Generative Part-Based Gabor Object Detector

Object detection is a fundamental task of computer vision that is utilized as a core part in a number of industrial and scientific applications, for example, in robotics, where objects need to be correctly detected and localized prior to being grasped and manipulated. Existing object detectors vary in (i) the amount of supervision they need for training, (ii) the type of a learning method adopted (generative or discriminative) and (iii) the amount of spatial information used in the object model (model-free, using no spatial information in the object model, or model-based, with the explicit spatial model of an object). Although some existing methods report good performance in the detection of certain objects, the results tend to be application specific and no universal method has been found that clearly outperforms all others in all areas. This work proposes a novel generative part-based object detector. The generative learning procedure of the developed method allows learning from positive examples only. The detector is based on finding semantically meaningful parts of the object (i.e. a part detector) that can provide additional information to object location, for example, pose. The object class model, i.e. the appearance of the object parts and their spatial variance, constellation, is explicitly modelled in a fully probabilistic manner. The appearance is based on bio-inspired complex-valued Gabor features that are transformed to part probabilities by an unsupervised Gaussian Mixture Model (GMM). The proposed novel randomized GMM enables learning from only a few training examples. The probabilistic spatial model of the part configurations is constructed with a mixture of 2D Gaussians. The appearance of the parts of the object is learned in an object canonical space that removes geometric variations from the part appearance model. Robustness to pose variations is achieved by object pose quantization, which is more efficient than previously used scale and orientation shifts in the Gabor feature space. Performance of the resulting generative object detector is characterized by high recall with low precision, i.e. the generative detector produces large number of false positive detections. Thus a discriminative classifier is used to prune false positive candidate detections produced by the generative detector improving its precision while keeping high recall. Using only a small number of positive examples, the developed object detector performs comparably to state-of-the-art discriminative methods.

Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Bio- ja lääkintäoikeuden kehitysnäkymiä

Vuoden 2004 väittelijän palkinnon saajan puhe VII Oikeuskulttuurin päivässä 11.11.2005

Kuiva-, bio-, hyöty- ja ongelmajätteiden keskitetysti kilpailutettu kuljetusjärjestelmä Etelä-Karjalassa

Tutkimuksen tarkoituksena oli tuottaa tietoa kuiva-, bio-, hyöty- ja ongelmajätteiden keskitetysti kilpailutetun kuljetusjärjestelmän eduista ja haitoista Etelä-Karjalan Jätehuolto Oy:n alueella. Tutkimuksessa esitellään jätteenkuljetusjärjestelmien ominaisuudet ja niiden suunnittelu sekä jätehuoltoa ja jätteenkuljetuksia koskeva lainsäädäntö. Keskitetysti kilpailutettu jätteenkuljetusjärjestelmä mitoitettiin järjestelmän nykytilan kuvauksen sekä muualla Suomessa kilpailutuksesta saatujen kokemusten avulla. Järjestelmää arvioitiin vertaamalla kaluston tarvetta, kuormapainoja sekä kuljetuskustannuksia nykyiseen tilanteeseen. Lopuksi arvioitiin jatkokehitystarpeita ja tarvittavia toimenpiteitä, kun keskitettyyn kilpailuttamiseen siirrytään. Jätteenkuljetusten keskitetyllä kilpailuttamisella voidaan saavuttaa etuja nykyiseen kuntakohtaiseen jätteenkuljetukseen verrattuna. Edut syntyvät kun päällekkäiset ajot sekä siirtoajot vähenevät ja kuormakoot kasvavat. Kuljetukset voidaan hoitaa pienemmällä kalustomäärällä, jolloin myös kuljetuskustannukset laskevat.

Economics of combined power plant and pyrolysis bio-oil production

There are reasons of necessity in bio-fuel use and bio-energy fast development. It includes the material about bio-energy technologies, applications and methods. There are basic thermodynamics and economic theories. The economic calculation presents the comparison between two combinations. There are boiler plant below 20 MW in combination with ablative pyrolysis plant for bio-oil production and CHP plant below 100 MW in combination with the RTP pyrolysis bio-oil production technology. It provides a material about wood chips and bio-oil characteristics and explains it nature, presents the situation around the bio-fuel market or bio-fuel trade. There is a description of pyrolysis technologies such as ablative and RTP. The liquid product of the pyrolysis processes is bio-oil. The bio-oil could be different even of the same production process, because of the raw material nature and characteristics. The calculation shows advantages and weaknesses of combinations and obtained a proof of suppositions. The next thing, proven by this work is the fact that to get more efficiency from energy project it is good possibility to built plants in combinations.

