Gypsum-DL: an open-source program for preparing small-molecule libraries for structure-based virtual screening

Computational techniques such as structure-based virtual screening require carefully prepared 3D models of potential small-molecule ligands. Though powerful, existing commercial programs for virtual-library preparation have restrictive and/or expensive licenses. Freely available alternatives, though often effective, do not fully account for all possible ionization, tautomeric, and ring-conformational variants. We here present Gypsum-DL, a free, robust open-source program that addresses these challenges. As input, Gypsum-DL accepts virtual compound libraries in SMILES or flat SDF formats. For each molecule in the virtual library, it enumerates appropriate ionization, tautomeric, chiral, cis/trans isomeric, and ring-conformational forms. As output, Gypsum-DL produces an SDF file containing each molecular form, with 3D coordinates assigned. To demonstrate its utility, we processed 1558 molecules taken from the NCI Diversity Set VI and 56,608 molecules taken from a Distributed Drug Discovery (D3) combinatorial virtual library. We also used 4463 high-quality protein-ligand complexes from the PDBBind database to show that Gypsum-DL processing can improve virtual-screening pose prediction. Gypsum-DL is available free of charge under the terms of the Apache License, Version 2.0

Intelligent Tutoring System Authoring Tools for Non-Programmers

An intelligent tutoring system (ITS) is a software application that tries to replicate the performance of a human tutor by supporting the theory of learning by doing . ITSs have been shown to improve the performance of a student in wide range of domains. Despite their benefits, ITSs have not seen widespread use due to the complexity involved in their development. Developing an ITS from scratch requires expertise in several fields including computer science, cognitive psychology and artificial intelligence. In order to decrease the skill threshold required to build ITSs, several authoring tools have been developed. In this thesis, I document several contributions to the field of intelligent tutoring in the form of extensions to an existing ITS authoring tool, research studies on authoring tool paradigms and the design of authoring tools for non-programmers in two complex domains - natural language processing and 3D game environments. The Extensible Problem Specific Tutor (xPST) is an authoring tool that helps rapidly develop model-tracing like tutors on existing interfaces such as webpages. xPST\u27s language was made more expressive with the introduction of new checktypes required for answer checking in problems belonging to domains such as geometry and statistics. A web-based authoring (WAT) tool was developed for the purpose of tutor management and deployment and to promote non-programmer authoring of ITSs. The WAT was used in a comparison study between two authoring tool paradigms - GUI based and text based, in two different problem domains - statistics and geometry. User-programming of natural language processing (NLP) in ITSs is not common with authoring toolkits. Existing NLP techniques do not offer sufficient power to non-programmers and the NLP is left to expert developers or machine learning algorithms. We attempted to address this challenge by developing a domain-independent authoring tool, ConceptGrid that is intended to help non-programmers develop ITSs that perform natural language processing. ConceptGrid has been integrated into xPST. When templates created using ConceptGrid were tested, they approached the accuracy of human instructors in scoring student responses. 3D game environments belong to another domain for which authoring tools are uncommon. Authoring game-based tutors is challenging due to the inherent domain complexity and dynamic nature of the environment. We attempt to address this challenge through the design of authoring tool that is intended to help non-programmers develop game-based ITSs

NHBC Foundation: improving recruitment of young people into home building : a literature review

This literature review was undertaken to support research into young people's attitudes to careers in house building. The review is based on database searches supplemented by the evidence gathered during stakeholder interviews and through requests made to the wider careers and home building sectors. In order to fully answer the main research questions, the literature mapping the barriers faced by young people to working within the sector was explored. Based on the review a set of criteria for analysing and categorising industry sector initiatives will also be developed. The criteria will be presented as a separate compendium of opportunities.National House Builders Council Foundatio

An Intelligent Debugging Tutor For Novice Computer Science Students

Debugging is a necessary aspect of computer science that can be difficult for novices and experienced programmers alike. This skill is mainly self-taught and is generally gained through trial and error, perhaps with some assistance from a professor or other expert figure. Novices encountering their first software defects may have few avenues open to them depending on the environment in which they are learning to program. The evident problem here is that the potential for a student to become stuck, frustrated, and/or losing confidence in their ability to pursue computer science is great. For a student to be successful when working professionally or progressing through academia they need to be able to function independently; trusting their own knowledge on par or above that of others so that their productivity does not rely on the knowledge of someone else. In order to solve this problem an Intelligent Tutoring System for teaching debugging skills to the novice utilizing Case Based Reasoning, Static Program Slicing, and the student\u27s preferred learning style was proposed. Case acquisition and automatic Exercise Generation were also explored. The system built for this research program was evaluated using novice students at the College and High School levels. Results of this evaluation produced statistically significant results at the p\u3c.05 and p\u3c.01 levels, with generated exercises exhibiting significance at the p\u3c.01 level. These results prove that the methodology chosen is a valid approach for the problem described, that the system does in fact teach students how to debug programs, and that the system is capable of successfully generating exercises on the fly

