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arXiv · 1503.00555

Learning Immune-Defectives Graph through Group Tests

Abhinav Ganesan·Sidharth Jaggi·Venkatesh Saligrama
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Abstract

This paper deals with an abstraction of a unified problem of drug discovery and pathogen identification. Pathogen identification involves identification of disease-causing biomolecules. Drug discovery involves finding chemical compounds, called lead compounds, that bind to pathogenic proteins and eventually inhibit the function of the protein. In this paper, the lead compounds are abstracted as inhibitors, pathogenic proteins as defectives, and the mixture of "ineffective" chemical compounds and non-pathogenic proteins as normal items. A defective could be immune to the presence of an inhibitor in a test. So, a test containing a defective is positive iff it does not contain its "associated" inhibitor. 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. We propose a probabilistic non-adaptive pooling design, a probabilistic two-stage adaptive pooling design and decoding algorithms for learning the IDG. For the two-stage adaptive-pooling design, we show that the sample complexity of the number of tests required to guarantee recovery of the inhibitors, defectives, and their associations with high probability, i.e., the upper bound, exceeds the proposed lower bound by a logarithmic multiplicative factor in the number of items. For the non-adaptive pooling design too, we show that the upper bound exceeds the proposed lower bound by at most a logarithmic multiplicative factor in the number of items.

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Abhinav Ganesan, Sidharth Jaggi, Venkatesh Saligrama. 2015-01-26. Learning Immune-Defectives Graph through Group Tests. https://arxiv.org/abs/1503.00555

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