Miracle-dz/UniFAR-FTUs huggingface dataset:
DMS: A Package for Multiscale Molecular Dynamics

Advances in multiscale theory and computation provide a novel paradigm for simulating many-classical particle systems. The Deductive Multiscale Simulator (DMS) is a multiscale molecular dynamics (MD) program built on two of these advances, i.e., multiscale Langevin (ML) and multiscale factorization (MF). Both capture the coevolution of the the coarse-grained (CG) state and the microstate. This provides these methods with great efficiency over conventional MD. Neither involve the introduction of phenomenological governing equations for the CG state with attendant uncertainty in both their form of the governing equations and the data needed to calibrate them. The design and implementation of DMS as an open source computational platform is presented here. DMS is written in Python, uses Gromacs to achieve the microphase, and then advances the microstate via a CG-guided evolution. DMS uses MDAnalysis, a Python library for analyzing MD trajectories, to perform computations required to construct CG-related variables and an ensemble of microstates. DMS is structured to allow for user-specific methods and CG variables. All computations require only an interatomic force field and an initial atom-resolved state.
EXPRESSIVE VIRTUAL 3D CITY MODELS

Virtual 3D city models include components such as 3D building models, transportation network models, and vegetation models. Traditional applications of virtual 3D city models focus on presenting photorealistic views. The potential of 3D city models, however, goes beyond virtual reality. In general, virtual 3D city models can serve as user interfaces to complex, spatial urban information, that is, for exploration, analysis, and communication of thematic and spatial information. For the last decades, the intrinsic concepts of real-time 3D computer graphics lead to near-photorealistic, interactive virtual 3D city models. With the recent advent of non-photorealistic 3D rendering, a new genre in computer graphics, a repertoire of illustrative, expressive, and artistic graphics techniques becomes viable to developers and designers of virtual city models. This contribution outlines main techniques and discusses consequences for cartographic information display based on 3D city models.
Visual Mining of Science Citation Data for Benchmarking Scientific and Technological Competitiveness of World Countries

In this paper we present a study where we visually analyzed science citation data to investigate the competitiveness of world countries in selected categories of science. The dataset that we worked on in our study includes the number of papers published and the number of citations made in the ESI (Essential Science Indicators) database in 2004. The dataset lists these values for practically every country in the world. In analyzing the data, we employ methods and software tools developed and used in the data mining and information visualization fields of the Computer Science. Some of the questions for which we look for answers in this study are the following: (a) Which countries are most competitive in the selected categories of science? (i.e. Engineering, Computer Science, Economics & Business) (b) What type of correlations exist between different categories of science? For example, do countries with many published papers in the field of Engineering science also have many papers published on Computer Science or Economics & Business? (c) Which countries produce the most influential papers? This analysis is needed since a country may have many papers published but these papers may be cited very rarely. (d) Can we gain useful and actionable insights by combining science citation data with socioeconomic and geographical data?
Pronominal Resolution in Automatic Text Summarisation

Automatic text summarisation is the technique where a computer program summarises a text. One summarisation technique is to, on linguistical and statistical grounds, extract sentences that are central to the text and use them to form a shorter text, the summary. In this case, automatically summarised text can sometimes result in dangling anaphors (i.e. broken anaphoric references). This is due to the fact that the sentences are extracted without making any deeper linguistic analysis of the text. We will in this thesis show a novel method to resolve some types of pronouns and to summarise the text such that coherence and important information is preserved. The method is implemented as a text pre-processor, called PRM (Pronoun Resolution Module) written in Perl. PRM uses lists of likely focuses (Sidner 1984), here called focus applicants. These lists are by order of insertion sorted in order of likelihood. Choice of applicant for an anaphor is based upon salience (represented by the antecedents position in a list) and semantic likelihood (based on what list the antecedent is to be found in). The latter is determined by using semantic information in a noun lexicon. This method enables us to resolve anaphors non-linearly. The domain is Swedish HTML-tagged newspaper text. A live version of the automatic summariser SweSum and PRM can be found at http://www.nada. kth.se/~xmartin.
Filthy Rich Clients: Developing Animated and Graphical Effects for Desktop Java Applications (The Java Series)

