Related papers: ERA: Efficient Serial and Parallel Suffix Tree Con…

The suffix array, perhaps the most important data structure in modern string processing, is often augmented with the longest common prefix (LCP) array which stores the lengths of the LCPs for lexicographically adjacent suffixes of a string.…

A \itbf{cover} of a string $x = x[1..n]$ is a proper substring $u$ of $x$ such that $x$ can be constructed from possibly overlapping instances of $u$. A recent paper \cite{FIKPPST13} relaxes this definition --- an \itbf{enhanced cover} $u$…

The two most common data-structures for genome indexing, FM-indices and hash-tables, exhibit a fundamental trade-off between memory footprint and performance. We present Ranger, a new indexing technique for nucleotide sequences that is both…

Transformers have revolutionized deep learning with applications in natural language processing, computer vision, and beyond. However, their computational demands make it challenging to deploy them on low-power edge devices. This paper…

Computational protein structure determination involves optimization in a problem space much too large to exhaustively search. Existing approaches include optimization algorithms such as gradient descent and simulated annealing, but these…

We propose new succinct representations of ordinal trees, which have been studied extensively. It is known that any $n$-node static tree can be represented in $2n + o(n)$ bits and a number of operations on the tree can be supported in…

Aligning millions of short DNA or RNA reads, of 75 to 250 base pairs each, to a reference genome is a significant computation problem in bioinformatics. We present a flexible and fast FPGA-based short read alignment tool. Our aligner makes…

The architecture of a coarse-grained reconfigurable array (CGRA) processing element (PE) has a significant effect on the performance and energy efficiency of an application running on the CGRA. This paper presents an automated approach for…

The problem of RNA secondary structure design (also called inverse folding) is the following: given a target secondary structure, one aims to create a sequence that folds into, or is compatible with, a given structure. In several practical…

Computing the Euclidean minimum spanning tree (EMST) is a computationally demanding step of many algorithms. While work-efficient serial and multithreaded algorithms for computing EMST are known, designing an efficient GPU algorithm is…

Parallel search algorithms harness the multithreading capability of modern processors to achieve faster planning. One such algorithm is PA*SE (Parallel A* for Slow Expansions), which parallelizes state expansions to achieve faster planning…

Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…

FastText has established itself as a fundamental algorithm for learning word representations, demonstrating exceptional capability in handling out-of-vocabulary words through character-level n-gram embeddings. However, its hash-based…

State of the art (SOTA) neural text to speech (TTS) models can generate natural-sounding synthetic voices. These models are characterized by large memory footprints and substantial number of operations due to the long-standing focus on…

Long Short-Term Memory (LSTM) is widely used in speech recognition. In order to achieve higher prediction accuracy, machine learning scientists have built larger and larger models. Such large model is both computation intensive and memory…

Data structures used in software development have inbuilt redundancy to improve software reliability and to speed up performance. Examples include a Doubly Linked List which allows a faster deletion due to the presence of the previous…

A heterogeneous memory has a single address space with fast access to some addresses (a fast tier of DRAM) and slow access to other addresses (a capacity tier of CXL-attached memory or NVM). A tiered memory system aims to maximize the…

Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet…

Suffix trees have emerged to be very fast for pattern searching yielding O (m) time, where m is the pattern size. Unfortunately their high memory requirements make it impractical to work with huge amounts of data. We present a memory…

Protein structure prediction helps to understand gene translation and protein function, which is of growing interest and importance in structural biology. The AlphaFold model, which used transformer architecture to achieve atomic-level…