Efficient Testing Algorithm Research Articles

Near-Optimal Noisy Group Testing via Separate Decoding of Items

The group testing problem consists of determining a small set of defective items from a larger set of items based on a number of tests, and is relevant in applications such as medical testing, communication protocols, pattern matching, and more. In this paper, we revisit an efficient algorithm for noisy group testing in which each item is decoded separately (Malyutov and Mateev, 1980), and develop novel performance guarantees via an information-theoretic framework for general noise models. For the special cases of no noise and symmetric noise, we find that the asymptotic number of tests required for vanishing error probability is within a factor $\log 2 \approx 0.7$ of the information-theoretic optimum at low sparsity levels, and that with a small fraction of allowed incorrectly decoded items, this guarantee extends to all sublinear sparsity levels. In addition, we provide a converse bound showing that if one tries to move slightly beyond our low-sparsity achievability threshold using separate decoding of items and i.i.d. randomized testing, the average number of items decoded incorrectly approaches that of a trivial decoder.

Quantum conditional query complexity

We define and study a new type of quantum oracle, the quantum conditional oracle, which provides oracle access to the conditional probabilities associated with an underlying distribution. Amongst other properties, we (a) obtain highly efficient quantum algorithms for identity testing, equivalence testing and uniformity testing of probability distributions; (b) study the power of these oracles for testing properties of boolean functions, and obtain an algorithm for checking whether an n-input m-output boolean function is balanced or e-far from balanced; and (c) give an algorithm, requiring O˜(n/e) queries, for testing whether an n-dimensional quantum state is maximally mixed or not.

A new perspective on clustered planarity as a combinatorial embedding problem

The clustered planarity problem (c-planarity) asks whether a hierarchically clustered graph admits a planar drawing such that the clusters can be nicely represented by regions. We introduce the cd-tree data structure and give a new characterization of c-planarity. It leads to efficient algorithms for c-planarity testing in the following cases. (i) Every cluster and every co-cluster (complement of a cluster) has at most two connected components. (ii) Every cluster has at most five outgoing edges.Moreover, the cd-tree reveals interesting connections between c-planarity and planarity with constraints on the order of edges around vertices. On one hand, this gives rise to a bunch of new open problems related to c-planarity, on the other hand it provides a new perspective on previous results.

Testing DNA code words properties of regular languages

One aspect of DNA Computing is the possibility of using DNA molecules for solving some “complicated” computational problems. In this context, the DNA code word design problem assumes a fundamental role: given a problem encoded in DNA strands and biochemical processes, the final computation is a concatenation of the input DNA strands that must allow us to recover the solution of the given problem in terms of the input (unique decipherability). Thus the initial set of DNA strands must be a code. In addition, it should satisfy some restrictions, called here DNA properties, in order to prevent them from interacting in undesirable ways. So a new interest towards the design of efficient algorithms for testing whether a language X is a code, has arisen from (wet) DNA Computing, but, as far as we know, only when X is a finite set. In this paper we provide an algorithm for testing whether an infinite but regular set of words is a code that avoids some DNA properties among unwanted intermolecular and intramolecular hybridizations.

Straight-Line Triangle Representations via Schnyder Labelings

A straight-line triangle representation (SLTR) of a planar graph is a straight-line drawing such that all the faces including the outer face are triangles. Such a drawing can be viewed as a tiling of a triangle with triangles where the input graph is the skeletal structure. A characterization based on flat angle assignments, i.e., selections of angles of the graph that are of size π in the representation, has been presented in earlier work. The drawback of this characterization of SLTRs is that we have no efficient algorithm for testing whether a given graph admits a flat angle assignment that fulfills the conditions. In this paper we present a new characterization based on Schnyder woods. For graphs with few Schnyder woods there exists a polynomial algorithm to check whether the conditions of this characterization are satisfied. However, there are planar 3-connected graphs on n vertices, which have 3.209n Schnyder woods. We also present a translation of the new characterization into a 2-commodity flow problem. Deciding whether a 2-commodity flow problem has an integral solution is known to be NP-complete. Hence, it is still open to decide whether the recognition of graphs that admit a straight line triangle representation is polynomially tractable.

An Analysis of Industrial SRAM Test Results—A Comprehensive Study on Effectiveness and Classification of March Test Algorithms

This paper deals with efficient test algorithm identification of embedded SRAMs. The approach is based on silicon test results of automotive microcontroller devices, which tries to identify efficient tests by removing unnecessary test patterns that cover the same subset of faults. Results of an industrial case under 29 test algorithms and a large amount of chips are obtained; among them, efficient ones are identified.