Virtual Reality Games for Motor Rehabilitation

This paper presents a fuzzy logic based method to track user satisfaction without the need for devices to monitor users physiological conditions. User satisfaction is the key to any product’s acceptance; computer applications and video games provide a unique opportunity to provide a tailored environment for each user to better suit their needs. We have implemented a non-adaptive fuzzy logic model of emotion, based on the emotional component of the Fuzzy Logic Adaptive Model of Emotion (FLAME) proposed by El-Nasr, to estimate player emotion in UnrealTournament 2004. In this paper we describe the implementation of this system and present the results of one of several play tests. Our research contradicts the current literature that suggests physiological measurements are needed. We show that it is possible to use a software only method to estimate user emotion

A browser-based tool for designing query interfaces to scientific databases

Scientists in the biological sciences need to retrieve information from a variety of data collections, traditionally maintained in SQL databases, in order to conduct research. Because current assistant tools are designed primarily for business and financial users, scientists have been forced to use the notoriously difficult command-line SQL interface, supplied as standard by most database vendors. The goal of our research has been to establish the requirements of scientific researchers and develop specialized query assistance tools to help them query data collections across the Internet. This thesis describes our work in developing HyperSQL, a Web-to-database scripting language, and most importantly, Query Designer, a user-oriented tool for designing query interfaces directly on Web browsers. Current browsers (i.e., Netscape, Internet Explorer) do not easily interoperate with databases without extensive "CGI" (Common Gateway Interface) programming. HyperSQL is a scripting language that enables database administrators to construct forms-based query interfaces intended for end-users who are not proficient with SQL. Query results are formatted as hypertext-clickable links which can be used to browse the database for related information, bring up Web pages, or access remote search engines. HyperSQL query interfaces are independent of the database computer, making it possible to construct different interfaces targeting distinct groups of users. Capitalizing on our experience with HyperSQL, we developed Query Designer, a user-oriented tool for building query interfaces directly on Web browsers. No experience in SQL and HTML programming is necessary. After choosing a target database, the user can build a personalized query interface by making menu selections and filling out forms--the tool automatically establishes network connections, and composes HTML and SQL code. The automatically generated query form can be used immediately to issue a query, customized, or saved for later use. Results returned from the database are dynamically formatted into hypertext for navigating related information in the database

