Miracle-dz/UniFAR-FTUs huggingface dataset:
Exploring Static Checking for Software Assurance

A key missing link in the creation of practically secure systems is finding a cost effective way to demonstrate and preserve correspondence between a software design and its implementation. This paper explores the use of software model checking techniques to validate selected design invariants in the EROS operating system kernel. Several global consistency policies in the EROS kernel can be expressed as finite state automata. Using the MOPS static checker, we have been able to validate the EROS kernel implementation against these automata. In the process, we have confirmed the practical utility of the basic verification technique, identified a number of desirable enhancements in MOPS, and located a small number of bugs in the EROS implementation. Current commodity assurance processes have no objectively verifiable benefit, while the formal verification needed for high assurance evaluation is expensive and requires specialized expertise. To date, no effective middle ground solution has emerged. Our work with EROS and MOPS suggests that domain specific application of software model checking is a practical and powerful technique for software assurance and maintenance.
Decoding heterogeneous big data in an integrative way

Biotechnologies in post-genomic era, especially those that generate data in highthroughput, bring opportunities and challenges that are never faced before. And one of them is how to decode big heterogeneous data for clues that are useful for biological questions. With the exponential growth of a variety of data, comes with more and more applications of systematic approaches that investigate biological questions in an integrative way. Systematic approaches inherently require integration of heterogeneous information, which is urgently calling for a lot more efforts. In this thesis, the effort is mainly devoted to the development of methods and tools that help to integrate big heterogeneous information. In Chapter 2, we employed a heuristic strategy to summarize/integrate genes that are essential for the determination of mouse retinal cells in the format of network. These networks with experimental evidence could be rediscovered in the analysis of high-throughput data set and thus would be useful in the leverage of high-throughput data. In Chapter 3, we described EnRICH, a tool that we developed to help qualitatively integrate heterogeneous intra-organism information. We also introduced how EnRICH could be applied to the construction of a composite network from different sources, and demonstrated how we used EnRICH to successfully prioritize retinal disease genes. Following the work of Chapter 3 (intra-organism information integration), in Chapter 4 we stepped to the development of method and tool that can help deal with inter-organism information integration. The method we proposed is able to match genes in a one-to-one fashion between any two genomes. In summary, this thesis contributes to integrative analysis of big heterogeneous data by its work on the integration of intraand inter-organism information
Real-time performance of a movement-sensitive neuron in the blowfly visual system: coding and information transfer in short spike sequences

We develop model-independent methods for characterizing the information carried by particular features of a neural spike train as it encodes continuously varying stimuli. These methods consist, in essence, of an inverse statistical approach; instead of asking for the statistics of neural responses to a given stimulus we describe the probability distribution of stimuli that give rise to a certain short pattern of spikes. These ‘response-conditional ensembles’ contain all the information about the stimulus that a hypothetical observer of the spike train may obtain. The structure of these distributions thus provides a quantitative picture of the neural code, and certain integrals of these distributions determine the absolute information in bits carried by a given spike sequence. These methods are applied to a movement-sensitive neuron (H1) in the visual system of the blowfly Calliphora erythrocephala. The stimulus is chosen as the time-varying angular velocity of a (spatially) random pattern, and we consider segments of the spike train of up to three spikes with specified spike-intervals. We demonstrate that, with extensive analysis, a single experiment of roughly one hour’s duration is sufficient to provide reliable estimates of the relevant probability distributions. From the experimentally determined probability distributions we are able to draw several conclusions. (1) Under the conditions of our experiment, observation of a single spike carries roughly 0.36 bits of information, but spike pairs carry an interval-dependent signal that can be much larger than 0.72 bits; estimates of the total information capacity are in rough agreement with the maximum possible capacity given the signal-to-noise characteristics of the photoreceptors. (2) On average a single spike signals the occurrence of a velocity waveform that is positive (movement in the excitatory direction) at all times before the spike, whereas spike pairs can signal both positive and negative velocities, depending on the inter-spike interval. (3) Although inter-spike intervals are crucial in extracting all the coded information, the code is robust to several millisecond errors in the estimate of spike arrival times. (4) Short spike sequences give reliable information about specific features of the stimulus waveform, and this specificity can be quantified. (5) Our results suggest approximate strategies for reading the neural code – reconstructing the stimulus from observations of the spike train – and some preliminary reconstructions are presented. Some tentative attempts are made to relate our results to the more general questions of coding and computation in the nervous system.
An adaptive overflow technique for B-trees (extended abstract)

