Data Representation in Machine Learning Methods with its Application to Compilation Optimization and Epitope Prediction

In this dissertation we explore the application of machine learning algorithms to compilation phase order optimization, and epitope prediction. The common thread running through these two disparate domains is the type of data being dealt with. In both problem domains we are dealing with categorical data, with its representation playing a significant role in the performance of classification algorithms. We first present a neuroevolutionary approach which orders optimization phases to generate compiled programs with performance superior to those compiled using LLVM\u27s -O3 optimization level. Performance improvements calculated as the speed of the compiled program\u27s execution ranged from 27% for the ccbench program, to 40.8% for bzip2. This dissertation then explores the problem of data representation of 3D biological data, such as amino acids. A new approach for distributed representation of 3D biological data through the process of embedding is proposed and explored. Analogously to word embedding, we developed a system that uses atomic and residue coordinates to generate distributed representation for residues, which we call 3D Residue BioVectors. Preliminary results are presented which demonstrate that even the low dimensional 3D Residue BioVectors can be used to predict conformational epitopes and protein-protein interactions, with promising proficiency. The generation of such 3D BioVectors, and the proposed methodology, opens the door for substantial future improvements, and application domains. The dissertation then explores the problem domain of linear B-Cell epitope prediction. This problem domain deals with predicting epitopes based strictly on the protein sequence. We present the DRREP system, which demonstrates how an ensemble of shallow neural networks can be combined with string kernels and analytical learning algorithm to produce state of the art epitope prediction results. DRREP was tested on the SARS subsequence, the HIV, Pellequer, AntiJen datasets, and the standard SEQ194 test dataset. AUC improvements achieved over the state of the art ranged from 3% to 8%. Finally, we present the SEEP epitope classifier, which is a multi-resolution SMV ensemble based classifier which uses conjoint triad feature representation, and produces state of the art classification results. SEEP leverages the domain specific knowledge based protein sequence encoding developed within the protein-protein interaction research domain. Using an ensemble of multi-resolution SVMs, and a sliding window based pre and post processing pipeline, SEEP achieves an AUC of 91.2 on the standard SEQ194 test dataset, a 24% improvement over the state of the art

24th International Conference on Information Modelling and Knowledge Bases

In the last three decades information modelling and knowledge bases have become essentially important subjects not only in academic communities related to information systems and computer science but also in the business area where information technology is applied. The series of European – Japanese Conference on Information Modelling and Knowledge Bases (EJC) originally started as a co-operation initiative between Japan and Finland in 1982. The practical operations were then organised by professor Ohsuga in Japan and professors Hannu Kangassalo and Hannu Jaakkola in Finland (Nordic countries). Geographical scope has expanded to cover Europe and also other countries. Workshop characteristic - discussion, enough time for presentations and limited number of participants (50) / papers (30) - is typical for the conference. Suggested topics include, but are not limited to: 1. Conceptual modelling: Modelling and specification languages; Domain-specific conceptual modelling; Concepts, concept theories and ontologies; Conceptual modelling of large and heterogeneous systems; Conceptual modelling of spatial, temporal and biological data; Methods for developing, validating and communicating conceptual models. 2. Knowledge and information modelling and discovery: Knowledge discovery, knowledge representation and knowledge management; Advanced data mining and analysis methods; Conceptions of knowledge and information; Modelling information requirements; Intelligent information systems; Information recognition and information modelling. 3. Linguistic modelling: Models of HCI; Information delivery to users; Intelligent informal querying; Linguistic foundation of information and knowledge; Fuzzy linguistic models; Philosophical and linguistic foundations of conceptual models. 4. Cross-cultural communication and social computing: Cross-cultural support systems; Integration, evolution and migration of systems; Collaborative societies; Multicultural web-based software systems; Intercultural collaboration and support systems; Social computing, behavioral modeling and prediction. 5. Environmental modelling and engineering: Environmental information systems (architecture); Spatial, temporal and observational information systems; Large-scale environmental systems; Collaborative knowledge base systems; Agent concepts and conceptualisation; Hazard prediction, prevention and steering systems. 6. Multimedia data modelling and systems: Modelling multimedia information and knowledge; Contentbased multimedia data management; Content-based multimedia retrieval; Privacy and context enhancing technologies; Semantics and pragmatics of multimedia data; Metadata for multimedia information systems. Overall we received 56 submissions. After careful evaluation, 16 papers have been selected as long paper, 17 papers as short papers, 5 papers as position papers, and 3 papers for presentation of perspective challenges. We thank all colleagues for their support of this issue of the EJC conference, especially the program committee, the organising committee, and the programme coordination team. The long and the short papers presented in the conference are revised after the conference and published in the Series of “Frontiers in Artificial Intelligence” by IOS Press (Amsterdam). The books “Information Modelling and Knowledge Bases” are edited by the Editing Committee of the conference. We believe that the conference will be productive and fruitful in the advance of research and application of information modelling and knowledge bases. Bernhard Thalheim Hannu Jaakkola Yasushi Kiyok

