Exploiting network topology for large-scale inference of nonlinear reaction models

The development of chemical reaction models aids understanding and prediction in areas ranging from biology to electrochemistry and combustion. A systematic approach to building reaction network models uses observational data not only to estimate unknown parameters, but also to learn model structure. Bayesian inference provides a natural approach to this data-driven construction of models. Yet traditional Bayesian model inference methodologies that numerically evaluate the evidence for each model are often infeasible for nonlinear reaction network inference, as the number of plausible models can be combinatorially large. Alternative approaches based on model-space sampling can enable large-scale network inference, but their realization presents many challenges. In this paper, we present new computational methods that make large-scale nonlinear network inference tractable. First, we exploit the topology of networks describing potential interactions among chemical species to design improved "between-model" proposals for reversible-jump Markov chain Monte Carlo. Second, we introduce a sensitivity-based determination of move types which, when combined with network-aware proposals, yields significant additional gains in sampling performance. These algorithms are demonstrated on inference problems drawn from systems biology, with nonlinear differential equation models of species interactions

On Nondeterministic Derandomization of Freivalds\u27 Algorithm: Consequences, Avenues and Algorithmic Progress

Motivated by studying the power of randomness, certifying algorithms and barriers for fine-grained reductions, we investigate the question whether the multiplication of two n x n matrices can be performed in near-optimal nondeterministic time O~(n^2). Since a classic algorithm due to Freivalds verifies correctness of matrix products probabilistically in time O(n^2), our question is a relaxation of the open problem of derandomizing Freivalds\u27 algorithm. We discuss consequences of a positive or negative resolution of this problem and provide potential avenues towards resolving it. Particularly, we show that sufficiently fast deterministic verifiers for 3SUM or univariate polynomial identity testing yield faster deterministic verifiers for matrix multiplication. Furthermore, we present the partial algorithmic progress that distinguishing whether an integer matrix product is correct or contains between 1 and n erroneous entries can be performed in time O~(n^2) - interestingly, the difficult case of deterministic matrix product verification is not a problem of "finding a needle in the haystack", but rather cancellation effects in the presence of many errors. Our main technical contribution is a deterministic algorithm that corrects an integer matrix product containing at most t errors in time O~(sqrt{t} n^2 + t^2). To obtain this result, we show how to compute an integer matrix product with at most t nonzeroes in the same running time. This improves upon known deterministic output-sensitive integer matrix multiplication algorithms for t = Omega(n^{2/3}) nonzeroes, which is of independent interest

Entropy, Randomization, Derandomization, and Discrepancy

The star discrepancy is a measure of how uniformly distributed a finite point set is in the d-dimensional unit cube. It is related to high-dimensional numerical integration of certain function classes as expressed by the Koksma-Hlawka inequality. A sharp version of this inequality states that the worst-case error of approximating the integral of functions from the unit ball of some Sobolev space by an equal-weight cubature is exactly the star discrepancy of the set of sample points. In many applications, as, e.g., in physics, quantum chemistry or finance, it is essential to approximate high-dimensional integrals. Thus with regard to the Koksma- Hlawka inequality the following three questions are very important: (i) What are good bounds with explicitly given dependence on the dimension d for the smallest possible discrepancy of any n-point set for moderate n? (ii) How can we construct point sets efficiently that satisfy such bounds? (iii) How can we calculate the discrepancy of given point sets efficiently? We want to discuss these questions and survey and explain some approaches to tackle them relying on metric entropy, randomization, and derandomization

On Nondeterministic Derandomization of {F}reivalds' Algorithm: {C}onsequences, Avenues and Algorithmic Progress

Motivated by studying the power of randomness, certifying algorithms and barriers for fine-grained reductions, we investigate the question whether the multiplication of two $n\times n$ matrices can be performed in near-optimal nondeterministic time $\tilde{O}(n^2)$. Since a classic algorithm due to Freivalds verifies correctness of matrix products probabilistically in time $O(n^2)$, our question is a relaxation of the open problem of derandomizing Freivalds' algorithm. We discuss consequences of a positive or negative resolution of this problem and provide potential avenues towards resolving it. Particularly, we show that sufficiently fast deterministic verifiers for 3SUM or univariate polynomial identity testing yield faster deterministic verifiers for matrix multiplication. Furthermore, we present the partial algorithmic progress that distinguishing whether an integer matrix product is correct or contains between 1 and $n$ erroneous entries can be performed in time $\tilde{O}(n^2)$ -- interestingly, the difficult case of deterministic matrix product verification is not a problem of "finding a needle in the haystack", but rather cancellation effects in the presence of many errors. Our main technical contribution is a deterministic algorithm that corrects an integer matrix product containing at most $t$ errors in time $\tilde{O}(\sqrt{t} n^2 + t^2)$. To obtain this result, we show how to compute an integer matrix product with at most $t$ nonzeroes in the same running time. This improves upon known deterministic output-sensitive integer matrix multiplication algorithms for $t = \Omega(n^{2/3})$ nonzeroes, which is of independent interest

Algorithms and Hardness for Robust Subspace Recovery

We consider a fundamental problem in unsupervised learning called \emph{subspace recovery}: given a collection of $m$ points in $\mathbb{R}^n$, if many but not necessarily all of these points are contained in a $d$-dimensional subspace $T$ can we find it? The points contained in $T$ are called {\em inliers} and the remaining points are {\em outliers}. This problem has received considerable attention in computer science and in statistics. Yet efficient algorithms from computer science are not robust to {\em adversarial} outliers, and the estimators from robust statistics are hard to compute in high dimensions. Are there algorithms for subspace recovery that are both robust to outliers and efficient? We give an algorithm that finds $T$ when it contains more than a $\frac{d}{n}$ fraction of the points. Hence, for say $d = n/2$ this estimator is both easy to compute and well-behaved when there are a constant fraction of outliers. We prove that it is Small Set Expansion hard to find $T$ when the fraction of errors is any larger, thus giving evidence that our estimator is an {\em optimal} compromise between efficiency and robustness. As it turns out, this basic problem has a surprising number of connections to other areas including small set expansion, matroid theory and functional analysis that we make use of here.Comment: Appeared in Proceedings of COLT 201

The ?-t-Net Problem

We study a natural generalization of the classical ?-net problem (Haussler - Welzl 1987), which we call the ?-t-net problem: Given a hypergraph on n vertices and parameters t and ? ? t/n, find a minimum-sized family S of t-element subsets of vertices such that each hyperedge of size at least ? n contains a set in S. When t=1, this corresponds to the ?-net problem. We prove that any sufficiently large hypergraph with VC-dimension d admits an ?-t-net of size O((1+log t)d/? log 1/?). For some families of geometrically-defined hypergraphs (such as the dual hypergraph of regions with linear union complexity), we prove the existence of O(1/?)-sized ?-t-nets. We also present an explicit construction of ?-t-nets (including ?-nets) for hypergraphs with bounded VC-dimension. In comparison to previous constructions for the special case of ?-nets (i.e., for t=1), it does not rely on advanced derandomization techniques. To this end we introduce a variant of the notion of VC-dimension which is of independent interest