Abstrac t We present a new overflow technique for the B-tree. The technique is a hybrid of partial expansions and unbalanced splits. This technique is asymmetric and adaptive. Considering a growing file (only insertions), the storage utilization is 77% for random keys, 70% for sorted keys, and over 75% for non-uniform distributed keys. Similar results are achieved when we have deletions mixed with insertions. One of the main properties of this technique is that the storage utilization is very stable with respect to changes of the data distribution. This technique may be used for other bucket-based file structures, like extendible hashing or bounded disorder files.
Feature-Oriented Modelling Using Event-B

Event-B is a formal method for specification and verification of reactive systems. Its Rodin toolkit provides comprehensive support for modelling, refinement and analysis using theorem proving, animation and model checking. There has always been a need to reuse existing models and their associated proofs when modelling related systems to save time and effort. Software product lines (SPLs) focus on the problem of reuse by providing ways to build software products having commonalities and managing variations within products of the same family. Feature modelling is a well know technique to manage variability and configure products within the SPLs. We have combined the two approaches to formally specify SPLs using Event-B. This will contribute the concept of formalism to SPLs and re-usability to Event-B. Existing feature modelling notations were adapted and extended to include refinement mechanism of Event-B. An Eclipse-based graphical feature modelling tool has been developed as a plug-in to the Rodin platform. We have modelled the `production cell' case-study in Event-B, an industrial metal processing plant, which has previously been specified in a number of formalisms. We have also highlighted future directions based on our experience with this framework so far.
On-line stochastic processes in data compression

Program Authorized to OOer Degree Date In presenting this dissertation in partial fullllment of the requirements for the Doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. I further agree that extensive copying of this dissertation is allowable only for scholarly purposes, consistent with \fair use" as prescribed in the U.S. to whom the author has granted \the right to reproduce and sell (a) copies of the manuscript in microform and/or (b) printed copies of the manuscript made from microform. " The ability to predict the future based upon the past in nite-alphabet sequences has many applications, including communications, data security, pattern recognition, and natural language processing. By Shannon's theory and the breakthrough development of arithmetic coding, any sequence, a 1 a 2 a n , can be encoded in a number of bits that is essentially equal to the minimal information-lossless codelength, P i ? log 2 p(a i ja 1 a i? 1). The goal of universal on-line modeling, and therefore of universal data compression, is to deduce the model of the input sequence a 1 a 2 a n that can estimate each p(a i ja 1 a i? 1) knowing only a 1 a 2 a i? 1 so that the expected value of ? log p(a i ja 1 a i? 1) is minimized. Thus, data compression has become both a routine application of on-line modeling techniques and a means for accurately measuring their empirical performance. The on-line modeling algorithm, Prediction By Partial Matching (PPM), has set the performance standard in data compression research since its introduction in 1984. PPM's success stems from its ad hoc probability estimator, which dynamically blends distinct frequency distributions contained in a single model into a probability estimate for each input symbol. Meanwhile, the most conclusive asymptotic results use an information-theoretic metric to dynamically select a model from a set of competing models, and then use that selected model to estimate the currently scanned symbol's probability. Our hypothesis is that these apparently unrelated approaches can be combined to produce a semantically coherent technique that is arguably universal and which consistently outperforms existing techniques on actual data. To prove our hypothesis, we rst give a semantics that uniies both forms of on-line modeling. Then we show how related but linguistically distinct model families t the semantics, and give a new frequency update mechanism that is …
BOSF: BY-OWNER SCRIPT FILTERING

Cross-Site Scripting (XSS) attacks are one of the most prevalent security threats all over the world. Although various defense methods have been proposed, most of them lack usability. Motivated by this reason, we present a location-based solution, called By-Owner Script Filtering (BOSF), which determines whether a script on a webpage can be executed or not using either the rules defined in the webpage or the information fetched from our database based on the ownership. BOSF is effective against various XSS attacks with minimal performance overheads, and more importantly, it places little requirements on developers and users.
Analysis and visualization of gene expression data