Gelatin as an additive in bio-based barrier films

The main objective of the present study was to verify the approach on starch-gelatin blending for the paperboard coating formulations with enhanced barrier and mechanical properties. Based on that, another objective was to find out, how the approach will function with wood-based polysaccharides (CMC, EHEC and HPC) by analyzing their barrier properties and convertibility. The last objective was to find out, if pigments can be used in the composition of polysaccharide-protein blends without causing any negative effect on stated properties. The whole process chain of the barrier coating development was studied in the research. The methodology applied included pilot-scale coating and converting trials for the evaluation of mechanical properties of obtained coatings, namely their exposure to cracking with the loss of barrier properties. The results obtained indicated that the combination of starch with gelatin, in fact, improves the grease barrier properties and flexibility of starch-based coatings, thereby confirming the offered approach. The similar results were obtained for CMC, exhibited elevated barrier properties and surface coverage, proving that the approach also functions with wood-based polysaccharides. The introduction of equal amounts of talc gave various effects at different gelatin dosages on barrier properties of wood-based polysaccharides. Mainly, the elevation of grease barrier properties was observed. The convertibility of talc-filled coatings was not sufficient.

Työvoiman ja koulutuksen tarvetutkimus 2009 : Yhteenveto bio- ja lääkealan työnantajahaastatteluista Asiantuntijaraadin SWOT-analyysi 2.3.2010

Varsinais-Suomen ELY-keskus teettää säännöllisesti maakunnan valikoiduille toimialoille työvoiman ja koulutuksen tarvetutkimuksia (TKTT). Tähän raporttiin on koottu bio- ja terveysalan TKTT-prosessin kaikki osiot: toimialan tilastotiedot, yrityshaastattelut syksyltä 2009, 2.3.2010 järjestetyn asiantuntijaraadin yhteenveto ja Delfoi-kierroksen tulokset. Varsinais-Suomi on kotimaassa lääketieteellisen bioalan kärkeä ja kansainvälistä huippua tietyillä tutkimusalueilla. Tässä työssä toimiala luokitellaan määritelmällä ”bioja terveysala”, johon kuuluvat lääkkeiden kehitys- ja valmistus, diagnostiikka, bioalan palvelut ja biomateriaalit. Toimialalla oli yrityksiä vuonna 2008 tehdyn kartoituksen perusteella noin 100, liikevaihdon ollessa yhteensä noin 522 miljoonaa €. Ala työllisti suoraan yli 2500 henkilöä, jonka lisäksi on huomioitava merkittävä alihankintaverkosto. Bio- ja terveysalan yrityskenttä jakautuu useisiin pienyrityksiin ja muutamiin suuryrityksiin, jotka työllistävät pääosan alan henkilöstöstä. Bioalan kehitystä koordinoi Turku Science Parkin BioTurku, joka on luonut vuonna 2009 uusimman strategian kasvuodotusten toteuttamiseksi. Viime vuosina Varsinais-Suomeen on syntynyt erityisesti biopalvelu- ja liiketoiminnankehitysyrityksiä. Alan koulutusta tarjotaan runsaasti, pääasiassa yliopistoissa ja ammattikorkeakoulussa. Aloituspaikkoja vuonna 2009 oli Turussa yhteensä 174. TKTT-haastattelut tehtiin yrityksissä loka-marraskuussa 2009: niissä haastateltiin 24 toimijaa, jotka työllistivät kaikkiaan 1849 henkilöä. Muutaman suuren yrityksen ansiosta määrä vastaa noin 70 % alan koko työvoimasta, mutta kattaa myös kaikki toimialamäärittelyssä esitetyt alaluokat Varsinais-Suomessa. Tutkimuskohteista pkyrityksiin lukeutui 80 %, mutta kokonaishenkilöstöstä 86 % työskenteli kolmen suurimman yrityksen palveluksessa. Yritysten näkymät vuonna 2009 olivat tilastollisesti optimistisia taloustilanteeseen nähden, ja lama on selvästikin taittumassa alalla. Vuoden kuluessa työllistävyyskehitys on kuitenkin vielä varovaista. Henkilöstön nettomäärä haastatelluissa yrityksissä lisääntyy syksyyn 2010 mennessä noin 11 henkilöllä. Suurin kasvu (20 %) on alle 10 henkeä työllistävissä mikroyrityksissä, ja työvoiman vähenemä koostuu pääasiassa suurempien yritysten eläkkeelle siirtyvistä työntekijöistä. Bio- ja terveysalalla on moninaisia tutkimukseen ja tuotantoon liittyviä toimenkuvia. Yleisimpiä ammattinimikkeitä haastatelluissa yrityksissä olivat kemisti, laborantti, insinööri ja tuotantotyöntekijä. Diagnostiikka-alan alihankintatöissä tarvitaan elektroniikka-asentajia. Henkilöstön ikärakenne painottuu 25-39-vuotiaisiin, joita on yli 40 % työvoimasta. Nuoria alle 24-vuotiaita työntekijöitä on erittäin vähän, mutta toisaalta vain 2 % työntekijöistä on eläköitymässä kahden vuoden kuluessa. Haastattelutulosten mukaan syksyllä 2009 noin puolessa yrityksistä elettiin nousukauden alkua, ja lamaan itsensä sijoitti viidennes. Syksyllä 2010 yrityksistä jo 95 % uskoo olevansa suhdannekäyrän positiivisella puolella, mutta kasvupotentiaalia on vielä huomattavasti. Haastatteluhetkellä työvoiman käyttöaste oli pääosin sopiva ja vain neljällä yrityksellä alhainen.

