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.

Two-phase flow measurements with spacer grid in a rod bundle geometry

Heat transfer effectiveness in nuclear rod bundles is of great importance to nuclear reactor safety and economics. An important design parameter is the Critical Heat Flux (CHF), which limits the transferred heat from the fuel to the coolant. The CHF is determined by flow behaviour, especially the turbulence created inside the fuel rod bundle. Adiabatic experiments can be used to characterize the flow behaviour separately from the heat transfer phenomena in diabatic flow. To enhance the turbulence, mixing vanes are attached to spacer grids, which hold the rods in place. The vanes either make the flow swirl around a single sub-channel or induce cross-mixing between adjacent sub-channels. In adiabatic two-phase conditions an important phenomenon that can be investigated is the effect of the spacer on canceling the lift force, which collects the small bubbles to the rod surfaces leading to decreased CHF in diabatic conditions and thus limits the reactor power. Computational Fluid Dynamics (CFD) can be used to simulate the flow numerically and to test how different spacer configurations affect the flow. Experimental data is needed to validate and verify the used CFD models. Especially the modeling of turbulence is challenging even for single-phase flow inside the complex sub-channel geometry. In two-phase flow other factors such as bubble dynamics further complicate the modeling. To investigate the spacer grid effect on two-phase flow, and to provide further experimental data for CFD validation, a series of experiments was run on an adiabatic sub-channel flow loop using a duct-type spacer grid with different configurations. Utilizing the wire-mesh sensor technology, the facility gives high resolution experimental data in both time and space. The experimental results indicate that the duct-type spacer grid is less effective in canceling the lift force effect than the egg-crate type spacer tested earlier.

Fundraising and investor relations in social enterprise: Marketing your way out of the pioneer gap in African off-grid renewable energy

Social enterprises apply the best of business for the pursuit of social or environmental mission while also generating revenues. Globally, nearly 1,3 billion people lack access to electricity, as well as another billion having access to only low quality and infrequent electricity. Off-grid renewable energy, like solar, will increasingly have a key role in the solution of the energy access issue. The pioneer gap in off-grid renewable energy consists of financing (or funding) gaps and capacity gaps, to do with both the early stage of the enterprises in question, as well as the early stage of the whole industry. The gaps are emphasised by specific characteristics of off-grid renewable energy business models and the requirements of operating in bottom-of-the-pyramid markets. The marketing perspective to fundraising is chosen to uncover the possible role enterprises themselves have in bridging the pioneer gap. The purpose of this thesis is to study how social enterprises operating in off-grid renewable energy in Africa utilise marketing activities in their investor relations in bridging the pioneer gap. This main research question is divided into the following sub-questions:  How does the pioneer gap affect fundraising for these enterprises?  How are the funding needs for these enterprises characterised?  How do these enterprises build trust in their investor relations? The theoretic framework is built on relationship marketing and investor relations, with an emphasis on creation of trust. The research is conducted as a thematical case study. Primary data is gathered via semi-structured interviews with six solar energy companies and two accelerators. According to the findings, the main components affecting trust-creation are diminished information asymmetry and perceived risk, mission alignment as well as a personal fit or relationship with the investor. Therefore, an enterprise can utilise e.g. the following marketing activities in their investor relations to bridge the pioneer gap: ensuring investor material, the enterprise story and presenting of them is clear, concise and complete to “package” the enterprise as an investment; taking investor needs and motivations into account as well as utilising existing investors as ambassadors.

Piilevien asiakastarpeiden tunnistaminen – repertory grid -tekniikka

Tässä työssä tutkitaan asiakaslähtöisyyttä tuotekehityksessä ja piilevien asiakastarpeiden selvittämistä ja hyödyntämistä asiakaslähtöisyydessä. Tavoitteena on selvittää asiakaslähtöisyyden tärkeyttä ja etuja tuotekehityksessä, sekä käydä läpi erilaisia asiakastarpeiden selvittämismetodeja erityisesti keskittyen repertory grid –tekniikkaan (RGT). Asiakaslähtöisyys tuo yrityksille merkittävää kilpailuetua tuotekehityksen alkupäähän. Erityisesti piilevät asiakastarpeet voivat mahdollistaa tuoteinnovaatioita, joilla saavutetaan huomattavasti parempaa asiakastyytyväisyyttä ja etulyöntiasemaa kilpailijoihin nähden. Piileviä asiakastarpeita voi tunnistaa repertory grid –tekniikalla, jota on avattu tässä työssä. Tekniikka mahdollistaa piilevien asiakastarpeiden tunnistamisen, mikä osaltaan edistää etulyöntiaseman antavia asiakaslähtöisiä tuoteinnovaatioita, joilla yritys voi differoitua muista markkinoilla olevista yrityksistä. Asiakaslähtöisyyden tulee tuotekehityksen lähtökohdan lisäksi olla osa yrityksen strategiaa ja kulttuuria, jotta yritys voi menestyä asiakaslähtöisyydellä.

