相关论文: copMEM: Finding maximal exact matches via sampling…

We consider the problem of communicating exogenous information by means of Markov decision process trajectories. This setting, which we call a Markov coding game (MCG), generalizes both source coding and a large class of referential games.…

We improve on GenASM, a recent algorithm for genomic sequence alignment, by significantly reducing its memory footprint and bandwidth requirement. Our algorithmic improvements reduce the memory footprint by 24$\times$ and the number of…

We present efficient parallel algorithms for computing maximal matchings in hypergraphs. Our algorithm finds locally maximal edges in the hypergraph and adds them in parallel to the matching. In the CRCW PRAM models our algorithms achieve…

Empirical Dynamic Modeling (EDM) is a nonlinear time series causal inference framework. The latest implementation of EDM, cppEDM, has only been used for small datasets due to computational cost. With the growth of data collection…

Contrast maximization (CMAX) is a direct geometric framework for event-based motion estimation, but its iterative warp-and-accumulate pipeline incurs input-dependent computation and frequent memory accesses, challenging real-time, low-power…

Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…

Extreme learning machine (ELM) is an extremely fast learning method and has a powerful performance for pattern recognition tasks proven by enormous researches and engineers. However, its good generalization ability is built on large numbers…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

Comparing and aligning large datasets is a pervasive problem occurring across many different knowledge domains. We introduce and study MREC, a recursive decomposition algorithm for computing matchings between data sets. The basic idea is to…

Humans have $23$ pairs of homologous chromosomes. The homologous pairs are almost identical pairs of chromosomes. For the most part, differences in homologous chromosome occur at certain documented positions called single nucleotide…

An approach for approximately calculating the number of genes in a genome is presented, which takes into account the average protein length expected for the species. A number of virus, bacterial and eukaryotic genomes are scrutinized.…

Each human genome is a 3 billion base pair set of encoding instructions. Decoding the genome using deep learning fundamentally differs from most tasks, as we do not know the full structure of the data and therefore cannot design…

Schema matching is the process of identifying correspondences between the elements of two given schemata, essential for database management systems, data integration, and data warehousing. For datasets across different scenarios, the…

We study the problem of minimizing total completion time on parallel machines subject to varying processing capacity. In this paper, we develop an approximation scheme for the problem under the data stream model where the input data is…

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…

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…

Analysis of DNA samples is an important step in forensics, and the speed of analysis can impact investigations. Comparison of DNA sequences is based on the analysis of short tandem repeats (STRs), which are short DNA sequences of 2-5 base…

While well-known methods to list the intersections of either a list of segments or a complex polygon aim at achieving optimal time-complexity they often do so at the cost of memory comsumption and complex code. Real-life software…

Long-term memory is essential for conversational agents to maintain coherence, track persistent tasks, and provide personalized interactions across extended dialogues. However, existing approaches as Retrieval-Augmented Generation (RAG) and…

The identification of homologous gene families across multiple genomes is a central task in bacterial pangenomics traditionally requiring computationally demanding all-against-all comparisons. PanDelos addresses this challenge with an…