The Oracle Problem in Software Testing: A Survey

Testing involves examining the behaviour of a system in order to discover potential faults. Given an input for a system, the challenge of distinguishing the corresponding desired, correct behaviour from potentially incorrect behavior is called the “test oracle problem”. Test oracle automation is important to remove a current bottleneck that inhibits greater overall test automation. Without test oracle automation, the human has to determine whether observed behaviour is correct. The literature on test oracles has introduced techniques for oracle automation, including modelling, specifications, contract-driven development and metamorphic testing. When none of these is completely adequate, the final source of test oracle information remains the human, who may be aware of informal specifications, expectations, norms and domain specific information that provide informal oracle guidance. All forms of test oracles, even the humble human, involve challenges of reducing cost and increasing benefit. This paper provides a comprehensive survey of current approaches to the test oracle problem and an analysis of trends in this important area of software testing research and practice

Higher Order Mutation Testing

Mutation testing is a fault-based software testing technique that has been studied widely for over three decades. To date, work in this field has focused largely on first order mutants because it is believed that higher order mutation testing is too computationally expensive to be practical. This thesis argues that some higher order mutants are potentially better able to simulate real world faults and to reveal insights into programming bugs than the restricted class of first order mutants. This thesis proposes a higher order mutation testing paradigm which combines valuable higher order mutants and non-trivial first order mutants together for mutation testing. To overcome the exponential increase in the number of higher order mutants a search process that seeks fit mutants (both first and higher order) from the space of all possible mutants is proposed. A fault-based higher order mutant classification scheme is introduced. Based on different types of fault interactions, this approach classifies higher order mutants into four categories: expected, worsening, fault masking and fault shifting. A search-based approach is then proposed for locating subsuming and strongly subsuming higher order mutants. These mutants are a subset of fault mask and fault shift classes of higher order mutants that are more difficult to kill than their constituent first order mutants. Finally, a hybrid test data generation approach is introduced, which combines the dynamic symbolic execution and search based software testing approaches to generate strongly adequate test data to kill first and higher order mutants

Digital control networks for virtual creatures

Robot control systems evolved with genetic algorithms traditionally take the form of floating-point neural network models. This thesis proposes that digital control systems, such as quantised neural networks and logical networks, may also be used for the task of robot control. The inspiration for this is the observation that the dynamics of discrete networks may contain cyclic attractors which generate rhythmic behaviour, and that rhythmic behaviour underlies the central pattern generators which drive lowlevel motor activity in the biological world. To investigate this a series of experiments were carried out in a simulated physically realistic 3D world. The performance of evolved controllers was evaluated on two well known control tasks—pole balancing, and locomotion of evolved morphologies. The performance of evolved digital controllers was compared to evolved floating-point neural networks. The results show that the digital implementations are competitive with floating-point designs on both of the benchmark problems. In addition, the first reported evolution from scratch of a biped walker is presented, demonstrating that when all parameters are left open to evolutionary optimisation complex behaviour can result from simple components

Fundamental Approaches to Software Engineering

This open access book constitutes the proceedings of the 24th International Conference on Fundamental Approaches to Software Engineering, FASE 2021, which took place during March 27–April 1, 2021, and was held as part of the Joint Conferences on Theory and Practice of Software, ETAPS 2021. The conference was planned to take place in Luxembourg but changed to an online format due to the COVID-19 pandemic. The 16 full papers presented in this volume were carefully reviewed and selected from 52 submissions. The book also contains 4 Test-Comp contributions

