In this paper, we consider the question of determining whether a function f has property P or is e-far from any function with property P. A property testing algorithm is given a sample of the value of f on instances drawn according to some distribution. In some cases, it is also allowed to query f on instances of its choice. We study this question for different properties and establish some connections to problems in learning theory and approximation.In particular, we focus our attention on testing graph properties. Given access to a graph G in the form of being able to query whether an edge exists or not between a pair of vertices, we devise algorithms to test whether the underlying graph has properties such as being bipartite, k-Colorable, or having a p-Clique (clique of density p with respect to the vertex set). Our graph property testing algorithms are probabilistic and make assertions that are correct with high probability, while making a number of queries that is independent of the size of the graph. Moreover, the property testing algorithms can be used to efficiently (i.e., in time linear in the number of vertices) construct partitions of the graph that correspond to the property being tested, if it holds for the input graph.

Property Testing and its connection to Learning and Approximation

Boolean functions are perhaps the most basic objects of study in theoretical computer science. They also arise in other areas of mathematics, including combinatorics, statistical physics, and mathematical social choice. The field of analysis of Boolean functions seeks to understand them via their Fourier transform and other analytic methods. This text gives a thorough overview of the field, beginning with the most basic definitions and proceeding to advanced topics such as hypercontractivity and isoperimetry. Each chapter includes a "highlight application" such as Arrow's theorem from economics, the Goldreich-Levin algorithm from cryptography/learning theory, Hstad's NP-hardness of approximation results, and "sharp threshold" theorems for random graph properties. The book includes roughly 450 exercises and can be used as the basis of a one-semester graduate course. It should appeal to advanced undergraduates, graduate students, and researchers in computer science theory and related mathematical fields.

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Analysis of Boolean Functions

Analysis of Boolean Functions: List of Notation

Expression.- Spectral Clustering Gene Ontology Terms to Group Genes by Function.- Dynamic De-Novo Prediction of microRNAs Associated with Cell Conditions: A Search Pruned by Expression.- Clustering Gene Expression Series with Prior Knowledge.- A Linear Time Biclustering Algorithm for Time Series Gene Expression Data.- Time-Window Analysis of Developmental Gene Expression Data with Multiple Genetic Backgrounds.- Phylogeny.- A Lookahead Branch-and-Bound Algorithm for the Maximum Quartet Consistency Problem.- Computing the Quartet Distance Between Trees of Arbitrary Degree.- Using Semi-definite Programming to Enhance Supertree Resolvability.- An Efficient Reduction from Constrained to Unconstrained Maximum Agreement Subtree.- Pattern Identification in Biogeography.- On the Complexity of Several Haplotyping Problems.- A Hidden Markov Technique for Haplotype Reconstruction.- Algorithms for Imperfect Phylogeny Haplotyping (IPPH) with a Single Homoplasy or Recombination Event.- Networks.- A Faster Algorithm for Detecting Network Motifs.- Reaction Motifs in Metabolic Networks.- Reconstructing Metabolic Networks Using Interval Analysis.- Genome Rearrangements.- A 1.375-Approximation Algorithm for Sorting by Transpositions.- A New Tight Upper Bound on the Transposition Distance.- Perfect Sorting by Reversals Is Not Always Difficult.- Minimum Recombination Histories by Branch and Bound.- Sequences.- A Unifying Framework for Seed Sensitivity and Its Application to Subset Seeds.- Generalized Planted (l,d)-Motif Problem with Negative Set.- Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI).- The Peres-Shields Order Estimator for Fixed and Variable Length Markov Models with Applications to DNA Sequence Similarity.- Multiple Structural RNA Alignment with Lagrangian Relaxation.- Faster Algorithms for Optimal Multiple Sequence Alignment Based on Pairwise Comparisons.- Ortholog Clustering on a Multipartite Graph.- Linear Time Algorithm for Parsing RNA Secondary Structure.- A Compressed Format for Collections of Phylogenetic Trees and Improved Consensus Performance.- Structure.- Optimal Protein Threading by Cost-Splitting.- Efficient Parameterized Algorithm for Biopolymer Structure-Sequence Alignment.- Rotamer-Pair Energy Calculations Using a Trie Data Structure.- Improved Maintenance of Molecular Surfaces Using Dynamic Graph Connectivity.- The Main Structural Regularities of the Sandwich Proteins.- Discovery of Protein Substructures in EM Maps.

