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

The Hamming distance function Ham_{n,d} returns 1 on all pairs of inputs x and y that differ in at most d coordinates and returns 0 otherwise. We initiate the study of the information complexity of the Hamming distance function.

We give a new optimal lower bound for the information complexity of the Ham_{n,d} function in the small-error regime where the protocol is required to err with probability at most epsilon < d/n. We also give a new conditional lower bound for the information complexity of Ham_{n,d} that is optimal in all regimes. These results imply the first new lower bounds on the communication complexity of the Hamming distance function for the shared randomness two-way communication model since Pang and El-Gamal (1986). These results also imply new lower bounds in the areas of property testing and parity decision tree complexity.

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The Information Complexity Of Hamming Distance

Modern software systems have grown significantly in their size and complexity, therefore understanding how software systems behave when there are many configuration options, also called features, is no longer a trivial task. This is primarily due to the potentially complex interactions among the features. In this paper, we propose a novel mathematical model for performance-relevant, or quantitative in general, feature interactions, based on the theory of Boolean functions. Moreover, we provide two algorithms for detecting all such interactions with little measurement effort and potentially guaranteed accuracy and confidence level. Empirical results on real-world configurable systems demonstrated the feasibility and effectiveness of our approach.

A mathematical model of performance-relevant feature interactions

Given oracle access to some boolean function f, how many queries do we need to test whether f is linear? Or monotone? Or whether its output is completely determined by a small number of the input variables? This thesis studies these and related questions in the framework of property testing introduced by Rubinfeld and Sudan ('96). 
The results of this thesis are grouped into three main lines of research. I. We determine nearly optimal bounds on the number of queries required to test k-juntas (functions that depend on at most k variables) and k-linearity (functions that return the parity of exactly k of the input bits). These two problems are fundamental in the study of boolean functions and the bounds obtained for these two properties lead to tight or improved bounds on the query complexity for testing many other properties including, for example, testing sparse polynomials, testing low Fourier degree, and testing computability by small-size decision trees. We give a partial characterization of the set of functions for which we can test isomorphism—that is, identity up to permutation of the labels of the variables—with a constant number of queries. This result provides some progress on the question of characterizing the set of properties of boolean functions that can be tested with a constant number of queries. II. We establish new connections between property testing and other areas of computer science. First, we present a new reduction between testing problems and communication problems. We use this reduction to obtain many new lower bounds in property testing from known results in communication complexity. Second, we introduce a new model of property testing that closely minors the active learning model. We show how testing results in this new model may be used to improve the efficiency of model selection algorithms in learning theory. 
The results presented in this thesis are obtained by applying tools from various mathematical areas, including probability theory, the analysis of boolean functions, orthogonal polynomials, and extremal combinatorics.

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Testing properties of boolean functions

We consider the problem of learning distributions in the presence of irrelevant features. This problem is formalized by introducing a new notion of k-junta distributions. Informally, a distribution D over the domain X is a k-junta distribution with respect to another distribution U over the same domain if there is a set J ⊆ [n] of size |J | ≤ k that captures the difference between D and U . We show that it is possible to learn k-junta distributions with respect to the uniform distribution over the Boolean hypercube {0, 1} in time poly(n, 1/ ). This result is obtained via a new Fourier-based learning algorithm inspired by the Low-Degree Algorithm of Linial, Mansour, and Nisan (1993). We also consider the problem of testing whether an unknown distribution is a k-junta distribution with respect to the uniform distribution. We give a nearly-optimal algorithm for this task. Both the analysis of the algorithm and the lower bound showing its optimality are obtained by establishing connections between the problem of testing junta distributions and testing uniformity of weighted collections of distributions.

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Learning and Testing Junta Distributions

One of the motivations for property testing of boolean functions is the idea that testing can serve as a preprocessing step before learning. However, in most machine learning applications, it is not possible to request for labels of fictitious examples constructed by the algorithm. Instead, the dominant query paradigm in applied machine learning, called active learning, is one where the algorithm may query for labels, but only on points in a given polynomial-sized (unlabeled) sample, drawn from some underlying distribution D. In this work, we bring this well-studied model in learning to the domain of testing. 
We show that for a number of important properties, testing can still yield substantial benefits in this setting. This includes testing unions of intervals, testing linear separators, and testing various assumptions used in semi-supervised learning. In addition to these specific results, we also develop a general notion of the testing dimension of a given property with respect to a given distribution. We show this dimension characterizes (up to constant factors) the intrinsic number of label requests needed to test that property. We develop such notions for both the active and passive testing models. We then use these dimensions to prove a number of lower bounds, including for linear separators and the class of dictator functions. 
Our results show that testing can be a powerful tool in realistic models for learning, and further that active testing exhibits an interesting and rich structure. Our work in addition brings together tools from a range of areas including U-statistics, noise-sensitivity, self-correction, and spectral analysis of random matrices, and develops new tools that may be of independent interest.

Eric Blais

Papers

The Information Complexity Of Hamming Distance

A mathematical model of performance-relevant feature interactions

Testing properties of boolean functions

Learning and Testing Junta Distributions

Active Property Testing