Novel agents with inhibitory activity against the Burkholderia cepacia complex

Pulmonary bacterial infections account for 95% of morbidity and mortality in cystic fibrosis (CF) patients, and include a limited spectrum of bacteria; Staphylococcus aureus, Haemophilus influenzae, Pseudomonas aeruginosa, and members of the Burkholderia cepacia complex (Bcc). "B. cepacia" was first recognised in the late 1970's as a cause of life threatening respiratory infections in CF. Initial clinical observations noted that 20% of colonised CF patients developed "cepacia syndrome", a rapid and fatal necrotising pneumonia. In addition, epidemiological evidence highlighted the potential spread of certain "B. cepacia''' strains, that most isolates were highly resistant to conventional antibiotics and consequently, Bcc infections are untreatable. Subsequent taxonomic studies have identified the Bcc that contains ten distinct species ofbacteria previously termed "5. cepacia". Clinical distribution ofBcc species in CF is restricted to mainly B. cenocepacia (50%), B. multivorans (38%) and B. vietnamiensis (7%)The aim of this study was to investigate novel antimicrobial agents against the Bcc and other problematic and emerging CF associated bacterial pathogens including multi-resistant epidemic P. aeruginosa strains, methicillin resistant S. aureus (MRSA), and Stenotrophomonas maltophilia. The novel antimicrobial strategies examined were based on three main themes: First, the use of natural honey, second, the potential use of bacteriophage and their associated lytic enzymes and third, novel mammalian cationic ß-defensins. The project utilised a vast collection of bacterial isolates and included relevant clinical, environmental and epidemic strains. The susceptibility to conventional antibiotics was measured, and resistance was shown to vary across the Bcc. In general, clinical isolates were statistically more resistant to conventional antibiotics than environmental isolates.Members of the Bcc, and an extended panel ofresistant organisms were shown to be sensitive to New Zealand manuka honey (NZMh). The MICs ranged from 9 to 17% (w/v), and the MBCs ranged from 9 to 20% (w/v). The antimicrobial component of NZMh was investigated, and focussed on osmolality, pH and H₂O₂. All were found to contribute to the antibacterial activity, although none were solely responsible for the activity. Killing-curves suggested that NZMh kills within 24 hours. The NZMh preparation was applied to a CF patient infected with B. cenocepacia J2315, and clinical data highlighted possible benefits to the patient.Novel Bcc specific bacteriophages were identified from environmental samples and from lysogeny studies. The spectrum of activity of the novel bacteriophages, and previously reported Bcc bacteriophage (NS1 and NS2), was determined using a panel comprising 66 isolates of the Bcc, 55 isolates representing other pseudomonads, and 40 B. pseudomallei strains. The novel phages were shown to be very promiscuous and had activity across the Bcc, with some active against P. aeruginosa, B. gladioli, and B. pseudomallei. The wide spectrum of activity was detrimental to therapeutic use, therefore, the phage-encoded lytic enzymes were the focus for further study: bacteriophage therapy with a novel twist. Two enzymes were investigated: the B. cepacia bacteriophage Bcep781 endolysin and the P. aeruginosa phage D3 endolysin. The Bcep781 phage and phage DNA was not available, therefore the endolysin gene was synthesized using recursive PCR. Briefly, twenty-two overlapping oligonucleotides encoding the entire gene were synthesized and constructed into the endolysin gene using a single PCR reaction. Both genes were cloned into an expression plasmid and the enzymes were recombinantly expressed as 6-His fusion proteins in BL21 E. coli cells. Bcep781 endolysin was purified using nickel-affinity chromatography, and the D3 lysin was purified using a Resource S® purification protocol. High-resolution mass spectrometry analysis highlighted discrepancies in both lysins, and neither proved to active against relevant bacteria tested.The activity of cationic antimicrobial peptides (CAMPs) including: a synthetic novel murine ß-defensin (Defrl) with 5-cysteine residues, which forms a covalently bound dimer; its 6-cysteine analog (Def-cys); a chemically reduced Defrl; polymyxin B and colistin; were assessed against the Bcc, as well as several multi-resistant bacterial CF pathogens. Two Bcc isolates, B. cepacia type strain ATCC 25416 and B. cenocepacia type strain J2315, were found to be inherently resistant to all CAMPs utilised in this study. Epidemic P. aeruginosa isolates were found to have a MIC of 6 μg/ml for Defrl and a MIC of 50-100 μg/ml for Def-cys, suggesting a possible relationship between defensin structure and function. Similarly, the MIC of 6 μg/ml was also noted for S. maltophilia and Ralstonia sp. that were found to be resistant to polymyxin B and colistin. The recombinant production of Defrl was also attempted in a number of expression systems in E. coli. However, although Defrl was successfully expressed, the recombinant proteins were highly insoluble. This study showed that resistance varies within the Bee. However, the data show that NZMh exerts a bactericidal effect on members of the Bcc, including B. cenocepacia J2315, and that such activity may be utilised clinically. The novel Bcc bacteriophage may prove to be a useful panel for further study, either as vectors for horizontal gene transfer or as therapeutic agents. The data confirm previous observations that the Bcc are inherently resistant to CAMPs, including a novel 5- cysteine defensin. Despite this finding, synthetic Defrl was shown to be active against a panel of multi-resistant pathogens associated with infections in CF. Further research is required to optimise the recombinant expression of Bcep781 endolysin, D3 lysin, and Defrl, to enable their use in the treatment of multiply resistant infections in CF and the wider hospital environment

