Semantic distillation: a method for clustering objects by their contextual specificity

TL;DR

This paper introduces a novel fuzzy hierarchical clustering method called semantic distillation, inspired by quantum measurement theory, to analyze and cluster experimental data such as DNA array gene specificity.

Contribution

It unifies concepts from IR, statistical analysis, and quantum measurement to develop a new clustering technique for complex experimental data.

Findings

Successfully applied to DNA array data

Effectively clusters genes by specificity

Demonstrates cross-disciplinary approach

Abstract

Techniques for data-mining, latent semantic analysis, contextual search of databases, etc. have long ago been developed by computer scientists working on information retrieval (IR). Experimental scientists, from all disciplines, having to analyse large collections of raw experimental data (astronomical, physical, biological, etc.) have developed powerful methods for their statistical analysis and for clustering, categorising, and classifying objects. Finally, physicists have developed a theory of quantum measurement, unifying the logical, algebraic, and probabilistic aspects of queries into a single formalism. The purpose of this paper is twofold: first to show that when formulated at an abstract level, problems from IR, from statistical data analysis, and from physical measurement theories are very similar and hence can profitably be cross-fertilised, and, secondly, to propose a novel method of fuzzy hierarchical clustering, termed \textit{semantic distillation} -- strongly inspired from the theory of quantum measurement --, we developed to analyse raw data coming from various types of experiments on DNA arrays. We illustrate the method by analysing DNA arrays experiments and clustering the genes of the array according to their specificity.