Combinatorial generation via permutation languages

In this work we present a general and versatile algorithmic framework for exhaustively generating a large variety of different combinatorial objects, based on encoding them as permutations. This approach provides a unified view on many known results and allows us to prove many new ones. In particular, we obtain the following four classical Gray codes as special cases: the Steinhaus-Johnson-Trotter algorithm to generate all permutations of an $n$-element set by adjacent transpositions; the binary reflected Gray code to generate all $n$-bit strings by flipping a single bit in each step; the Gray code for generating all $n$-vertex binary trees by rotations due to Lucas, van Baronaigien, and Ruskey; the Gray code for generating all partitions of an $n$-element ground set by element exchanges due to Kaye. We present two distinct applications for our new framework: The first main application is the generation of pattern-avoiding permutations, yielding new Gray codes for different families of permutations that are characterized by the avoidance of certain classical patterns, (bi)vincular patterns, barred patterns, Bruhat-restricted patterns, mesh patterns, monotone and geometric grid classes, and many others. We thus also obtain new Gray code algorithms for the combinatorial objects that are in bijection to these permutations, in particular for five different types of geometric rectangulations, also known as floorplans, which are divisions of a square into $n$ rectangles subject to certain restrictions. The second main application of our framework are lattice congruences of the weak order on the symmetric group~$S_n$. Recently, Pilaud and Santos realized all those lattice congruences as $(n-1)$-dimensional polytopes, called quotientopes, which generalize hypercubes, associahedra, permutahedra etc. Our algorithm generates the equivalence classes of each of those lattice congruences, by producing a Hamilton path on the skeleton of the corresponding quotientope, yielding a constructive proof that each of these highly symmetric graphs is Hamiltonian. We thus also obtain a provable notion of optimality for the Gray codes obtained from our framework: They translate into walks along the edges of a polytope

On palimpsests in neural memory: an information theory viewpoint

The finite capacity of neural memory and the reconsolidation phenomenon suggest it is important to be able to update stored information as in a palimpsest, where new information overwrites old information. Moreover, changing information in memory is metabolically costly. In this paper, we suggest that information-theoretic approaches may inform the fundamental limits in constructing such a memory system. In particular, we define malleable coding, that considers not only representation length but also ease of representation update, thereby encouraging some form of recycling to convert an old codeword into a new one. Malleability cost is the difficulty of synchronizing compressed versions, and malleable codes are of particular interest when representing information and modifying the representation are both expensive. We examine the tradeoff between compression efficiency and malleability cost, under a malleability metric defined with respect to a string edit distance. This introduces a metric topology to the compressed domain. We characterize the exact set of achievable rates and malleability as the solution of a subgraph isomorphism problem. This is all done within the optimization approach to biology framework.Accepted manuscrip

Combinatorial generation via permutation languages. I. Fundamentals

In this work we present a general and versatile algorithmic framework for exhaustively generating a large variety of different combinatorial objects, based on encoding them as permutations. This approach provides a unified view on many known results and allows us to prove many new ones. In particular, we obtain the following four classical Gray codes as special cases: the Steinhaus-Johnson-Trotter algorithm to generate all permutations of an $n$-element set by adjacent transpositions; the binary reflected Gray code to generate all $n$-bit strings by flipping a single bit in each step; the Gray code for generating all $n$-vertex binary trees by rotations due to Lucas, van Baronaigien, and Ruskey; the Gray code for generating all partitions of an $n$-element ground set by element exchanges due to Kaye. We present two distinct applications for our new framework: The first main application is the generation of pattern-avoiding permutations, yielding new Gray codes for different families of permutations that are characterized by the avoidance of certain classical patterns, (bi)vincular patterns, barred patterns, boxed patterns, Bruhat-restricted patterns, mesh patterns, monotone and geometric grid classes, and many others. We also obtain new Gray codes for all the combinatorial objects that are in bijection to these permutations, in particular for five different types of geometric rectangulations, also known as floorplans, which are divisions of a square into $n$ rectangles subject to certain restrictions. The second main application of our framework are lattice congruences of the weak order on the symmetric group~$S_n$. Recently, Pilaud and Santos realized all those lattice congruences as $(n-1)$-dimensional polytopes, called quotientopes, which generalize hypercubes, associahedra, permutahedra etc. Our algorithm generates the equivalence classes of each of those lattice congruences, by producing a Hamilton path on the skeleton of the corresponding quotientope, yielding a constructive proof that each of these highly symmetric graphs is Hamiltonian. We thus also obtain a provable notion of optimality for the Gray codes obtained from our framework: They translate into walks along the edges of a polytope

General BER Expression for One-Dimensional Constellations

A novel general ready-to-use bit-error rate (BER) expression for one-dimensional constellations is developed. The BER analysis is performed for bit patterns that form a labeling. The number of patterns for equally spaced M-PAM constellations with different BER is analyzed.Comment: To appear in the Proceedings of the IEEE Global Communications Conference (GLOBECOM) 2012. Remark 3 modifie

Codes for Asymmetric Limited-Magnitude Errors With Application to Multilevel Flash Memories

Several physical effects that limit the reliability and performance of multilevel flash memories induce errors that have low magnitudes and are dominantly asymmetric. This paper studies block codes for asymmetric limited-magnitude errors over q-ary channels. We propose code constructions and bounds for such channels when the number of errors is bounded by t and the error magnitudes are bounded by ℓ. The constructions utilize known codes for symmetric errors, over small alphabets, to protect large-alphabet symbols from asymmetric limited-magnitude errors. The encoding and decoding of these codes are performed over the small alphabet whose size depends only on the maximum error magnitude and is independent of the alphabet size of the outer code. Moreover, the size of the codes is shown to exceed the sizes of known codes (for related error models), and asymptotic rate-optimality results are proved. Extensions of the construction are proposed to accommodate variations on the error model and to include systematic codes as a benefit to practical implementation

On the Exact BER of Bit-Wise Demodulators for One-Dimensional Constellations

The optimal bit-wise demodulator for M-ary pulse amplitude modulation (PAM) over the additive white Gaussian noise channel is analyzed in terms of uncoded bit-error rate (BER). New closed-form BER expressions for 4-PAM with any labeling are developed. Moreover, closed-form BER expressions for 11 out of 23 possible bit patterns for 8-PAM are presented, which enable us to obtain the BER for 8-PAM with some of the most popular labelings, including the binary reflected Gray code and the natural binary code. Numerical results show that, regardless of the labeling, there is no difference between the optimal demodulator and the symbol-wise demodulator for any BER of practical interest (below 0.1)

On BICM receivers for TCM transmission

Recent results have shown that the performance of bit-interleaved coded modulation (BICM) using convolutional codes in nonfading channels can be significantly improved when the interleaver takes a trivial form (BICM-T), i.e., when it does not interleave the bits at all. In this paper, we give a formal explanation for these results and show that BICM-T is in fact the combination of a TCM transmitter and a BICM receiver. To predict the performance of BICM-T, a new type of distance spectrum for convolutional codes is introduced, analytical bounds based on this spectrum are developed, and asymptotic approximations are also presented. It is shown that the minimum distance of the code is not the relevant optimization criterion for BICM-T. Optimal convolutional codes for different constrain lengths are tabulated and asymptotic gains of about 2 dB are obtained. These gains are found to be the same as those obtained by Ungerboeck's one-dimensional trellis coded modulation (1D-TCM), and therefore, in nonfading channels, BICM-T is shown to be asymptotically as good as 1D-TCM.Comment: Submitted to the IEEE Transactions on Communication