Related papers: A massively parallel algorithm for constructing th…
String sorting is an important part of tasks such as building index data structures. Unfortunately, current string sorting algorithms do not scale to massively parallel distributed-memory machines since they either have latency (at least)…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of the…
Transformers have emerged as the cornerstone of state-of-the-art natural language processing models, showcasing exceptional performance across a wide range of AI applications. However, the memory demands posed by the self-attention…
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…
Machine learning potentials have achieved great success in accelerating atomistic simulations. Many of them relying on atom-centered local descriptors are natural for parallelization. More recent message passing neural network (MPNN) models…
In the area of Pattern Recognition and Matching, finding a Longest Common Subsequence plays an important role. In this paper, we have proposed one algorithm based on parallel computation. We have used OpenMP API package as middleware to…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
This thesis develops signal-processing algorithms and implementation schemes under constraints of minimal parallelism and memory space, with the goal of improving energy efficiency of low-power computing hardware. We propose (i) a…
We investigate distributed memory parallel sorting algorithms that scale to the largest available machines and are robust with respect to input size and distribution of the input elements. The main outcome is that four sorting algorithms…
We show that the Longest Common Prefix Array of a text collection of total size n on alphabet [1, {\sigma}] can be computed from the Burrows-Wheeler transformed collection in O(n log {\sigma}) time using o(n log {\sigma}) bits of working…
The future of main memory appears to lie in the direction of new technologies that provide strong capacity-to-performance ratios, but have write operations that are much more expensive than reads in terms of latency, bandwidth, and energy.…
We introduce FFN Fusion, an architectural optimization technique that reduces sequential computation in large language models by identifying and exploiting natural opportunities for parallelization. Our key insight is that sequences of…
We engineer algorithms for sorting huge data sets on massively parallel machines. The algorithms are based on the multiway merging paradigm. We first outline an algorithm whose I/O requirement is close to a lower bound. Thus, in contrast to…
FM-index is an efficient data structure for string search and is widely used in next-generation sequencing (NGS) applications such as sequence alignment and de novo assembly. Recently, FM-indexing is even performed down to the read level,…
We describe a grammar for DNA sequencing reads from which we can compute the BWT directly. Our motivation is to perform in succinct space genomic analyses that require complex string queries not yet supported by repetition-based…
Introduced about thirty years ago in the field of Data Compression, the Burrows-Wheeler Transform (BWT) is a string transformation that, besides being a booster of the performance of memoryless compressors, plays a fundamental role in the…
In this paper, we study a parallel version of Galton-Watson processes for the random generation of tree-shaped structures. Random trees are useful in many situations (testing, binary search, simulation of physics phenomena,...) as attests…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…
Large Language Models (LLMs) have ushered in a new wave of artificial intelligence advancements impacting every scientific field and discipline. We live in a world where most of the data around us, e.g., text, audio, and music, has a…
Summary: BWA-MEM is a new alignment algorithm for aligning sequence reads or long query sequences against a large reference genome such as human. It automatically chooses between local and end-to-end alignments, supports paired-end reads…