Shrimping under working conditions

We propose that mutated forms of death are emerging with neoliberalism’s biopolitical financialisation of life. Thinking of such forms as commercial extinction and social death, how do we begin to frame these outside of a quantified rhetoric of surplus? These questions aim to provoke a discussion about these terms that can be interpreted as modes of exhaustion, while maintaining particular biological, social or economic conditions of life. When we are confronted with capitalism’s failure to fulfil resource exhaustion, a model of conservation by dispossession1 might emerge within what Rosi Braidotti calls “new and subtler degrees of death and extinction” (2013, 115). In this text we want to think with other conditions of death and extinction that can help to move beyond the missing item of an inventory, a carved rock along a fossil road or a set of pre-emptive actions to be executed beyond a certain threshold. Thus, we ask if there could be figures, which rather than narrating death as a biological or geological concept, open it up to other equally violent forces that are nevertheless materially situated. More importantly, will we ever be able to think of extinction beyond ideas of absence or frame death from social or economic realms as an emerging mode of living? In order to address many of these questions we dissect a critical example of extinction, that of the brown shrimp (Crangon crangon) as it flips between commercial (albeit not yet biotic) death in the ex-fishing grounds of the South East corner of the UK, and the social death embedded in the labour-power of the ex-processing factories of the Special Economic Zones of Tangier and Tetuan in Morocco

Erasure

How does erasure execute knowledge production? The following is a tour through a collection of erasure that provides a glimpse into the many directions that this question may take us, through the lens of a series of artistic interventions, academic research, experiments and artefacts. I present these items from a collector’s point of view. For achieving completion of this collection of erasures would be, in the words of Jean Baudrillard, like death. That is to say that the desire to complete the series, to achieve the perfection of its imaginary ending, is that which creates the elusive object of desire. As such, in the same way that a collection can always extend itself laterally, or spark a new one ([1968] 1996, 113), I am presenting it as an object of desire, fuelled by the impetus of neoliberal growth, which can never be complete and will forever expand into new meanings of execution, always towards the elusive erasure of death

Data Browser 06: Executing Practices

This collection brings together artists, curators, programmers, theorists and heavy internet browsers whose practices make critical intervention into the broad concept of execution. It draws attention to their political strategies, asking: who and what is involved with those practices, and for whom or what are these practices performed, and how? From the contestable politics of emoji modifier mechanisms and micro-temporalities of computational processes to genomic exploitation and the curating of digital content, the chapters account for gendered, racialised, spatial, violent, erotic, artistic and other embedded forms of execution. Together they highlight a range of ways in which execution emerges and how it participates within networked forms of liveliness

From the projected to the transmitted image: the 2.0 construction of tourist destination image and identity in Catalonia

This thesis aims to explore online projected and perceived images of a tourist destination, to assess their mutual correspondence, and to shed light on the role of online user-generated images in destination image formation. It also seeks to analyse the spatial distribution of image by tourists and the complex image identity issues concerning a destination. To achieve this, online image sources regarding the case study of Catalonia were analysed through massive computerized quantitative content analysis of some 25,000 travel blog and review entries (perceived image) and around 3,000 official tourism webpages (projected image). The results showed significant dissonance between tourists’ images and official images of the destination in several aspects, notably its attraction factors and cultural identity. Tourists' destination images were found to be greatly concentrated on certain elements and spaces. Finally, this thesis proposes the concept of "transmitted image" to reflect the new central role of tourists’ online images in the creation, dissemination and formation of destination image. Keywords: tourist destination image; destination identity; online image; perceived image; projected image; transmitted image; travel blog; travel review; official tourism websites; Web 2.0; quantitative content analysis; Catalonia.Aquesta tesi té com a objectiu explorar les imatges projectades i percebudes online d’una destinació turística, examinar la seva correspondència mútua, i contribuir a aclarir el rol de les imatges online generades pels usuaris en la formació de la imatge d’una destinació. Amb aquests propòsits, es van analitzar fonts d’imatge online sobre el cas d’estudi de Catalunya a través d’una anàlisi computeritzada quantitativa de contingut massiu d’aproximadament 25.000 entrades de travel blogs i travel reviews (imatge percebuda) i aproximadament 3.000 pàgines de webs oficials (imatge projectada). Els resultats mostren que hi ha una dissonància important entre les imatges dels turistes i les imatges oficials de la destinació en diversos aspectes, notablement en els seus factors d’atracció i identitat cultural. S’ha trobat que les imatges dels turistes sobre la destinació estaven altament concentrades en certs elements i espais. Finalment, aquesta tesi proposa el concepte d’ “imatge transmesa” per tal de reflectir el nou rol central de les imatges online dels turistes en la creació, disseminació i formació de la imatge d’una destinació. Paraules clau: imatge d’una destinació turística; identitat de la destinació; imatge online; imatge percebuda; imatge projectada; imatge transmesa; blog de viatges; review de viatges; webs oficials de turisme; web 2.0; anàlisi de contingut quantitatiu; Catalunya.Esta tesis tiene como objetivo explorar las imágenes proyectadas y percibidas online de un destino turístico, examinar su correspondencia mutua, y contribuir a aclarar el rol de las imágenes online generadas por los usuarios en la formación de la imagen de un destino. Con estos propósitos, se analizaron fuentes de imagen online sobre el caso de estudio de Cataluña a través de un análisis computerizado cuantitativo de contenido masivo de aproximadamente 25.000 entradas de travel blogs y travel reviews (imagen percibida) y aproximadamente 3.000 páginas de webs oficiales (imagen proyectada). Los resultados muestran que hay una disonancia importante entre las imágenes de los turistas y las imágenes oficiales del destino en varios aspectos, notablemente en sus factores de atracción e identidad cultural. Se ha encontrado que las imágenes de los turistas sobre el destino estaban altamente concentradas en ciertos elementos y espacios. Finalmente, esta tesis propone el concepto de “imagen transmitida” para reflejar el nuevo rol central de las imágenes online de los turistas en la creación, diseminación y formación de la imagen de un destino. Palabras clave: imagen de un destino turístico; identidad del destino; imagen online; imagen percibida; imagen proyectada; imagen transmitida; blog de viajes; review de viajes; webs oficiales de turismo; web 2.0; análisis de contenido cuantitativo; Cataluña.Cette thèse a pour objectif d’explorer les images projetées et perçues en ligne d'une destination touristique, examiner sa correspondance mutuelle, et contribuer à clarifier le rôle des images en ligne générées par les usagers dans la formation de l'image d'une destination. Dans ce but, des sources d’image en ligne sur le cas d'étude de la Catalogne ont été analysées à travers d'une analyse informatisée quantitative d'un contenu massif d'à peu près 25.000 travel blogs et travel reviews (image perçue) et à peu près 3.000 pages de sites web officiels (image projetée). Les résultats montrent qu'il y a une dissonance importante entre les images des touristes et les images officielles de la destination selon quelques aspects, surtout dans ses facteurs d'attraction et d'identité culturelle. On a trouvé que les images des touristes sur la destination étaient hautement concentrées dans certains éléments et des espaces. Finalement, cette thèse propose le concept d’ "image transmise" pour refléter le nouveau rôle central des images en ligne des touristes dans la création, la dissémination et la formation de l'image d'une destination. Mots clés: image d'une destination touristique; identité de la destination; image en ligne; image perçue; image projetée; image transmise; blog de voyage; review de voyage; sites web officiels de tourisme; web 2.0; analyse de contenu quantitatif; Catalogne