Today, gene expression data is acquired with increasing speed with increasing quality and depth. High throughput technologies like DNA microarrays and next generation sequencing technologies have led to a rising pace of new discoveries in the biomedical field. These technologies are complemented by high throughput pipelines for proteomics and metabolomics profiling. Altogether, vast amounts of primary measured data, complementary data from other omics and meta information from many sources is available for researchers. This data needs to be jointly analyzed and visualized in context of external data and meta information. In this thesis, new tools and concepts are introduced for the purpose of visualizing gene expression data in the context of meta information and complementary data from other “omics” experiments. First, the application of generic visualization tools to resequencing microarrays, which are used for finding mutations in single genes is discussed. For this final step of gene expression analysis, an application called ResqMi, (“Resequencing using Microarrays”) is presented that allows to use generic and adapted visualization tools on resequencing microarrays, in order to improve quality control, data analysis and revision of problematic base calls. The focus of this work is on the visualization of gene expression data. Here, new tools for the visualization of gene expression data in the context of meta information from processing results and external sources, like functional annotations are introduced. For the visualization of clustered gene expression data, profile logos extend the concept of sequence logos to expression data. Chromograms and tag clouds, tools for visualizing different properties of collections of nominal data are applied in combination in order to explore temporal, spatial and other patters in annotations of gene expression data. Furthermore, enhanced tabular views of summarized gene annotations and genes ranked by statistical values are discussed for comparative visualization of textual and numeric meta data. Graph based visualizations of gene expression and meta data are more generic and investigated in greater detail. Most tools for visualizing biological pathways do not make full use of gene expression or meta information data. Here, a variety of ways to include gene expression data into biological network visualizations is investigated and implemented, based both on the node rendering and the layout of the graph. This allows dense, high dimensional visualizations. Specialized tools that are optimized for working with pathways in KEGG and BioPax formats, are presented as well as MGV (the Mayday Graph Viewer), a general tool for visualizing a wide range of biological networks that offers a full range of options within a rich, extensible user interface. Options for integration and creation of network data, data organization and analysis within the graph framework are investigated. MGV furthermore incorporates tools for integrating
Cheminement de décrocheurs et de décrocheuses

L’objectif de cette etude a methodologie mixte menee aupres de 32 decrocheurs est d’identifier les facteurs de risque d’abandon scolaire et de decrire leurs cheminements dans leurs milieux de vie. Un volet quantitatif sert a identifier les facteurs de risque, alors qu’un volet qualitatif permet de decrire le vecu des participants. Les resultats montrent que les participants ont fait face a un cumul de facteurs de risque alors qu’ils etaient inscrits a l’ecole secondaire. Aussi le discours des jeunes montre-t-il que, pour plusieurs, les difficultes vecues a l’enfance dans la famille les ont conduits progressivement vers l’abandon. Les difficultes rencontrees en milieu scolaire sont parfois attribuables a l’eleve, parfois a son interaction avec ce milieu et ses intervenants.
Dagstuhl-Workshop MBEES: Modellbasierte Entwicklung eingebetteter Systeme III, Schloss Dagstuhl, Germany, 15.-18. Januar 2007, Tagungsband Modellbasierte Entwicklung eingebetteter Systeme

The development of embedded systems is a challenging task because of the distributed, reactive and real-time nature of such systems. Distribution of embedded components across buses and networks causes high interaction complexity. We propose a model-based development approach to handle this complexity. We model the individual functionalities of the system – the services – independently from each other in an interaction modeling and architecture definition language. Methodological steps allow us to refine and modify the models. A development process determines the order in which to perform the steps. Our service-oriented development methodology spans the entire development process from requirements analysis to implementation, verification and validation. We have developed integrated tool support that governs this process; it provides an effective means to apply and evaluate our approach. In this paper we introduce our service-oriented methodology and describe our tool as part of an integrated tool suite supporting this process by means of an automotive example: the Central Locking System (CLS).
Features of Visual Representation

Systems of receptive elds (RFs) are probably the most prominent and ubiquitous computational mechanism employed in biological information processing, and, in particular, in vision. A natural question suggested by the hierarchy of RF types found in the visual pathway is, what is it good for? It may seem that the answer is to be found, jointly, in the many models of visual function based on population coding of various stimulus qualities, especially as some of these models draw explicit parallels between the representations they employ and the RFs found in biological vision. However, mere invocation of the idea of population coding, if not accompanied by a computational (in the sense of Marr, 1982) statement of what it is that the visual system does with its representations, simply begs the question: At all levels of the visual system, complex objects appear to be coded by the activity of populations, or networks, of cells, and the representation of a particular object may be widely distributed throughout one or more visual areas. That said, the goal of the anatomical pathway for object recognition becomes less obvious. The photoreceptors are a population of cells, for example, and they are necessarily capable of coding, by their population response, any conceivable stimulus. Why are subsequent populations needed? (Desimone and Ungerleider, 1989, p.268). A number of recent works that do address the computational problem of representation tend to employ information-theoretic terms such as redundancy reduction and eecient coding This seminar series will survey and compare the diierent computational characterizations of the features of visual representation, and will discuss the relevance of the proposed approaches to the problem of representing 3D shape.
Part–Of–Speech Tagging using by Hidden Markov Model and Named Entity Recognition