Layout-Based Refined NPSF Model for DRAM Characterization and Testing

As dynamic random access memories (DRAMs) are becoming denser with technology scaling, more complex fault behaviors emerge; examples are leakage, coupling effects, and cell neighborhoods interaction. The neighborhood pattern sensitive fault (NPSF) model is suitable to address such faulty behaviors and identify them during the characterization and/or test of new DRAM chips. However, NPSF test algorithms are extremely time-consuming and therefore not economically affordable. In this brief, we show how layout information can be used to refine and significantly simplify the NPSF model and reduce the test time complexity. As a case study, the folded DRAM array is considered. A realistic NPSF model, the $\Delta$ -type neighborhood, is introduced together with a time efficient test algorithm which is more than two-times cheaper than traditional ones. Even when incorporating bit-line influence and word-line coupling effects, along with NPSFs, the test algorithm time complexity almost remains unaltered. Therefore, the proposed approach makes NPSF testing economically affordable, and hence, suitable for the characterization/test of dense DRAMs in the nanoera.

Rigid Two-Dimensional Frameworks with Two Coincident Points

Let G = (V, E) be a graph and $${u, v \in V}$$ u , v ? V be two distinct vertices. We give a necessary and sufficient condition for the existence of an infinitesimally rigid two-dimensional bar-and-joint framework (G, p), in which the positions of u and v coincide. We also determine the rank function of the corresponding modified generic rigidity matroid on ground-set E. The results lead to efficient algorithms for testing whether a graph has such a coincident realization with respect to a designated vertex pair and, more generally, for computing the rank of G in the matroid.

Counting minimal semi-Sturmian words

A finite Sturmian word w is a balanced word over the binary alphabet {a,b}, that is, for all subwords u and v of w of equal length, ||u|a−|v|a|≤1, where |u|a and |v|a denote the number of occurrences of the letter a in u and v, respectively. There are several other characterizations, some leading to efficient algorithms for testing whether a finite word is Sturmian. These algorithms find important applications in areas such as pattern recognition, image processing, and computer graphics. Recently, Blanchet-Sadri and Lensmire considered finite semi-Sturmian words of minimal length and provided an algorithm for generating all of them using techniques from graph theory. In this paper, we exploit their approach in order to count the number of minimal semi-Sturmian words. We also present some other results that come from applying this graph theoretical framework to subword complexity.

Impact of the Yosemite Hantavirus Outbreak on Hantavirus Antibody Testing at a National Reference Laboratory

In conjunction with the 2012 Yosemite hantavirus outbreak, the number of sera our facility tested for hantavirus antibodies increased. We tracked test results and used the data set to determine if a more efficient testing algorithm was possible. Sera were screened using laboratory-developed pan-hantavirus IgG and IgM enzyme immunoassays (EIAs), with an index of >1.10 defined as positive. Sera that were IgM positive by screening (screen IgM(+)) were tested for Sin Nombre virus (SNV)-specific IgM using a laboratory-developed EIA; screen IgM(+) IgG(+) sera were also tested for SNV IgG using a laboratory-developed immunoblot assay. SNV antibody-positive samples were sent to state public health laboratories (PHL) or the CDC for confirmation. Of 3,946 sera tested from July through December 2012, 205 were screen IgM(+) IgG negative (IgG(-)); 7/205 were SNV IgM(+), but only 1/5 sent to PHL/CDC was confirmed as SNV IgM(+). Of 61 screen IgM(+) IgG(+) sera, 16 were SNV antibody positive; 13/16 sera (from 11 patients) went to PHL/CDC, where SNV infection was confirmed for all patients. Of 12 confirmed patients, 7 had been exposed at Yosemite. A modified algorithm defining screen indices of ≥2.00 as positive identified 11/12 confirmed cases while reducing the number of sera requiring SNV-specific antibody testing by 65%; the patient missed was not tested until 3 months after the onset of symptoms. Hantavirus antibody testing at our facility identified 12 SNV-infected patients, including 7 exposed at Yosemite. Some screen IgM(+) IgG(-) SNV IgM(+) results were false positives, emphasizing the value of PHL/CDC confirmatory testing. We identified a modified algorithm requiring analysis of fewer specimens for SNV-specific antibodies without loss of sensitivity.