Evaluating humanoid embodied conversational agents in mobile guide applications

Evolution in the area of mobile computing has been phenomenal in the last few years. The exploding increase in hardware power has enabled multimodal mobile interfaces to be developed. These interfaces differ from the traditional graphical user interface (GUI), in that they enable a more “natural” communication with mobile devices, through the use of multiple communication channels (e.g., multi-touch, speech recognition, etc.). As a result, a new generation of applications has emerged that provide human-like assistance in the user interface (e.g., the Siri conversational assistant (Siri Inc., visited 2010)). These conversational agents are currently designed to automate a number of tedious mobile tasks (e.g., to call a taxi), but the possible applications are endless. A domain of particular interest is that of Cultural Heritage, where conversational agents can act as personalized tour guides in, for example, archaeological attractions. The visitors to historical places have a diverse range of information needs. For example, casual visitors have different information needs from those with a deeper interest in an attraction (e.g., - holiday learners versus students). A personalized conversational agent can access a cultural heritage database, and effectively translate data into a natural language form that is adapted to the visitor’s personal needs and interests. The present research aims to investigate the information needs of a specific type of visitors, those for whom retention of cultural content is important (e.g., students of history, cultural experts, history hobbyists, educators, etc.). Embodying a conversational agent enables the agent to use additional modalities to communicate this content (e.g., through facial expressions, deictic gestures, etc.) to the user. Simulating the social norms that guide the real-world human-to-human interaction (e.g., adapting the story based on the reactions of the users), should at least theoretically optimize the cognitive accessibility of the content. Although a number of projects have attempted to build embodied conversational agents (ECAs) for cultural heritage, little is known about their impact on the users’ perceived cognitive accessibility of the cultural heritage content, and the usability of the interfaces they support. In particular, there is a general disagreement on the advantages of multimodal ECAs in terms of users’ task performance and satisfaction over nonanthropomorphised interfaces. Further, little is known about what features influence what aspects of the cognitive accessibility of the content and/or usability of the interface. To address these questions I studied the user experiences with ECA interfaces in six user studies across three countries (Greece, UK and USA). To support these studies, I introduced: a) a conceptual framework based on well-established theoretical models of human cognition, and previous frameworks from the literature. The framework offers a holistic view of the design space of ECA systems b) a research technique for evaluating the cognitive accessibility of ECA-based information presentation systems that combine data from eye tracking and facial expression recognition. In addition, I designed a toolkit, from which I partially developed its natural language processing component, to facilitate rapid development of mobile guide applications using ECAs. Results from these studies provide evidence that an ECA, capable of displaying some of the communication strategies (e.g., non-verbal behaviours to accompany linguistic information etc.) found in the real-world human guidance scenario, is not affecting and effective in enhancing the user’s ability to retain cultural content. The findings from the first two studies, suggest than an ECA has no negative/positive impact on users experiencing content that is similar (but not the same) across different locations (see experiment one, in Chapter 7), and content of variable difficulty (see experiment two, in Chapter 7). However, my results also suggest that improving the degree of content personalization and the quality of the modalities used by the ECA can result in both effective and affecting human-ECA interactions. Effectiveness is the degree to which an ECA facilitates a user in accomplishing the navigation and information tasks. Similarly, affecting is the degree to which the ECA changes the quality of the user’s experience while accomplishing the navigation and information tasks. By adhering to the above rules, I gradually improved my designs and built ECAs that are affecting. In particular, I found that an ECA can affect the quality of the user’s navigation experience (see experiment three in Chapter 7), as well as how a user experiences narrations of cultural value (see experiment five, in Chapter 8). In terms of navigation, I found sound evidence that the strongest impact of the ECAs nonverbal behaviours is on the ability of users to correctly disambiguate the navigation of an ECA instructions provided by a tour guide system. However, my ECAs failed to become effective, and to elicit enhanced navigation or retention performances. Given the positive impact of ECAs on the disambiguation of navigation instructions, the lack of ECA-effectiveness in navigation could be attributed to the simulated mobile conditions. In a real outdoor environment, where users would have to actually walk around the castle, an ECA could have elicited better navigation performance, than a system without it. With regards to retention performance, my results suggest that a designer should not solely consider the impact of an ECA, but also the style and effectiveness of the question-answering (Q&A) with the ECA, and the type of user interacting with the ECA (see experiments four and six, in Chapter 8). I found that that there is a correlation between how many questions participants asked per location for a tour, and the information they retained after the completion of the tour. When participants were requested to ask the systems a specific number of questions per location, they could retain more information than when they were allowed to freely ask questions. However, the constrained style of interaction decreased their overall satisfaction with the systems. Therefore, when enhanced retention performance is needed, a designer should consider strategies that should direct users to ask a specific number of questions per location for a tour. On the other hand, when maintaining the positive levels of user experiences is the desired outcome of an interaction, users should be allowed to freely ask questions. Then, the effectiveness of the Q&A session is of importance to the success/failure of the user’s interaction with the ECA. In a natural-language question-answering system, the system often fails to understand the user’s question and, by default, it asks the user to rephrase again. A problem arises when the system fails to understand a question repeatedly. I found that a repetitive request to rephrase the same question annoys participants and affects their retention performance. Therefore, in order to ensure effective human-ECA Q&A, the repeat messages should be built in a way to allow users to figure out how to ask the system questions to avoid improper responses. Then, I found strong evidence that an ECA may be effective for some type of users, while for some others it may be not. I found that an ECA with an attention-grabbing mechanism (see experiment six, in Chapter 8), had an inverse effect on the retention performance of participants with different gender. In particular, it enhanced the retention performance of the male participants, while it degraded the retention performance of the female participants. Finally, a series of tentative design recommendations for the design of both affecting and effective ECAs in mobile guide applications in derived from the work undertaken. These are aimed at ECA researchers and mobile guide designers

Intelligence by Design: Principles of Modularity and Coordination for Engineerin

All intelligence relies on search --- for example, the search for an intelligent agent's next action. Search is only likely to succeed in resource-bounded agents if they have already been biased towards finding the right answer. In artificial agents, the primary source of bias is engineering. This dissertation describes an approach, Behavior-Oriented Design (BOD) for engineering complex agents. A complex agent is one that must arbitrate between potentially conflicting goals or behaviors. Behavior-oriented design builds on work in behavior-based and hybrid architectures for agents, and the object oriented approach to software engineering. The primary contributions of this dissertation are: 1.The BOD architecture: a modular architecture with each module providing specialized representations to facilitate learning. This includes one pre-specified module and representation for action selection or behavior arbitration. The specialized representation underlying BOD action selection is Parallel-rooted, Ordered, Slip-stack Hierarchical (POSH) reactive plans. 2.The BOD development process: an iterative process that alternately scales the agent's capabilities then optimizes the agent for simplicity, exploiting tradeoffs between the component representations. This ongoing process for controlling complexity not only provides bias for the behaving agent, but also facilitates its maintenance and extendibility. The secondary contributions of this dissertation include two implementations of POSH action selection, a procedure for identifying useful idioms in agent architectures and using them to distribute knowledge across agent paradigms, several examples of applying BOD idioms to established architectures, an analysis and comparison of the attributes and design trends of a large number of agent architectures, a comparison of biological (particularly mammalian) intelligence to artificial agent architectures, a novel model of primate transitive inference, and many other examples of BOD agents and BOD development