Related papers: Unfolding Ordered Matrices into BioFabric Motifs

The technique presented here identifies tethered mould designs, optimised for growing cultured tissue with very highly-aligned cells. It is based on a microscopic biophysical model for polarised cellular hydrogels. There is an unmet need…

Enhancing the efficiency of iterative computation on graphs has garnered considerable attention in both industry and academia. Nonetheless, the majority of efforts focus on expediting iterative computation by minimizing the running time per…

The biologically inspired framework of port-graphs has been successfully used to specify complex systems. It is the basis of the PORGY modelling tool. To facilitate the specification of proof normalisation procedures via graph rewriting, in…

Hypergraphs, describing networks where interactions take place among any number of units, are a natural tool to model many real-world social and biological systems. In this work we propose a principled framework to model the organization of…

Probabilistic biological network growth models have been utilized for many tasks including but not limited to capturing mechanism and dynamics of biological growth activities, null model representation, capturing anomalies, etc. Well-known…

In complex systems, groups of interacting objects may form prevalent and persistent spatiotemporal patterns, which we refer to as motifs. These motifs can exhibit features that reveal how individual objects interact with one another.…

Graphs are ubiquitous data structures for representing interactions between entities. With an emphasis on the use of graphs to represent chemical molecules, we explore the task of learning to generate graphs that conform to a distribution…

Graphs provide a natural way to represent data by encoding information about objects and the relationships between them. With the ever-increasing amount of data collected and generated, locating specific patterns of relationships between…

In this paper a novel biclustering algorithm based on artificial intelligence (AI) is introduced. The method called EBIC aims to detect biologically meaningful, order-preserving patterns in complex data. The proposed algorithm is probably…

Bifiltered graphs are a versatile tool for modelling relations between data points across multiple grades of a two-dimensional scale. They are especially popular in topological data analysis, where the homological properties of the induced…

Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to…

Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…

Link prediction plays an important role in network analysis and applications. Recently, approaches for link prediction have evolved from traditional similarity-based algorithms into embedding-based algorithms. However, most existing…

We introduce a variation of the scheduling with precedence constraints problem that has applications to molecular folding and production management. We are given a bipartite graph $H=(B,S)$. Vertices in $B$ are thought of as goods or…

While deep learning has achieved great success in many fields, one common criticism about deep learning is its lack of interpretability. In most cases, the hidden units in a deep neural network do not have a clear semantic meaning or…

Exploring statistics of locally connected subgraph patterns (also known as network motifs) has helped researchers better understand the structure and function of biological and online social networks (OSNs). Nowadays the massive size of…

Fashion recommendation systems are highly desired by customers to find visually-collocated fashion items, such as clothes, shoes, bags, etc. While existing methods demonstrate promising results, they remain lacking in flexibility and…

Triangle listing is an important topic significant in many practical applications. Efficient algorithms exist for the task of triangle listing. Recent algorithms leverage an orientation framework, which can be thought of as mapping an…

Analysis of higher-order organizations, usually small connected subgraphs called motifs, is a fundamental task on complex networks. This paper studies a new problem of testing higher-order clusterability: given query access to an undirected…

Folding garments reliably and efficiently is a long standing challenge in robotic manipulation due to the complex dynamics and high dimensional configuration space of garments. An intuitive approach is to initially manipulate the garment to…