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With the advance in genome sequencing technology, the lengths of deoxyribonucleic acid (DNA) sequencing results are rapidly increasing at lower prices than ever. However, the longer lengths come at the cost of a heavy computational burden…
High-level automation is increasingly critical in AI, driven by rapid advances in large language models (LLMs) and AI agents. However, LLMs, despite their general reasoning power, struggle significantly in specialized, data-sensitive tasks…
This paper introduces a high-throughput software tool framework called {\it sam2bam} that enables users to significantly speedup pre-processing for next-generation sequencing data. The sam2bam is especially efficient on single-node…
Recently, 3D Gaussian Splatting (3DGS) has excelled in novel view synthesis (NVS) with its real-time rendering capabilities and superior quality. However, it encounters challenges for high-resolution novel view synthesis (HRNVS) due to the…
Geometric constraints between feature matches are critical in 3D point cloud registration problems. Existing approaches typically model unordered matches as a consistency graph and sample consistent matches to generate hypotheses. However,…
Raw nanopore signal analysis is a common approach in genomics to provide fast and resource-efficient analysis without translating the signals to bases (i.e., without basecalling). However, existing solutions cannot interpret raw signals…
Haplotype-resolved de novo assembly is the ultimate solution to the study of sequence variations in a genome. However, existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the…
For single-cell or metagenomic sequencing projects, it is necessary to sequence with a very high mean coverage in order to make sure that all parts of the sample DNA get covered by the reads produced. This leads to huge datasets with lots…
We consider the problem of efficiently managing massive data in a large-scale distributed environment. We consider data strings of size in the order of Terabytes, shared and accessed by concurrent clients. On each individual access, a…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
In just the last decade, a multitude of bio-technologies and software pipelines have emerged to revolutionize genomics. To further their central goal, they aim to accelerate and improve the quality of de novo whole-genome assembly starting…
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can be…
The Maximum Weighted Independent Set (MWIS) problem, which considers a graph with weights assigned to nodes and seeks to discover the "heaviest" independent set, that is, a set of nodes with maximum total weight so that no two nodes in the…
Microbes are essentially yet convolutedly linked with human lives on the earth. They critically interfere in different physiological processes and thus influence overall health status. Studying microbial species is used to be constrained to…
Due to the ubiquity of graph data on the web, web graph mining has become a hot research spot. Nonetheless, the prevalence of large-scale web graphs in real applications poses significant challenges to storage, computational capacity and…
Given an input graph G and a node v in G, homogeneous network embedding (HNE) maps the graph structure in the vicinity of v to a compact, fixed-dimensional feature vector. This paper focuses on HNE for massive graphs, e.g., with billions of…
Haptic-assisted virtual assembly and prototyping has seen significant attention over the past two decades. However, in spite of the appealing prospects, its adoption has been slower than expected. We identify the main roadblocks as the…
In order to support the real-time interaction with LLMs and the instant search or the instant recommendation on social media, it becomes an imminent problem to build a k-NN graph or an indexing graph for the massive number of vectorized…
Minimal perfect hash functions provide space-efficient and collision-free hashing on static sets. Existing algorithms and implementations that build such functions have practical limitations on the number of input elements they can process,…
Genome assembly is a fundamental problem in Bioinformatics, where for a given set of overlapping substrings of a genome, the aim is to reconstruct the source genome. The classical approaches to solving this problem use assembly graphs, such…