. The response pattern of two alternative models, based on local FB analysis and on raw luminance, strongly diverged from the human behavior patterns. These results suggest that human performance can be constrained by the type of information conveyed by polar patterns, and consequently that humans might use FB-like spatial patterns in face processing.

Enthalpy-entropy compensation based on isotherms of mango

Moisture equilibrium data of mango pulp were determined using the static gravimetric method. Adsorption and desorption isotherms were obtained in the range of 30-70 ºC, to water activities (a w) from 0.02 to 0.97. The application of the GAB model to the experimental results, using direct nonlinear regression analysis, provided agreement between experimental and calculated values. The net isosteric heat of sorption was estimated from equilibrium sorption data, using the Clausius-Clapeyron equation. Isosteric heats of sorption were found to increase with increasing temperature and could be well adjusted by an exponential relationship. The enthalpy-entropy compensation theory was applied to sorption isotherms and plots of deltaH versus deltaS provided the isokinetic temperatures, indicating an enthalpy controlled sorption process.

Digital content and making it viral in social media

Tutkimuksen tavoite on selvittää digitaalisen sisällön ominaisuuksia, jotka vaikuttavat ryhtyvätkö kuluttajat jakamaan, tykkäämään ja kommentoimaan sitä sosiaalisessa mediassa. Tällä pyritään auttamaan yrityksiä ymmärtämään paremmin viraalisuutta, jotta he pystyisivät tuottamaan ja julkaisemaan nettisivuillaan ja sosiaalisessa mediassa parempaa sisältöä, jota kuluttajat jakaisivat enemmän. Tutkimus toteutetaan muodostamalla hypoteeseja mahdollisista ominaisuuksista kirjallisuuden perusteella ja testaamalla niitä regressioanalyyseillä empiirisessä osiossa. Tulokset paljastavat yhdeksän piirrettä, jotka lisäävät viraalisuutta: kiinnostavuus, neutraalisuus, yllättävyys, viihdyttävyys, epäkäytännöllisyys, artikkelin ja Facebook julkaisun pituus, eri sisältö taktiikoiden käyttö (erityisesti blogit ja kuvat lisäävät viraalisuutta) sekä kun mielipidevaikuttaja tai kuuluisuus jakaa sisällön.

Evaluation of phenolic compounds content and in vitro antioxidant activity of red wines produced from Vitis labrusca grapes

Wine production in the northern Curitiba, Paraná, Brazil, specifically the communes of Colombo and Almirante Tamandaré, is based mainly on the utilization of Vitis labrusca grapes var. Bordô (Ives). Total sugar content, pH, and total acidity were analyzed in red wine samples from 2007 and 2008 vintages following official methods of analysis. Moreover, total phenolic, flavonoid, and tannin contents were analyzed by colorimetric methodologies and the antioxidant activity was determined using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical methodology. Phenolic compounds were identified by high performance liquid chromatography. The total phenolic content of wine samples presented concentrations varying between 1582.35 and 2896.08 mg gallic acid.L-1 since the major part corresponds to flavonoid content. In these compounds' concentration range, a direct relationship between phenolic compounds content and levels of antioxidant activity was not observed. Among the identified phenolic compounds, chlorogenic, caffeic, and syringic acids were found to be the major components. Using three principal components, it was possible to explain 81.36% of total variance of the studied samples. Principal Components Analysis does not differentiate between vintages.

Application of carnauba-based wax maintains postharvest quality of 'Ortanique' tangor

This study aimed at evaluating compositional changes in the quality of 'Ortanique' tangor after coating with the carnauba-based waxes Aruá Tropical® or Star Light®. The storage conditions studied simulated those of local marketing (22 ± 2 °C, 60 ± 5% RH). Non-destructive analysis, mass loss, peel color, and sensory evaluation, were performed upon coating and every three days up to the fifteenth day of storage. Destructive analysis, peel moisture content, chlorophyll of the peel, pulp color, juice content, soluble solids (SS), titratable acidity (TA), pH, and soluble solids to titratable acidity ratio, were performed upon coating and every four days up to the sixteenth day of storage. The assay was conducted using an entirely randomized design, with three replications (destructive analyses) or ten replications (non-destructive analyses), in a split plot scheme. Wax-coating, especially Aruá Tropical®, maintained fruit freshness by reducing mass loss and peel dehydration and retaining green color. Peel moisture content, chlorophyll content, and juice content had lower rates in the wax coated fruits. Puncture force, soluble solids, titratable acidity, pH, and soluble solids to titratable acidity ratio varied vary little over the course of storage. Sensory evaluation showed that the application of Aruá Tropical keeps 'Ortanique' tangor fresher for 6 days longer for commercialization.

