相关论文: Computing Maximal Unique Matches with the r-index
Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…
The study of approximate matching in the Massively Parallel Computations (MPC) model has recently seen a burst of breakthroughs. Despite this progress, however, we still have a far more limited understanding of maximal matching which is one…
Profile hidden Markov models (pHMMs) are widely employed in various bioinformatics applications to identify similarities between biological sequences, such as DNA or protein sequences. In pHMMs, sequences are represented as graph…
Mutation analysis has many applications, such as assessing the quality of test cases, fault localization, test input generation, security analysis, etc. Such applications involve running test suite against a large number of program mutants…
Large matrix multiplication is a cornerstone of modern machine learning workloads, yet traditional approaches suffer from cubic computational complexity (e.g., $\mathcal{O}(n^3)$ for a matrix of size $n\times n$). We present Low-Rank GEMM,…
Frequent Subgraph Mining (FSM) is the process of identifying common subgraph patterns that surpass a predefined frequency threshold. While FSM is widely applicable in fields like bioinformatics, chemical analysis, and social network anomaly…
The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…
Deep neural networks have achieved significant improvements in information retrieval (IR). However, most existing models are computational costly and can not efficiently scale to long documents. This paper proposes a novel End-to-End neural…
Universal Multimodal Retrieval (UMR) aims to enable search across various modalities using a unified model, where queries and candidates can consist of pure text, images, or a combination of both. Previous work has attempted to adopt…
Finite mixture models have been widely used for the modelling and analysis of data from heterogeneous populations. Maximum likelihood estimation of the parameters is typically carried out via the Expectation-Maximization (EM) algorithm. The…
In an effort to develop topic modeling methods that can be quickly applied to large data sets, we revisit the problem of maximum-likelihood estimation in topic models. It is known, at least informally, that maximum-likelihood estimation in…
While Mixture of Experts (MoE) models achieve remarkable efficiency by activating only subsets of parameters, they suffer from high memory access costs during inference. Memory-layer architectures offer an appealing alternative with very…
This paper explores the enhancement of solution diversity in evolutionary algorithms (EAs) for the maximum matching problem, concentrating on complete bipartite graphs and paths. We adopt binary string encoding for matchings and use Hamming…
Recent advancements in image customization exhibit a wide range of application prospects due to stronger customization capabilities. However, since we humans are more sensitive to faces, a significant challenge remains in preserving…
While recent advances in large language models (LLMs) have significantly enhanced performance across diverse natural language tasks, the high computational and financial costs associated with their deployment remain substantial barriers.…
In this work, we present a literature review for full-text and keyword indexes as well as our contributions (which are mostly practice-oriented). The first contribution is the FM-bloated index, which is a modification of the well-known…
AI models are increasing in size and recent advancement in the community has shown that unlike HPC applications where double precision datatype are required, lower-precision datatypes such as fp8 or int4 are sufficient to bring the same…
The $r$-index represented a breakthrough in compressed indexing of repetitive text collections, outperforming its alternatives by orders of magnitude in query time. Its space usage, $O(r)$ where $r$ is the number of runs in the…
Maximal Biclique Enumeration (MBE) holds critical importance in graph theory with applications extending across fields such as bioinformatics, social networks, and recommendation systems. However, its computational complexity presents…
The rapid advancement of deep neural networks has significantly improved various tasks, such as image and speech recognition. However, as the complexity of these models increases, so does the computational cost and the number of parameters,…