Insights into bacterial colony morphology evolution and diversification during infection development in cystic fibrosis

Tese de Doutoramento em Engenharia Biomédica.Pseudomonas aeruginosa infections are the major cause of high morbidity and mortaiity in cystic fibrosis (CF) patients. Despite the long and aggressive antibiotic treatments, P. aeruginosa still persists causing chronic infections. Its Iong-persistence is due to sophisticated mechanisms of adaptation, including cional diversification into specialized CF-adapted phenotypes. While CF community awaits the development of effective therapies targeting conductance regulator mutations, the gold standard of CF disease management is the eradication of P. aeruginosa from CF lungs as soon as detected. Early eradication of P. aeruginosa avoids or, at ieast, retards the development of chronic infections preserving lung function. But to achieve a successful eradication, it is need understanding the eariy adaptations mechanisms used by P. aeruginosa for antimicrobial agents target them. Up to now these mechanisms are unclear. Being so, this project aimed to determine the early adaptations undergone by P. aeruginosa after CF lungs colonization and their driven forces in several clinical scenarios. Alterations in colony morphology are one of the indicators of cional diversification of bacteria in CF iungs and are also associated with different virulence factors expression and antibiotic resistance. Therefore, it was take the advantage of this macroscopic feature of P. aeruginosa to monitor its evolution in CF environment after in vitro initial colonization. Despite its potential, colony morphology characterisation method exhibit has some restrictions, such as the unclear impact of the experimental parameters in colony morphogenesis and detection of colony diversity, variability of vocabulary and inconsistent concepts about morphoiogical traits and the time to return results. Therefore, before analysing P. aeruginosa clonal diversification in CF environment, it was attempted to introduce some improvements on this method related to standardisation of the experimental parameters and vocabulary and speed up colony analysis in three different studies. The results of the first study demonstrated that ali experimental parameters anaiysed, including colony growth time, colony density per plate, culture media, bacterial mode of growth and bacterial genetic background influenced colony morphogenesis and the detection of bacterial diversity. Therefore, a set of guidelines was created and proposed to clinical community in order to standardise the experimental parameters. Further, a morphological classification system to unambiguously characterise and describe bacterial colonies was constructed based on literature. The system was deeply tested and demonstrated to be accurate for bacterial colonies characterisation. The third study, it was aimed to introduce some quickness and highthroughput features to coiony morpholog' characterisation verifying whether MALDI-TOF MS could distinguished morphotypes. MALDI-TOF MS colony classification did not totaily match with manual colony characterisation, leading to conclude that MALDI-TOF MS provided additional information about colony variants not visible at naked eye. MALDI-TOF MS cannot thus "replace" colony morphology method but rather complement it. The data obtained in the first study demonstrated that colony morphology characterisation could be used as a reliable method to detect biofilm-derived colony morphotypes. So, it was tried to find out a colony morphology variant characteristic of biofllm lifestyle, which' could be used as a marker of P. aeruginosa bioflim growth and the development of chronic infections. Thrèsults revealed that bioflim population diversity was highly strain-dependent, hindering the unambiguous establishrrent of a coiony variant marker of P. aeruginosa biof'ilms. Nonetheless, small colony variants (SCV) demonstrated to be a strong hint of bioflim growth. In order to investigate the early adaptations undergone by P. aeruginosa after CF Iungs colonisation, bacteria grow in artificial sputum medium during ten days in the presence and absence of ciprofloxacin, an antibiotic often used in CF context. Data revealed that substantial phenotypic diversity is likely to be present in P. aeruginosa populations shortly after CF