Heri-Graphs: A Dataset Creation Framework for Multi-Modal Machine Learning on Graphs of Heritage Values and Attributes with Social Media

Values (why to conserve) and Attributes (what to conserve) are essential concepts of cultural heritage. Recent studies have been using social media to map values and attributes conveyed by the public to cultural heritage. However, it is rare to connect heterogeneous modalities of images, texts, geo-locations, timestamps, and social network...

Advances in Graph Signal Processing: Fast graph construction & Node-adaptive graph signal reconstruction

This thesis consists of two parts in both data science and signal processing over graphs. In the first part of this thesis, we aim to solve the problem of graph construction in big data scenario, which is critical for practical tasks, like collaborative filtering in recommender systems, spectral embedding or clustering in learning algorithms. We...

Accelerating DNA Variant Calling Algorithms on High Performance Computing Systems

Next generation sequencing (NGS) technologies have transformed the landscape of genomic research. With the significant advances in NGS technologies, DNA sequencing is more affordable and accessible than ever before. Meanwhile, many DNA sequence analysis tools have been developed to derive useful information from the raw sequencing data produced...

An Efficient GPU-based de Bruijn Graph Construction Algorithm for Micro-Assembly

In order to improve the accuracy of indel detection, micro-assembly is used in multiple variant callers, such as the GATK HaplotypeCaller to reassemble reads in a specific region of the genome. Assembly is a computationally intensive process that causes runtime bottlenecks. In this paper, we propose a GPU-based de Bruijn graph construction...