1 citations · 3 across the 7 of their papers we have counts for
8 papers
CAP: Commutative Algebra Prediction of Protein-Nucleic Acid Binding Affinities
Mushal Zia, Faisal Suwayyid, Yuta Hozumi +3
An accurate prediction of protein-nucleic acid binding affinity is vital for deciphering genomic processes, yet existing approaches often struggle in reconciling high accuracy with…
Commutative Algebra Modeling of Mutation and Disease Association
JunJie Wee, Faisal Suwayyid, Mushal Zia +3
Genetic mutations can lead to disease by disrupting molecular interactions, altering protein stability, inducing misfolding, and promoting protein aggregation. Although existing pr…
CAKR: Commutative algebra k-mer representations for genomics
Faisal Suwayyid, Yuta Hozumi, Mushal Zia +3
Despite the availability of various sequence analysis models, comparative genomic analysis remains a challenge in genomics, genetics, and phylogenetics. Commutative algebra, a fund…
CAML: Commutative algebra machine learning -- a case study on protein-ligand binding affinity prediction
Hongsong Feng, Faisal Suwayyid, Mushal Zia +4
Recently, Suwayyid and Wei have introduced commutative algebra as an emerging paradigm for machine learning and data science. In this work, we integrate commutative algebra machine…
Revealing the Shape of Genome Space via K-mer Topology
Yuta Hozumi, Guo-Wei Wei
Despite decades of effort, understanding the shape of genome space in biology remains a challenge due to the similarity, variability, diversity, and plasticity of evolutionary rela…
Multiscale differential geometry learning of networks with applications to single-cell RNA sequencing data
Hongsong Feng, Sean Cottrell, Yuta Hozumi +1
Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expres…
Analyzing Single Cell RNA Sequencing with Topological Nonnegative Matrix Factorization
Yuta Hozumi, Guo-Wei Wei
Single-cell RNA sequencing (scRNA-seq) is a relatively new technology that has stimulated enormous interest in statistics, data science, and computational biology due to the high d…
K-Nearest-Neighbors Induced Topological PCA for scRNA Sequence Data Analysis
Sean Cottrell, Yuta Hozumi, Guo-Wei Wei
Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differen…