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.

/pdf/analysis-of-boolean-functions-4kueie1j8m.pdf

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

The function f: { − 1, 1}n → { − 1, 1} is a k-junta if it depends on at most k of its variables. We consider the problem of tolerant testing of k-juntas, where the testing algorithm must accept any function that is ϵ-close to some k-junta and reject any function that is ϵ'-far from every k'-junta for some ϵ' = O(ϵ) and k' = O(k). Our first result is an algorithm that solves this problem with query complexity polynomial in k and 1/ϵ. This result is obtained via a new polynomial-time approximation algorithm for submodular function minimization (SFM) under large cardinality constraints, which holds even when only given an approximate oracle access to the function. Our second result considers the case where k' = k. We show how to obtain a smooth tradeoff between the amount of tolerance and the query complexity in this setting. Specifically, we design an algorithm that given ρ ∈ (0, 1/2) accepts any function that is [EQUATION]-close to some k-junta and rejects any function that is ϵ-far from every k-junta. The query complexity of the algorithm is [EQUATION]. Finally, we show how to apply the second result to the problem of tolerant isomorphism testing between two unknown Boolean functions f and g. We give an algorithm for this problem whose query complexity only depends on the (unknown) smallest k such that either f or g is close to being a k-junta.

Tolerant junta testing and the connection to submodular optimization and function isomorphism

We show that every algorithm for testing $n$-variate Boolean functions for monotonicity must have query complexity $\tilde{\Omega}(n^{1/4})$. All previous lower bounds for this problem were designe...

A Polynomial Lower Bound for Testing Monotonicity

The embodiments discussed herein involve flood filling a region with anti-aliasing. In forming a fill region, a candidate pixel can be included in the region based on a color of the pixel and also a color of a neighbor of the point. The inclusion basis may be a color distance between a seed color and the points, and a color distance between the seed color and the point's neighbor. Points in the region may be weighted according to their color distance relative to the seed color, where the color distance can also take into account alpha values. Flood filling may be anti-aliased by assigning alpha values to pixels in gaps between corners of the fill region, where an alpha value may be proportional to a point's contribution to the gap. Dimples in a fill region may be tested for and used to determine which of two flood fill algorithms to use.

Graphics Processing Method and System

The celebrated minimax principle of Yao (1977) says that for any Boolean-valued function $f$ with finite domain, there is a distribution $\mu$ over the domain of $f$ such that computing $f$ to error $\epsilon$ against inputs from $\mu$ is just as hard as computing $f$ to error $\epsilon$ on worst-case inputs. Notably, however, the distribution $\mu$ depends on the target error level $\epsilon$: the hard distribution which is tight for bounded error might be trivial to solve to small bias, and the hard distribution which is tight for a small bias level might be far from tight for bounded error levels. 
In this work, we introduce a new type of minimax theorem which can provide a hard distribution $\mu$ that works for all bias levels at once. We show that this works for randomized query complexity, randomized communication complexity, some randomized circuit models, quantum query and communication complexities, approximate polynomial degree, and approximate logrank. We also prove an improved version of Impagliazzo's hardcore lemma. 
Our proofs rely on two innovations over the classical approach of using Von Neumann's minimax theorem or linear programming duality. First, we use Sion's minimax theorem to prove a minimax theorem for ratios of bilinear functions representing the cost and score of algorithms. 
Second, we introduce a new way to analyze low-bias randomized algorithms by viewing them as "forecasting algorithms" evaluated by a proper scoring rule. The expected score of the forecasting version of a randomized algorithm appears to be a more fine-grained way of analyzing the bias of the algorithm. We show that such expected scores have many elegant mathematical properties: for example, they can be amplified linearly instead of quadratically. We anticipate forecasting algorithms will find use in future work in which a fine-grained analysis of small-bias algorithms is required.

A New Minimax Theorem for Randomized Algorithms

We study the complexity of approximating Boolean functions with disjunctive normal forms (DNFs) and other depth-2 circuits, exploring two main directions: universal bounds on the approximability of all Boolean functions, and the approximability of the parity function. In the first direction, our main positive results are the first nontrivial universal upper bounds on approximability by DNFs: (a) every Boolean function can be $\epsilon$-approximated by a DNF of size $O_\epsilon(2^n/\log n)$, and (b) every Boolean function can be $\epsilon$-approximated by a DNF of width $c_\epsilon\, n$, where $c_\epsilon < 1$. Our techniques extend broadly to give strong universal upper bounds on approximability by various depth-2 circuits that generalize DNFs, including the intersection of halfspaces, low-degree Polynomial threshold functions, and unate functions. We show that the parameters of our constructions almost match the information-theoretic inapproximability of a random function. In the second direction our mai...

Eric Blais

Papers

Tolerant junta testing and the connection to submodular optimization and function isomorphism

A Polynomial Lower Bound for Testing Monotonicity

Graphics Processing Method and System

A New Minimax Theorem for Randomized Algorithms

Approximating Boolean Functions with Depth-2 Circuits