DVMS 1.5: A user manual (the data visualization and modeling system)

The data available during the drug discovery process is vast in amount and diverse in nature. To gain useful information from such data, an effective visualisation tool is required. To provide better visualisation facilities to the domain experts (screening scientist, biologist, chemist, etc.),we developed a software which is based on recently developed principled visualisation algorithms such as Generative Topographic Mapping (GTM) and Hierarchical Generative Topographic Mapping (HGTM). The software also supports conventional visualisation techniques such as Principal Component Analysis, NeuroScale, PhiVis, and Locally Linear Embedding (LLE). The software also provides global and local regression facilities . It supports regression algorithms such as Multilayer Perceptron (MLP), Radial Basis Functions network (RBF), Generalised Linear Models (GLM), Mixture of Experts (MoE), and newly developed Guided Mixture of Experts (GME). This user manual gives an overview of the purpose of the software tool, highlights some of the issues to be taken care while creating a new model, and provides information about how to install & use the tool. The user manual does not require the readers to have familiarity with the algorithms it implements. Basic computing skills are enough to operate the software.

Design and implementation of graphical user interfaces for complex simulations

The development of increasingly powerful computers, which has enabled the use of windowing software, has also opened the way for the computer study, via simulation, of very complex physical systems. In this study, the main issues related to the implementation of interactive simulations of complex systems are identified and discussed. Most existing simulators are closed in the sense that there is no access to the source code and, even if it were available, adaptation to interaction with other systems would require extensive code re-writing. This work aims to increase the flexibility of such software by developing a set of object-oriented simulation classes, which can be extended, by subclassing, at any level, i.e., at the problem domain, presentation or interaction levels. A strategy, which involves the use of an object-oriented framework, concurrent execution of several simulation modules, use of a networked windowing system and the re-use of existing software written in procedural languages, is proposed. A prototype tool which combines these techniques has been implemented and is presented. It allows the on-line definition of the configuration of the physical system and generates the appropriate graphical user interface. Simulation routines have been developed for the chemical recovery cycle of a paper pulp mill. The application, by creation of new classes, of the prototype to the interactive simulation of this physical system is described. Besides providing visual feedback, the resulting graphical user interface greatly simplifies the interaction with this set of simulation modules. This study shows that considerable benefits can be obtained by application of computer science concepts to the engineering domain, by helping domain experts to tailor interactive tools to suit their needs.

Accessing networked services : a user interface design problem

This research investigates the general user interface problems in using networked services. Some of the problems are: users have to recall machine names and procedures to. invoke networked services; interactions with some of the services are by means of menu-based interfaces which are quite cumbersome to use; inconsistencies exist between the interfaces for different services because they were developed independently. These problems have to be removed so that users can use the services effectively. A prototype system has been developed to help users interact with networked services. This consists of software which gives the user an easy and consistent interface with the various services. The prototype is based on a graphical user interface and it includes the following appJications: Bath Information & Data Services; electronic mail; file editor. The prototype incorporates an online help facility to assist users using the system. The prototype can be divided into two parts: the user interface part that manages interactlon with the user; the communicatIon part that enables the communication with networked services to take place. The implementation is carried out using an object-oriented approach where both the user interface part and communication part are objects. The essential characteristics of object-orientation, - abstraction, encapsulation, inheritance and polymorphism - can all contribute to the better design and implementation of the prototype. The Smalltalk Model-View-Controller (MVC) methodology has been the framework for the construction of the prototype user interface. The purpose of the development was to study the effectiveness of users interaction to networked services. Having completed the prototype, tests users were requested to use the system to evaluate its effectiveness. The evaluation of the prototype is based on observation, i.e. observing the way users use the system and the opinion rating given by the users. Recommendations to improve further the prototype are given based on the results of the evaluation. based on the results of the evah:1ation. . .'. " "', ':::' ,n,<~;'.'

