255 research outputs found
Group Testing with Probabilistic Tests: Theory, Design and Application
Identification of defective members of large populations has been widely
studied in the statistics community under the name of group testing. It
involves grouping subsets of items into different pools and detecting defective
members based on the set of test results obtained for each pool.
In a classical noiseless group testing setup, it is assumed that the sampling
procedure is fully known to the reconstruction algorithm, in the sense that the
existence of a defective member in a pool results in the test outcome of that
pool to be positive. However, this may not be always a valid assumption in some
cases of interest. In particular, we consider the case where the defective
items in a pool can become independently inactive with a certain probability.
Hence, one may obtain a negative test result in a pool despite containing some
defective items. As a result, any sampling and reconstruction method should be
able to cope with two different types of uncertainty, i.e., the unknown set of
defective items and the partially unknown, probabilistic testing procedure.
In this work, motivated by the application of detecting infected people in
viral epidemics, we design non-adaptive sampling procedures that allow
successful identification of the defective items through a set of probabilistic
tests. Our design requires only a small number of tests to single out the
defective items. In particular, for a population of size and at most
defective items with activation probability , our results show that tests is sufficient if the sampling procedure should
work for all possible sets of defective items, while
tests is enough to be successful for any single set of defective items.
Moreover, we show that the defective members can be recovered using a simple
reconstruction algorithm with complexity of .Comment: Full version of the conference paper "Compressed Sensing with
Probabilistic Measurements: A Group Testing Solution" appearing in
proceedings of the 47th Annual Allerton Conference on Communication, Control,
and Computing, 2009 (arXiv:0909.3508). To appear in IEEE Transactions on
Information Theor
Code Construction and Decoding Algorithms for Semi-Quantitative Group Testing with Nonuniform Thresholds
We analyze a new group testing scheme, termed semi-quantitative group
testing, which may be viewed as a concatenation of an adder channel and a
discrete quantizer. Our focus is on non-uniform quantizers with arbitrary
thresholds. For the most general semi-quantitative group testing model, we
define three new families of sequences capturing the constraints on the code
design imposed by the choice of the thresholds. The sequences represent
extensions and generalizations of Bh and certain types of super-increasing and
lexicographically ordered sequences, and they lead to code structures amenable
for efficient recursive decoding. We describe the decoding methods and provide
an accompanying computational complexity and performance analysis
Compressed Genotyping
Significant volumes of knowledge have been accumulated in recent years
linking subtle genetic variations to a wide variety of medical disorders from
Cystic Fibrosis to mental retardation. Nevertheless, there are still great
challenges in applying this knowledge routinely in the clinic, largely due to
the relatively tedious and expensive process of DNA sequencing. Since the
genetic polymorphisms that underlie these disorders are relatively rare in the
human population, the presence or absence of a disease-linked polymorphism can
be thought of as a sparse signal. Using methods and ideas from compressed
sensing and group testing, we have developed a cost-effective genotyping
protocol. In particular, we have adapted our scheme to a recently developed
class of high throughput DNA sequencing technologies, and assembled a
mathematical framework that has some important distinctions from 'traditional'
compressed sensing ideas in order to address different biological and technical
constraints.Comment: Submitted to IEEE Transaction on Information Theory - Special Issue
on Molecular Biology and Neuroscienc
Superselectors: Efficient Constructions and Applications
We introduce a new combinatorial structure: the superselector. We show that
superselectors subsume several important combinatorial structures used in the
past few years to solve problems in group testing, compressed sensing,
multi-channel conflict resolution and data security. We prove close upper and
lower bounds on the size of superselectors and we provide efficient algorithms
for their constructions. Albeit our bounds are very general, when they are
instantiated on the combinatorial structures that are particular cases of
superselectors (e.g., (p,k,n)-selectors, (d,\ell)-list-disjunct matrices,
MUT_k(r)-families, FUT(k, a)-families, etc.) they match the best known bounds
in terms of size of the structures (the relevant parameter in the
applications). For appropriate values of parameters, our results also provide
the first efficient deterministic algorithms for the construction of such
structures
Practical High-Throughput, Non-Adaptive and Noise-Robust SARS-CoV-2 Testing
We propose a compressed sensing-based testing approach with a practical
measurement design and a tuning-free and noise-robust algorithm for detecting
infected persons. Compressed sensing results can be used to provably detect a
small number of infected persons among a possibly large number of people. There
are several advantages of this method compared to classical group testing.
Firstly, it is non-adaptive and thus possibly faster to perform than adaptive
methods which is crucial in exponentially growing pandemic phases. Secondly,
due to nonnegativity of measurements and an appropriate noise model, the
compressed sensing problem can be solved with the non-negative least absolute
deviation regression (NNLAD) algorithm. This convex tuning-free program
requires the same number of tests as current state of the art group testing
methods. Empirically it performs significantly better than theoretically
guaranteed, and thus the high-throughput, reducing the number of tests to a
fraction compared to other methods. Further, numerical evidence suggests that
our method can correct sparsely occurring errors.Comment: 8 Pages, 1 Figur
Boolean Compressed Sensing and Noisy Group Testing
The fundamental task of group testing is to recover a small distinguished
subset of items from a large population while efficiently reducing the total
number of tests (measurements). The key contribution of this paper is in
adopting a new information-theoretic perspective on group testing problems. We
formulate the group testing problem as a channel coding/decoding problem and
derive a single-letter characterization for the total number of tests used to
identify the defective set. Although the focus of this paper is primarily on
group testing, our main result is generally applicable to other compressive
sensing models.
The single letter characterization is shown to be order-wise tight for many
interesting noisy group testing scenarios. Specifically, we consider an
additive Bernoulli() noise model where we show that, for items and
defectives, the number of tests is for arbitrarily
small average error probability and for a worst case
error criterion. We also consider dilution effects whereby a defective item in
a positive pool might get diluted with probability and potentially missed.
In this case, it is shown that is and
for the average and the worst case error
criteria, respectively. Furthermore, our bounds allow us to verify existing
known bounds for noiseless group testing including the deterministic noise-free
case and approximate reconstruction with bounded distortion. Our proof of
achievability is based on random coding and the analysis of a Maximum
Likelihood Detector, and our information theoretic lower bound is based on
Fano's inequality.Comment: In this revision: reorganized the paper, added citations to related
work, and fixed some bug
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