Coding limits on the number of transcription factors

Transcription factor proteins bind specific DNA sequences to control the expression of genes. They contain DNA binding domains which belong to several super-families, each with a specific mechanism of DNA binding. The total number of transcription factors encoded in a genome increases with the number of genes in the genome. Here, we examined the number of transcription factors from each super-family in diverse organisms. We find that the number of transcription factors from most super-families appears to be bounded. For example, the number of winged helix factors does not generally exceed 300, even in very large genomes. The magnitude of the maximal number of transcription factors from each super-family seems to correlate with the number of DNA bases effectively recognized by the binding mechanism of that super-family. Coding theory predicts that such upper bounds on the number of transcription factors should exist, in order to minimize cross-binding errors between transcription factors. This theory further predicts that factors with similar binding sequences should tend to have similar biological effect, so that errors based on mis-recognition are minimal. We present evidence that transcription factors with similar binding sequences tend to regulate genes with similar biological functions, supporting this prediction. The present study suggests limits on the transcription factor repertoire of cells, and suggests coding constraints that might apply more generally to the mapping between binding sites and biological function.Comment: http://www.weizmann.ac.il/complex/tlusty/papers/BMCGenomics2006.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1590034/ http://www.biomedcentral.com/1471-2164/7/23

On similarity prediction and pairwise clustering

We consider the problem of clustering a finite set of items from pairwise similarity information. Unlike what is done in the literature on this subject, we do so in a passive learning setting, and with no specific constraints on the cluster shapes other than their size. We investigate the problem in different settings: i. an online setting, where we provide a tight characterization of the prediction complexity in the mistake bound model, and ii. a standard stochastic batch setting, where we give tight upper and lower bounds on the achievable generalization error. Prediction performance is measured both in terms of the ability to recover the similarity function encoding the hidden clustering and in terms of how well we classify each item within the set. The proposed algorithms are time efficient

Indexability, concentration, and VC theory

Degrading performance of indexing schemes for exact similarity search in high dimensions has long since been linked to histograms of distributions of distances and other 1-Lipschitz functions getting concentrated. We discuss this observation in the framework of the phenomenon of concentration of measure on the structures of high dimension and the Vapnik-Chervonenkis theory of statistical learning.Comment: 17 pages, final submission to J. Discrete Algorithms (an expanded, improved and corrected version of the SISAP'2010 invited paper, this e-print, v3

On the Measurement of Privacy as an Attacker's Estimation Error

A wide variety of privacy metrics have been proposed in the literature to evaluate the level of protection offered by privacy enhancing-technologies. Most of these metrics are specific to concrete systems and adversarial models, and are difficult to generalize or translate to other contexts. Furthermore, a better understanding of the relationships between the different privacy metrics is needed to enable more grounded and systematic approach to measuring privacy, as well as to assist systems designers in selecting the most appropriate metric for a given application. In this work we propose a theoretical framework for privacy-preserving systems, endowed with a general definition of privacy in terms of the estimation error incurred by an attacker who aims to disclose the private information that the system is designed to conceal. We show that our framework permits interpreting and comparing a number of well-known metrics under a common perspective. The arguments behind these interpretations are based on fundamental results related to the theories of information, probability and Bayes decision.Comment: This paper has 18 pages and 17 figure