lungs colonization. Ciprofloxacin concentrations at this simulated early stage of disease demonstrated to play dose-dependent role. lnhibitory concentrations of ciprofloxacin, established based on the MIC of biofllm celI, were effective in bacterial eradication, in contrast to the sub-inhibitory doses that triggered P. aeruginosa diversification into new "fitter" variants. lmpaired swimming motility was one of the first signs of adaptation noticed in ali P. aeruginosa clonal variants, either in the presence or absence of ciprofloxacin. It was speculated that this adaptation was triggered by the environmental CF conditions due to the absence of mutators. Being so, impaired swimming motility was considered a potential disease marker for early P. aeruginosa adaptation and infection development. It was also found that some coiony morphology traits, including sheath, size and colour, could be useful indicators of antimicrobial resistance towards some antibiotics and of some virulence factors expression. During the development of this project the comparison of morphological traits and phenotypic data among colony morphotypes was a hard task. So, to easily perform this kind of analyses it was created a new ontology-based tool for the description of colony morphologies formed by bacteria, called MorphoCol. MorphoCoi establishes and standardises in consistent way the minimum information necessary to describe colony morphotypes and also the phenotypic data related to the colony-forming bacteria. In near future, this knowledgebase will transform the findings of this project and upcoming results related to colony morphology variation into valuable information for clinical decision making. The overali data will have great impact on CF disease management because relevant improvements were introduced in the colony morphology characterisation method that will strengthen clinical diagnosis. Clonai diversification in CF lungs and other host sites could be now better monitored and accurately described. Moreover, the identification of a putative CF disease marker of eariy P. aeruginosa adaptation and infection development will also assist in the design of tailored effective antimicrobial therapies.Pseudomonas aeruginosa é a maior causa das elevadas taxas de morbidez e mortalidade associada a pacientes com fibrose cística (FC). Apesar dos longos e agressivos tratamentos com antibióticos, a P. aeruginosa persiste originando infecções crónicas. A sua longa persistência deve-se a sofisticados mecanismos de adaptação, designadamente a diversificação clonal em fenótipos altamente adaptados às condições de FC. Enquanto a comunidade médica aguarda pelo desenvolvimento de terapias eficazes direcionadas ao regulador mutacional de condutância, o standard terapêutico seguido é a erradicação da P. aeruginosa logo que detetada. A erradicação atempada da P. aeruginosa evita ou, pelo menos retarda, o desenvolvimento de infecções crónicas, preservando assim a função respiratória. Contudo, para obter a erradicação bacteriana é necessário perceber os mecanismos iniciais de adaptação da P. aeruginosa para que os agentes antimicrobianos os possam bloquear. Assim sendo, este projeto pretendeu determinar quais as adaptações iniciais da P. aeruginosa após colonização das vias respiratórias de pacientes com FC e as suas respetivas forças impulsionadoras para diversas situações clínicas. As alterações na morfologia de colónia é um dos indicadores de diversificação clonal das bactérias em ambiente de FC. Estas alterações estão igualmente associadas à expressão diferencial de factores de virulência e à resistência a antibióticos. Assim, utilizou-se esta característica macroscópica da P. aeruginosa para monitorizar a sua evolução e adaptação em ambiente FC. Apesar do seu potencial, a caracterização de morfologia de colónias apresenta algumas restrições, tais como o impacto incerto dos parâmetros experimentais na morfogénese das colónias e na detecção de diversidade de colónias, a variabilidade de vocabulário e conceitos inconsistentes sobre os traços morfológicos, e o tempo de obtenção de resultados. Assim, antes da análise da diversidade clonal da P. aeruginosa em ambiente FC, tentou-se introduzir alguns melhoramentos neste método em três diferentes estudos, nomeadamente na estandardização dos parâmetros experimentais e vocabulário, bem como acelerar a obtenção de