Identification and Classification Problems on Pooling Designs for Inhibitor Models

@article{Chang2010IdentificationAC,
  title={Identification and Classification Problems on Pooling Designs for Inhibitor Models},
  author={Huilan Chang and Hong-Bin Chen and Hung-Lin Fu},
  journal={Journal of computational biology : a journal of computational molecular cell biology},
  year={2010},
  volume={17 7},
  pages={
          927-41
        }
}
  • Huilan Chang, Hong-Bin Chen, H. Fu
  • Published 15 July 2010
  • Computer Science
  • Journal of computational biology : a journal of computational molecular cell biology
Pooling designs are common tools to efficiently distinguish positive clones from negative clones in clone library screening. In some applications, there is a third type of clones called "inhibitors" whose effect is in a sense to obscure the positive clones in pools. Various inhibitor models have been proposed in the literature. We address the inhibitor problems of designing efficient nonadaptive procedures for both identification and classification problems, and improve previous results in… 
View on PubMed
ir.nctu.edu.tw
17 Citations
Highly Influential Citations
2
Background Citations
9
Methods Citations
3
Results Citations
2

17 Citations

Citation Type

Citation Type

Learning immune-defectives graph through group tests
TLDR
The goal of this paper is to identify the defectives, inhibitors, and their “associations” with high probability, or in other words, learn the Immune-Defectives Graph using group tests.
Learning Immune-Defectives Graph through Group Tests
TLDR
The goal of this paper is to identify the defectives, inhibitors, and their “associations” with high probability, or in other words, learn the Immune Defectives Graph (IDG).
An Almost Optimal Algorithm for Generalized Threshold Group Testing with Inhibitors
TLDR
A new generalization of the GTI model in which there are two unknown thresholds h and g is considered and the response to a test is YES both in the case when the queried subset contains at least one defective item and less than h inhibitors, and inThe present article derives lower bounds on the minimum number of tests required to determine the defective items under this model and presents an algorithm that uses an almost optimal number of Tests.
Non-adaptive group testing with inhibitors
TLDR
A probabilistic non-adaptive pooling design with a low complexity decoding algorithm for group testing with inhibitors is proposed and it is shown that the sample complexity of the number of tests required for guaranteed recovery with vanishing error probability scales as T = O(d log n) and equation in the regimes r = O (d) and d = o(r) respectively.
Learning Immune-Defectives Graph Through Group Tests
TLDR
The goal of this paper is to identify the defectives, inhibitors, and their “associations” with high probability, or in other words, learn the immune defectives graph (IDG) efficiently through group tests, and propose a Probabilistic non-adaptive pooling design, a probabilistic two-stage adaptive poolingDesign, and decoding algorithms for learning the IDG.
Sublinear decoding schemes for non-adaptive group testing with inhibitors
TLDR
Two decoding schemes for efficiently identifying the defective items and the inhibitors in the presence of $e$ erroneous outcomes in time are presented, each column of the measurement matrices associated with the proposed schemes can be nonrandomly generated in polynomial order of the number of rows.
Threshold Group Testing on Inhibitor Model
TLDR
This article provides nonadaptive algorithms to conquer the threshold group testing on k-inhibitor model where error-tolerance is considered and provides a two-stage algorithm to identify all inhibitors and find a g-approximate set.
Pooled Screening for Synergistic Interactions Subject to Blocking and Noise
The complex molecular networks in the cell can give rise to surprising interactions: gene deletions that are synthetically lethal, gene overexpressions that promote stemness or differentiation,…
Efficient and error-tolerant schemes for non-adaptive complex group testing and its application in complex disease genetics
TLDR
This work considers complex group testing (CmplxGT) in which a set of defective items consists of subsets of positive items (called \textit{positive complexes}), and presents a scheme that efficiently identifies all positive complexes.
Group Testing for Efficiently Sampling Hypergraphs When Tests Have Variable Costs
TLDR
This work generates test problems with variable numbers of defective sets and a tunable positive:negative test cost ratio to compare the efficiency of deterministic and stochastic adaptive group splitting algorithms for identifying defective edges in hypergraphs and shows that the optimal initial group size is a function of both the prevalence of defective set and the positive: negative test ratio.
...
1
2
...

References

SHOWING 1-10 OF 35 REFERENCES
Error-Tolerant Pooling Designs with Inhibitors
TLDR
This paper gives a pooling design, as well as a two-stage scheme, for the inhibitor model with unreliable outcomes, and the number of pools required by the schemes are quite comparable to the three- stage scheme.
The identification of positive clones in a general inhibitor model
New combinatorial structures with applications to efficient group testing with inhibitors
  • A. D. Bonis
  • Computer Science, Mathematics
    J. Comb. Optim.
  • 2008
TLDR
An efficient trivial two-stage algorithm is given for GTI in the case when the exact number of positives is known and an improved lower bound on the number of tests required by any algorithm (using any number of stages) is derived.
Improved Algorithms for Group Testing with Inhibitors
An upper bound of the number of tests in pooling designs for the error-tolerant complex model
TLDR
An upper bound of the number of tests required in a pooling design for the complex model (with given design parameters) where experimental errors are allowed is given.
Sets pooling designs
AbstractPooling desings have previously been used for the efficient identification of distinguished elements of a finite setU. Group testing underlies these designs: For any $$S \subseteq U$$ , a…
Pooling designs for clone library screening in the inhibitor complex model
TLDR
A very efficient pooling design for the general inhibitor complex model is proposed and extended to the error-tolerant case and a lower bound and an upper bound of tests are given in a nonadaptive pooling designs for some inhibitor complex models.
Optimal Two-Stage Algorithms for Group Testing Problems
TLDR
This work provides an optimal two-stage algorithm that uses a number of tests of the same order as the information-theoretic lower bound on the problem and provides efficient algorithms for the case in which there is a Bernoulli probability distribution on the possible sets.
Trivial two-stage group testing for complexes using almost disjunct matrices
Group Testing With Blockers and Synergism
Discovery and development of a new drug can cost hundreds of millions of dollars. Pharmaceutical companies have used group testing methodology routinely as one of the efficient high throughput…
...
1
2
3
4
...