Stuart Watt

Turalt Inc. · Research and Development

Importance Real-world data sets that combine clinical and genomic data may be subject to left truncation (when potential study participants are not included because they have already passed the milestone of interest at the time of study recruitment). The lapse between diagnosis and molecular testing can present analytic challenges and threaten the...

Importance Contemporary observational cancer research requires associating genomic biomarkers with reproducible end points; overall survival (OS) is a key end point, but interpretation can be challenging when multiple lines of therapy and prolonged survival are common. Progression-free survival (PFS), time to treatment discontinuation (TTD), and ti...

The cBioPortal for Cancer Genomics provides intuitive visualization and analysis of complex cancer genomics data. The public site (http://cbioportal.org/) is accessed by more than 1,500 researchers per day, and there are now dozens of local instances of the software that host private data sets at cancer centers around the globe. We have recently re...

Motivation: Alignment-based sequence similarity searches, while accurate for some type of sequences, can produce incorrect results when used on more divergent but functionally related sequences that have undergone the sequence rearrangements observed in many bacterial and viral genomes. Here, we propose a classification model that exploits the comp...

This paper reports on an approach to the analysis of form (layout and formatting) during genre recognition recorded using eye tracking. The researchers focused on eight di erent types of e-mail, such as calls for papers, newsletters and spam, which were chosen to represent di erent genres. The study involved the collection of oculographic behaviour...

Next-generation sequencing technologies provide an unparallelled opportunity for the characterization and discovery of known and novel viruses. Because viruses are known to have the highest mutation rates when compared to eukaryotic and bacterial organisms, we assess the extent to which eleven well-known alignment algorithms (BLAST, BLAT, BWA, BWA-...

11016 Background: NGS techniques enable the identification of actionable mutations in clinical tumor samples. The objective of this study is to assess feasibility and explore the impact of real-time targeted NGS on therapeutic decision-making. Methods: Patients (pts) with advanced solid tumors underwent a biopsy of a metastatic lesion. The first ph...

Using sequencing information to guide clinical decision-making requires coordination of a diverse set of people and activities. In clinical genomics, the process typically includes sample acquisition, template preparation, genome data generation, analysis to identify and confirm variant alleles, interpretation of clinical significance, and reportin...

The successes of targeted drugs with companion predictive biomarkers and the technological advances in gene sequencing have generated enthusiasm for evaluating personalized cancer medicine strategies using genomic profiling. We assessed the feasibility of incorporating real-time analysis of somatic mutations within exons of 19 genes into patient ma...

Evidence shows the vital role that the quality of feedback plays on students' performance and on the overall increase of learning opportunities that good feedback creates for students. Based on this evidence, the Open University developed Open Mentor (OM), a system to support tutors enhance their feedback practice. Open Mentor Technology transfer (...

It is now well established that nearly 20% of human cancers are caused by infectious agents, and the list of human oncogenic pathogens will grow in the future for a variety of cancer types. Whole tumor transcriptome and genome sequencing by next-generation sequencing technologies presents an unparalleled opportunity for pathogen detection and disco...

Table S1. Short tandem repeat sequence (STR) analysis in OVCA0016. Table S1 shows that the top 10 results with the highest arbitrary evaluation value (EV) are 293T and other corresponding variants (HKb20, ProPak-X.36, ProPak-A.52...).

Assessment has been identified as one of the major challenges faced by Higher Education Institutions (Whitelock, et al, 2007). As a response to the challenge, in a project funded by the Joint Information Systems Committee (JISC) the Open University developed Open Mentor (OM), a learning support tool for tutors to help them reflect on the quality of...

Proceedings: AACR 103rd Annual Meeting 2012‐‐ Mar 31‐Apr 4, 2012; Chicago, IL Background:We are conducting a multicenter clinical trial to evaluate the feasibility of including next-generation sequencing in routine clinical care. Study goals are to determine patient acceptance of research biopsies for genomic sequencing, optimal methods and proced...

Assessment has been identified as one of the major challenges faced by Higher Education Institutions (Whitelock, et al, 2007). As a response to the challenge, in a project funded by the Joint Information Systems Committee (JISC) the Open University developed Open Mentor (OM), a learning support tool for tutors to help them reflect on the quality of...

e13107 Background: Clinical genomics uses information from a patient's genome in clinical decision-making, an example of personalized medicine. The OICR/UHN Genomics Cohort Study is assessing the feasibility and developing standard operating procedures for clinical genomics in late stage cancer patients to enable larger trials. Tumor DNA from conse...

Assessment has been identified as one of the major challenges faced by Higher Education Institutions (Whitelock, et al, 2007). As a response to the challenge, in a project funded by the Joint Information Systems Committee (JISC) Open Mentor (OM) was developed as a learning support tool for tutors to help them reflect on the quality of feedback give...

