Chunxiao Zhang, Zhiyan Liu, Aravind B R, Hariharasudan A
Synergizing language learning: SmallTalk AI In industry 4.0 and Education 4.0
PeerJ. Computer science
dictionary learning dl implemented via matrix factorization mf commonly used computational biology tackle ubiquitous clustering problems method favored due conceptual simplicity relatively low computational complexity however dl algorithms produce results lack interpretability terms real biological data additionally optimized graphstructured data hence often fail handle scalable manner order address limitations propose novel dl algorithm called online convex network dictionary learning online cvxndl unlike classical dl algorithms online cvxndl implemented via mf designed handle extremely large datasets virtue online nature importantly enables interpretation dictionary elements serve cluster representatives convex combinations real measurements moreover algorithm applied data network structure incorporating specialized subnetwork sampling techniques demonstrate utility approach apply cvxndl 3dgenome rnapii chiadrop data goal identifying important longrange interaction patterns longrange dictionary elements chiadrop probes higherorder interactions produces data form hypergraphs whose nodes represent genomic fragments hyperedges represent observed physical contacts hypergraph model analysis objective creating interpretable dictionary longrange interaction patterns accurately represent global chromatin physical contact maps use dictionary information one also associate contact maps rna transcripts infer cellular functions accomplish task hand focus rnapiienriched chiadrop data drosophila melanogaster s2 cell lines results offer two key insights first demonstrate online cvxndl retains accuracy classical dl mf methods simultaneously ensuring unique interpretability scalability second identify distinct collections proximal distal interaction patterns involving chromatin elements shared related processes across different chromosomes well patterns unique specific chromosomes associate dictionary elements biological properties corresponding chromatin regions employ gene ontology go enrichment analysis perform multiple rna coexpression studies