Average case analysis of marking algorithms

The Lindstrom marking algorithm uses bounded workspace. Its time complexity is O(n^2) in all cases, but it has been assumed that the average case time complexity O(n lg n). It is proven that the average case time complexity is H(n^2). Similarly, the average size of the Wegbreit bit stack is shown to be H(n)

vDNN: Virtualized Deep Neural Networks for Scalable, Memory-Efficient Neural Network Design

The most widely used machine learning frameworks require users to carefully tune their memory usage so that the deep neural network (DNN) fits into the DRAM capacity of a GPU. This restriction hampers a researcher's flexibility to study different machine learning algorithms, forcing them to either use a less desirable network architecture or parallelize the processing across multiple GPUs. We propose a runtime memory manager that virtualizes the memory usage of DNNs such that both GPU and CPU memory can simultaneously be utilized for training larger DNNs. Our virtualized DNN (vDNN) reduces the average GPU memory usage of AlexNet by up to 89%, OverFeat by 91%, and GoogLeNet by 95%, a significant reduction in memory requirements of DNNs. Similar experiments on VGG-16, one of the deepest and memory hungry DNNs to date, demonstrate the memory-efficiency of our proposal. vDNN enables VGG-16 with batch size 256 (requiring 28 GB of memory) to be trained on a single NVIDIA Titan X GPU card containing 12 GB of memory, with 18% performance loss compared to a hypothetical, oracular GPU with enough memory to hold the entire DNN.Comment: Published as a conference paper at the 49th IEEE/ACM International Symposium on Microarchitecture (MICRO-49), 201

Compressed Data Structures for Dynamic Sequences

We consider the problem of storing a dynamic string $S$ over an alphabet $\Sigma=\{\,1,\ldots,\sigma\,\}$ in compressed form. Our representation supports insertions and deletions of symbols and answers three fundamental queries: $\mathrm{access}(i,S)$ returns the $i$-th symbol in $S$, $\mathrm{rank}_a(i,S)$ counts how many times a symbol $a$ occurs among the first $i$ positions in $S$, and $\mathrm{select}_a(i,S)$ finds the position where a symbol $a$ occurs for the $i$-th time. We present the first fully-dynamic data structure for arbitrarily large alphabets that achieves optimal query times for all three operations and supports updates with worst-case time guarantees. Ours is also the first fully-dynamic data structure that needs only $nH_k+o(n\log\sigma)$ bits, where $H_k$ is the $k$-th order entropy and $n$ is the string length. Moreover our representation supports extraction of a substring $S[i..i+\ell]$ in optimal $O(\log n/\log\log n + \ell/\log_{\sigma}n)$ time

Garbage collection in distributed systems

PhD ThesisThe provision of system-wide heap storage has a number of advantages. However, when the technique is applied to distributed systems automatically recovering inaccessible variables becomes a serious problem. This thesis presents a survey of such garbage collection techniques but finds that no existing algorithm is entirely suitable. A new, general purpose algorithm is developed and presented which allows individual systems to garbage collect largely independently. The effects of these garbage collections are combined, using recursively structured control mechanisms, to achieve garbage collection of the entire heap with the minimum of overheads. Experimental results show that new algorithm recovers most inaccessible variables more quickly than a straightforward garbage collection, giving an improved memory utilisation

Lightweight LCP Construction for Very Large Collections of Strings

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several applications, especially in biological contexts. Nowadays, the input data for many problems are big collections of strings, for instance the data coming from "next-generation" DNA sequencing (NGS) technologies. In this paper we present the first lightweight algorithm (called extLCP) for the simultaneous computation of the longest common prefix array and the Burrows-Wheeler transform of a very large collection of strings having any length. The computation is realized by performing disk data accesses only via sequential scans, and the total disk space usage never needs more than twice the output size, excluding the disk space required for the input. Moreover, extLCP allows to compute also the suffix array of the strings of the collection, without any other further data structure is needed. Finally, we test our algorithm on real data and compare our results with another tool capable to work in external memory on large collections of strings.Comment: This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ The final version of this manuscript is in press in Journal of Discrete Algorithm

Garbage Collection of Linked Data Structures: An Example in a Network Oriented Database Management System

A unified view of the numerous existing algorithms for performing garbage collection of linked data structure has been presented. An implementation of a garbage collection tool in a network oriented database management system has been described

Quantum query complexity of state conversion

State conversion generalizes query complexity to the problem of converting between two input-dependent quantum states by making queries to the input. We characterize the complexity of this problem by introducing a natural information-theoretic norm that extends the Schur product operator norm. The complexity of converting between two systems of states is given by the distance between them, as measured by this norm. In the special case of function evaluation, the norm is closely related to the general adversary bound, a semi-definite program that lower-bounds the number of input queries needed by a quantum algorithm to evaluate a function. We thus obtain that the general adversary bound characterizes the quantum query complexity of any function whatsoever. This generalizes and simplifies the proof of the same result in the case of boolean input and output. Also in the case of function evaluation, we show that our norm satisfies a remarkable composition property, implying that the quantum query complexity of the composition of two functions is at most the product of the query complexities of the functions, up to a constant. Finally, our result implies that discrete and continuous-time query models are equivalent in the bounded-error setting, even for the general state-conversion problem.Comment: 19 pages, 2 figures; heavily revised with new results and simpler proof

Computational speedups using small quantum devices

Suppose we have a small quantum computer with only M qubits. Can such a device genuinely speed up certain algorithms, even when the problem size is much larger than M? Here we answer this question to the affirmative. We present a hybrid quantum-classical algorithm to solve 3SAT problems involving n>>M variables that significantly speeds up its fully classical counterpart. This question may be relevant in view of the current quest to build small quantum computers.Comment: 5+12 page

Active Self-Assembly of Algorithmic Shapes and Patterns in Polylogarithmic Time

We describe a computational model for studying the complexity of self-assembled structures with active molecular components. Our model captures notions of growth and movement ubiquitous in biological systems. The model is inspired by biology's fantastic ability to assemble biomolecules that form systems with complicated structure and dynamics, from molecular motors that walk on rigid tracks and proteins that dynamically alter the structure of the cell during mitosis, to embryonic development where large-scale complicated organisms efficiently grow from a single cell. Using this active self-assembly model, we show how to efficiently self-assemble shapes and patterns from simple monomers. For example, we show how to grow a line of monomers in time and number of monomer states that is merely logarithmic in the length of the line. Our main results show how to grow arbitrary connected two-dimensional geometric shapes and patterns in expected time that is polylogarithmic in the size of the shape, plus roughly the time required to run a Turing machine deciding whether or not a given pixel is in the shape. We do this while keeping the number of monomer types logarithmic in shape size, plus those monomers required by the Kolmogorov complexity of the shape or pattern. This work thus highlights the efficiency advantages of active self-assembly over passive self-assembly and motivates experimental effort to construct general-purpose active molecular self-assembly systems