Mathematics inspired by Darwin. Adaptive dynamics of dispersal and cooperation

In 1859, Charles Darwin published his theory of evolution by natural selection, the process occurring based on fitness benefits and fitness costs at the individual level. Traditionally, evolution has been investigated by biologists, but it has induced mathematical approaches, too. For example, adaptive dynamics has proven to be a very applicable framework to the purpose. Its core concept is the invasion fitness, the sign of which tells whether a mutant phenotype can invade the prevalent phenotype. In this thesis, four real-world applications on evolutionary questions are provided. Inspiration for the first two studies arose from a cold-adapted species, American pika. First, it is studied how the global climate change may affect the evolution of dispersal and viability of pika metapopulations. Based on the results gained here, it is shown that the evolution of dispersal can result in extinction and indeed, evolution of dispersalshould be incorporated into the viability analysis of species living in fragmented habitats. The second study is focused on the evolution of densitydependent dispersal in metapopulations with small habitat patches. It resulted a very surprising unintuitive evolutionary phenomenon, how a non-monotone density-dependent dispersal may evolve. Cooperation is surprisingly common in many levels of life, despite of its obvious vulnerability to selfish cheating. This motivated two applications. First, it is shown that density-dependent cooperative investment can evolve to have a qualitatively different, monotone or non-monotone, form depending on modelling details. The last study investigates the evolution of investing into two public-goods resources. The results suggest one general path by which labour division can arise via evolutionary branching. In addition to applications, two novel methodological derivations of fitness measures in structured metapopulations are given.

Bio-ethanol valorization towards C4s including 1-butanol over metal modified alumina and zeolite catalysts

Bio-ethanol has been used as a fuel additive in modern society aimed at reducing CO2-emissions and dependence on oil. However, ethanol is unsuitable as fuel supplement in higher proportions due to its physico-chemical properties. One option to counteract the negative effects is to upgrade ethanol in a continuous fixed bed reactor to more valuable C4 products such as 1-butanol providing chemical similarity with traditional gasoline components. Bio-ethanol based valorization products also have other end-uses than just fuel additives. E.g. 1-butanol and ethyl acetate are well characterised industrial solvents and platform chemicals providing greener alternatives. The modern approach is to apply heterogeneous catalysts in the investigated reactions. The research was concentrated on aluminium oxide (Al2O3) and zeolites that were used as catalysts and catalyst supports. The metals supported (Cu, Ni, Co) gave very different product profiles and, thus, a profound view of different catalyst preparation methods and characterisation techniques was necessary. Additionally, acidity and basicity of the catalyst surface have an important role in determining the product profile. It was observed that ordinary determination of acid strength was not enough to explain all the phenomena e.g. the reaction mechanism. One of the main findings of the thesis is based on the catalytically active site which originates from crystallite structure. As a consequence, the overall evaluation of different by-products and intermediates was carried out by combining the information. Further kinetic analysis was carried out on metal (Cu, Ni, Co) supported self-prepared alumina catalysts. The thesis gives information for further catalyst developments aimed to scale-up towards industrially feasible operations.

