Δομημένη εξαγωγή πληροφοριών από σελίδες ιατρικών και διατροφικών δεδομένων με χρήση του Information Extraction

106 σ.Αντικείμενο της παρούσας διπλωματικής εργασίας αποτελεί η μελέτη και εφαρμογή μεθόδων για την εξαγωγή πληροφοριών (Ιnformation Extraction, IE) από κείμενα σχετικά με ιατρικοφαρμαευτικά και διατροφικά δεδομένα και τη δομημένη παρουσίασή τους σε μορφή html πινάκων. Γίνεται, επίσης, χρήση ενός λογισμικού που διατίθεται ελέυθερα στους χρήστες (GATE), καθώς και ενός συνόλου κανόνων και γραμματικών (JAPE) που υποβοηθούν στον εντοπισμό των δεδομένων που ζητούνται. Παρουσιάζεται, παράλληλα, μία εφαρμογή (pipeline) που είναι σχεδιασμένη κατάλληλα για να τρέχει πάνω σε ένα σύνολο εγγράφων (corpus) και να δημιουργεί ένα σύνολο σχολιασμών (annotations). Τέλος, εφαρμόζεται ένα στάδιο που λαμβάνει τα αποτελέσματα της εφαρμογής και τα κατηγοριοποιεί στην επιθυμητή μορφή. Η εργασία στο συνολό της περιλαμβάνει πέρα από ένα γενικό θεωρητικό υπόβαθρο, τη χρήση ειδικών διαδραστικών περιβαλλόντων (Integrated Development Environment, IDE) απαραίτητων για την επίτευξη του αρχικού στόχου. Στο κεφάλαιο 1, γίνεται μια γενική εισαγωγή σε τρόπους επεξεργασίας φυσικών γλωσσών (Natural Language Processing, NLP) εισάγωντας το γενικότερο πλαίσιο στο οποίο θα κινηθεί η εν λόγω εργασία. Προσδιορίζονται, επίσης, και έννοιες απαραίτητες για τη συνέχεια, όπως αυτή της εξαγωγής δεδομένων (IE). Στο κεφάλαιο 2, παρουσιάζεται το κυριότερο θεωρητικό υπόβαθρο της εργασίας, καθώς περιλαμβάνει την ανάλυση του GATE, ενός συστηματος λογισμικού στο οποίο θα στηριχθεί η εξαγωγή των δεδομένων μας. Περιλαμβάνει, ακόμα, και την ανάλυση του διαδραστικού περιβάλλοντος του GATE (GATE Developer) και του ΙΕ συστήματός του (ANNIE), που θα χρησιμοποιηθούν στη συνέχεια. Στο κεφάλαιο 3, περιγράφεται σε θεωρητικό επίπεδο η γλώσσα που παράγει τους σχολιασμούς κειμένων με χρήση ειδικών κανόνων και γραμματικών. Αποτελεί ένα βασικό εργαλείο για τη δημιουργία της εφαρμογής που θα εξάγει τα δεδομένα. Στο κεφάλαιο 4, προσδιορίζεται ο τρόπος σύνδεσης όλων των ανώτερων στοιχείων και πληροφοριών για τη δημιουργία της εφαρμογής που επιτυγχάνει τον τελικό στόχο. Αναφέρεται, δηλαδή, σε ένα αναλυτικό βαθμό ο τρόπος σχεδιασμού της εφαρμογής, παρουσιάζοντας ταυτόχρονα τμήματα κώδικα προγραμματισμού της και αποτελέσματα από την εκτελεσή της. Στο κεφάλαιο 5, γίνεται μία γενική σύνοψη της εργασίας , προβολή συμπερασμάτων που προέκυψαν, καθώς και προτροπή νέων ιδεών για μελλοντική ανάπτυξη της δουλειάς που παρουσιάστηκε.The purpose of this diploma thesis is the design and implementation of methods that achieve Information Extraction (IE) from texts, relevant to biomedical and nutritional data and their structured presentation in html tables. Additionally, an open-source software for text engineering (GATE) is used, and a set of rules and grammars (JAPE) to assist in identifying the requested data. Furthermore, an application (pipeline) is utilized that is designed especially to run on a set of documents (corpus) and create a set of annotations that facilitate superior work. A final stage is applied, that takes the results of the above application and categorizes them in a desired form. The document includes apart from a theoretical background review of the basic concepts involved in the aforementioned tool flow, the description of the use of special Integrated Development Environments (IDEs) necessary to achieve the original goal. In Chapter 1, a general introduction is made, covering the field of Natural Language Processing (NLP), providing motivation for this work. Moreover, lots of necessary concepts, such as the Information extraction (IE) are determined, critical for the comprehension of the rest of the chapters. Chapter 2 presents the main theoretical background of the entire diploma thesis, as it involves the analysis of GATE, a general architecture of text engineering which will support the information extraction of our data. It also includes the analysis of the integrated development environment of GATE (GATE Developer) and the information extraction system of GATE (ANNIE), which will be subsequently used. Chapter 3 describes the way of creating text annotations using the Java Annotation Pattern Engine (JAPE). It is an essential tool for the creation of our application which will perform the IE. In Chapter 4, we analyze the way of connecting all data and information mentioned, to create the application that achieves the ultimate goal. Additionally, a detailed process of the application design is highlighted, while presenting snippets of its code and results of its execution. In Chapter 5, the diploma thesis is summarised, giving conclusions and introducing new ideas for further development of the presented work.Γεώργιος Δ. Παντερή