Filthy Rich Clients refers to ultra-graphically rich applications that ooze cool. They suck the user in from the outset and hang on to them with a death grip of excitement. Filthy Rich Clients: Developing Animated and Graphical Effects for Desktop Java™ Applications shows you how to build better, more effective, cooler desktop applications that intensify the user experience.The keys to Filthy Rich Clients are graphical and animated effects. These kinds of effects provide ways of enhancing the user experience of the application through more attractive GUIs, dynamic effects that give your application a pulse, and animated transitions that keep your user connected to the logical flow of the application. The book also discusses how to do so effectively, making sure to enrich applications in sensible ways.In-depth coverage includes Graphics and GUI fundamentals: Dig deep into the internals of how Swing and Java 2D work together to display GUI applications onscreen. Learn how to maximize the flexibility of these libraries and use them most effectively. Performance: Follow in-depth discussions and tips throughout the book that will help you write high-performing GUI applications. Images: Understand how images are created and used to make better Java applications. Advanced graphics: Learn more about elements of Swing and Java 2D that are of particular benefit to Filthy Rich Clients. Animation: Discover general concepts of animation, as well as how to use the facilities provided in the Java platform. Learn new utility libraries that vastly simplify animations in Java. Effects: Learn how to create, customize, and use static and animated effects-the mainstays of Filthy Rich Clients. Code examples illustrate key concepts, and the book's companion Web site, http://filthyrichclients.org, includes extensive demos, utility libraries, additional information on related technologies, and more.Informal, fun, and, most of all, useful, this book is great for any developer working with Java to build desktop applications.
Comparing Improved Language Models for Sentence Retrieval inQuestion Answering

A retrieval system is a very important part in a question answering framework. It reduces the number of documents to be considered for finding an answer. For further refinement, the documents are split up into smaller chunks to deal with topic variability in larger documents. In our case, we divided the documents into single sentences. Then a language model based approach was used to re-rank the sentence collection. For this purpose, we developed a new language model toolkit. It implements all standard language modeling techniques and is more flexible than other tools in terms of backingoff strategies, model combinations and design of the retrieval vocabulary. With the aid of this toolkit we conducted re-ranking experiments with standard language model based smoothing methods. On top of these algorithms we developed some new, improved models including dynamic stop word reduction and stemming. We also experimented with query expansion depending on the type of a query. On a TREC corpus, we demonstrate that our proposed approaches provide a performance superior to the standard methods. In terms of Proceedings of the 17th Meeting of Computational Linguistics in the Netherlands Edited by: Peter Dirix, Ineke Schuurman, Vincent Vandeghinste, and Frank Van Eynde. Copyright c 2007 by the individual authors.
Hardware Performance Monitoring in Memory of NUMAchine Multiprocessor

This thesis reflects on the aspects of hardware performance monitoring in multiprocessors. More specifically, it deals with the hardware designed and implemented for performance monitoring in the main memory of the cache-coherent, shared-memory NUMAchine multiprocessor. It also elaborates on the factors that affect performances and some of the cost-effective hardware features used in NUMAchine to measure these factors without intruding on software performance.Hardware monitoring in the memory of NUMAchine is used to measure performance during peak memory activity based on the transaction types, to collect statistical data on page accesses and finally to probe on cache line accesses at a fine or coarse granularity level. Also described is how these hardware performance measurements provide insight into various bottlenecks that cause performance degradation in multiprocessors.
Studies in the psychology of computer text editing systems

Six studies of user interaction with on-line computer text editing systems are reported. Editing times· for benchmark tasks on several editing systems were collected to gauge the range of performance across systems. Using the measured times, it was possible to predict when an editing system would outperform a typewriter. To model the user's behavior in greater detail, an information processing model of editing performance is proposed describing the user's "goals", "operators", "methods", and "selection rules". An important issue in such a nlOdelis how the model's accuracy depends on the grain of analysis. To find out, the model was recast at nine different levels of grain size and the accuracy of the different versions compared. From observations of users on several different systems, it was discovered that on each task, the users go through a similar sequence of task assimilation, target location, target modification, and verification. This concept of a "unit task cycle" was used to predict rough performance times for a proposed system prior to system specification. With respect to the target location part of a task, four devices for pointing to a target were compared and modeled. Using Fitts's Law, it is argued that the time for the best of these devices, the mouse, approaches the theoretical minimum. Finally, a Monte Carlo simulation model using gamma-distributed operator times and stochastic method selection rules is described, with which sequences of user actions, time per task, and the distribution of time can be predicted. The picture of user behavior that emerges from these studie~ is related to, but distinct from, behavior in classical problem-solving studies. The main difference is that the methods are almost certain of success. For any subproblem the user simply recalls the solution from his experience rather than working it out. Hence there is no search. Such behavior is expected to be found in many cognitive tasks in industrial work and daily life which people perform repetitively, tasks the report calls "routine cognitive skills. "
Adapting Problem Frames to eXtreme Programming