Efficient Two-Stage Group Testing Algorithms for Genetic Screening

Efficient two-stage group testing algorithms that are particularly suited for rapid and less-expensive DNA library screening and other large scale biological group testing efforts are investigated in this paper. The main focus is on novel combinatorial constructions in order to minimize the number of individual tests at the second stage of a two-stage disjunctive testing procedure. Building on recent work by Levenshtein (2003) and Tonchev (2008), several new infinite classes of such combinatorial designs are presented.

Special Section on the Forty-Second Annual ACM Symposium on Theory of Computing (STOC 2010)

This issue of SICOMP contains eight selected papers from the Forty-Second Annual ACM Symposium on Theory of Computing (STOC 2010), held June 6--8, 2010, in Cambridge, Massachusetts. The STOC proceedings contained 78 papers, which the program committee selected from 279 submissions. The program committee consisted of Timothy Chan, Ken Clarkson, Constantinos Daskalakis, Irit Dinur, Faith Ellen, Alan Frieze, Parikshit Gopalan, Piotr Indyk, Valentine Kabanets, Yael Tauman Kalai, Howard Karloff, Robert Kleinberg, Assaf Naor, Noam Nisan, Chris Peikert, Jaikumar Radhakrishnan, Oded Regev, Alexander Russell, Leonard Schulman (chair), Aravind Srinivasan, Santosh Vempala, and Andrew Yao. Eight of the STOC papers appear in this special section, each expanded and subjected to the standard thorough reviewing process of the journal. They cover a diverse collection of topics: In “Improving Exhaustive Search Implies Superpolynomial Lower Bounds," R. Ryan Williams shows that there are natural problems in NP and BPP for which algorithms that improve over the naïve deterministic simulation even quite slightly, imply lower bounds such as NEXP $\not\in$ P/poly and LOGSPACE $\neq$ NP. Williams also proves certain unconditional time-space lower bounds for improving on exhaustive search; the length of the witness-string in some standard verification protocol is a key parameter here. In “An Effective Dichotomy for the Counting Constraint Satisfaction Problem," Martin Dyer and David Richerby consider the counting constraint satisfaction problem (\#CSP). This problem asks how many ways there are to satisfy a system of constraints on a set of variables, where a constraint is a relation chosen from a fixed finite set. This class is shown to have a decidable dichotomy, depending on the form of the relations. The dichotomy is that each problem in the class either is in FP or is \#P-complete, with no intermediate cases. In “Pseudorandom Generators for Polynomial Threshold Functions," Raghu Meka and David Zuckerman develop improved (and in many cases the first nontrivial) pseudorandom generators for low-degree polynomial threshold functions; related explicit constructions are also developed. A key ingredient is the use of invariance principles to construct pseudorandom generators. In “Local List-Decoding and Testing of Random Linear Codes from High Error," Swastik Kopparty and Shubhangi Saraf give efficient local list-decoding and testing algorithms for “sparse" random linear codes, and subexponential time algorithms for list-decoding random linear codes, which tolerate error rates approaching $1/2$. In “How to Compress Interactive Communication," Boaz Barak, Mark Braverman, Xi Chen, and Anup Rao attack the important direct sum problem in communication complexity: is the complexity of evaluating $n$ copies of a function ever significantly less than $n$ times the complexity of evaluating it once? By defining a new notion of information cost for protocols --- the so-called internal information cost --- and providing new protocol compression schemes, they prove that computing $n$ copies of any function requires communicating at least $\sqrt{n}$ times as many bits as computing one copy of the function. In “A Deterministic Single Exponential Time Algorithm for Most Lattice Problems based on Voronoi Cell Computations," Daniele Micciancio and Panagiotis Voulgaris provide the first $\exp(O(n))$-time algorithms for the closest vector problem (CVP) and shortest independent vectors problem (SIVP); their algorithm is, moreover, deterministic. Likewise they provide a deterministic algorithm for the shortest vector problem (SVP), whose $\exp(O(n))$ runtime is an improvement over the best known bounds for randomized algorithms. In “Perfect Matchings in $O(n \log n)$ Time in Regular Bipartite Graphs," Ashish Goel, Michael Kapralov, and Sanjeev Khanna provide a randomized algorithm that finds a perfect matching in a $d$-regular $n$-node bipartite graph in time $O(n \log n)$, notably, within time that may be sublinear in the input size and is independent of the degree. In “Efficiency Improvements in Constructing Pseudorandom Generators from One-Way Functions," Iftach Haitner, Omer Reingold, and Salil Vadhan give a new construction of pseudorandom generators from one-way functions that both simplifies and tightens the acclaimed original construction of Hastad, Impagliazzo, Levin, and Luby. We thank the authors, the STOC program committee, the STOC external reviewers, and the journal referees for all their work to make this special issue possible.