Background: As the development of molecularly targeted agents is increasingly linked to predictive biomarkers, there is a need for novel strategies of cancer genome characterization at the point of care. This study assesses the feasibility of biopsying pts with advanced solid cancers for MP using both targeted exome sequencing and targeted mutation...

Introduction: What is Text Categorisation?How to Build a Text Categorisation SystemEvaluating Text Categorisation SystemsGenre: Text Structure and PurposeRelated Techniques: Information FilteringApplications of Text CategorisationSummary and the Future of Text CategorisationExercisesReferences

This chapter is about how we might assess the difference between human minds and machine minds. It is divided into two parts. The first briefly explores how machines might decide whether humans are intelligent, and parallels Turing’s 1950 article closely. The second explores a hypothetical legal case in somewhat more detail, looking at Turing’s Tes...

Over the past 10 years, learning and teaching have benefited from greater use of social constructivist and situated learning, through more widespread adoption of the ideas of Dewey, Piaget, Vygotsky and Bruner (e.g., Lave and Wenger 1991; Brown 2004). However, assessment has consistently failed to follow through these innovations, substantially bec...

One of the more challenging aspects in the current e-assessment milieu is to provide a set of electronic interactive tasks that will allow students more free text entry and provide immediate feedback to them. The specific objective of the project was to construct some simple tools in the form of Moodle extensions that allow a Moodle author to ask f...

The categorization of documents is traditionally topic-based. This paper presents a complementary analysis of research and experiments on genre to show that encouraging results can be obtained by using genre structure (form) features. We conducted an experiment to assess the effectiveness of using eXtensible Mark-Up Language (XML) tag information,...

We present a novel approach to mine word similarity in Textual Case Based Reasoning. We exploit indirect associations of words, in addition to direct ones for estimating their similarity. If word A co-occurs with word B, we say A and B share a first order association between them. If A co-occurs with B in some documents, and B with C in some others...

Latent Semantic Indexing (LSI) has been shown to be effective in recovering from synonymy and pol- ysemy in text retrieval applications. However, since LSI ignores class labels of training documents, LSI generated representations are not as effective in classification tasks. To address this limitation, a process called 'sprinkling' is presented. Sp...

This chapter examines the ways in which currently available software applications can support the creative process in general, and designers, in particular, working in virtual teams. It follows the main stages in the design process, examining how existing software can support the creative process. Emerging innovations for each stage of the design p...

This chapter examines the ways in which currently available software applications can support the creative process in general, and designers, in particular, working in virtual teams. It follows the main stages in the design process, examining how existing software can support the creative process. Emerging innovations for each stage of the design p...

One of the problems with tutor feedback to students is that a balanced combination of socio emotive and cognitive support is required from the teaching staff, and the feedback needs to be relevant to the assigned grade. Is it possible to capitalise on technology to build training systems for tutors in Higher Education, that will support them with t...

This paper describes the participation of the Information Retrieval and Interaction group of Robert Gordon University in the INEX 2006 ad hoc track. We focused on two questions: “What potential evidence do human assessors use to identify relevant XML elements?” and “How can this evidence be used by computers for the same task?”. Our main strategy w...

This paper describes the participation of the Information Re-trieval and Interaction group of Robert Gordon University in the INEX 2006 ad hoc track. We focused on two questions: "What potential evi-dence do human assessors use to identify relevant XML elements?" and "How can this evidence be used by computers for the same task?". Our main strategy...

Case Retrieval Networks (CRNs) facilitate flexible and efficient retrieval in Case-Based Reasoning (CBR) systems. While CRNs scale up well to handle large numbers of cases in the case-base, the retrieval efficiency is still critically determined by the number of feature values (referred to as Information Entities) and by the nature of similarity re...

We report here an evaluation of a story segmentation technique based on narrative discourse text. The research was carried out using three different term weighting functions with Hearst's TextTiling algorithm (Hearst 1997) for detecting subject boundaries within text. We explored also the effectiveness of three interacting factors in this algorithm...

Agents have for a while been a key concept in artificial intelligence, but often all that the word refers to is a computational process or task with a capability for autonomous action, either alone or in an artificial society of similar agents. However, the artificial nature of these societies restricts the flexibility of agents to a point where so...

Latent Semantic Indexing (LSI) has been shown to be effective in recovering from synonymy and polysemy in text retrieval applications. However, since LSI ignores class labels of training documents, LSI generated representations are not as effective in classification tasks. To address this limitation, a process called ‘sprinkling’ is presented. Sprin...

