Professor Pedro Ferreira

Abstract:

Background

Assessing the outcome of motif mining algorithms is an essential task, as the number of reported motifs can be very large. Significance measures play a central role in automatically ranking those motifs, and therefore alleviating the analysis work. Spotting the most interesting and relevant motifs is then dependent on the choice of the right measures. The combined use of several measures may provide more robust results. However caution has to be taken in order to avoid spurious evaluations.

Results

From the set of conducted experiments, it was verified that several of the selected significance measures show a very similar behavior in a wide range of situations therefore providing redundant information. Some measures have proved to be more appropriate to rank highly conserved motifs, while others are more appropriate for weakly conserved ones. Support appears as a very important feature to be considered for correct motif ranking. We observed that not all the measures are suitable for situations with poorly balanced class information, like for instance, when positive data is significantly less than negative data. Finally, a visualization scheme was proposed that, when several measures are applied, enables an easy identification of high scoring motifs.

Conclusion

In this work we have surveyed and categorized 14 significance measures for pattern evaluation. Their ability to rank three types of deterministic motifs was evaluated. Measures were applied in different testing conditions, where relations were identified. This study provides some pertinent insights on the choice of the right set of significance measures for the evaluation of deterministic motifs extracted from protein databases.

Abstract:

We study the cosmological stability of a class of theories with a dynamical preferred frame. For a range of actions, we find cosmological solutions which are compatible with observations of the recent history of the Universe: a matter dominated era followed by accelerated expansion. We then study the evolution of linear perturbations on these backgrounds and find conditions on the parameters of the theory which allow for the growth of structure sourced by the new degrees of freedom.

Abstract:

It is widely accepted that the Universe underwent a period of thermal equilibrium at very early times. One expects a residue of this primordial state to be imprinted on the large scale structure of space time. In this paper we study the morphology of this thermal residue in a universe whose early dynamics is governed by a scalar field. We calculate the amplitude of fluctuations on large scales and compare it to the imprint of vacuum fluctuations. We then use the observed power spectrum of fluctuations on the cosmic microwave background to place a constraint on the temperature of the Universe before and during inflation. We also present an alternative scenario where the fluctuations are predominantly thermal and near scale-invariant.