A Program for Year-Round Surveillance of Respiratory Syndromes Needs More Efficient Testing Algorithms to Quickly Identify Causative Pathogens in Specimens That Test Negative for Influenza Virus

A Program for Year-Round Surveillance of Respiratory Syndromes Needs More Efficient Testing Algorithms to Quickly Identify Causative Pathogens in Specimens That Test Negative for Influenza Virus

On Isomorphism Testing of Groups with Normal Hall Subgroups

A normal Hall subgroup N of a group G is a normal subgroup with its order coprime with its index. Schur-Zassenhaus theorem states that every normal Hall subgroup has a complement subgroup, that is a set of coset representatives H which also forms a subgroup of G. In this paper, we present a framework to test isomorphism of groups with at least one normal Hall subgroup, when groups are given as multiplication tables. To establish the framework, we first observe that a proof of Schur-Zassenhaus theorem is constructive, and formulate a necessary and sufficient condition for testing isomorphism in terms of the associated actions of the semidirect products, and isomorphisms of the normal parts and complement parts. We then focus on the case when the normal subgroup is abelian. Utilizing basic facts of representation theory of finite groups and a technique by Le Gall (STACS 2009), we first get an efficient isomorphism testing algorithm when the complement has bounded number of generators. For the case when the complement subgroup is elementary abelian, which does not necessarily have bounded number of generators, we obtain a polynomial time isomorphism testing algorithm by reducing to generalized code isomorphism problem, which asks whether two linear subspaces are the same up to permutation of coordinates. A solution to the latter can be obtained by a mild extension of the singly exponential (in the number of coordinates) time algorithm for code isomorphism problem developed recently by Babai et al. (SODA 2011). Enroute to obtaining the above reduction, we study the following computational problem in representation theory of finite groups: given two representations ρ and τ of a group H over \( \mathbb{Z}_p^d \), p a prime, determine if there exists an automorphism : H → H, such that the induced representation ρ𝜙 = ρ ◦ 𝜙 and τ are equivalent, in time poly(|H|, p d).

A New Method for March Test Algorithm Generation and Its Application for Fault Detection in RAMs

In this paper, all linked and unlinked static and two-operation dynamic faults are considered. A classification for their description is introduced. To generate a test algorithm for detection of all the considered faults, it was shown that it is not an easy problem. For this purpose, a new structure-oriented method is developed. Based on the proposed method, an efficient test algorithm March LSD of complexity 75N is generated for the detection of the considered linked static and dynamic faults.

Biomarkers that currently affect clinical practice: EGFR, ALK, MET, KRAS.

New drugs such as pemetrexed, the epidermal growth factor receptor (egfr) tyrosine kinase inhibitors, and the Alk inhibitor crizotinib have recently enabled progress in the management of advanced non-small-cell lung cancer (nsclc). More drugs, especially Met inhibitors, will follow. However, the benefits of these agents are not uniform across the spectrum of nsclc, and optimizing their utility requires some degree of subgrouping of nsclc by the presence or absence of certain biomarkers.The biomarkers of current or imminent value are EGFR and KRAS mutational status, ALK rearrangements, and MET immunohistochemistry. As a predictor of benefit for anti-egfr monoclonal antibodies, EGFR immunohistochemistry is also of potential interest.Some of the foregoing biomarkers (EGFR, ALK, MET) are direct drivers of the malignant phenotype. As such, they are, quite rationally, the direct targets of inhibitory drugs. However, KRAS, while definitely a driver, has resisted attempts at direct pharmacologic manipulation, and its main value might lie in its role as part of an efficient testing algorithm, because KRAS mutations appear to exclude EGFR and ALK mutations. The indirect value of KRAS in determining sensitivity to other targeted agents or to pemetrexed remains controversial. The other biomarkers (EGFR, ALK, MET) may also have indirect value as predictors of sensitivity to chemotherapy in general, to pemetrexed specifically, and to radiotherapy and molecularly targeted agents.These biomarkers have all enabled the co-development of new drugs with companion diagnostics, and they illustrate the paradigm that will govern progress in oncology in the immediate future. However, in nsclc, the acquisition of sufficient biopsy material remains a stubborn obstacle to the evolution of novel targeted therapies.

