Temporal networks in biology and medicine: a survey on models, algorithms, and tools.

The use of static graphs for modelling and analysis of biological and biomedical data plays a key role in biomedical research. However, many real-world scenarios present dynamic behaviours resulting in both node and edges modification as well as feature evolution. Consequently, ad-hoc models for capturing these evolutions along the time have been introduced, also referred to as dynamic, temporal, time-varying graphs. Here, we focus on temporal graphs, i.e., graphs whose evolution is represented by a sequence of time-ordered snapshots. Each snapshot represents a graph active in a particular timestamp. We survey temporal graph models and related algorithms, presenting fundamentals aspects and the recent advances. We formally define temporal graphs, focusing on the problem setting and we present their main applications in biology and medicine. We also present temporal graph embedding and the application to recent problems such as epidemic modelling. Finally, we further state some promising research directions in the area. Main results of this study include a systematic review of fundamental temporal network problems and their algorithmic solutions considered in the literature, in particular those having application in computational biology and medicine. We also include the main software developed in this context.

A novel algorithm for finding top-k weighted overlapping densest connected subgraphs in dual networks.

The use of networks for modelling and analysing relations among data is currently growing. Recently, the use of a single networks for capturing all the aspects of some complex scenarios has shown some limitations. Consequently, it has been proposed to use Dual Networks (DN), a pair of related networks, to analyse complex systems. The two graphs in a DN have the same set of vertices and different edge sets. Common subgraphs among these networks may convey some insights about the modelled scenarios. For instance, the detection of the Top-k Densest Connected subgraphs, i.e. a set k subgraphs having the largest density in the conceptual network which are also connected in the physical network, may reveal set of highly related nodes. After proposing a formalisation of the approach, we propose a heuristic to find a solution, since the problem is computationally hard. A set of experiments on synthetic and real networks is also presented to support our approach.