Examining university student satisfaction and barriers to taking online remote exams

Recent years have seen a surge in the popularity of online exams at universities, due to the greater convenience and flexibility they offer both students and institutions. Driven by the dearth of empirical data on distance learning students' satisfaction levels and the difficulties they face when taking online exams, a survey with 562 students at The Open University (UK) was conducted to gain insights into their experiences with this type of exam. Satisfaction was reported with the environment and exams, while work commitments and technical difficulties presented the greatest barriers. Gender, race and disability were also associated with different levels of satisfaction and barriers. This study adds to the increasing number of studies into online exams, demonstrating how this type of exam can still have a substantial effect on students experienced in online learning systems and technologies

Character on Trial: Reading and Judgement in Henry Fielding's Works

To be placed above the Reach of Deceit is to be placed above the Rank of a human Being - Henry Fielding, A Clear State of the Case of Elizabeth Canning, 1753. Throughout his literary and legal careers, Fielding was concerned with the difficulties of reading and judging character accurately. He saw society as being rife with deceptive and duplicitous individuals and articulated his concerns in his writing, offering various advices to his readers. This thesis examines Fielding’s changing approaches to characterization and his proposed methods for judging character. There is a strong tradition within Fielding criticism, particularly prevalent in the mid-twentieth century, of seeing Fielding’s characters as ‘essential’, that is to say, innate and unchanging: the product of his theory of ‘Conservation of Character’. As such, his characters are often deemed easy-to-read and lacking fully-determined internal lives. Since the mid-1990s, however, critics have begun to argue that his characters are more dynamic than first supposed. While critics have noted the role of judgement in Fielding’s novels, it has not yet been explored in depth in his plays. With some notable exceptions, few studies have explored the interrelation between his novels and plays in a sustained way. I argue that Fielding examines questions of discerning character in both his plays and his novels, and that the early plays are essential for understanding the concepts which are central to his theory of judgement. This thesis contributes to studies of Fielding in three ways: by intervening in long-standing discussions of Fielding’s characterization; by analysing themes of good nature, perception and gossip which develop from his early dramatic work into the better-known novels; and by exploring its relationship to wider ideas about character in the eighteenth-century theatre and novel. Beginning with his plays, I consider Fielding’s presentation of the judgement of character in a range of his works from 1728-1753. I suggest that the early plays gave Fielding the space in which to experiment with the presentation of character and his relationship to his audience. His novels build upon concepts first introduced in the plays, such as good nature, perception and gossip, which he suggests are key to perceiving character. Fielding encourages his audiences and readers to engage with character as a process of discovery (as it is in life), but does not punish or mock them when they make mistakes. In doing so, he gives his audiences and readers indulgences he could ill afford in his magisterial career: time for judgement and the luxury of occasionally being proved wrong