Dimension Extractors and Optimal Decompression

A *dimension extractor* is an algorithm designed to increase the effective dimension -- i.e., the amount of computational randomness -- of an infinite binary sequence, in order to turn a "partially random" sequence into a "more random" sequence. Extractors are exhibited for various effective dimensions, including constructive, computable, space-bounded, time-bounded, and finite-state dimension. Using similar techniques, the Kucera-Gacs theorem is examined from the perspective of decompression, by showing that every infinite sequence S is Turing reducible to a Martin-Loef random sequence R such that the asymptotic number of bits of R needed to compute n bits of S, divided by n, is precisely the constructive dimension of S, which is shown to be the optimal ratio of query bits to computed bits achievable with Turing reductions. The extractors and decompressors that are developed lead directly to new characterizations of some effective dimensions in terms of optimal decompression by Turing reductions.Comment: This report was combined with a different conference paper "Every Sequence is Decompressible from a Random One" (cs.IT/0511074, at http://dx.doi.org/10.1007/11780342_17), and both titles were changed, with the conference paper incorporated as section 5 of this new combined paper. The combined paper was accepted to the journal Theory of Computing Systems, as part of a special issue of invited papers from the second conference on Computability in Europe, 200

Stable Leader Election in Population Protocols Requires Linear Time

A population protocol *stably elects a leader* if, for all $n$, starting from an initial configuration with $n$ agents each in an identical state, with probability 1 it reaches a configuration $\mathbf{y}$ that is correct (exactly one agent is in a special leader state $\ell$) and stable (every configuration reachable from $\mathbf{y}$ also has a single agent in state $\ell$). We show that any population protocol that stably elects a leader requires $\Omega(n)$ expected "parallel time" --- $\Omega(n^2)$ expected total pairwise interactions --- to reach such a stable configuration. Our result also informs the understanding of the time complexity of chemical self-organization by showing an essential difficulty in generating exact quantities of molecular species quickly.Comment: accepted to Distributed Computing special issue of invited papers from DISC 2015; significantly revised proof structure and intuitive explanation

Design of Geometric Molecular Bonds

An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the affinity of the DNA base A for T, but not for C, G, or another A. Recent experimental breakthroughs in DNA nanotechnology demonstrate that a particular nonspecific like-like bond ("blunt-end DNA stacking" that occurs between the ends of any pair of DNA double-helices) can be used to create specific "macrobonds" by careful geometric arrangement of many nonspecific blunt ends, motivating the need for sets of macrobonds that are orthogonal: two macrobonds not intended to bind should have relatively low binding strength, even when misaligned. To address this need, we introduce geometric orthogonal codes that abstractly model the engineered DNA macrobonds as two-dimensional binary codewords. While motivated by completely different applications, geometric orthogonal codes share similar features to the optical orthogonal codes studied by Chung, Salehi, and Wei. The main technical difference is the importance of 2D geometry in defining codeword orthogonality.Comment: Accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communication

Finite-State Dimension and Lossy Decompressors

This paper examines information-theoretic questions regarding the difficulty of compressing data versus the difficulty of decompressing data and the role that information loss plays in this interaction. Finite-state compression and decompression are shown to be of equivalent difficulty, even when the decompressors are allowed to be lossy. Inspired by Kolmogorov complexity, this paper defines the optimal *decompression *ratio achievable on an infinite sequence by finite-state decompressors (that is, finite-state transducers outputting the sequence in question). It is shown that the optimal compression ratio achievable on a sequence S by any *information lossless* finite state compressor, known as the finite-state dimension of S, is equal to the optimal decompression ratio achievable on S by any finite-state decompressor. This result implies a new decompression characterization of finite-state dimension in terms of lossy finite-state transducers.Comment: We found that Theorem 3.11, which was basically the motive for this paper, was already proven by Sheinwald, Ziv, and Lempel in 1991 and 1995 paper