Computational approaches to complex biological networks

The need of understanding and modeling the biological networks is one of the raisons d'\ueatre and of the driving forces behind the emergence of Systems Biology. Because of its holistic approach and because of the widely different level of complexity of the networks, different mathematical methods have been developed during the years. Some of these computational methods are used in this thesis in order to investigate various properties of different biological systems. The first part deals with the prediction of the perturbation of cellular metabolism induced by drugs. Using Flux Balance Analysis to describe the reconstructed genome-wide metabolic networks, we consider the problem of identifying the most selective drug synergisms for given therapeutic targets. The second part of this thesis considers gene regulatory and large social networks as signed graphs (activation/deactivation or friendship/hostility are rephrased as positive/negative coupling between spins). Using the analogy with an Ising spin glass an analysis of the energy landscape and of the content of \u201cdisorder\u201d 'is carried out. Finally, the last part concerns the study of the spatial heterogeneity of the signaling pathway of rod photoreceptors. The electrophysiological data produced by our collaborators in the Neurobiology laboratory have been analyzed with various dynamical systems giving an insight into the process of ageing of photoreceptors and into the role diffusion in the pathway

Unpacking polarization: Antagonism and Alignment in Signed Networks of Online Interaction

Online polarization research currently focuses on studying single-issue opinion distributions or computing distance metrics of interaction network structures. Limited data availability often restricts studies to positive interaction data, which can misrepresent the reality of a discussion. We introduce a novel framework that aims at combining these three aspects, content and interactions, as well as their nature (positive or negative), while challenging the prevailing notion of polarization as an umbrella term for all forms of online conflict or opposing opinions. In our approach, built on the concepts of cleavage structures and structural balance of signed social networks, we factorize polarization into two distinct metrics: Antagonism and Alignment. Antagonism quantifies hostility in online discussions, based on the reactions of users to content. Alignment uses signed structural information encoded in long-term user-user relations on the platform to describe how well user interactions fit the global and/or traditional sides of discussion. We can analyse the change of these metrics through time, localizing both relevant trends but also sudden changes that can be mapped to specific contexts or events. We apply our methods to two distinct platforms: Birdwatch, a US crowd-based fact-checking extension of Twitter, and DerStandard, an Austrian online newspaper with discussion forums. In these two use cases, we find that our framework is capable of describing the global status of the groups of users (identification of cleavages) while also providing relevant findings on specific issues or in specific time frames. Furthermore, we show that our four metrics describe distinct phenomena, emphasizing their independent consideration for unpacking polarization complexities

A Comparison of Supervised Machine Learning Classification Techniques and Theory-Driven Approaches for the Prediction of Subjective Mental Workload

In the modern world of technological progress, systems and interfaces are becoming more and more complex. As a consequence, it is a crucial to design the human-computer interaction in the most optimal way to improve the user experience. The construct of Mental Workload is a valid metric that can be used for such a goal. Among the different ways of measuring Mental Workload, self-reporting procedures are the most adopted for their ease of use and application. This research is focused on the application of Machine Learning as an alternative to theory-driven approaches for Mental Workload measurement. In particular, the study is aimed at comparing the classification accuracy of a set of induced models, from an existing dataset, to the mental workload indexes generated by well-known subjective mental workload assessment techniques - namely the Nasa Task Load Index and the Workload profile instruments