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Multi-membership gene regulation in pathway based microarray analysis

This article is available through the Brunel Open Access Publishing Fund. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.Background: Gene expression analysis has been intensively researched for more than a decade. Recently, there has been elevated interest in the integration of microarray data analysis with other types of biological knowledge in a holistic analytical approach. We propose a methodology that can be facilitated for pathway based microarray data analysis, based on the observation that a substantial proportion of genes present in biochemical pathway databases are members of a number of distinct pathways. Our methodology aims towards establishing the state of individual pathways, by identifying those truly affected by the experimental conditions based on the behaviour of such genes. For that purpose it considers all the pathways in which a gene participates and the general census of gene expression per pathway. Results: We utilise hill climbing, simulated annealing and a genetic algorithm to analyse the consistency of the produced results, through the application of fuzzy adjusted rand indexes and hamming distance. All algorithms produce highly consistent genes to pathways allocations, revealing the contribution of genes to pathway functionality, in agreement with current pathway state visualisation techniques, with the simulated annealing search proving slightly superior in terms of efficiency. Conclusions: We show that the expression values of genes, which are members of a number of biochemical pathways or modules, are the net effect of the contribution of each gene to these biochemical processes. We show that by manipulating the pathway and module contribution of such genes to follow underlying trends we can interpret microarray results centred on the behaviour of these genes.The work was sponsored by the studentship scheme of the School of Information Systems, Computing and Mathematics, Brunel Universit

Learning,Generating and Adapting Wave Gestures for Expressive Human-Robot Interaction

This study proposes a novel imitation learning approach for the stochastic generation of human-like rhythmic wave gestures and their modulation for effective non-verbal communication through a probabilistic formulation using joint angle data from human demonstrations. This is achieved by learning and modulating the overall expression characteristics of the gesture (e.g., arm posture, waving frequency and amplitude) in the frequency domain. The method was evaluated on simulated robot experiments involving a robot with a manipulator of 6 degrees of freedom. The results show that the method provides efficient encoding and modulation of rhythmic movements and ensures variability in their execution.Comment: 3 pages, 3 figure

Cytokinesis in bloodstream stage Trypanosoma brucei requires a family of katanins and spastin

Microtubule severing enzymes regulate microtubule dynamics in a wide range of organisms and are implicated in important cell cycle processes such as mitotic spindle assembly and disassembly, chromosome movement and cytokinesis. Here we explore the function of several microtubule severing enzyme homologues, the katanins (KAT80, KAT60a, KAT60b and KAT60c), spastin (SPA) and fidgetin (FID) in the bloodstream stage of the African trypanosome parasite, Trypanosoma brucei. The trypanosome cytoskeleton is microtubule based and remains assembled throughout the cell cycle, necessitating its remodelling during cytokinesis. Using RNA interference to deplete individual proteins, we show that the trypanosome katanin and spastin homologues are non-redundant and essential for bloodstream form proliferation. Further, cell cycle analysis revealed that these proteins play essential but discrete roles in cytokinesis. The KAT60 proteins each appear to be important during the early stages of cytokinesis, while downregulation of KAT80 specifically inhibited furrow ingression and SPA depletion prevented completion of abscission. In contrast, RNA interference of FID did not result in any discernible effects. We propose that the stable microtubule cytoskeleton of T. brucei necessitates the coordinated action of a family of katanins and spastin to bring about the cytoskeletal remodelling necessary to complete cell divisio

Gastric Outlet Obstruction due to Cytomegalovirus Infection in an Immunocompromised Patient

A case of gastric outlet obstruction accompanied by diffuse gastritis and gastric ulcer due to cytomegalovirus infection is presented. The patient, a woman aged 67 years with a long history of rheumatoid arthritis under immunosuppressive treatment (methotrexate), was admitted to our department complaining mostly of abdominal pain located in the epigastrium and the right abdomen. Upper gastrointestinal endoscopy revealed the presence of gastritis accompanied by ulcer in the prepyloric area and gastric outlet obstruction due to cytomegalovirus infection which was confirmed histologically. The patient responded well – although after many weeks – to specific treatment with antiviral treatment (ganciclovir). It is concluded that gastric outlet obstruction caused by cytomegalovirus infection can be observed in immunocompromised patients. The clinician must search for possible cytomegalovirus infection in all immunocompromised patients presenting with a clinical picture of gastric outlet obstruction by obtaining enough biopsies and by asking the histopathologist to specifically stain the specimen for the presence of cytomegalovirus, especially if infection by Helicobacter pylori is not present