Lightweight software development methods like eXtreme Programming (XP) can benefit from the expansion of their practices by the judicious application of techniques from other methods. This paper shows how Problem Frames can be coupled with the “stories” method of requirements capture used in XP to further explore the problem space and synergistically derive requirements.
Local Binary Patterns for Still Images

The local binary pattern operator is an image operator which transforms an image into an array or image of integer labels describing small-scale appearance of the image. These labels or their statistics, most commonly the histogram, are then used for further image analysis. The most widely used versions of the operator are designed for monochrome still images but it has been extended also for color (multi channel) images as well as videos and volumetric data. This chapter covers the different versions of the actual LBP operator in spatial domain [42, 45, 53], while Chap. 3 deals with spatiotemporal LBP [88]. Parts II to IV of this book discuss how the labels are then used in different computer vision tasks.
Learning to hear: the emergence of spectro-temporal response flelds in a model of auditory cortex.

The responses of cortical neurons are often characterized by measuring their spectro-temporal response flelds (strfs) which embody the stimulus ‘preferences’ of a cortical unit. A range of in vivo strfs with varying properties have been reported in various species, although none in humans. Using a computational model it has been shown that responses of ensembles of artiflcial strfs, or linear kernels derived from limited sets of formative stimuli, preserve information about utterance class and prosody as well as the identity and sex of the speaker in a model speech classiflcation system. In this work we help to put this idea on a biologically plausible footing by developing a simple model thalamo-cortical system built of conductance based neurons and synapses some of which exhibit spike-timedependent plasticity. We show that such a model develops an ensemble of strfs with varying temporal properties and exhibiting a range of heterotopic integration when exposed to various sets of formative stimuli. The proposed model, with its simple architecture, learning rule, and modest number of neurons (< 1000), is suitable for implementation in neuromorphic analogue VLSI hardware and hence could form the basis of a developmental, real time, neuromorphic sound classiflcation system.
Using HTML Formatting to Aid in Natural Language Processing on the World Wide Web

Because of its magnitude and the fact that it is not computer understandable, the World Wide Web has become a prime candidate for automatic natural language tasks. This thesis argues that there is information in the layout of a web page, and that by looking at the HTML formatting in addition to the text on a page, one can improve performance in tasks such as learning to classify segments of documents. A rich representation for web pages, the HTML Struct Tree, is described. A parsing algorithm for creating Struct Trees is presented, as well as a set of experiments that use Struct Trees as a feature set for learning to extract a company's name and location from its Web pages. Through these experiments we found that it is useful to consider the layout of a page for these tasks.
A Cultural Historical Activity Theory Approach in Natural Sciences Education Laboratory Lessons towards Reforming Teachers Training.

This paper focuses on connecting natural sciences education with Cultural Historical Activity Theory (CHAT). In this sense, natural sciences education is considered as a lifelong learning procedure, not seen as an individual but as a collective activity. Moreover, learning becomes a human activity in which theory and praxis are strongly connected and learning outcomes are obviously seen in society and culture. The paper is a review of five years research on natural sciences education from a CHAT perspective in the Department of Early Childhood Education in the University of Ioannina, Greece. Effort is put on using CHAT as a theoretical framework in order to analyze and design natural sciences education activities. In this regard, teaching natural sciences in a university laboratory becomes a dynamic activity system which involves multiple participants (university teachers, lab assistants, students, early grade pupils etc.). All the participants act towards some common goals, considering scientific knowledge as cultural, historical and social process and using meditative and analyzing tools. Scientific concepts are taught as part of the natural curriculum of natural sciences education at the early grades which is strongly connected with CHAT. At this level scientific learning is connected with inquiring in authentic environments, practicing skills of observation, classification, communication etc., and making sense of the relations and interactions that take place in the world around us. The research question addressed in this paper is to highlight some qualitative dimensions of the socio-cultural aspect of teaching natural sciences in the early grades. Research data have been collected during practical application of lab activities in the early childhood classrooms by observing, video recording, interviewing and analyzing. This part involves university teachers, lab assistants, students, early childhood teachers, early grade pupils who work as a community towards reforming of natural sciences education.
Improving spatial awareness in an indoor environment withwireless positioning technology

