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Converting a set of sequencing reads into a lossless compact data structure that encodes all the relevant biological information is a major challenge. The classical approaches are to build the string graph or the de Bruijn graph. Each has…
\textit{Graph Neural Network} (GNN) is a promising approach for analyzing graph-structured data that tactfully captures their dependency information via node-level message passing. It has achieved state-of-the-art performances in many…
Dataset deduplication is widely recognized as a crucial preprocessing step that enhances data quality and improves the performance of large language models. A commonly used method for this process is the MinHash Locality-Sensitive Hashing…
A minimal perfect hash function (MPHF) bijectively maps a set S of objects to the first |S| integers. It can be used as a building block in databases and data compression. RecSplit [Esposito et al., ALENEX'20] is currently the most space…
Meta-graph is currently the most powerful tool for similarity search on heterogeneous information networks,where a meta-graph is a composition of meta-paths that captures the complex structural information. However, current relevance…
Metagenomics has led to significant advancements in many fields. Metagenomic analysis commonly involves the key tasks of determining the species present in a sample and their relative abundances. These tasks require searching large…
Maximal clique enumeration is a fundamental graph mining task, but its utility is often limited by computational intractability and highly redundant output. To address these challenges, we introduce \emph{$\rho$-dense aggregators}, a novel…
Autoregressive transformers are spectacular models for short sequences but scale poorly to long sequences such as high-resolution images, podcasts, code, or books. We proposed Megabyte, a multi-scale decoder architecture that enables…
Most real-world datasets are inherently heterogeneous graphs, which involve a diversity of node and relation types. Heterogeneous graph embedding is to learn the structure and semantic information from the graph, and then embed it into the…
The SPAdes assembler for metagenome assembly is a long-running application commonly used at the NERSC supercomputing site. However, NERSC, like many other sites, has a 48-hour limit on resource allocations. The solution is to chain together…
Mixed communities of organisms are found in many environments (from the human gut to marine ecosystems) and can have profound impact on human health and the environment. Metagenomics studies the genomic material of such communities through…
Parameter estimation via unbinned maximum likelihood fits is a central technique in particle physics. This article introduces MoreFit, which aims to provide a more optimised, rapid and efficient fitting solution for unbinned maximum…
Microbes have a profound impact on our health and environment, but our understanding of the diversity and function of microbial communities is severely limited. Through DNA sequencing of microbial communities (metagenomics), DNA fragments…
Contig assembly is the first stage that most assemblers solve when reconstructing a genome from a set of reads. Its output consists of contigs -- a set of strings that are promised to appear in any genome that could have generated the…
We present MegaTrain, a memory-centric system that efficiently trains 100B+ parameter large language models at full precision on a single GPU. Unlike traditional GPU-centric systems, MegaTrain stores parameters and optimizer states in host…
The improvements in recent CNN-based object detection works, from R-CNN [11], Fast/Faster R-CNN [10, 31] to recent Mask R-CNN [14] and RetinaNet [24], mainly come from new network, new framework, or novel loss design. But mini-batch size, a…
Metagenomics enables the reconstruction of microbial genomes in complex microbial communities without the need for culturing. Since assembly typically results in fragmented genomes the grouping of genome fragments (contigs) belonging to the…
Fitting complicated models to large datasets is a bottleneck of many analyses. We present GooFit, a library and tool for constructing arbitrarily-complex probability density functions (PDFs) to be evaluated on nVidia GPUs or on multicore…
A large number of real-world graphs or networks are inherently heterogeneous, involving a diversity of node types and relation types. Heterogeneous graph embedding is to embed rich structural and semantic information of a heterogeneous…
Sparse Convolution (SC) is widely used for processing 3D point clouds that are inherently sparse. Different from dense convolution, SC preserves the sparsity of the input point cloud by only allowing outputs to specific locations. To…