Évolution géologique de la marge ouest-ibérique

This paper is a summary of the results of the authors recent researches about the Western Iberian continental margin. During the Mesozoic, the margin is affected by two consecutive extensional phases interpreted as the result from two episodes of rifting in the Atlantic. Then during Cenozoic, subsidence was interrupted by compression and related deformation, specially during Eocene time. Ante-mesozoic basement controls the structural and sedimentary evolution of the margin

Balancing Bounded Treewidth Circuits

Algorithmic tools for graphs of small treewidth are used to address questions in complexity theory. For both arithmetic and Boolean circuits, it is shown that any circuit of size $n^{O(1)}$ and treewidth $O(\log^i n)$ can be simulated by a circuit of width $O(\log^{i+1} n)$ and size $n^c$, where $c = O(1)$, if $i=0$, and $c=O(\log \log n)$ otherwise. For our main construction, we prove that multiplicatively disjoint arithmetic circuits of size $n^{O(1)}$ and treewidth $k$ can be simulated by bounded fan-in arithmetic formulas of depth $O(k^2\log n)$. From this we derive the analogous statement for syntactically multilinear arithmetic circuits, which strengthens a theorem of Mahajan and Rao. As another application, we derive that constant width arithmetic circuits of size $n^{O(1)}$ can be balanced to depth $O(\log n)$, provided certain restrictions are made on the use of iterated multiplication. Also from our main construction, we derive that Boolean bounded fan-in circuits of size $n^{O(1)}$ and treewidth $k$ can be simulated by bounded fan-in formulas of depth $O(k^2\log n)$. This strengthens in the non-uniform setting the known inclusion that $SC^0 \subseteq NC^1$. Finally, we apply our construction to show that {\sc reachability} for directed graphs of bounded treewidth is in $LogDCFL$

Arithmetic Branching Programs with Memory

We extend the well known characterization of VPws as the class of polynomials computed by polynomial size arithmetic branching programs to other complexity classes. In order to do so we add additional memory to the computation of branching programs to make them more expressive. We show that allowing different types of memory in branching programs increases the computational power even for constant width programs. In particular, this leads to very natural and robust characterizations of VP and VNP by branching programs with memory. 1

Processing Succinct Matrices and Vectors

We study the complexity of algorithmic problems for matrices that are represented by multi-terminal decision diagrams (MTDD). These are a variant of ordered decision diagrams, where the terminal nodes are labeled with arbitrary elements of a semiring (instead of 0 and 1). A simple example shows that the product of two MTDD-represented matrices cannot be represented by an MTDD of polynomial size. To overcome this deficiency, we extended MTDDs to MTDD_+ by allowing componentwise symbolic addition of variables (of the same dimension) in rules. It is shown that accessing an entry, equality checking, matrix multiplication, and other basic matrix operations can be solved in polynomial time for MTDD_+-represented matrices. On the other hand, testing whether the determinant of a MTDD-represented matrix vanishes PSPACE$-complete, and the same problem is NP-complete for MTDD_+-represented diagonal matrices. Computing a specific entry in a product of MTDD-represented matrices is #P-complete.Comment: An extended abstract of this paper will appear in the Proceedings of CSR 201

Algorithm engineering for optimal alignment of protein structure distance matrices

Protein structural alignment is an important problem in computational biology. In this paper, we present first successes on provably optimal pairwise alignment of protein inter-residue distance matrices, using the popular Dali scoring function. We introduce the structural alignment problem formally, which enables us to express a variety of scoring functions used in previous work as special cases in a unified framework. Further, we propose the first mathematical model for computing optimal structural alignments based on dense inter-residue distance matrices. We therefore reformulate the problem as a special graph problem and give a tight integer linear programming model. We then present algorithm engineering techniques to handle the huge integer linear programs of real-life distance matrix alignment problems. Applying these techniques, we can compute provably optimal Dali alignments for the very first time

CSA: Comprehensive comparison of pairwise protein structure alignments

htmlabstractCSA is a web server for the computation, evaluation and comprehensive comparison of pairwise protein structure alignments. Its exact alignment engine computes either optimal, top-scoring alignments or heuristic alignments with quality guarantee for the inter-residue distance-based scorings of contact map overlap, PAUL, DALI and MATRAS. These and additional, uploaded alignments are compared using a number of quality measures and intuitive visualizations. CSA brings new insight into the structural relationship of the protein pairs under investigation and is a valuable tool for studying structural similarities. It is available at http://csa.project.cwi.nl

THE COMPLEXITY OF POLYNOMIALS AND THEIR COEFFICIENT FUNCTIONS

Abstract. We study the link between the complexity of a polynomial and that of its coefficient functions. Valiant’s theory is a good setting for this, and we start by generalizing one of Valiant’s observations, showing that the class VNP is stable for coefficients functions, and that this is true of the class VP iff VP = VNP, an eventuality which would be as surprising as the equality of the classes P and NP in the Boolean case. We extend the definition of Valiant’s classes to polynomials of unbounded degree, thus defining the classes VPnb and VNPnb. Over rings of positive characteristic the same kind of results hold in this case, and we also prove that VP = VNP iff VPnb = VNPnb. Finally, we use our extension of Valiant’s results to show that iterated partial derivatives can be efficiently computed iff VP = VNP. This is also true for the case of polynomials of unbounded degree, if the characteristic of the ring is positive. 1