The contribution of indoor wireless technology to solve the indoor wayfinding problem is potentially big. However, no structured way of describing indoor environments exists today. Also indoor wireless positioning technologies are just emerging and there is not yet a dominant technology. In this thesis a structure to functionally describe indoor environments is developed. Elements of indoor environments are identified. Using these functional elements it is possible to describe a position at four different layers of abstraction, ranging from local view to a rough view of the environment, based on the main functions. After experimental results indoor GPS is ruled out as wireless indoor positioning technology. Experiments with WLAN show that this technology is able to provide high accuracy at a low cost. This technology combined with the developed structure opens up possibilities for various applications, particularly in the area of indoor wayfinding and navigation systems. Especially the possibility to functionally describe the indoor environment at different layers of granularity will improve the spatial awareness of users.
LICAI+: A Comprehension-Based Model of The Recall of Action Sequences

This paper presents a model of occasional use of functions of an application by an experienced user of an environment like Windows 95 or the MacOS. We have developed a simulation model, LICAI+, that assumes that users store episodic records of correct steps discovered by exploration or told to them during training. They then use the application display and their goal as retrieval cues in attempts to recall these episodes later. The model predicts, and supporting data show, that tasks that violate the label-following strategy are not only hard to learn by exploration but also difficult to remember even if the correct steps have been previously presented.
Isolation, Resource Management and Sharing in the Kaffeos Java Runtime System

Single-language runtime systems, in the form of Java virtual machines, are widely deployed platforms for executing untrusted mobile code. These runtimes provide some of the features that operating systems provide: interapplication memory protection and basic system services. They do not, however, provide the ability to isolate applications from each other. Neither do they provide the ability to limit the resource consumption of applications. Consequently, the performance of current systems degrades severely in the presence of malicious or buggy code that exhibits ill-behaved resource usage. In this dissertation, we show that Java runtime systems can be extended to provide a process model, and that such a process model can provide robust and efficient support for untrusted applications. Processes are an operating system abstraction in which each process executes as if it were run in its own virtual machine. We have designed and prototyped KaffeOS, which is a Java runtime system that provides support for processes. KaffeOS isolates processes and manages the physical resources available to them, in particular: CPU and memory. Each process is given its own heap, which can be separately garbage collected. Unlike existing Java virtual machines, KaffeOS can safely terminate processes without adversely affecting the integrity of the system, and it can fully reclaim a terminated process’s resources. The novel aspects of the KaffeOS architecture include the application of a user/kernel boundary as a structuring principle to runtime systems, the employment of garbage collection techniques for resource management and isolation, and a model for direct sharing of objects between untrusted applications. The difficulty in designing KaffeOS lay in balancing the goals of isolation and resource management against the goal of allowing direct sharing of objects. We built a prototype of our design and ran the SPEC JVM 98 benchmarks to evaluate its performance for well-behaved applications. We found that for those applications, our KaffeOS prototype is no more than 8% slower than the freely available JVM on which it is based, which is an acceptable penalty for the safety that it provides. At the same time, our KaffeOS prototype can support more applications than a hardware-based approach on the same platform. We demonstrate that in the presence of malicious or buggy code that engages in a denial-of-service attack directed against resources, KaffeOS-based systems can contain the attack, remove resources from the attacked applications, and continue to provide robust service to other clients.
Graphs & Digraphs, Fifth Edition

Continuing to provide a carefully written, thorough introduction, Graphs & Digraphs, Fifth Edition expertly describes the concepts, theorems, history, and applications of graph theory. Nearly 50 percent longer than its bestselling predecessor, this edition reorganizes the material and presents many new topics. New to the Fifth Edition New or expanded coverage of graph minors, perfect graphs, chromatic polynomials, nowhere-zero flows, flows in networks, degree sequences, toughness, list colorings, and list edge colorings New examples, figures, and applications to illustrate concepts and theorems Expanded historical discussions of well-known mathematicians and problems More than 300 new exercises, along with hints and solutions to odd-numbered exercises at the back of the book Reorganization of sections into subsections to make the material easier to read Bolded definitions of terms, making them easier to locate Despite a field that has evolved over the years, this student-friendly, classroom-tested text remains the consummate introduction to graph theory. It explores the subjects fascinating history and presents a host of interesting problems and diverse applications.