Optimization is a fundamental tool in modern science. Numerous important tasks in biology, economy, physics and computer science can be cast as optimization problems. Consider the example of machine learning: recent advances have shown that even the most sophisticated tasks involving decision making, can be reduced to solving certain optimization problems. These advances however, bring several new challenges to the field of algorithm design. The first of them is related to the ever-growing size of instances, these optimization problems need to be solved for. In practice, this forces the algorithms for these problems to run in time linear or nearly linear in their input size. The second challenge is related to the emergence of new, harder and harder problems which need to be dealt with. These problems are in most cases considered computationally intractable because of complexity barriers such as NP completeness, or because of non-convexity. Therefore, efficiently computable relaxations for these problems are typically desired.

The material of this thesis is divided into two parts. In the first part we attempt to address the first challenge. The recent tremendous progress in developing fast algorithm for such fundamental problems as maximum flow or linear programming, demonstrate the power of continuous techniques and tools such as electrical flows, fast Laplacian solvers and interior point methods. In this thesis we study new algorithms of this type based on continuous dynamical systems inspired by the study of a slime mold Physarum polycephalum. We perform a rigorous mathematical analysis of these dynamical systems and extract from them new, fast algorithms for problems such as minimum cost flow, linear programming and basis pursuit.

In the second part of the thesis we develop new tools to approach the second challenge. Towards this, we study a very general form of discrete optimization problems and its extension to sampling and counting, capturing a host of important problems such as counting matchings in graphs, computing permanents of matrices or sampling from constrained determinantal point processes. We present a very general framework, based on polynomials, for dealing with these problems computationally. It is based, roughly, on encoding the problem structure in a multivariate polynomial and then recovering the solution by means of certain continuous relaxations. This leads to several questions on how to reason about such relaxations and how to compute them. We resolve them by relating certain analytic properties of the arising polynomials, such as the location of their roots or convexity, to the combinatorial structure of the underlying problem.

We believe that the ideas and mathematical techniques developed in this thesis are only a beginning and they will inspire more work on the use of dynamical systems and polynomials in the design of fast algorithms.