Identifying reasons for failure in biomedical research and publishing

The regular assessment of Brazilian scientific output means that individual university departments need to constantly improve the quantity and quality of their scientific output. A significant proportion of this output involves the work of Master’s and Doctoral students, but getting this work published in a suitable journal can often prove to be a challenge. Although students’ lack of fluency in English is a contributing factor, many of the problems observed have an early origin in the formulation of the research problem and its relevance to current research trends in the international literature. In short, more time needs to be spent in the library and less in the laboratory, and more effort needs to be made in teaching students basic research skills such as the effective use of bibliographic databases like PubMed, Web of Science and Scopus.

Doubly fed wind turbine performance in variable grid conditions

Wind turbines based on doubly fed induction generators (DFIG) become the most popular solution in high power wind generation industry. While this topology provides great performance with the reduced power rating of power converter, it has more complicated structure in comparison with full-rated topologies, and therefore leads to complexity of control algorithms and electromechanical processes in the system. The purpose of presented study is to present a proper vector control scheme for the DFIG and overall control for the WT to investigate its behavior at different wind speeds and in different grid voltage conditions: voltage sags, magnitude and frequency variations. The key principles of variable-speed wind turbine were implemented in simulation model and demonstrated during the study. Then, based on developed control scheme and mathematical model, the set of simulation is made to analyze reactive power capabilities of the DFIG wind turbine. Further, the rating of rotor-side converter is modified to not only generate active rated active power, but also to fulfill Grid Codes. Results of modelling and analyzing of the DFIG WT behavior under different speeds and different voltage conditions are presented in the work.

Repertory grid adaptations in detecting connotative trends and social behaviour problems in education

Please consult the paper edition of this thesis to read. It is available on the 5th Floor of the Library at Call Number: Z 9999 E38 K66 1983

The orientalist sore : biomedical discourses, capital and urban warfare in the colonial present

Mémoire numérisé par la Division de la gestion de documents et des archives de l'Université de Montréal.

Concept oriented biomedical information retrieval

Le domaine biomédical est probablement le domaine où il y a les ressources les plus riches. Dans ces ressources, on regroupe les différentes expressions exprimant un concept, et définit des relations entre les concepts. Ces ressources sont construites pour faciliter l’accès aux informations dans le domaine. On pense généralement que ces ressources sont utiles pour la recherche d’information biomédicale. Or, les résultats obtenus jusqu’à présent sont mitigés : dans certaines études, l’utilisation des concepts a pu augmenter la performance de recherche, mais dans d’autres études, on a plutôt observé des baisses de performance. Cependant, ces résultats restent difficilement comparables étant donné qu’ils ont été obtenus sur des collections différentes. Il reste encore une question ouverte si et comment ces ressources peuvent aider à améliorer la recherche d’information biomédicale. Dans ce mémoire, nous comparons les différentes approches basées sur des concepts dans un même cadre, notamment l’approche utilisant les identificateurs de concept comme unité de représentation, et l’approche utilisant des expressions synonymes pour étendre la requête initiale. En comparaison avec l’approche traditionnelle de "sac de mots", nos résultats d’expérimentation montrent que la première approche dégrade toujours la performance, mais la seconde approche peut améliorer la performance. En particulier, en appariant les expressions de concepts comme des syntagmes stricts ou flexibles, certaines méthodes peuvent apporter des améliorations significatives non seulement par rapport à la méthode de "sac de mots" de base, mais aussi par rapport à la méthode de Champ Aléatoire Markov (Markov Random Field) qui est une méthode de l’état de l’art dans le domaine. Ces résultats montrent que quand les concepts sont utilisés de façon appropriée, ils peuvent grandement contribuer à améliorer la performance de recherche d’information biomédicale. Nous avons participé au laboratoire d’évaluation ShARe/CLEF 2014 eHealth. Notre résultat était le meilleur parmi tous les systèmes participants.