resultados. Os resultados do primeiro estudo demonstraram que todos os parâmetros experimentais analisados (tempo de crescimento das colónias, densidade de colónias por placa de cultura, meio de cultura, modo de crescimento bacteriano e os antecedentes genéticos) influenciaram a morfogénese das colónias e na detecção de diversidade bacteriana. Assim sendo, foi elaborado e proposto um conjunto de linhas de orientação para estandardização dos parâmetros experimentais. Posteriormente, foi construído um sistema de classificação para inequivocamente caracterizar a morfologia de colónias com base na literatura. Este sistema foi amplamente testado e demonstrou-se adequado para a caracterização de colónias bacterianas. No terceiro estudo tentou-se introduzir alguma celeridade e aumento do débito de resultados verificando se MALDI-TOF MS seria capaz de distinguir os moríótipos. Esta técnica forneceu uma classificação dos morfótipos ligeiramente diferente comparativamente à classificação manual. Tal, leva a concluir que MALDI-TOF MS fornece informação adicional sobre os morfótipos que não foi observável macroscopicamente. Assim, o MALDITOF MS não pode assim substituir" o método de caracterização manual de morfologia de colónias mas pode ser um método complementar. Os dados obtidos com o primeiro estudo demonstraram que a caracterização de morfologia de colónias pode ser usado na detecção de morfótipos derivados de biofilmes. Assim, tentou-se identificar um variante morfológico característico do crescimento em biofilmes que possa ser posteriormente usado para detectar este modo de crescimento e, consequentemente o desenvolvimento de infecções crónicas. Os resultados revelaram que diversidade população dos biofilmes foi dependente da estirpe, dificultando assim a identificação do variante morfológico característico de biofilme. Ainda assim, verificou-se que as small colony vanants (SCV) são um forte indicador do crescimento séssil. De forma a investigar as adaptações iniciais da P. aeruginosa após colonização de vias respiratórias com FC, as bactérias foram crescidas em muco artificial (MA) na presença e ausência de ciprofloxacina durante 10 dias. Os resultados deste estudo revelaram que é provável a existência de diversidade fenotípica logo após a colonização das vias respiratórias. As diferentes concentrações de ciprofloxacina testadas demonstraram desempenhar uma ação dose-dependente. Concentrações inibitórias, estabelecidas com base na MIC de células de biofilme, foram eficazes na erradicação da P. aeruginosa em MA, contrariamente às concentrações sub-inibitórias. Estas concentrações "acionaram" a diversificação fenotípica em variantes melhor adaptados ao ambiente FC. A limitada capacidade de swimming foi um dos sinais de adaptação inicial da P. aeruginosa verificada em todos os variantes fenótipicos. Foi assim especulado que esta adaptação foi promovida pelas condições típicas de FC devido à ausência de mutators. Como tal, a capacidade limitada de swimming foi considerada um potencial marcador dos estágios iniciais do desenvolvimento de infecções em FC. Foi igualmente verificado que alguns traço morfológicos de colónias, nomeadamente a bainha, tamanho e cor, foram indicadores de alterações na expressão de fatores de virulência e resistência a antibióticos. Durante o desenvolvimento deste projeto a comparação de traços morfológicos das colónias, bem como de dados fenótipos foi uma tarefa árdua. Neste sentido, foi desenvolvida uma base de dados, designada por MorphoCol, para a descrição de morfologia de colónias formadas por bactérias. MorphoCol estabelece e uniformiza a informação mínima necessária de uma forma estruturada e consistente. Num futuro próximo, esta base de dados transformará os resultados deste projeto e outros subsequentes em informação relevante para a tomada de decisão clínica. O conjunto de resultados obtidos neste projeto terá um impacto considerável na gestão clínica da FC devido aos consideráveis melhoramentos introduzidos no método de caracterização de colónias pois fortalecerão o diagnóstico clínico. A diversificação clonal nas vias respiratórias de FC e nos outros locais pode ser assim melhor monitorizada e descrita adequadamente. Para além disso, a identificação de possíveis marcadores para estágios iniciais de adaptação de P. aeruginosa em FC ajudarão na definição de terapias antimicrobianas eficazes

