Related papers: MEGAHIT: An ultra-fast single-node solution for la…

Summary: FermiKit is a variant calling pipeline for Illumina data. It de novo assembles short reads and then maps the assembly against a reference genome to call SNPs, short insertions/deletions (INDELs) and structural variations (SVs).…

We propose scaling up 3D scene reconstruction by training with synthesized data. At the core of our work is MegaSynth, a procedurally generated 3D dataset comprising 700K scenes - over 50 times larger than the prior real dataset DL3DV -…

Heterogeneous graph neural networks (HGNNs) were proposed for representation learning on structural data with multiple types of nodes and edges. To deal with the performance degradation issue when HGNNs become deep, researchers combine…

In this paper, we propose a multi-resolution deep-learning architecture to semantically segment dense large-scale pointclouds. Dense pointcloud data require a computationally expensive feature encoding process before semantic segmentation.…

Repetitive DNA (repeats) poses significant challenges for accurate and efficient genome assembly and sequence alignment. This is particularly true for metagenomic data, where genome dynamics such as horizontal gene transfer, gene…

Modeling heterogeneity by extraction and exploitation of high-order information from heterogeneous information networks (HINs) has been attracting immense research attention in recent times. Such heterogeneous network embedding (HNE)…

De novo genome assembly, i.e., rebuilding the sequence of an unknown genome from redundant and erroneous short sequences, is a key but computationally intensive step in many genomics pipelines. The exponential growth of genomic data is…

The main challenge in de novo assembly of NGS data is certainly to deal with repeats that are longer than the reads. This is particularly true for RNA- seq data, since coverage information cannot be used to flag repeated sequences, of which…

Graphs are ubiquitous, and they can model unique characteristics and complex relations of real-life systems. Although using machine learning (ML) on graphs is promising, their raw representation is not suitable for ML algorithms. Graph…

Metagenomic disease prediction commonly relies on species abundance tables derived from large, incomplete reference catalogs, constraining resolution and discarding valuable information contained in DNA reads. To overcome these limitations,…

How can we find meaningful clusters in a graph robustly against noise edges? Graph clustering (i.e., dividing nodes into groups of similar ones) is a fundamental problem in graph analysis with applications in various fields. Recent studies…

Graph analytics are vital in fields such as social networks, biomedical research, and graph neural networks (GNNs). However, traditional CPUs and GPUs struggle with the memory bottlenecks caused by large graph datasets and their…

Charged particle track reconstruction is a foundational task in collider experiments and the main computational bottleneck in particle reconstruction. Graph neural networks (GNNs) have shown strong performance for this problem, but costly…

De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…

A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…

The maximum entropy method (MEM) is a well known deconvolution technique in radio-interferometry. This method solves a non-linear optimization problem with an entropy regularization term. Other heuristics such as CLEAN are faster but highly…

We formally introduce a systematic (de/re)-composition approach, based on the algebraic formalism of "Multi-Dimensional Homomorphisms (MDHs)". Our approach is designed as general enough to be applicable to a wide range of data-parallel…

Deep learning thrives with large neural networks and large datasets. However, larger networks and larger datasets result in longer training times that impede research and development progress. Distributed synchronous SGD offers a potential…

Motivation: Accurate data analysis and quality control is critical for metagenomic studies. Though many tools exist to analyze metagenomic data there is no consistent framework to integrate and run these tools across projects. Currently,…

We present SuperKMeans: a k-means variant designed for clustering collections of high-dimensional vector embeddings. SuperKMeans' clustering is up to 7x faster than FAISS and Scikit-Learn on modern CPUs and up to 4x faster than cuVS on GPUs…