Numerical algebraic geometry for model selection and its application to the life sciences

Researchers working with mathematical models are often confronted by the related problems of parameter estimation, model validation, and model selection. These are all optimization problems, well-known to be challenging due to non-linearity, non-convexity and multiple local optima. Furthermore, the challenges are compounded when only partial data is available. Here, we consider polynomial models (e.g., mass-action chemical reaction networks at steady state) and describe a framework for their analysis based on optimization using numerical algebraic geometry. Specifically, we use probability-one polynomial homotopy continuation methods to compute all critical points of the objective function, then filter to recover the global optima. Our approach exploits the geometric structures relating models and data, and we demonstrate its utility on examples from cell signaling, synthetic biology, and epidemiology.Comment: References added, additional clarification

Numerical Algebraic Geometry: A New Perspective on String and Gauge Theories

The interplay rich between algebraic geometry and string and gauge theories has recently been immensely aided by advances in computational algebra. However, these symbolic (Gr\"{o}bner) methods are severely limited by algorithmic issues such as exponential space complexity and being highly sequential. In this paper, we introduce a novel paradigm of numerical algebraic geometry which in a plethora of situations overcomes these short-comings. Its so-called 'embarrassing parallelizability' allows us to solve many problems and extract physical information which elude the symbolic methods. We describe the method and then use it to solve various problems arising from physics which could not be otherwise solved.Comment: 36 page

Trifocal Relative Pose from Lines at Points and its Efficient Solution

We present a new minimal problem for relative pose estimation mixing point features with lines incident at points observed in three views and its efficient homotopy continuation solver. We demonstrate the generality of the approach by analyzing and solving an additional problem with mixed point and line correspondences in three views. The minimal problems include correspondences of (i) three points and one line and (ii) three points and two lines through two of the points which is reported and analyzed here for the first time. These are difficult to solve, as they have 216 and - as shown here - 312 solutions, but cover important practical situations when line and point features appear together, e.g., in urban scenes or when observing curves. We demonstrate that even such difficult problems can be solved robustly using a suitable homotopy continuation technique and we provide an implementation optimized for minimal problems that can be integrated into engineering applications. Our simulated and real experiments demonstrate our solvers in the camera geometry computation task in structure from motion. We show that new solvers allow for reconstructing challenging scenes where the standard two-view initialization of structure from motion fails.Comment: This material is based upon work supported by the National Science Foundation under Grant No. DMS-1439786 while most authors were in residence at Brown University's Institute for Computational and Experimental Research in Mathematics -- ICERM, in Providence, R