VITAL is a research and development project which aims to provide methodological and software support for developing large, embedded KBS applications. VITAL is novel in that its ambition is to develop a methodology-based workbench covering the whole KBS life-cycle, from requirements specification to implementation, and to integrate and deploy a num...

Blogs are highly rich in opinion making their au- tomatic processing appealing to marketing compa- nies, the media, costumer centres, etc. TREC ran a Blog track in 2006 with two tasks: opinion retrieval and an open task. This document reports the ex- periments conducted at The Robert Gordon Uni- versity (RGU) where we used Statistical Language Mode...

A person reading a book needs to gain insights based on the text. In most books, stories, themes, and references are organized structurally and purposefully. In previous work, we presented the design of an e-Book user interface that reveals the multi-structural information to support reading for comprehension[1]. In this paper, we describe techniqu...

In this paper we present the concept of Federated Information Sharing Communities (FISC), which leverages organisational and social relationships with document content to provide community-centred information sharing and communication environments. Prominence is given to capabilities that go beyond the generic retrieval of documents to include the...

Current e-Book browsers provide minimal support for comprehending the organization, narrative structure, and themes, of large complex books. In order to build an understanding of such books, readers should be provided with user interfaces that present, and relate, the organizational, narrative and thematic structures. We propose adapting informatio...

In this paper we describe the concept of Federated Information Sharing Communities (FISC), and associated architecture, which provide a way for organisations, distributed workgroups and individuals to build up a federated community based on their common interests over the World Wide Web. To support communities, we develop capabilities that go beyon...

In this demonstration, we will show a context-aware information system intended for mobile users. The demonstration involves special-purpose hardware devices, called 'context tags', which can work with mobile devices such as mobile phones, to provide ambient information to users on the move. Key to the framework is special support for content servi...

Virtual Learning Environments provide the possibility of offering additional support to tutors, monitors and students in writing and grading essays and reports. They enable monitors to focus on the assignments that need most attention. This paper reports the findings from phase one of a feasibility study to assist the monitoring of student essays....

Virtual Learning Environments provide the possibility of offering additional support to tutors, monitors and students in writing and grading essays and reports. They enable monitors to focus on the assignments that need most attention. This paper reports the findings from phase one of a feasibility study to assist the monitoring of student essays....

The internet offers considerable potential for open and distance learning in psychology. Research reveals an abundance of psychology demonstrations and experiments available online, directed both at students and potential research participants. Although expertise is being developed to overcome the technical problems associated with this medium, the...

Opening up large amounts of loosely structured information for easy access and use is a complex problem. This paper describes two systems that address different aspects of the problem, but which use common technology and similar underlying principles. Open Book is a web-based newslet- ter, which automatically links stories with each other, and with...

The widespread use of computers and of the internet have brought about human information overload, particularly in the areas of internet searches and email management. This has made Knowledge Management a necessity, particularly in a business context. Agent technology – with its metaphor of agents as assistants – has shown promise in the area of in...

Nowadays, document management is a challenging necessity, especially for businesses. A particularly difficult but essential document management task is that of email management within corporate mailing lists. This paper will show how information extraction, retrieval and integration can be combined to deliver a powerful software tool to extract inf...

This paper discusses an electronic course survey system designed to support evaluation of a modular programme in management taught through distance education. The scale and communication issues raised by distance education, when compounded by a complex rolling modular programme, make conventional evaluation complicated, slow and expensive. To overc...

This is a conference paper. This paper reports the findings from a preliminary study, which set out to test a number of metrics and heuristics that will form the basis of an electronic monitoring system for postgraduate level assignments. Such a (web-based) system would augment the University’s electronic ‘Tutor Marked Assignment’ (e-TMA) infrastru...

Cognitive modelling involves building computational models of psychological theories in order to learn more about them, and is a major research area allied to psychology and artificial intelligence. The main problem is that few psychology students have previous programming experience. The course lecturer can avoid the problem by presenting the area...

. VITAL is a research and development project which aims to provide methodological and software support for developing large, embedded KBS applications. VITAL is novel in that its ambition is to develop a methodology-based workbench covering the whole KBS lifecycle, from requirements specification to implementation, and to integrate and deploy a nu...

Knowledge management systems are used widely in many different organizations, yet there are few models and theories which can be used to help introduce and apply them successfully. In this paper, we analyze some of the more common problems for knowledge management systems. Using this background, we adapt models and theories from social and organiza...

: This document describes the remote message passing system developed in T3.1.1 to prove the technical feasibility of Lisp-to-C++ communication between different processes and machines. Author: Stuart Watt Collaborators (VITAL Partners): SYSECA - SYSECA TEMPS REEL (Coordinator) NOTT - UNIVERSITY OF NOTTINGHAM BULL - BULL CEDIAG AC - ANDERSEN CONSUL...

