An empirical comparison of exact nearest neighbour algorithms

Abstract. Nearest neighbour search (NNS) is an old problem that is of practical importance in a number of fields. It involves finding, for a given point q, called the query, one or more points from a given set of points that are nearest to the query q. Since the initial inception of the problem a great number of algorithms and techniques have been proposed for its solution. However, it remains the case that many of the proposed algorithms have not been compared against each other on a wide variety of datasets. This research attempts to fill this gap to some extent by presenting a detailed empirical comparison of three prominent data structures for exact NNS: KD-Trees, Metric Trees, and Cover Trees. Our results suggest that there is generally little gain in using Metric Trees or Cover Trees instead of KD-Trees for the standard NNS problem.

Microbial Forensics: Predicting Phenotypic Characteristics and Environmental Conditions from Large-Scale Gene Expression Profiles

<div><p>A tantalizing question in cellular physiology is whether the cellular state and environmental conditions can be inferred by the expression signature of an organism. To investigate this relationship, we created an extensive normalized gene expression compendium for the bacterium <i>Escherichia coli</i> that was further enriched with meta-information through an iterative learning procedure. We then constructed an ensemble method to predict environmental and cellular state, including strain, growth phase, medium, oxygen level, antibiotic and carbon source presence. Results show that gene expression is an excellent predictor of environmental structure, with multi-class ensemble models achieving balanced accuracy between 70.0% (±3.5%) to 98.3% (±2.3%) for the various characteristics. Interestingly, this performance can be significantly boosted when environmental and strain characteristics are simultaneously considered, as a composite classifier that captures the inter-dependencies of three characteristics (medium, phase and strain) achieved 10.6% (±1.0%) higher performance than any individual models. Contrary to expectations, only 59% of the top informative genes were also identified as differentially expressed under the respective conditions. Functional analysis of the respective genetic signatures implicates a wide spectrum of Gene Ontology terms and KEGG pathways with condition-specific information content, including iron transport, transferases, and enterobactin synthesis. Further experimental phenotypic-to-genotypic mapping that we conducted for knock-out mutants argues for the information content of top-ranked genes. This work demonstrates the degree at which genome-scale transcriptional information can be predictive of latent, heterogeneous and seemingly disparate phenotypic and environmental characteristics, with far-reaching applications.</p></div