P-Glycoprotein Expression in Canine Lymphomas

P-glycoprotein (P-gp) is a membrane glycoprotein which can act as an efflux pump for certain chemotherapeutic drugs and thereby confers resistance to these drugs on the host cell. The P-gp isoform encoded by the human mdrl gene has been implicated as a factor in clinical resistance in human tumours. To investigate the role of P-gp in acquired clinical resistance, dogs with malignant lymphoma which were referred to Glasgow University Veterinary College for treatment, were given an anthracycline based protocol until first relapse. Tumour samples were obtained from these dogs at diagnosis and at time of disease progression. P-gp expression in these samples was assessed by immunohistochemistry using a monoclonal antibody which detects all known P-gp isoforms and by dot-blot analysis using a human mdrl specific probe. Multiple members of the mdr gene family exist in every species studied and only the mdrl isoform(s) is implicated in drug resistance. Investigations of the canine mdr gene family revealed that the dog has four potential members of this family. The homologue of the human mdrl gene was expressed in normal canine liver, kidney and adrenal and at a lower level in the caudal gastro-intestinal tract. Skeletal and cardiac muscle tissue has strong P-gp expression but this did not appear to be of the mdrl homologue isoform. Immunohistochemistry revealed that normal, reactive and lymphomatous nodes contain a P-gp positive dendritic cell population. These P-gp positive cells are morphologically identical to S-100 positive cells and so may represent an antigen presenting cell population. The presence of these cells could confound accurate interpretation of the dot- blot analysis and so imunohistochemistry was used as the main criterion to determine P-gp positivity in the malignant cell population. Within tumour cells, P-gp expression at time of diagnosis was a rare occurrence (less than 5%) but was significantly more common in drug resistant tumours (p=0.0113). However, even within the drug refractory tumours, P-gp expression was not ubiquitous; only 25% of tumours were P-gp positive and therefore P-gp does not appear to be a major cause of treatment failure in canine lymphoma. Statistical analysis of the results revealed that P-gp was associated with advanced stage disease. Advanced stage at presentation seemed a more important predictor of subsequent P-gp expression than the amount or type of drugs received prior to relapse. Treatment with corticosteroids prior to chemotherapy had a profound effect on the ability to achieve remission but again this was not related to the presence of P-gp. Canine T cell lymphomas are reported to have a poorer clinical performance than B cell tumours. T cell tumours were positively identified in this group of dogs by genotyping using a feline constant region probe of the T cell receptor p chain gene. 10/45 tumours were identified as having p chain rearrangements by this technique. The T cell genotype was a poor prognostic indicator by univariate analysis but none of the T cell tumours expressed P- gp, either before treatment or at relapse, indicating that P-gp is not a major cause of treatment failure in T cell lymphomas

