Related papers: XORRO: Rapid Paired-End Read Overlapper

We present a parallel algorithm and scalable implementation for genome analysis, specifically the problem of finding overlaps and alignments for data from "third generation" long read sequencers. While long sequences of DNA offer enormous…

In this article, we establish a class of new accelerated modulus-based iteration methods for solving the linear complementarity problem. When the system matrix is an $H_+$-matrix, we present appropriate criteria for the convergence…

We propose an efficient protocol for secure comparison of integers when both integers are shared between two parties. Such protocols are useful for implementing secure auctions. The proposed protocol's computational complexity is roughly…

Current computational methods for exon-intron structure prediction from a cluster of transcript (EST, mRNA) data do not exhibit the time and space efficiency necessary to process large clusters of over than 20,000 ESTs and genes longer than…

The volume of scientific literature is growing exponentially, leading to underutilized discoveries, duplicated efforts, and limited cross-disciplinary collaboration. Retrieval Augmented Generation (RAG) offers a way to assist scientists by…

Bitmap indexes must be compressed to reduce input/output costs and minimize CPU usage. To accelerate logical operations (AND, OR, XOR) over bitmaps, we use techniques based on run-length encoding (RLE), such as Word-Aligned Hybrid (WAH)…

We present BackboneLearn: an open-source software package and framework for scaling mixed-integer optimization (MIO) problems with indicator variables to high-dimensional problems. This optimization paradigm can naturally be used to…

Recurrent neural networks are powerful tools for handling incomplete data problems in computer vision, thanks to their significant generative capabilities. However, the computational demand for these algorithms is too high to work in real…

With streaming floating-point numbers being increasingly prevalent, effective and efficient compression of such data is critical. Compression schemes must be able to exploit the similarity, or smoothness, of consecutive numbers and must be…

This paper presents BiPaR, a bilingual parallel novel-style machine reading comprehension (MRC) dataset, developed to support multilingual and cross-lingual reading comprehension. The biggest difference between BiPaR and existing reading…

Cycles are one of the fundamental subgraph patterns and being able to enumerate them in graphs enables important applications in a wide variety of fields, including finance, biology, chemistry, and network science. However, to enable cycle…

In the realm of Large Language Model (LLM) inference, the inherent structure of transformer models coupled with the multi-GPU tensor parallelism strategy leads to a sequential execution of computation and communication. This results in…

Clustering the nodes of a graph is a cornerstone of graph analysis and has been extensively studied. However, some popular methods are not suitable for very large graphs: e.g., spectral clustering requires the computation of the spectral…

Parallelization techniques have become ubiquitous for accelerating inference and training of deep neural networks. Despite this, several operations are still performed in a sequential manner. For instance, the forward and backward passes…

Near-duplicate text alignment is the task of identifying, among the texts in a corpus, all the subsequences (substrings) that are similar to a given query. Traditional approaches rely on seeding-extension-filtering heuristics, which lack…

The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…

Word error rate of an ocr is often higher than its character error rate. This is especially true when ocrs are designed by recognizing characters. High word accuracies are critical to tasks like the creation of content in digital libraries…

Important papers have appeared recently on the problem of indexing binary strings for jumbled pattern matching, and further lowering the time bounds in terms of the input size would now be a breakthrough with broad implications. We can…

The high-throughput short-reads RNA-seq protocols often produce paired-end reads, with the middle portion of the fragments being unsequenced. We explore if the full-length fragments can be computationally reconstructed from the sequenced…

Compressed bitmap indexes are used in databases and search engines. Many bitmap compression techniques have been proposed, almost all relying primarily on run-length encoding (RLE). However, on unsorted data, we can get superior performance…