Implementation of network entropy algorithms on hpc machines, with application to high-dimensional experimental data

Network Theory is a prolific and lively field, especially when it approaches Biology. New concepts from this theory find application in areas where extensive datasets are already available for analysis, without the need to invest money to collect them. The only tools that are necessary to accomplish an analysis are easily accessible: a computing machine and a good algorithm. As these two tools progress, thanks to technology advancement and human efforts, wider and wider datasets can be analysed. The aim of this paper is twofold. Firstly, to provide an overview of one of these concepts, which originates at the meeting point between Network Theory and Statistical Mechanics: the entropy of a network ensemble. This quantity has been described from different angles in the literature. Our approach tries to be a synthesis of the different points of view. The second part of the work is devoted to presenting a parallel algorithm that can evaluate this quantity over an extensive dataset. Eventually, the algorithm will also be used to analyse high-throughput data coming from biology.

Transportation theory and planning

The aim of this research is to analyze the transport system and its subcomponents in order to highlight which are the design tools for physical and/or organizational projects related to transport supply systems. A characteristic of the transport systems is that the change of their structures can recoil on several entities, groups of entities, which constitute the community. The construction of a new infrastructure can modify both the transport service characteristic for all the user of the entire network; for example, the construction of a transportation infrastructure can change not only the transport service characteristics for the users of the entire network in which it is part of, but also it produces economical, social, and environmental effects. Therefore, the interventions or the improvements choices must be performed using a rational decision making approach. This approach requires that these choices are taken through the quantitative evaluation of the different effects caused by the different intervention plans. This approach becomes even more necessary when the decisions are taken in behalf of the community. Then, in order to understand how to develop a planning process in Transportation I will firstly analyze the transport system and the mathematical models used to describe it: these models provide us significant indicators which can be used to evaluate the effects of possible interventions. In conclusion, I will move on the topics related to the transport planning, analyzing the planning process, and the variables that have to be considered to perform a feasibility analysis or to compare different alternatives. In conclusion I will perform a preliminary analysis of a new transit system which is planned to be developed in New York City.

Tor network forensics and hidden service deanonymization

The cybernetics revolution of the last years improved a lot our lives, having an immediate access to services and a huge amount of information over the Internet. Nowadays the user is increasingly asked to insert his sensitive information on the Internet, leaving its traces everywhere. But there are some categories of people that cannot risk to reveal their identities on the Internet. Even if born to protect U.S. intelligence communications online, nowadays Tor is the most famous low-latency network, that guarantees both anonymity and privacy of its users. The aim of this thesis project is to well understand how the Tor protocol works, not only studying its theory, but also implementing those concepts in practice, having a particular attention for security topics. In order to run a Tor private network, that emulates the real one, a virtual testing environment has been configured. This behavior allows to conduct experiments without putting at risk anonymity and privacy of real users. We used a Tor patch, that stores TLS and circuit keys, to be given as inputs to a Tor dissector for Wireshark, in order to obtain decrypted and decoded traffic. Observing clear traffic allowed us to well check the protocol outline and to have a proof of the format of each cell. Besides, these tools allowed to identify a traffic pattern, used to conduct a traffic correlation attack to passively deanonymize hidden service clients. The attacker, controlling two nodes of the Tor network, is able to link a request for a given hidden server to the client who did it, deanonymizing him. The robustness of the traffic pattern and the statistics, such as the true positive rate, and the false positive rate, of the attack are object of a potential future work.