Just-in-Time Data Structures

Today, software engineering practices focus on finding the single "right" data representation (i.e., data structure) for a program. The right data representation, however, might not exist: relying on a single representation of the data for the lifetime of the program can be suboptimal in terms of performance. We explore the idea of developing data structures for which changing the data representation is an intrinsic property. To this end we introduce Just-in-Time Data Structures, which enable representation changes at runtime, based on declarative input from a performance expert programmer. Just-in-Time Data Structures are an attempt to shift the focus from finding the "right" data structure to finding the right sequence of data representations. We present JitDS-Java, an extension to the Java language, to develop Just-in-Time Data Structures. Further, we show two example programs that benefit from changing the representation at runtime

A framework for space-efficient string kernels

String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a number of exact string kernels, like the $k$-mer kernel, the substrings kernels, a number of length-weighted kernels, the minimal absent words kernel, and kernels with Markovian corrections, can all be computed in $O(nd)$ time and in $o(n)$ bits of space in addition to the input, using just a $\mathtt{rangeDistinct}$ data structure on the Burrows-Wheeler transform of the input strings, which takes $O(d)$ time per element in its output. The same bounds hold for a number of measures of compositional complexity based on multiple value of $k$, like the $k$-mer profile and the $k$-th order empirical entropy, and for calibrating the value of $k$ using the data

Lossless fault-tolerant data structures with additive overhead

12th International Symposium, WADS 2011, New York, NY, USA, August 15-17, 2011. ProceedingsWe develop the first dynamic data structures that tolerate δ memory faults, lose no data, and incur only an O(δ ) additive overhead in overall space and time per operation. We obtain such data structures for arrays, linked lists, binary search trees, interval trees, predecessor search, and suffix trees. Like previous data structures, δ must be known in advance, but we show how to restore pristine state in linear time, in parallel with queries, making δ just a bound on the rate of memory faults. Our data structures require Θ(δ) words of safe memory during an operation, which may not be theoretically necessary but seems a practical assumption.Center for Massive Data Algorithmics (MADALGO

Tight Cell Probe Bounds for Succinct Boolean Matrix-Vector Multiplication

The conjectured hardness of Boolean matrix-vector multiplication has been used with great success to prove conditional lower bounds for numerous important data structure problems, see Henzinger et al. [STOC'15]. In recent work, Larsen and Williams [SODA'17] attacked the problem from the upper bound side and gave a surprising cell probe data structure (that is, we only charge for memory accesses, while computation is free). Their cell probe data structure answers queries in $\tilde{O}(n^{7/4})$ time and is succinct in the sense that it stores the input matrix in read-only memory, plus an additional $\tilde{O}(n^{7/4})$ bits on the side. In this paper, we essentially settle the cell probe complexity of succinct Boolean matrix-vector multiplication. We present a new cell probe data structure with query time $\tilde{O}(n^{3/2})$ storing just $\tilde{O}(n^{3/2})$ bits on the side. We then complement our data structure with a lower bound showing that any data structure storing $r$ bits on the side, with $n < r < n^2$ must have query time $t$ satisfying $t r = \tilde{\Omega}(n^3)$. For $r \leq n$, any data structure must have $t = \tilde{\Omega}(n^2)$. Since lower bounds in the cell probe model also apply to classic word-RAM data structures, the lower bounds naturally carry over. We also prove similar lower bounds for matrix-vector multiplication over $\mathbb{F}_2$