Algorithms in Bioinformatics: 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings (Lecture Notes in Computer Science / Lecture Notes in Bioinformatics)

1 Introduction.- 2 Experiments, Deficiencies, Distances v.- 2.1 Comparing Risk Functions.- 2.2 Deficiency and Distance between Experiments.- 2.3 Likelihood Ratios and Blackwell's Representation.- 2.4 Further Remarks on the Convergence of Distri butions of Likelihood Ratios.- 2.5 Historical Remarks.- 3 Contiguity - Hellinger Transforms.- 3.1 Contiguity.- 3.2 Hellinger Distances, Hellinger Transforms.- 3.3 Historical Remarks.- 4 Gaussian Shift and Poisson Experiments.- 4.1 Introduction.- 4.2 Gaussian Experiments.- 4.3 Poisson Experiments.- 4.4 Historical Remarks.- 5 Limit Laws for Likelihood Ratios.- 5.1 Introduction.- 5.2 Auxiliary Results.- 5.2.1 Lindeberg's Procedure.- 5.2.2 Levy Splittings.- 5.2.3 Paul Levy's Symmetrization Inequalities.- 5.2.4 Conditions for Shift-Compactness.- 5.2.5 A Central Limit Theorem for Infinitesimal Arrays.- 5.2.6 The Special Case of Gaussian Limits.- 5.2.7 Peano Differentiable Functions.- 5.3 Limits for Binary Experiments.- 5.4 Gaussian Limits.- 5.5 Historical Remarks.- 6 Local Asymptotic Normality.- 6.1 Introduction.- 6.2 Locally Asymptotically Quadratic Families.- 6.3 A Method of Construction of Estimates.- 6.4 Some Local Bayes Properties.- 6.5 Invariance and Regularity.- 6.6 The LAMN and LAN Conditions.- 6.7 Additional Remarks on the LAN Conditions.- 6.8 Wald's Tests and Confidence Ellipsoids.- 6.9 Possible Extensions.- 6.10 Historical Remarks.- 7 Independent, Identically Distributed Observations.- 7.1 Introduction.- 7.2 The Standard i.i.d. Case: Differentiability in Quadratic Mean.- 7.3 Some Examples.- 7.4 Some Nonparametric Considerations.- 7.5 Bounds on the Risk of Estimates.- 7.6 Some Cases Where the Number of Observations Is Random.- 7.7 Historical Remarks.- 8 On Bayes Procedures.- 8.1 Introduction.- 8.2 Bayes Procedures Behave Nicely.- 8.3 The Bernstein-von Mises Phenomenon.- 8.4 A Bernstein-von Mises Result for the i.i.d. Case.- 8.5 Bayes Procedures Behave Miserably.- 8.6 Historical Remarks.- Author Index.

Asymptotics in Statistics–Some Basic Concepts

We show how the communication complexity method introduced in (Blais, Brody, Matulef 2012) can be used to prove lower bounds on the number of queries required to test properties of functions with non-hypercube domains. We use this method to prove strong, and in many cases optimal, lower bounds on the query complexity of testing fundamental properties of functions over hypergrid domains: monotonicity, the Lipschitz property, separate convexity, convexity and monotonicity of higher-order derivatives. There is a long line of work on upper bounds and lower bounds for many of these properties that uses a diverse set of combinatorial techniques. Our method provides a unified treatment of lower bounds for all these properties based on Fourier analysis. A key ingredient in our new lower bounds is a set of Walsh functions, a canonical Fourier basis for the set of functions on the line. The orthogonality of the Walsh functions lets us use a product construction to extend our method from properties of functions over the line to properties of functions over hypergrids. Our product construction applies to properties over hypergrids that can be expressed in terms of axis-parallel directional derivatives, such as monotonicity, the Lipschitz property and separate convexity. We illustrate the robustness of our method by making it work for convexity, which is the property of the Hessian matrix of second derivatives being positive semidefinite and thus cannot be described by axis-parallel directional derivatives alone. Such robustness contrasts with the state of the art in the upper bounds for testing properties over hypergrids: methods that work for other properties are not applicable for testing convexity, for which no nontrivial upper bounds are known for d ≥ 2.