Bio- ja maakaasu liikennepolttoaineena Suomessa

Työssä tarkastellaan bio- ja maakaasun käyttöä Suomen tieliikenteen polttoaineena. Työn lähtökohtana on selvittää kaasukäyttöisten ajoneuvojen käytön kannattavuutta Suomessa ja niiden etuja muihin polttoaineisiin nähden. Tutkielmassa perehdytään erityisesti biokaasun käyttöön fossiilisten polttoaineiden korvaajana ja mitä vaatimuksia sen käytön lisääminen edellyttää. Työssä perehdytään kaasujen tuotantomenetelmiin, jakeluun, taloudelliseen kannattavuuteen, ympäristöystävällisyyteen ja tulevaisuuden näkymiin.

Innovation Process and Organizational Adoption of Disruptive Innovation: Empirical Evidence from Finnish Bio-Economy Companies.

The thesis aims to build a coherent view and understanding of the innovation process and organizational technology adoption in Finnish bio-economy companies with a focus on innovations of a disruptive nature. Disruptive innovations are exceptional hence in order to create generalizations and a unified view of the subject the perspective is also on less radical innovations. Other interests of the thesis are how ideas are discovered and generated and how the nature of the innovation and size of the company affect the technology adoption and innovation process. The data was collected by interviewing six small and six large Finnish bio-economy companies. The results suggest companies regardless of size consider innovation as a core asset in the competitive markets. Organizations want to be considered innovators and early adopters yet these qualities are limited by certain, mainly resource-based factors. In addition the industry, scalability and Finland’s geographical location when seeking funding provide certain challenges. The innovation process may be considered relatively similar whether the idea or technology stems from an internal or external source suggesting the technology adoption process can in fact be linked to the innovation process theories. Thus the thesis introduces a new theoretical model which based on the results of the study and the theories of technology adoption and innovation process aims on characterizing how ideas and technology from both external and internal sources generate into innovations. The innovation process is in large bio-economy companies most often similar to or a modified version of the stage-gate model, while small companies generally have less structured processes. Nevertheless the more disruptive the innovation, the less it fits in the structured processes. This implies disruptive innovation cannot be put in a certain mould but it is rather processed case-by-case.

Bio and chemocatalysis for stereo and regioselective one-pot reaction applications

The development of cost efficient, selective and sustainable chemical processes for production of chiral building blocks is of great importance in synthetic and industrial organic chemistry. One way to reach these objectives is to carry out several reactions steps in one vessel at one time. Furthermore, when this kind of one-pot multi step reactions are catalyzed by heterogeneous chemo- and bio-catalysts, which can be separated from the reaction products by filtration, practical access to chiral small molecules for further utilization can be obtained. The initial reactions studied in this thesis are the two step dynamic kinetic resolution of rac-2-hydroxy-1-indanone and the regioselective hydrogenation of 1,2-indanedione. These reactions are then combined in a new heterogeneously catalyzed one-pot reaction sequence enabling simple recovery of the catalysts by filtration, facilitating simple reaction product isolation. Conclusively, the readily available 1,2-indanedione is by the presented one-pot sequence, utilizing heterogeneous enzyme and transition metal based catalysts, transferred with high regio- and stereoselectivity to a useful chiral vicinal hydroxyl ketone structure. Additional and complementary investigation of homogeneous half-sandwich ruthenium complexes for catalyzing the epimerization of chiral secondary alcohols of five natural products containing additional non-functionalized stereocenters was conducted. In principle, this kind of epimerization reactions of single stereocenters could be utilized for converting inexpensive starting materials, containing other stereogenic centers, into diastereomeric mixtures from which more valuable compounds can be isolated by traditional isolation techniques.