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Affordable, high-quality whole-genome assemblies have made it possible to construct rich pangenomes that capture haplotype diversity across many species. As these datasets grow, they motivate the development of specialized techniques…
A randomized algorithm for computing a data sparse representation of a given rank structured matrix $A$ (a.k.a. an $H$-matrix) is presented. The algorithm draws on the randomized singular value decomposition (RSVD), and operates under the…
Graph Auto-Encoders (GAEs) are powerful tools for graph representation learning. In this paper, we develop a novel Hierarchical Cluster-based GAE (HC-GAE), that can learn effective structural characteristics for graph data analysis. To this…
Single individual haplotyping is an NP-hard problem that emerges when attempting to reconstruct an organism's inherited genetic variations using data typically generated by high-throughput DNA sequencing platforms. Genomes of diploid…
Accurate identification of haplotypes in sequenced human genomes can provide invaluable information about population demography and fine-scale correlations along the genome, thus empowering both population genomic and medical association…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
This paper studies the haplotype assembly problem from an information theoretic perspective. A haplotype is a sequence of nucleotide bases on a chromosome, often conveniently represented by a binary string, that differ from the bases in the…
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…
Graph Neural Networks (GNNs) have demonstrated significant success in learning from graph-structured data but often struggle on heterophilous graphs, where connected nodes differ in features or class labels. This limitation arises from…
Graphs can be used to represent a wide variety of data belonging to different domains. Graphs can capture the relationship among data in an efficient way, and have been widely used. In recent times, with the advent of Big Data, there has…
Hypergraphs serve as an effective model for depicting complex connections in various real-world scenarios, from social to biological networks. The development of Hypergraph Neural Networks (HGNNs) has emerged as a valuable method to manage…
Given a graph G where each node is associated with a set of attributes, attributed network embedding (ANE) maps each node v in G to a compact vector Xv, which can be used in downstream machine learning tasks. Ideally, Xv should capture node…
Persistent homology is a tool that can be employed to summarize the shape of data by quantifying homological features. When the data is an object in $\mathbb{R}^d$, the (augmented) persistent homology transform ((A)PHT) is a family of…
Graphical models find numerous applications in biology, chemistry, sociology, neuroscience, etc. While substantial progress has been made in graph estimation, it remains largely unexplored how to select significant graph signals with…
While linear mixed model (LMM) has shown a competitive performance in correcting spurious associations raised by population stratification, family structures, and cryptic relatedness, more challenges are still to be addressed regarding the…
Although graph-based learning has attracted a lot of attention, graph representation learning is still a challenging task whose resolution may impact key application fields such as chemistry or biology. To this end, we introduce GRALE, a…
We investigate efficient learning from higher-order graph convolution and learning directly from adjacency matrices for node classification. We revisit the scaled graph residual network and remove ReLU activation from residual layers and…
Graph neural networks (GNN) have been proven to be mature enough for handling graph-structured data on node-level graph representation learning tasks. However, the graph pooling technique for learning expressive graph-level representation…
Understanding genetic variation, e.g., through mutations, in organisms is crucial to unravel their effects on the environment and human health. A fundamental characterization can be obtained by solving the haplotype assembly problem, which…
The architecture of the brain is too complex to be intuitively surveyable without the use of compressed representations that project its variation into a compact, navigable space. The task is especially challenging with high-dimensional…