Related papers: Automatically layout and visualize the biological …
Regular Path Queries (RPQs) are a type of graph query where answers are pairs of nodes connected by a sequence of edges matching a regular expression. We study the techniques to process such queries on a distributed graph of data. While…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Graph generation generally aims to create new graphs that closely align with a specific graph distribution. Existing works often implicitly capture this distribution through the optimization of generators, potentially overlooking the…
In this work, we introduce a new algorithm for analyzing a diagram, which contains visual and textual information in an abstract and integrated way. Whereas diagrams contain richer information compared with individual image-based or…
We give a self-contained introduction to the theory of directed graphs, leading up to the relationship between the Perron-Frobenius eigenvectors of a graph and its autocatalytic sets. Then we discuss a particular dynamical system on a fixed…
Given a set of graphs from some unknown family, we want to generate new graphs from that family. Recent methods use diffusion on either graph embeddings or the discrete space of nodes and edges. However, simple changes to embeddings (say,…
Graph theory provides fundamental concepts for many fields of science like statistical physics, network analysis and theoretical computer science. Here we give a pedagogical introduction to graph theory, divided into three sections. In the…
Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as…
Transcriptional regulation of gene expression is one of the main processes that affect cell diversification from a single set of genes. Regulatory proteins often interact with DNA regions located distally from the transcription start sites…
Probabilistic graphical models (PGMs) have become a popular tool for computational analysis of biological data in a variety of domains. But, what exactly are they and how do they work? How can we use PGMs to discover patterns that are…
This paper describes an ongoing multi-scale visual analytics approach for exploring and analyzing biomedical knowledge at scale.We utilize global and local views, hierarchical and flow-based graph layouts, multi-faceted search, neighborhood…
Multipath cohomology is a cohomology theory for directed graphs, which is defined using the path poset. The aim of this paper is to investigate combinatorial properties of path posets, and to provide computational tools for multipath…
How to represent the genetic code? Despite the fact that it is extensively known, the DNA mapping into proteins remains as one of the relevant discoveries of genetics. However, modern genomic signal processing usually requires converting…
Causal loop and stock and flow diagrams are broadly used in System Dynamics because they help organize relationships and convey meaning. Using the analytical work of Schoenberg (2019) to select what to include in a compressed model, this…
Gene expression datasets offer insights into gene regulation mechanisms, biochemical pathways, and cellular functions. Additionally, comparing gene expression profiles between disease and control patients can deepen the understanding of…
Cell formation is a critical step in the design of cellular manufacturing systems. Recently, it was tackled using a cut-based-graph-partitioning model. This model meets real-life production systems requirements as it uses the actual amount…
Schema induction builds a graph representation explaining how events unfold in a scenario. Existing approaches have been based on information retrieval (IR) and information extraction(IE), often with limited human curation. We demonstrate a…
We present an elaborate framework for formally modelling pathways in chemical reaction networks on a mechanistic level. Networks are modelled mathematically as directed multi-hypergraphs, with vertices corresponding to molecules and…
Graph reachability is the task of understanding whether two distinct points in a graph are interconnected by arcs to which in general a semantic is attached. Reachability has plenty of applications, ranging from motion planning to routing.…
The study of spectral graph determination is a fascinating area of research in spectral graph theory and algebraic combinatorics. This field focuses on examining the spectral characterization of various classes of graphs, developing methods…