The capacity of non-identical adaptive group testing

We consider the group testing problem, in the case where the items are defective independently but with non-constant probability. We introduce and analyse an algorithm to solve this problem by grouping items together appropriately. We give conditions under which the algorithm performs essentially optimally in the sense of information-theoretic capacity. We use concentration of measure results to bound the probability that this algorithm requires many more tests than the expected number. This has applications to the allocation of spectrum to cognitive radios, in the case where a database gives prior information that a particular band will be occupied.Comment: To be presented at Allerton 201

Poisson Group Testing: A Probabilistic Model for Boolean Compressed Sensing

We introduce a novel probabilistic group testing framework, termed Poisson group testing, in which the number of defectives follows a right-truncated Poisson distribution. The Poisson model has a number of new applications, including dynamic testing with diminishing relative rates of defectives. We consider both nonadaptive and semi-adaptive identification methods. For nonadaptive methods, we derive a lower bound on the number of tests required to identify the defectives with a probability of error that asymptotically converges to zero; in addition, we propose test matrix constructions for which the number of tests closely matches the lower bound. For semi-adaptive methods, we describe a lower bound on the expected number of tests required to identify the defectives with zero error probability. In addition, we propose a stage-wise reconstruction algorithm for which the expected number of tests is only a constant factor away from the lower bound. The methods rely only on an estimate of the average number of defectives, rather than on the individual probabilities of subjects being defective

Optimal Dorfman Group Testing For Symmetric Distributions

We study Dorfman's classical group testing protocol in a novel setting where individual specimen statuses are modeled as exchangeable random variables. We are motivated by infectious disease screening. In that case, specimens which arrive together for testing often originate from the same community and so their statuses may exhibit positive correlation. Dorfman's protocol screens a population of n specimens for a binary trait by partitioning it into nonoverlapping groups, testing these, and only individually retesting the specimens of each positive group. The partition is chosen to minimize the expected number of tests under a probabilistic model of specimen statuses. We relax the typical assumption that these are independent and indentically distributed and instead model them as exchangeable random variables. In this case, their joint distribution is symmetric in the sense that it is invariant under permutations. We give a characterization of such distributions in terms of a function q where q(h) is the marginal probability that any group of size h tests negative. We use this interpretable representation to show that the set partitioning problem arising in Dorfman's protocol can be reduced to an integer partitioning problem and efficiently solved. We apply these tools to an empirical dataset from the COVID-19 pandemic. The methodology helps explain the unexpectedly high empirical efficiency reported by the original investigators.Comment: 20 pages w/o references, 2 figure

