Multivariate sparse interpolation using randomized Kronecker substitutions

We present new techniques for reducing a multivariate sparse polynomial to a univariate polynomial. The reduction works similarly to the classical and widely-used Kronecker substitution, except that we choose the degrees randomly based on the number of nonzero terms in the multivariate polynomial, that is, its sparsity. The resulting univariate polynomial often has a significantly lower degree than the Kronecker substitution polynomial, at the expense of a small number of term collisions. As an application, we give a new algorithm for multivariate interpolation which uses these new techniques along with any existing univariate interpolation algorithm.Comment: 21 pages, 2 tables, 1 procedure. Accepted to ISSAC 201

Parallel sparse interpolation using small primes

To interpolate a supersparse polynomial with integer coefficients, two alternative approaches are the Prony-based "big prime" technique, which acts over a single large finite field, or the more recently-proposed "small primes" technique, which reduces the unknown sparse polynomial to many low-degree dense polynomials. While the latter technique has not yet reached the same theoretical efficiency as Prony-based methods, it has an obvious potential for parallelization. We present a heuristic "small primes" interpolation algorithm and report on a low-level C implementation using FLINT and MPI.Comment: Accepted to PASCO 201

Interpolation of Sparse Graph Signals by Sequential Adaptive Thresholds

This paper considers the problem of interpolating signals defined on graphs. A major presumption considered by many previous approaches to this problem has been lowpass/ band-limitedness of the underlying graph signal. However, inspired by the findings on sparse signal reconstruction, we consider the graph signal to be rather sparse/compressible in the Graph Fourier Transform (GFT) domain and propose the Iterative Method with Adaptive Thresholding for Graph Interpolation (IMATGI) algorithm for sparsity promoting interpolation of the underlying graph signal.We analytically prove convergence of the proposed algorithm. We also demonstrate efficient performance of the proposed IMATGI algorithm in reconstructing randomly generated sparse graph signals. Finally, we consider the widely desirable application of recommendation systems and show by simulations that IMATGI outperforms state-of-the-art algorithms on the benchmark datasets in this application.Comment: 12th International Conference on Sampling Theory and Applications (SAMPTA 2017

Machine learning-guided directed evolution for protein engineering

Machine learning (ML)-guided directed evolution is a new paradigm for biological design that enables optimization of complex functions. ML methods use data to predict how sequence maps to function without requiring a detailed model of the underlying physics or biological pathways. To demonstrate ML-guided directed evolution, we introduce the steps required to build ML sequence-function models and use them to guide engineering, making recommendations at each stage. This review covers basic concepts relevant to using ML for protein engineering as well as the current literature and applications of this new engineering paradigm. ML methods accelerate directed evolution by learning from information contained in all measured variants and using that information to select sequences that are likely to be improved. We then provide two case studies that demonstrate the ML-guided directed evolution process. We also look to future opportunities where ML will enable discovery of new protein functions and uncover the relationship between protein sequence and function.Comment: Made significant revisions to focus on aspects most relevant to applying machine learning to speed up directed evolutio