Interaction of peptides, peptidomimetics and other drug candidates with the DI/tripeptide transport system in intestinal epithelial cells, using the in vitro caco-2 cell culture system

An uptake system was developed using Caco-2 cell monolayers and the dipeptide, glycyl-[3H]L-proline, as a probe compound. Glycyl-[3H]L-proline uptake was via the di-/tripeptide transport system (DTS) and, exhibited concentration-, pH- and temperature-dependency. Dipeptides inhibited uptake of the probe, and the design of the system allowed competitors to be ranked against one another with respect to affinity for the transporter. The structural features required to ensure or increase interaction with the DTS were defined by studying the effect of a series of glycyl-L-proline and angiotensin-converting enzyme (ACE)-inhibitor (SQ-29852) analogues on the uptake of the probe. The SQ-29852 structure was divided into six domains (A-F) and competitors were grouped into series depending on structural variations within specific regions. Domain A was found to prefer a hydrophobic function, such as a phenyl group, and was intolerant to positive charges and H+ -acceptors and donors. SQ-29852 analogues were more tolerant of substitutions in the C domain, compared to glycyl-L-proline analogues, suggesting that interactions along the length of the SQ-29852 molecule may override the effects of substitutions in the C domain. SQ-29852 analogues showed a preference for a positive function, such as an amine group in this region, but dipeptide structures favoured an uncharged substitution. Lipophilic substituents in domain D increased affinity of SQ-29852 analogues with the DTS. A similar effect was observed for ACE-NEP inhibitor analogues. Domain E, corresponding to the carboxyl group was found to be tolerant of esterification for SQ-29852 analogues but not for dipeptides. Structural features which may increase interaction for one series of compounds, may not have the same effect for another series, indicating that the presence of multiple recognition sites on a molecule may override the deleterious effect of anyone change. Modifying current, poorly absorbed peptidomimetic structures to fit the proposed hypothetical model may improve oral bioavailability by increasing affinity for the DTS. The stereochemical preference of the transporter was explored using four series of compounds (SQ-29852, lysylproline, alanylproline and alanylalanine enantiomers). The L, L stereochemistry was the preferred conformation for all four series, agreeing with previous studies. However, D, D enantiomers were shown in some cases to be substrates for the DTS, although exhibiting a lower affinity than their L, L counterparts. All the ACE-inhibitors and β-lactam antibiotics investigated, produced a degree of inhibition of the probe, and thus show some affinity for the DTS. This contrasts with previous reports that found several ACE inhibitors to be absorbed via a passive process, thus suggesting that compounds are capable of binding to the transporter site and inhibiting the probe without being translocated into the cell. This was also shown to be the case for oligodeoxynucleotide conjugated to a lipophilic group (vitamin E), and highlights the possibility that other orally administered drug candidates may exert non-specific effects on the DTS and possibly have a nutritional impact. Molecular modelling of selected ACE-NEP inhibitors revealed that the three carbonyl functions can be oriented in a similar direction, and this conformation was found to exist in a local energy-minimised state, indicating that the carbonyls may possibly be involved in hydrogen-bond formation with the binding site of the DTS.

The interaction between the implementation of an occupational health and safety management system and safety culture:a case study in the rubber industry

A prominent theme emerging in Occupational Health and Safety (OSH) is the development of management systems. A range of interventions, according to a prescribed route detailed by one of the management systems, can be introduced into an organisation with some expectation of improved OSH performance. This thesis attempts to identify the key influencing factors that may impact upon the process of introducing interventions, (according to B88800: 1996, Guide to Implementing Occupational Health and Safety Management Systems) into an organisation. To help identify these influencing factors a review of possible models from the sphere of Total Quality Management (TQM) was undertaken and the most suitable TQM model selected for development and use in aSH. By anchoring the aSH model's development in the reviewed literature a range ofeare, medium and low level influencing factors were identified. This model was developed in conjunction with the research data generated within the case study organisation (rubber manufacturer) and applied to the organisation. The key finding was that the implementation of an OSH intervention was dependant upon three broad vectors of influence. These are the Incentive to introduce change within an organisation which refers to the drivers or motivators for OSH. Secondly the Ability within the management team to actually implement the changes refers to aspects, amongst others, such as leadership, commitment and perceptions of OSH. Ability is in turn itself influenced by the environment within which change is being introduced. TItis aspect of Receptivity refers to the history of the plant and characteristics of the workforce. Aspects within Receptivity include workforce profile and organisational policies amongst others. It was found that the TQM model selected and developed for an OSH management system intervention did explain the core influencing factors and their impact upon OSH performance. It was found that within the organisation the results that may have been expected from implementation of BS8800:1996 were not realised. The OSH model highlighted that given the organisation's starting point, a poor appreciation of the human factors of OSH, gave little reward for implementation of an OSH management system. In addition it was found that general organisational culture can effectively suffocate any attempts to generate a proactive safety culture.