Graph-based techniques for compression and reconstruction of sparse sources

The main goal of this thesis is to develop lossless compression schemes for analog and binary sources. All the considered compression schemes have as common feature that the encoder can be represented by a graph, so they can be studied employing tools from modern coding theory. In particular, this thesis is focused on two compression problems: the group testing and the noiseless compressed sensing problems. Although both problems may seem unrelated, in the thesis they are shown to be very close. Furthermore, group testing has the same mathematical formulation as non-linear binary source compression schemes that use the OR operator. In this thesis, the similarities between these problems are exploited. The group testing problem is aimed at identifying the defective subjects of a population with as few tests as possible. Group testing schemes can be divided into two groups: adaptive and non-adaptive group testing schemes. The former schemes generate tests sequentially and exploit the partial decoding results to attempt to reduce the overall number of tests required to label all members of the population, whereas non-adaptive schemes perform all the test in parallel and attempt to label as many subjects as possible. Our contributions to the group testing problem are both theoretical and practical. We propose a novel adaptive scheme aimed to efficiently perform the testing process. Furthermore, we develop tools to predict the performance of both adaptive and non-adaptive schemes when the number of subjects to be tested is large. These tools allow to characterize the performance of adaptive and non-adaptive group testing schemes without simulating them. The goal of the noiseless compressed sensing problem is to retrieve a signal from its lineal projection version in a lower-dimensional space. This can be done only whenever the amount of null components of the original signal is large enough. Compressed sensing deals with the design of sampling schemes and reconstruction algorithms that manage to reconstruct the original signal vector with as few samples as possible. In this thesis we pose the compressed sensing problem within a probabilistic framework, as opposed to the classical compression sensing formulation. Recent results in the state of the art show that this approach is more efficient than the classical one. Our contributions to noiseless compressed sensing are both theoretical and practical. We deduce a necessary and sufficient matrix design condition to guarantee that the reconstruction is lossless. Regarding the design of practical schemes, we propose two novel reconstruction algorithms based on message passing over the sparse representation of the matrix, one of them with very low computational complexity.El objetivo principal de la tesis es el desarrollo de esquemas de compresión sin pérdidas para fuentes analógicas y binarias. Los esquemas analizados tienen en común la representación del compresor mediante un grafo; esto ha permitido emplear en su estudio las herramientas de codificación modernas. Más concretamente la tesis estudia dos problemas de compresión en particular: el diseño de experimentos de testeo comprimido de poblaciones (de sangre, de presencia de elementos contaminantes, secuenciado de ADN, etcétera) y el muestreo comprimido de señales reales en ausencia de ruido. A pesar de que a primera vista parezcan problemas totalmente diferentes, en la tesis mostramos que están muy relacionados. Adicionalmente, el problema de testeo comprimido de poblaciones tiene una formulación matemática idéntica a los códigos de compresión binarios no lineales basados en puertas OR. En la tesis se explotan las similitudes entre todos estos problemas. Existen dos aproximaciones al testeo de poblaciones: el testeo adaptativo y el no adaptativo. El primero realiza los test de forma secuencial y explota los resultados parciales de estos para intentar reducir el número total de test necesarios, mientras que el segundo hace todos los test en bloque e intenta extraer el máximo de datos posibles de los test. Nuestras contribuciones al problema de testeo comprimido han sido tanto teóricas como prácticas. Hemos propuesto un nuevo esquema adaptativo para realizar eficientemente el proceso de testeo. Además hemos desarrollado herramientas que permiten predecir el comportamiento tanto de los esquemas adaptativos como de los esquemas no adaptativos cuando el número de sujetos a testear es elevado. Estas herramientas permiten anticipar las prestaciones de los esquemas de testeo sin necesidad de simularlos. El objetivo del muestreo comprimido es recuperar una señal a partir de su proyección lineal en un espacio de menor dimensión. Esto sólo es posible si se asume que la señal original tiene muchas componentes que son cero. El problema versa sobre el diseño de matrices y algoritmos de reconstrucción que permitan implementar esquemas de muestreo y reconstrucción con un número mínimo de muestras. A diferencia de la formulación clásica de muestreo comprimido, en esta tesis se ha empleado un modelado probabilístico de la señal. Referencias recientes en la literatura demuestran que este enfoque permite conseguir esquemas de compresión y descompresión más eficientes. Nuestras contribuciones en el campo de muestreo comprimido de fuentes analógicas dispersas han sido también teóricas y prácticas. Por un lado, la deducción de la condición necesaria y suficiente que debe garantizar la matriz de muestreo para garantizar que se puede reconstruir unívocamente la secuencia de fuente. Por otro lado, hemos propuesto dos algoritmos, uno de ellos de baja complejidad computacional, que permiten reconstruir la señal original basados en paso de mensajes entre los nodos de la representación gráfica de la matriz de proyección.Postprint (published version

Group testing:an information theory perspective

The group testing problem concerns discovering a small number of defective items within a large population by performing tests on pools of items. A test is positive if the pool contains at least one defective, and negative if it contains no defectives. This is a sparse inference problem with a combinatorial flavour, with applications in medical testing, biology, telecommunications, information technology, data science, and more. In this monograph, we survey recent developments in the group testing problem from an information-theoretic perspective. We cover several related developments: efficient algorithms with practical storage and computation requirements, achievability bounds for optimal decoding methods, and algorithm-independent converse bounds. We assess the theoretical guarantees not only in terms of scaling laws, but also in terms of the constant factors, leading to the notion of the {\em rate} of group testing, indicating the amount of information learned per test. Considering both noiseless and noisy settings, we identify several regimes where existing algorithms are provably optimal or near-optimal, as well as regimes where there remains greater potential for improvement. In addition, we survey results concerning a number of variations on the standard group testing problem, including partial recovery criteria, adaptive algorithms with a limited number of stages, constrained test designs, and sublinear-time algorithms.Comment: Survey paper, 140 pages, 19 figures. To be published in Foundations and Trends in Communications and Information Theor