Adaptive conflict-free optimization of rule sets for network security packet filtering devices

Packet filtering and processing rules management in firewalls and security gateways has become commonplace in increasingly complex networks. On one side there is a need to maintain the logic of high level policies, which requires administrators to implement and update a large amount of filtering rules while keeping them conflict-free, that is, avoiding security inconsistencies. On the other side, traffic adaptive optimization of large rule lists is useful for general purpose computers used as filtering devices, without specific designed hardware, to face growing link speeds and to harden filtering devices against DoS and DDoS attacks. Our work joins the two issues in an innovative way and defines a traffic adaptive algorithm to find conflict-free optimized rule sets, by relying on information gathered with traffic logs. The proposed approach suits current technology architectures and exploits available features, like traffic log databases, to minimize the impact of ACO development on the packet filtering devices. We demonstrate the benefit entailed by the proposed algorithm through measurements on a test bed made up of real-life, commercial packet filtering devices

Duplicate Defect Detection

Discovering and fixing faults is an unavoidable process in Software Engineering. It is always a good practice to document and organize fault reports. This facilitates the effectiveness of development and maintenance process. Bug Tracking Repositories, such as Bugzilla, are designed to provide fault reporting facilities for developers, testers and users of the system. Allowing anyone to contribute finding and reporting faults has an immediate impact on software quality. However, this benefit comes with one side-effect. Users often file reports that describe the same fault. This increases the triaging time spent by the maintainers. At the same time, important information required to fix the fault is likely to be distributed across different reports.;The objective of this thesis is twofold. First, we want to understand the dynamics of bug report filing for a large, long duration open source project, Firefox. Second, we present a new approach that can reduce the number of duplicate reports. The novel element in the proposed approach is the ability to concentrate the search for duplicates on specific portions of the bug repository. This improves the performance of Information Retrieval techniques and classification runtime of our algorithm. Our system can be deployed as a search tool to help reporters query the repository or it can be adopted to help maintainers detect duplicate reports. In both cases the performance is satisfactory. When tested as a search tool our system is able to detect up to 53% of duplicate reports. The approach adapted for maintainers has a maximum recall rate of 59%

The study of probability model for compound similarity searching

Information Retrieval or IR system main task is to retrieve relevant documents according to the users query. One of IR most popular retrieval model is the Vector Space Model. This model assumes relevance based on similarity, which is defined as the distance between query and document in the concept space. All currently existing chemical compound database systems have adapt the vector space model to calculate the similarity of a database entry to a query compound. However, it assumes that fragments represented by the bits are independent of one another, which is not necessarily true. Hence, the possibility of applying another IR model is explored, which is the Probabilistic Model, for chemical compound searching. This model estimates the probabilities of a chemical structure to have the same bioactivity as a target compound. It is envisioned that by ranking chemical structures in decreasing order of their probability of relevance to the query structure, the effectiveness of a molecular similarity searching system can be increased. Both fragment dependencies and independencies assumption are taken into consideration in achieving improvement towards compound similarity searching system. After conducting a series of simulated similarity searching, it is concluded that PM approaches really did perform better than the existing similarity searching. It gave better result in all evaluation criteria to confirm this statement. In terms of which probability model performs better, the BD model shown improvement over the BIR model

Application of coevolution-based methods and deep learning for structure prediction of protein complexes

The three-dimensional structures of proteins play a critical role in determining their biological functions and interactions. Experimental determination of protein and protein complex structures can be expensive and difficult. Computational prediction of protein and protein complex structures has therefore been an open challenge for decades. Recent advances in computational structure prediction techniques have resulted in increasingly accurate protein structure predictions. These techniques include methods that leverage information about coevolving residues to predict residue interactions and that apply deep learning techniques to enable better prediction of residue contacts and protein structures. Prior to the work outlined in this thesis, coevolution-based methods and deep learning had been shown to improve the prediction of single protein domains or single protein chains. Most proteins in living organisms do not function on their own but interact with other proteins either through transient interactions or by forming stable protein complexes. Knowledge of protein complex structures can be useful for biological and disease research, drug discovery and protein engineering. Unfortunately, a large number of protein complexes do not have experimental structures or close homolog structures that can be used as templates. In this thesis, methods previously developed and applied to the de novo prediction of single protein domains or protein monomer chains were modified and leveraged for the prediction of protein heterodimer and homodimer complexes. A number of coevolution-based tools and deep learning methods are explored for the purpose of predicting inter-chain and intra-chain residue contacts in protein dimers. These contacts are combined with existing protein docking methods to explore the prediction of homodimers and heterodimers. Overall, the work in this thesis demonstrates the promise of leveraging coevolution and deep-learning for the prediction of protein complexes, shows improvements in protein complex prediction tasks achieved using coevolution based methods and deep learning methods, and demonstrates remaining challenges in protein complex prediction

Learning-Assisted Automated Reasoning with Flyspeck

The considerable mathematical knowledge encoded by the Flyspeck project is combined with external automated theorem provers (ATPs) and machine-learning premise selection methods trained on the proofs, producing an AI system capable of answering a wide range of mathematical queries automatically. The performance of this architecture is evaluated in a bootstrapping scenario emulating the development of Flyspeck from axioms to the last theorem, each time using only the previous theorems and proofs. It is shown that 39% of the 14185 theorems could be proved in a push-button mode (without any high-level advice and user interaction) in 30 seconds of real time on a fourteen-CPU workstation. The necessary work involves: (i) an implementation of sound translations of the HOL Light logic to ATP formalisms: untyped first-order, polymorphic typed first-order, and typed higher-order, (ii) export of the dependency information from HOL Light and ATP proofs for the machine learners, and (iii) choice of suitable representations and methods for learning from previous proofs, and their integration as advisors with HOL Light. This work is described and discussed here, and an initial analysis of the body of proofs that were found fully automatically is provided

Web Services Discovery and Recommendation Based on Information Extraction and Symbolic Reputation

This paper shows that the problem of web services representation is crucial and analyzes the various factors that influence on it. It presents the traditional representation of web services considering traditional textual descriptions based on the information contained in WSDL files. Unfortunately, textual web services descriptions are dirty and need significant cleaning to keep only useful information. To deal with this problem, we introduce rules based text tagging method, which allows filtering web service description to keep only significant information. A new representation based on such filtered data is then introduced. Many web services have empty descriptions. Also, we consider web services representations based on the WSDL file structure (types, attributes, etc.). Alternatively, we introduce a new representation called symbolic reputation, which is computed from relationships between web services. The impact of the use of these representations on web service discovery and recommendation is studied and discussed in the experimentation using real world web services