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Lower Bounds for Testing Properties of Functions over Hypergrid Domains

We prove new lower bounds in the area of property testing of boolean functions. Specifically, we study the problem of testing whether a boolean function $f$ is isomorphic to a fixed function $g$ (i.e., is equal to $g$ up to permutation of the input variables). The analogous problem for testing graphs was solved by Fischer in 2005. The setting of boolean functions, however, appears to be more difficult, and no progress has been made since the initial study of the problem by Fischer et al. in 2004. Our first result shows that any non-adaptive algorithm for testing isomorphism to a function that ``strongly'' depends on $k$ variables requires $\log k - O(1)$ queries (assuming $k/n$ is bounded away from 1). This lower bound affirms and strengthens a conjecture appearing in the 2004 work of Fischer et al. Its proof relies on total variation bounds between hypergeometric distributions which may be of independent interest. Our second result concerns the simplest interesting case not covered by our first result: non-adaptively testing isomorphism to the Majority function on $k$ variables. Here we show that $\Omega(k^{1/12})$ queries are necessary (again assuming $k/n$ is bounded away from 1). The proof of this result relies on recently developed multidimensional invariance principle tools.

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Lower Bounds for Testing Function Isomorphism

In recent work, Kalai, Klivans, Mansour, and Servedio (2005) studied a variant of the "Low-Degree (Fourier) Algorithm" for learning under the uniform probability distribution on {0,1} n . They showed that the L 1 polynomial regression algorithm yields agnostic (tolerant to arbitrary noise) learning algorithms with respect to the class of threshold functions--under certain restricted instance distributions, including uniform on {0,1} n and Gaussian on ? n . In this work we show how all learning results based on the Low-Degree Algorithm can be generalized to give almost identical agnostic guarantees under arbitrary product distributions on instance spaces X 1×???×X n . We also extend these results to learning under mixtures of product distributions.

The main technical innovation is the use of (Hoeffding) orthogonal decomposition and the extension of the "noise sensitivity method" to arbitrary product spaces. In particular, we give a very simple proof that threshold functions over arbitrary product spaces have ?-noise sensitivity $O(\sqrt{\delta})$ , resolving an open problem suggested by Peres (2004).

Polynomial Regression under Arbitrary Product Distributions.

Two boolean functions f, g: {0, 1}n → {0, 1} are isomorphic if they are identical up to relabeling of the input variables. We consider the problem of testing whether two functions are isomorphic or far from being isomorphic with as few queries as possible.

In the setting where one of the functions is known in advance, we show that the non-adaptive query complexity of the isomorphism testing problem is &Theta(n). In fact, we show that the lower bound of Ω(n) queries for testing isomorphism to g holds for almost all functions g.

In the setting where both functions are unknown to the testing algorithm, we show that the query complexity of the isomorphism testing problem is Θ(2n/2). The bound in this result holds for both adaptive and non-adaptive testing algorithms.

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Testing Boolean function isomorphism

The function $f : \mathbb{F}_2^n \to \mathbb{F}_2$ is k-linear if it returns the sum (over $\mathbb{F}_2$) of exactly k coordinates of its input. We introduce strong lower bounds on the query complexity for testing whether a function is k-linear. We show that for any $k \le \frac n2$, at least k − o(k) queries are required to test k-linearity, and we show that when $k \approx \frac n2$, this lower bound is nearly tight since $\frac43 k + o(k)$ queries are sufficient to test k-linearity. We also show that non-adaptive testers require 2k − O(1) queries to test k-linearity.

Eric Blais

Papers

Lower Bounds for Testing Properties of Functions over Hypergrid Domains

Lower Bounds for Testing Function Isomorphism

Polynomial Regression under Arbitrary Product Distributions.

Testing Boolean function isomorphism

Tight Bounds for Testing k -Linearity