HPV Genotypes in High Grade Cervical Lesions and Invasive Cervical Carcinoma as Detected by Two Commercial DNA Assays, North Carolina, 2001–2006

BackgroundHPV typing using formalin fixed paraffin embedded (FFPE) cervical tissue is used to evaluate HPV vaccine impact, but DNA yield and quality in FFPE specimens can negatively affect test results. This study aimed to evaluate 2 commercial assays for HPV detection and typing using FFPE cervical specimens.MethodsFour large North Carolina pathology laboratories provided FFPE specimens from 299 women ages18 and older diagnosed with cervical disease from 2001 to 2006. For each woman, one diagnostic block was selected and unstained serial sections were prepared for DNA typing. Extracts from samples with residual lesion were used to detect and type HPV using parallel and serial testing algorithms with the Linear Array and LiPA HPV genotyping assays.FindingsLA and LiPA concordance was 0.61 for detecting any high-risk (HR) and 0.20 for detecting any low-risk (LR) types, with significant differences in marginal proportions for HPV16, 51, 52, and any HR types. Discordant results were most often LiPA-positive, LA-negative. The parallel algorithm yielded the highest prevalence of any HPV type (95.7%). HR type prevalence was similar using parallel (93.1%) and serial (92.1%) approaches. HPV16, 33, and 52 prevalence was slightly lower using the serial algorithm, but the median number of HR types per woman (1) did not differ by algorithm. Using the serial algorithm, HPV DNA was detected in >85% of invasive and >95% of pre-invasive lesions. The most common type was HPV16, followed by 52, 18, 31, 33, and 35; HPV16/18 was detected in 56.5% of specimens. Multiple HPV types were more common in lower grade lesions.ConclusionsWe developed an efficient algorithm for testing and reporting results of two commercial assays for HPV detection and typing in FFPE specimens, and describe HPV type distribution in pre-invasive and invasive cervical lesions in a state-based sample prior to HPV vaccine introduction.

A Formal Methodology for Network Protocol Fingerprinting

Network protocol fingerprinting refers to the process of identifying a protocol implementation by their input and output behaviors. It has been regarded as both a potential threat to network security and also as a useful mechanism for network management. Existing protocol fingerprinting tools share common disadvantages such as being protocol-specific and difficult to automate. This paper proposes a formal methodology for fingerprinting experiments using which we can model a broad spectrum of fingerprinting problems and design-efficient algorithms. We present a formal behavioral model that specifies a protocol principal by its states and transitions, then identify a complete taxonomy of fingerprint matching and discovery problems is identified based on 1) whether the fingerprinting experiment is active or passive and 2) the information available about the specifications and implementations. Algorithms to solve the problems are discussed. In particular, for fingerprint matching algorithm, we propose an efficient PEFSM online separation algorithm for active experiment and concurrent passive testing for passive experiments. For fingerprint discovery problem, there are two cases: if the protocol specification is available as a nondeterministic PEFSM, we apply across verification and back-tracing technique for active and passive discovery, respectively; if no specification is available, we take the machine learning approach and discover the fingerprint by active testing.

Soft Computing Approach for digital Circuit Layout based on Graph Partitioning

Soft computing based approaches are increasingly being used to solve different NP complete problems, the development of efficient parallel algorithms for digital circuit partitioning, circuit testing, logic minimization and simulation etc. is currently a field of increasing research activity. This paper describes evolutionary based approach for solving circuitpartitioning problem. That implies dividing a circuit into nonoverlapping sub circuits while minimizing the number of cuts after the division and balancing the load associated to each one. The paper shows the effective partitioning for achieving peak chip performance and reducing the cost and time of the design and manufacturing process.

An Efficient Stochastic Simulation Algorithm for Bayesian Unit Root Testing in Stochastic Volatility Models

In financial times series analysis, unit root test is one of the most important research issues. This paper is aimed to propose a new simple and efficient stochastic simulation algorithm for computing Bayes factor to detect the unit root of stochastic volatility models. The proposed algorithm is based on a classical thermodynamic integration technique named path sampling. Simulation studies show that the test procedure is efficient under moderate sample size. In the end, the performance of the proposed approach is investigated with a Monte Carlo simulation study and illustrated with a time series of S&P500 return data.