Anna Lombardi

Constructing and Analyzing a Large-Scale Gene-to-Gene Regulatory Network-Lasso-Constrained Inference and Biological Validation

We construct a gene-to-gene regulatory network from time-series data of expression levels for the whole genome of the yeast Saccharomyces cerevisae, in a case where the number of measurements is much smaller than the number of genes in the network. This network is analyzed with respect to present biological knowledge of all genes (according to the Gene Ontology database), and we find some of its large-scale properties to be in accordance with known facts about the organism. The linear modeling employed here has been explored several times, but due to lack of any validation beyond investigating individual genes, it has been seriously questioned with respect to its applicability to biological systems. Our results show the adequacy of the approach and make further investigations of the model meaningful.

Comparison and validation of community structures in complex networks

The issue of partitioning a network into communities has attracted a great deal of attention recently. Most authors seem to equate this issue with the one of finding the maximum value of the modularity, as defined by Newman. Since the problem formulated this way is believed to be NP-hard, most effort has gone into the construction of search algorithms, and less to the question of other measures of community structures, similarities between various partitionings and the validation with respect to external information.

A logic-based approach to model supervisory control systems

We present an approach to model supervisory control systems based on extended behaviour networks. In particular, we employ them to formalize the control theory of the supervisor. By separating the reasoning in the supervisor and the action implementation in the controller, the overall system architecture becomes modular, and therefore easily changeable and modifiable.

A model based project for 3D animation

Abstract As the computer game market is expanding, the demand for qualified programmers is increasing. Therefore more and more universities invest in education in this field, giving the students a broad knowledge in programming and graphics. What the students often miss is a competence in physical modelling that makes the simulation of the system close to reality. This paper presents the achievement of a project course where students are asked to model, simulate and animate a physical system. Physically based modelling is used and it has been very successful as it is shown by the excellent results produced during the course. Two examples are described: they are both based on physical modelling but two different approaches for implementation are used. First the animation of a golf strike is illustrated. The mathematical model is implemented in Simulink and the Virtual Reality Toolbox of Matlab together with 3D Studio Max have been used for the 3D visualization. The animation of an axial fan is also illustrated. In this case both the model and the 3D animation are implemented in C++.