This report was originally written in May 1992, following a HCRL internal seminar; and the content hasn't really changed since, although the views---and hopefully the wisdom---of the author have deviated from the text here. Comments will still be gratefully received; email address "S.N.K.Watt@open.ac.uk". Page 1 Introduction

This paper argues that the psychology of programming is at least partly 'psychological' in character, rather than being purely physical or computational. That is, when people are learning a programming language, or an execution model for a programming language, they think about them almost as homunculi — agents which act according to beliefs, desir...

Cognitive modelling involves building computational models of psychological theories in order to learn more about them, and is a major research area allied to psychology and artificial intelligence. The main problem is that few psychology students have previous programming experience. The course lecturer can avoid the problem by presenting the area...

VITAL is a research and development project which aims to provide methodological and software support for developing large, embedded KBS applications. VITAL is novel in that its ambition is to develop a methodology-ba sed workbench covering the whole KBS life- cycle, from requirements specification to implementatio n, and to integrate and deploy a...

Agents have for a while been a key concept in artificial intelligence, but often all that the word refers to is a computational process or task with a capability for autonomous action, either alone or in an artificial society of similar agents. However the artificial nature of these societies restricts the flexibility of agents to a point where soc...

This thesis is about common-sense psychology and its role in cognitive science. Put simply, the argument is that common-sense psychology is important because it offers clues to some complex problems in cognitive science, and because common-sense psychology has significant effects on our intuitions, both in science and on an everyday level. The thes...

An abstract is not available.

This report was originally written in May 1992, following a HCRL internal seminar; and the content hasn't really changed since, although the views---and hopefully the wisdom---of the author have deviated from the text here. Comments will still be gratefully received; email address "S.N.K.Watt@open.ac.uk". Page 1 Introduction

Agents have for a while been a key concept in artificial intelligence, but often all that the word refers to is a computational process or task with a capability for autonomous action, either alone or in an artificial society of similar agents. But the artificial nature of these societies restricts the flexibility of agents to a point where social...

This paper argues that the Turing test implicitly rests on a `naive psychology,' a naturally evolved psychological faculty which is used to predict and understand the behaviour of others in complex societies. This natural faculty is an important and implicit bias in the observer's tendency to ascribe mentality to the system in the test. The paper a...

This paper argues that artificial intelligence has failed to address the whole problem of common sense, and that this is the cause of a recent stagnation in the field. The big gap is in common sense---or naive---psychology, our natural human ability to see one another as minds rather than as bodies. This is especially important to artificial intell...

Complex development environments which use languages of diverse styles and purposes have special problems efficiently managing their data. Generally there are two alternatives; first, marking the text with extra codes, and second, using a tool capable of structuring the data, such as an object management system. For many purposes, something between...

A fundamental problem of AI is that of how to simulate a particular kind of behaviour -- that of intelligence. This paper describes an alternative approach to reproducing action systems by a geometric analysis of behaviour. If the behaviour to be reproduced has a particular character, a character identified by a self-affinity like that of fractal i...

Popple (1996) argues that the inverted Turing test should be seen as a replicable scientific experiment. I suggest that while the research method this implies may be appropriate, the Turing test itself should not be seen as a scientific test.

Groupware and computer-supported cooperative work (CSCW) systems are usually considered collaborative, but some kinds of group activity can actually be competitive. The author examines the differences between systems with one role and with several roles and how this potential conflict between the different roles arises. Design rules are provided to...

Groupware and computer supported cooperative work (CSCW) systems are usually considered collaborative, but some kinds of group activity can actually be competitive. People can have different roles which conflict because they are trying to satisfy different intermediate goals associated with their roles, even though there may appear to be a single c...

Hank is a visual cognitive modelling language designed specifically for psychology students. The aim in designing Hank was to create an experience of cognitive modelling that focused on gaining a new perspective on psychological models rather than programming for its own sake. Recent informal analyses have investigated the effectiveness of Hank in...

We present an approach to visualize textual case bases by "stacking" similar cases and features close to each other in an image derived from the case-feature matrix. We propose a complexity measure called GAME that exploits regularities in stacked images to evaluate the alignment between problem and solution components of cases. GAME class , a coun...

Many communities exist that learn and share information either partly or wholly online. These (wholly or partially) on-line communities share messages, documents, and other artefacts that contain useful community knowledge. Members of the community learn through this sharing process, and the growing archive they create forms a valuable learning res...

This is a conference paper. Assessment is one of the major challenges for higher education today. This is partly because it traditionally squares the desire for improved constructivist learning against the demand for institutional reliability and accountability. The call for a pedagogically-driven model for e-Assessment was acknowledged as part of...