A Randomised Schema Mutator for Evolutionary Database Optimisation

In this paper we focus on randomised evolutionary optimisation. We introduce a general framework for the optimisation of data models, based on the concept of evolution. This evolution is guided by a randomised schema mutator. Although our approach is expressed in terms of database optimisation, our ideas are applicable to other fields of randomised evolutionary optimisation of computer models, especially when similar (graph structured) models are used. Keywords and phrases: global optimisation, evolutionary optimisation, adaptive search, randomised algorithms, conceptual data models, transformation of data models, database optimisation. 1 Introduction 1.1 Intention of the paper In this paper we describe the underlying algorithm of a Prototype Evolutionary Database Optimiser, under development at the Department of Information Systems, University of Nijmegen, The Netherlands. The paper has three main contributions. Firstly, we introduce a formal framework for nondeterministic evolution..

Investigating the diagnostic potential of circulating tumour DNA (ctDNA) as a non-invasive liquid biopsy: from research to clinic.

Recent advances in oncology have led to the development of targeted therapies, enabling patients to be treated based on their tumour molecular profile. Whilst tumour biopsies are routinely used for profiling, they can be highly invasive, may not fully reflect the heterogeneity present within the tumour mass, or accurately represent the genomic profile as the tumour evolves over time. Recent interest has focussed on the use of circulating tumour DNA (ctDNA) as a non-invasive ‘liquid biopsy’. Cell-free ctDNA, released from cancer cells, is highly fragmented, and carries the same genetic modifications present in the originating tumour, so has potential to be an exquisitely specific biomarker. This thesis will focus on research I have performed over the last decade to investigate the diagnostic potential of ctDNA. I assessed the hypothesis that ctDNA is a clinically useful biomarker, able to correlate with disease burden, monitor tumour dynamics, and be used to guide treatment. I developed novel digital PCR and next generation sequencing (NGS) assays for the highly sensitive detection of ctDNA, and led the development and analytical validation of a clinical diagnostic ctDNA test to ISO15189:2012 regulatory standards, which is now being used in the clinic to stratify advanced non-small cell lung cancer patients to treatment. This thesis involves critical analysis of 14 publications that I have co-authored investigating the use of ctDNA in high-grade serous ovarian, breast and lung cancer, and the development of novel methods to improve sensitivity of detection. When I started this work in 2009, very little was known about the clinical relevance of ctDNA. Since this time, work by myself and others has led to an explosion of interest in this area, leading to significant advances in the use of ctDNA for cancer diagnosis, treatment selection, patient monitoring and detection of minimal residual disease

A series of case studies to enhance the social utility of RSS

RSS (really simple syndication, rich site summary or RDF site summary) is a dialect of XML that provides a method of syndicating on-line content, where postings consist of frequently updated news items, blog entries and multimedia. RSS feeds, produced by organisations or individuals, are often aggregated, and delivered to users for consumption via readers. The semi-structured format of RSS also allows the delivery/exchange of machine-readable content between different platforms and systems. Articles on web pages frequently include icons that represent social media services which facilitate social data. Amongst these, RSS feeds deliver data which is typically presented in the journalistic style of headline, story and snapshot(s). Consequently, applications and academic research have employed RSS on this basis. Therefore, within the context of social media, the question arises: can the social function, i.e. utility, of RSS be enhanced by producing from it data which is actionable and effective? This thesis is based upon the hypothesis that the fluctuations in the keyword frequencies present in RSS can be mined to produce actionable and effective data, to enhance the technology's social utility. To this end, we present a series of laboratory-based case studies which demonstrate two novel and logically consistent RSS-mining paradigms. Our first paradigm allows users to define mining rules to mine data from feeds. The second paradigm employs a semi-automated classification of feeds and correlates this with sentiment. We visualise the outputs produced by the case studies for these paradigms, where they can benefit users in real-world scenarios, varying from statistics and trend analysis to mining financial and sporting data. The contributions of this thesis to web engineering and text mining are the demonstration of the proof of concept of our paradigms, through the integration of an array of open-source, third-party products into a coherent and innovative, alpha-version prototype software implemented in a Java JSP/servlet-based web application architecture