Motif adjacency matrixOpen motifDirected networkBy introducing the missing edge matrix, three-node open motifs are represented.By using motifs to reconstruct the feature matrix of NMF, good results are obtained.By using linear and nonlinear methods, network is considered more comprehensively....
For high-order information, we first generate the corresponding motif adjacency matrices based on the defined motif structures. These matrices are then weighted and summed. Subsequently, we conduct spectral normalization on the result to form a comprehensive network representation \(M_{sum}\), as sh...
Spectral embedding with motif adjacency matrices Motif-based spectral clustering The methods are all designed to run quickly on large sparse networks, and are easy to install and use. Branches The main branch contains stable versions. The develop branch may be unstable, and is for development purpo...
j}\)as node j to i (Formula (10)). MS-GAT introduces motif structure information on this basis of GAT, M is the edge-based motif co-occurrence matrix (Formula (11)), simultaneously integrates adjacent matrix A and module matrix M, The new attention score\(\alpha _{i,j}\)(Formula ...
The geometry of evolved community matrix spectra Introduction Food webs are abstract representations of which species consume which others in an ecosystem1,2,3. In a network-based description, species are represented by nodes and their trophic interactions are represented by directed links, pointing fr...
Firstly, we can get an adjacency matrix easily, whose shape isN \times N, whereNis the number of nodes. Secondly, we can use a bunch of different methods to get features of every nodes. In the original paper of RolX, a concept of recursive feature is introduced. Therefore, a new featu...
[41,42] with protein-DNA interactions from MotifMap can yield a more comprehensive view of molecular mechanisms and networks. Integration of PPI data can also facilitate the identification of transcriptional complexes. For example, evidence for a complex based on adjacency of binding sites for two ...
capturehigher-orderinteractionsbetweennodeswork,weproposemoti-basedgraphattentionmodel,calledMotiConvolutionalNetworks,whichgeneralizespastapproachesusingweightedmulti-hopmotiadjacencymatricescapturehigher-orderneighborhoods.Anovelattentionmechanismisusedalloweachindividualnodemostrelevantneighborhoodapplyitsflter.Weevaluateour...
We address these shortcomings by exploring motif-based weighted spectral clustering methods. We present new and computationally useful matrix formulae for motif adjacency matrices on weighted networks, which can be used to construct efficient algorithms for any anchored or non-anchored motif on three ...
Specifically, to capture temporal information and higher-order features, we develop a method extracting temporal motif instances from temporal networks, and design an algorithm to compute the weighted motif adjacency matrix and the diagonal motif out-degree matrix, then define a motif transition matrix...