Based on these operators, we adapt and extend the PC-algorithm to estimate the functional directed graph, so that the computation time depends on the sparsity rather than the full size of the graph. We study the asymptotic properties of the two operators, derive their uniform convergence rates,...
Among them, Gene Ontology (GO) [5] is the most comprehensive source, which organizes the biological terms in a hierarchical tree structure in the form of a directed acyclic graph (DAG). Other popular sources are, for example, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways [6] and...
We propose a factor analysis model (FAM) for functional genomics and give a two-step algorithm, using genome-wide expression data for yeast and a subset of Gene-Ontology Biological Process functional annotations. We show that the predictive performance of our method is comparable to the current b...
At present, a popular similarity calculation strategy for GO terms is based on the Information Content (IC), which is to measure the importance of each term in the Directed Acyclic Graph (DAG) of GO [19]. And the similarity of the two GO terms depends on their respective IC, as well ...
Data from the GO website are downloaded in a structure called a directed acyclic graph (DAG), a name that denotes an unclosed structure where a particular child node associated with a GO term can have multiple parent nodes. GOFFA converts the DAG structure to a tree structure by constructing...
Next, a phylogenetic tree was constructed as a directed acyclic graph (DAG) to include all existing taxonomic units in the Greengenes database up to species level (excluding strains) as nodes of the DAG. Two kingdoms, Viruses and Viroids, were excluded from the tree because the datasets of ...
In this study, we propose a new deep learning framework, spatio-temporal directed acyclic graph with attention mechanisms (ST-DAG-Att), (1) to incorporate multiple spatio-temporal scales of functional time series and connectivity data; (2) to conduct spatial convolution of functional time series ...
NJW Spectral Clustering Algorithm Consider a datasetUformed by N points to be clustered. For each pair of points withinU, a similarity value can be defined assij=sji≥ 0 by any similarity measure.Ucan be represented by a weighted directed graphG= (V,E) where theS= [sij] matrix plays th...
Spatio-temporal directed acyclic graph learning with attention mechanisms on brain functional time series and connectivity. Med Image Anal. 2022;77:102370. https://doi.org/10.1016/j.media.2022.102370. Article PubMed Google Scholar Jiang J, Wang M, Alberts I, Sun X, Li T, Rominger A, et ...
The GO database schema models a directed acyclic graph (DAG) relationally, and the terms (graph nodes) and term-term relationships provide the conceptualizations of biological domains of knowledge [9]. High throughput annotation methods [10–13] can electronically annotate any uncharacterized protein ...