In this investigation we verify and confirm the availability of Hidden Markov Model that is widely used for English morphological analysis. Unfortunately it is impossible to identify Named Entity because of unknown word problem (that dosen’t appear in training deta), though it is an important issue in morphological analysis. Here to recognize Named Entity correctly, we introduce conjunction table using by 2 gram.
Analysis and efficient classification of P2P file sharing traffic

Since the advent of P2P networks they have grown to be the biggest source of internet traffic, superseding HTTP and FTP. For service providers P2P traffic results in in­ creased costs for both infrastructure and transportation. Interest is high to reliably identify the type of service to ensure quality of service. In this document we analyze P2P network ar­ chitectures and give an overview of existing identification mechanisms. In addition we devise a simple identification scheme suitable for implementation in resources restricted environ­ ments with limited computational power and memory. The scheme is based on behavior analysis and as such is not prone to traffic obfuscation techniques.
A modified FDTD method for the analysis of wide and dual band antennas

Abstract (Document Summary) This thesis uses a modified Finite-Difference Time-Domain (FDTD) method to examine several wide and dual band antenna structures. The FDTD method is a finite difference approximation to Maxwell's equation that is solved in the time domain. Frequency domain results are obtained by taking the Fourier transform of the time-domain result. Recent advances in the FDTD method such as the Convolutional Perfectly Matched Layer (CPML) were necessary for such analysis of certain structures and have been used for simulation in this thesis. Some improvements in the implementation of the boundary conditions and in the CPML implementation have been documented and the new Floating Perfectly Matched Layer (Floating PML) has been introduced. The historical and mathematical development of the FDTD method is also discussed. The code itself is written in object-oriented C++ and has been partially optimized for speed. It has been written so that microstrip and stripline structures are particularly easy to implement. Because the code fully implements Maxwell's equations, the radiation characteristics of antennas are correctly modeled when designing microstrip structures. The code has been verified with simple to more complicated antenna structures such as microstrip-fed dielectric resonator antennas (DRA)
Análise da evolução de software com séries temporais

A software system is never finished. Even after it was delivered, the software continues to evolve. For this reason, governments, businesses, open-source communities and spend a lot of resources regularly to correct, improve or adapt their software systems. In some works it is said that 90% of the resources of companies dedicated to software, are spent on maintenance activities. This indicates that only 10% is devoted to other activities including the development of new projects. This represents an opportunity, with better planning, to make the software process more efficient, which should yield significant economic benefits. The ability to develop software quickly and reliably is a major challenge in Software Engineering. One possible technique to help reducing costs without sacrificing software quality is the forecast of their behavior in the future. For project managers and developers to predict the evolution of the software will be useful, because it will help directing efforts for parts that require more intervention. Analysing the life history of the software, which is normally stored in the repositories of the projects or, in some cases, data repositories. In this dissertation we will analyse the evolution of the Eclipse IDE, using time series. Our analysis will cover not only the evolution over time but also allow predicting its evolution in the future. This will use the source code repository of the eclipse, in combination with the defects tracking system. Our work will help identifying possible areas or pieces of software that give rise to large numbers of evolution requests. One of the main deliverables of this research will be a case study of the evolution of a successfull, durable and widely used system, which differs from previous work on strengthening the use of time series analysis, a technique not sufficiently explored in the context of studying the evolution of software, particularly in forecasting the evolution of Eclipse.
Evaluating Memory Size for Energy Efficient Sorting

Sorting processes are responsible for a large portion of energy consumed by computers. This paper proposes an energy efficiency evaluation for the required memory size of a sorting algorithm. An experiment result shows the energy consumption of different kinds of sorting algorithms with different memory sizes and various input sizes. This study then determines the memory size of a sorting algorithm for achieving better energy efficiency.
Integration of Legacy Components in MechatronicUML Architectures

One of the main benefits of the component-based development paradigm is its support for reuse which is guided by the interface description of the components. This facilitates the construction of complex functionality by the flexible composition of components. However, the also required verification of the resulting system often becomes intractable in practice as no abstract model of the reused components, which can serve the verification purpose, is available for the integrated legacy components. In this paper, we present the integration of legacy components in a Mechatronic UML model by an incremental synthesis of the communication behavior of the embedded legacy components combined with compositional verification.