P?=NP as minimization of degree 4 polynomial, integration or Grassmann number problem, and new graph isomorphism problem approaches

While the P vs NP problem is mainly approached form the point of view of discrete mathematics, this paper proposes reformulations into the field of abstract algebra, geometry, fourier analysis and of continuous global optimization - which advanced tools might bring new perspectives and approaches for this question. The first one is equivalence of satisfaction of 3-SAT problem with the question of reaching zero of a nonnegative degree 4 multivariate polynomial (sum of squares), what could be tested from the perspective of algebra by using discriminant. It could be also approached as a continuous global optimization problem inside $[0,1]^n$, for example in physical realizations like adiabatic quantum computers. However, the number of local minima usually grows exponentially. Reducing to degree 2 polynomial plus constraints of being in $\{0,1\}^n$, we get geometric formulations as the question if plane or sphere intersects with $\{0,1\}^n$. There will be also presented some non-standard perspectives for the Subset-Sum, like through convergence of a series, or zeroing of $\int_0^{2\pi} \prod_i \cos(\varphi k_i) d\varphi$ fourier-type integral for some natural $k_i$. The last discussed approach is using anti-commuting Grassmann numbers $\theta_i$, making $(A \cdot \textrm{diag}(\theta_i))^n$ nonzero only if $A$ has a Hamilton cycle. Hence, the P$\ne$NP assumption implies exponential growth of matrix representation of Grassmann numbers. There will be also discussed a looking promising algebraic/geometric approach to the graph isomorphism problem -- tested to successfully distinguish strongly regular graphs with up to 29 vertices.Comment: 19 pages, 8 figure

A combinatorial optimization approach for diverse motif finding applications

BACKGROUND: Discovering approximately repeated patterns, or motifs, in biological sequences is an important and widely-studied problem in computational molecular biology. Most frequently, motif finding applications arise when identifying shared regulatory signals within DNA sequences or shared functional and structural elements within protein sequences. Due to the diversity of contexts in which motif finding is applied, several variations of the problem are commonly studied. RESULTS: We introduce a versatile combinatorial optimization framework for motif finding that couples graph pruning techniques with a novel integer linear programming formulation. Our approach is flexible and robust enough to model several variants of the motif finding problem, including those incorporating substitution matrices and phylogenetic distances. Additionally, we give an approach for determining statistical significance of uncovered motifs. In testing on numerous DNA and protein datasets, we demonstrate that our approach typically identifies statistically significant motifs corresponding to either known motifs or other motifs of high conservation. Moreover, in most cases, our approach finds provably optimal solutions to the underlying optimization problem. CONCLUSION: Our results demonstrate that a combined graph theoretic and mathematical programming approach can be the basis for effective and powerful techniques for diverse motif finding applications

Feynman integrals and hyperlogarithms

We study Feynman integrals in the representation with Schwinger parameters and derive recursive integral formulas for massless 3- and 4-point functions. Properties of analytic (including dimensional) regularization are summarized and we prove that in the Euclidean region, each Feynman integral can be written as a linear combination of convergent Feynman integrals. This means that one can choose a basis of convergent master integrals and need not evaluate any divergent Feynman graph directly. Secondly we give a self-contained account of hyperlogarithms and explain in detail the algorithms needed for their application to the evaluation of multivariate integrals. We define a new method to track singularities of such integrals and present a computer program that implements the integration method. As our main result, we prove the existence of infinite families of massless 3- and 4-point graphs (including the ladder box graphs with arbitrary loop number and their minors) whose Feynman integrals can be expressed in terms of multiple polylogarithms, to all orders in the epsilon-expansion. These integrals can be computed effectively with the presented program. We include interesting examples of explicit results for Feynman integrals with up to 6 loops. In particular we present the first exactly computed counterterm in massless phi^4 theory which is not a multiple zeta value, but a linear combination of multiple polylogarithms at primitive sixth roots of unity (and divided by $\sqrt{3}$). To this end we derive a parity result on the reducibility of the real- and imaginary parts of such numbers into products and terms of lower depth.Comment: PhD thesis, 220 pages, many figure