An information foraging theory based user study of an adaptive user interaction framework for content-based image retrieval

This paper presents the design and results of a task-based user study, based on Information Foraging Theory, on a novel user interaction framework - uInteract - for content-based image retrieval (CBIR). The framework includes a four-factor user interaction model and an interactive interface. The user study involves three focused evaluations, 12 simulated real life search tasks with different complexity levels, 12 comparative systems and 50 subjects. Information Foraging Theory is applied to the user study design and the quantitative data analysis. The systematic findings have not only shown how effective and easy to use the uInteract framework is, but also illustrate the value of Information Foraging Theory for interpreting user interaction with CBIR. © 2011 Springer-Verlag Berlin Heidelberg.

Applying Information Foraging Theory to understand user interaction with content-based image retrieval

The paper proposes an ISE (Information goal, Search strategy, Evaluation threshold) user classification model based on Information Foraging Theory for understanding user interaction with content-based image retrieval (CBIR). The proposed model is verified by a multiple linear regression analysis based on 50 users' interaction features collected from a task-based user study of interactive CBIR systems. To our best knowledge, this is the first principled user classification model in CBIR verified by a formal and systematic qualitative analysis of extensive user interaction data. Copyright 2010 ACM.

Enabling effective user interactions in content-based image retrieval

This paper presents an interactive content-based image retrieval framework—uInteract, for delivering a novel four-factor user interaction model visually. The four-factor user interaction model is an interactive relevance feedback mechanism that we proposed, aiming to improve the interaction between users and the CBIR system and in turn users overall search experience. In this paper, we present how the framework is developed to deliver the four-factor user interaction model, and how the visual interface is designed to support user interaction activities. From our preliminary user evaluation result on the ease of use and usefulness of the proposed framework, we have learnt what the users like about the framework and the aspects we could improve in future studies. Whilst the framework is developed for our research purposes, we believe the functionalities could be adapted to any content-based image search framework.

Multi-Agent Security System based on Neural Network Model of User's Behavior

It is proposed an agent approach for creation of intelligent intrusion detection system. The system allows detecting known type of attacks and anomalies in user activity and computer system behavior. The system includes different types of intelligent agents. The most important one is user agent based on neural network model of user behavior. Proposed approach is verified by experiments in real Intranet of Institute of Physics and Technologies of National Technical University of Ukraine "Kiev Polytechnic Institute”.

Comparing interaction techniques for serious games through brain-computer interfaces:a user perception evaluation study

This paper examines the application of commercial and non-invasive electroencephalography (EEG)-based brain-computer (BCIs) interfaces with serious games. Two different EEG-based BCI devices were used to fully control the same serious game. The first device (NeuroSky MindSet) uses only a single dry electrode and requires no calibration. The second device (Emotiv EPOC) uses 14 wet sensors requiring additional training of a classifier. User testing was performed on both devices with sixty-two participants measuring the player experience as well as key aspects of serious games, primarily learnability, satisfaction, performance and effort. Recorded feedback indicates that the current state of BCIs can be used in the future as alternative game interfaces after familiarisation and in some cases calibration. Comparative analysis showed significant differences between the two devices. The first device provides more satisfaction to the players whereas the second device is more effective in terms of adaptation and interaction with the serious game.

Integrating service user and practitioner expertise within a web-based system for collaborative mental-health risk and safety management

Objectives: To develop a decision support system (DSS), myGRaCE, that integrates service user (SU) and practitioner expertise about mental health and associated risks of suicide, self-harm, harm to others, self-neglect, and vulnerability. The intention is to help SUs assess and manage their own mental health collaboratively with practitioners. Methods: An iterative process involving interviews, focus groups, and agile software development with 115 SUs, to elicit and implement myGRaCE requirements. Results: Findings highlight shared understanding of mental health risk between SUs and practitioners that can be integrated within a single model. However, important differences were revealed in SUs' preferred process of assessing risks and safety, which are reflected in the distinctive interface, navigation, tool functionality and language developed for myGRaCE. A challenge was how to provide flexible access without overwhelming and confusing users. Conclusion: The methods show that practitioner expertise can be reformulated in a format that simultaneously captures SU expertise, to provide a tool highly valued by SUs. A stepped process adds necessary structure to the assessment, each step with its own feedback and guidance. Practice Implications: The GRiST web-based DSS (www.egrist.org) links and integrates myGRaCE self-assessments with GRiST practitioner assessments for supporting collaborative and self-managed healthcare.