Rosemary extract and celery-based products used as natural quality enhancers for colonial type salami with different ripening times

This study aimed to evaluate the use of rosemary (Rosmarinus officinalis) extract (RE), celery (Apium graveolis), and low levels of NO3 and NO2 as natural agents to enhance the quality of colonial salami. Salami was produced according to three treatments: (A) Control: 0.1% curing salt; (B) Rosemary: 0.05% curing salt + 0.5% RE (rosemary extract); and (C) Rosemary+celery: 0.14% Veg 503 + 0.27% Veg 504 (sea salt plus celery) + 0.5% of RE (rosemary extract). There was no effect (P > 0.05) of the treatments on water activity, Na content, and residual NO3 and NO2. Fatty acids C18:2 and C20:4 were reduced (P < 0.05) during the ripening period in the Control treatment indicating possible oxidation. The use of celery resulted in lower pH values (P < 0.05) in the salami. Reduced addition of NO3 and NO2 resulted in salami lighter in color (higher L* values, P < 0.05) at the 12th day of ripening. In conclusion, celery-based products proved to be an effective source of NO2 and NO3 for color development, but the low pH of the product indicates the need for better evaluation of its use in fermented salami. The RE (rosemary extract) reduced fat oxidation in salami, but this needs further evaluation.

Comparative analysis of vitamin A and iron content in food according to different food composition tables and nutritional evaluation software programs

The objective of this study was to analyze retinol equivalent and iron content in different food composition tables and nutritional evaluation software programs. A literature search was conduct to identify tables and software available in Brazil containing information about retinol equivalent and iron content that are currently used by nutritionists. Ten tables and five software programs were selected for this study. The methodology used to present the retinol equivalent and iron content was evaluated and no pattern to obtain such content was found in the tables and software programs analyzed. Only one of the tables had enough information for the calculation of retinol equivalents; this table is recommended to all Latin America As for the iron content, three of the tables analyzed stand out and therefore should be used; two of them are based on national foods and the other is recommended for use in all Latin America countries. None of the software programs evaluated use the conversion factors suggested by IVACG to assess the vitamin A content in foods. Special attention should be given to the content of iron provided in the software programs since they use tables as international sources and fortified foods.

Content marketing performance measurement system in the context of customer acquisition

This thesis examines how content marketing is used in B2B customer acquisition and how content marketing performance measurement system is built and utilized in this context. Literature related to performance measurement, branding and buyer behavior is examined in the theoretical part in order to identify the elements influence on content marketing performance measurement design and usage. Qualitative case study is chosen in order to gain deep understanding of the phenomenon studied. The case company is a Finnish software vendor, which operates in B2B markets and has practiced content marketing for approximately two years. The in-depth interviews were conducted with three employees from marketing department. According to findings content marketing performance measurement system’s infrastructure is based on target market’s decision making processes, company’s own customer acquisition process, marketing automation tool and analytics solutions. The main roles of content marketing performance measurement system are measuring performance, strategy management and learning and improvement. Content marketing objectives in the context of customer acquisition are enhancing brand awareness, influencing brand attitude and lead generation. Both non-financial and financial outcomes are assessed by single phase specific metrics, phase specific overall KPIs and ratings related to lead’s involvement.

Digital Content Marketing in the Business-to-Business Context. A Case Study on Marketing Communications Agencies.

Marketing has changed because of digitalization. Marketing is moving towards digital channels and more companies are transitioning from “pushing” advertising messages to “pull” marketing, that attracts audience with the content that interests and benefits the audience. This kind of marketing is called content marketing or “inbound” marketing. This study focuses on how marketing communications agencies utilize digital content marketing and what are the best practices with the selected digital content marketing channels. In this study, those channels include blogs, Facebook, Twitter, and LinkedIn. The qualitative research method was utilized in order to examine the phenomenon of digital content marketing in-depth. The chosen data collecting method was semi-structured interviewing. A total of seven marketing communications agencies, who currently utilize digital content marketing, were selected as case companies and interviewed. All the case companies are from the marketing communications industry because that industry can be assumed to be well adapted to digital content marketing techniques. There is a research gap about digital content marketing in the B2B context, which increases the novelty value of this research. The study examines what is digital content marketing, why B2B companies use digital content marketing, and how should digital content marketing be conducted through blogs and social media. The informants perceived digital marketing to be a fundamental part of their all marketing. They conduct digital content marketing for the following reasons: to increase sales, to improve their brand image and to demonstrate their own skills. Concrete results of digital content marketing for the case companies include sales leads, new clients, better brand image, and that recruiting is easier. The most important success factors with blogs and social media are the following: 1) Audience-centric thinking. All content planning should start from figuring out which themes interests the target audience. Social media channel choices should be based on where the target audience can be reached. 2) Companies should not talk only about themselves. Instead, content is made about themes that interests the target audience. On social media channels, only a fragment of all shared content is about the company. Rather, most of the shared content is industry-specific content that helps the potential client.