Investigations on Magnetic, Optical and Transport Properties of Magnetic Nanofluids for Engineering and Biomedical Applications

Department of Physics, Cochin University of Science & Technology

A DHT-Based Grid Resource Indexing and Discovery Scheme

This paper presents a DHT-based grid resource indexing and discovery (DGRID) approach. With DGRID, resource-information data is stored on its own administrative domain and each domain, represented by an index server, is virtualized to several nodes (virtual servers) subjected to the number of resource types it has. Then, all nodes are arranged as a structured overlay network or distributed hash table (DHT). Comparing to existing grid resource indexing and discovery schemes, the benefits of DGRID include improving the security of domains, increasing the availability of data, and eliminating stale data.

Towards Grid-Wide Modeling and Simulation

Modeling and simulation permeate all areas of business, science and engineering. With the increase in the scale and complexity of simulations, large amounts of computational resources are required, and collaborative model development is needed, as multiple parties could be involved in the development process. The Grid provides a platform for coordinated resource sharing and application development and execution. In this paper, we survey existing technologies in modeling and simulation, and we focus on interoperability and composability of simulation components for both simulation development and execution. We also present our recent work on an HLA-based simulation framework on the Grid, and discuss the issues to achieve composability.

Stimuli-responsive Novel Amphiphilic Polymers for Chemical and Biomedical Applications

Amphiphilic polymers are a class of polymers that self-assemble into different types of microstructure, depending on the solvent environment and external stimuli. Self assembly structures can exist in many different forms, such as spherical micelles, rod-like micelles, bi-layers, vesicles, bi-continuous structure etc. Most biological systems are basically comprised of many of these organised structures arranged in an intelligent manner, which impart functions and life to the system. We have adopted the atom transfer radical polymerization (ATRP) technique to synthesize various types of block copolymer systems that self-assemble into different microstructure when subject to an external stimuli, such as pH or temperature. The systems that we have studied are: (1) pH responsive fullerene (C60) containing poly(methacrylic acid) (PMAA-b-C60); (2) pH and temperature responsive fullerene containing poly[2-(dimethylamino)ethyl methacrylate] (C₆₀-b-PDMAEMA); (3) other responsive water-soluble fullerene systems. By varying temperature, pH and salt concentration, different types microstructure can be produced. In the presence of inorganic salts, fractal patterns at nano- to microscopic dimension were observed for negatively charged PMAA-b-C60, while such structure was not observed for positively charged PDMAEMA-b-C60. We demonstrated that negatively charged fullerene containing polymeric systems can serve as excellent nano-templates for the controlled growth of inorganic crystals at the nano- to micrometer length scale and the possible mechanism was proposed. The physical properties and the characteristics of their self-assembly properties will be discussed, and their implications to chemical and biomedical applications will be highlighted.

Compositional Data in Biomedical Research

Modern methods of compositional data analysis are not well known in biomedical research. Moreover, there appear to be few mathematical and statistical researchers working on compositional biomedical problems. Like the earth and environmental sciences, biomedicine has many problems in which the relevant scienti c information is encoded in the relative abundance of key species or categories. I introduce three problems in cancer research in which analysis of compositions plays an important role. The problems involve 1) the classi cation of serum proteomic pro les for early detection of lung cancer, 2) inference of the relative amounts of di erent tissue types in a diagnostic tumor biopsy, and 3) the subcellular localization of the BRCA1 protein, and it's role in breast cancer patient prognosis. For each of these problems I outline a partial solution. However, none of these problems is \solved". I attempt to identify areas in which additional statistical development is needed with the hope of encouraging more compositional data analysts to become involved in biomedical research

WMR navigation using local potential field corridors and narrow local occupancy grid perception

Path planning and control strategies applied to autonomous mobile robots should fulfil safety rules as well as achieve final goals. Trajectory planning applications should be fast and flexible to allow real time implementations as well as environment interactions. The methodology presented uses the on robot information as the meaningful data necessary to plan a narrow passage by using a corridor based on attraction potential fields that approaches the mobile robot to the final desired configuration. It employs local and dense occupancy grid perception to avoid collisions. The key goals of this research project are computational simplicity as well as the possibility of integrating this method with other methods reported by the research community. Another important aspect of this work consist in testing the proposed method by using a mobile robot with a perception system composed of a monocular camera and odometers placed on the two wheels of the differential driven motion system. Hence, visual data are used as a local horizon of perception in which trajectories without collisions are computed by satisfying final goal approaches and safety criteria