Signal processing and information fusing algorithms for the synthesis of an alternative electromyogram/eye gaze tracking computer cursor control system

This research pursued the conceptualization and real-time verification of a system that allows a computer user to control the cursor of a computer interface without using his/her hands. The target user groups for this system are individuals who are unable to use their hands due to spinal dysfunction or other afflictions, and individuals who must use their hands for higher priority tasks while still requiring interaction with a computer. ^ The system receives two forms of input from the user: Electromyogram (EMG) signals from muscles in the face and point-of-gaze coordinates produced by an Eye Gaze Tracking (EGT) system. In order to produce reliable cursor control from the two forms of user input, the development of this EMG/EGT system addressed three key requirements: an algorithm was created to accurately translate EMG signals due to facial movements into cursor actions, a separate algorithm was created that recognized an eye gaze fixation and provided an estimate of the associated eye gaze position, and an information fusion protocol was devised to efficiently integrate the outputs of these algorithms. ^ Experiments were conducted to compare the performance of EMG/EGT cursor control to EGT-only control and mouse control. These experiments took the form of two different types of point-and-click trials. The data produced by these experiments were evaluated using statistical analysis, Fitts' Law analysis and target re-entry (TRE) analysis. ^ The experimental results revealed that though EMG/EGT control was slower than EGT-only and mouse control, it provided effective hands-free control of the cursor without a spatial accuracy limitation, and it also facilitated a reliable click operation. This combination of qualities is not possessed by either EGT-only or mouse control, making EMG/EGT cursor control a unique and practical alternative for a user's cursor control needs. ^

A digital signal processing approach for affective sensing of a computer user through pupil diameter monitoring

Recent research has indicated that the pupil diameter (PD) in humans varies with their affective states. However, this signal has not been fully investigated for affective sensing purposes in human-computer interaction systems. This may be due to the dominant separate effect of the pupillary light reflex (PLR), which shrinks the pupil when light intensity increases. In this dissertation, an adaptive interference canceller (AIC) system using the H∞ time-varying (HITV) adaptive algorithm was developed to minimize the impact of the PLR on the measured pupil diameter signal. The modified pupil diameter (MPD) signal, obtained from the AIC was expected to reflect primarily the pupillary affective responses (PAR) of the subject. Additional manipulations of the AIC output resulted in a processed MPD (PMPD) signal, from which a classification feature, PMPDmean, was extracted. This feature was used to train and test a support vector machine (SVM), for the identification of stress states in the subject from whom the pupil diameter signal was recorded, achieving an accuracy rate of 77.78%. The advantages of affective recognition through the PD signal were verified by comparatively investigating the classification of stress and relaxation states through features derived from the simultaneously recorded galvanic skin response (GSR) and blood volume pulse (BVP) signals, with and without the PD feature. The discriminating potential of each individual feature extracted from GSR, BVP and PD was studied by analysis of its receiver operating characteristic (ROC) curve. The ROC curve found for the PMPDmean feature encompassed the largest area (0.8546) of all the single-feature ROCs investigated. The encouraging results seen in affective sensing based on pupil diameter monitoring were obtained in spite of intermittent illumination increases purposely introduced during the experiments. Therefore, these results confirmed the benefits of using the AIC implementation with the HITV adaptive algorithm to isolate the PAR and the potential of using PD monitoring to sense the evolving affective states of a computer user.

A practical system for hands-off computer interaction based on electromyogram (EMG)/eye gaze tracking (EGT)

Effective interaction with personal computers is a basic requirement for many of the functions that are performed in our daily lives. With the rapid emergence of the Internet and the World Wide Web, computers have become one of the premier means of communication in our society. Unfortunately, these advances have not become equally accessible to physically handicapped individuals. In reality, a significant number of individuals with severe motor disabilities, due to a variety of causes such as Spinal Cord Injury (SCI), Amyothrophic Lateral Sclerosis (ALS), etc., may not be able to utilize the computer mouse as a vital input device for computer interaction. The purpose of this research was to further develop and improve an existing alternative input device for computer cursor control to be used by individuals with severe motor disabilities. This thesis describes the development and the underlying principle for a practical hands-off human-computer interface based on Electromyogram (EMG) signals and Eye Gaze Tracking (EGT) technology compatible with the Microsoft Windows operating system (OS). Results of the software developed in this thesis show a significant improvement in the performance and usability of the EMG/EGT cursor control HCI.