Related papers: Matrix Graph Grammars as a Model of Computation
In recent years, there has been a growing interest in mapping data from different domains to graph structures. Among others, neural network models such as the multi-layer perceptron (MLP) can be modeled as graphs. In fact, MLPs can be…
Graph neural networks (GNNs) are a class of deep models that operate on data with arbitrary topology represented as graphs. We introduce an efficient memory layer for GNNs that can jointly learn node representations and coarsen the graph.…
While Language Models (LMs) are the workhorses of NLP, their interplay with structured knowledge graphs (KGs) is still actively researched. Current methods for encoding such graphs typically either (i) linearize them for embedding with LMs…
Graph Weighted Models (GWMs) have recently been proposed as a natural generalization of weighted automata over strings and trees to arbitrary families of labeled graphs (and hypergraphs). A GWM generically associates a labeled graph with a…
Recent work at the intersection of formal language theory and graph theory has explored graph grammars for graph modeling. However, existing models and formalisms can only operate on homogeneous (i.e., untyped or unattributed) graphs. We…
Large Language Models are increasingly used by students to explore advanced material in computer science, including graph theory. As these tools become integrated into undergraduate and graduate coursework, it is important to understand how…
Coarse-grained (CG) molecular dynamics (MD) simulations can simulate large molecular complexes over extended timescales by reducing degrees of freedom. A critical step in CG modeling is the selection of the CG mapping algorithm, which…
We propose the use of hyperedge replacement graph grammars for factor graphs, or factor graph grammars (FGGs) for short. FGGs generate sets of factor graphs and can describe a more general class of models than plate notation, dynamic…
Knowledge graph reasoning (KGR), aiming to deduce new facts from existing facts based on mined logic rules underlying knowledge graphs (KGs), has become a fast-growing research direction. It has been proven to significantly benefit the…
Well-designed open-source software drives progress in Machine Learning (ML) research. While static graph ML enjoys mature frameworks like PyTorch Geometric and DGL, ML for temporal graphs (TG), networks that evolve over time, lacks…
We consider graph Turing machines, a model of parallel computation on a graph, in which each vertex is only capable of performing one of a finite number of operations. This model of computation is a natural generalization of several…
Recent developments in Machine Learning approaches for modelling physical systems have begun to mirror the past development of numerical methods in the computational sciences. In this survey, we begin by providing an example of this with…
Graphs are ubiquitous real-world data structures, and generative models that approximate distributions over graphs and derive new samples from them have significant importance. Among the known challenges in graph generation tasks,…
Graph condensation (GC) has gained significant attention for its ability to synthesize smaller yet informative graphs. However, existing studies often overlook the robustness of GC in scenarios where the original graph is corrupted. In such…
Graphs are central to the chemical sciences, providing a natural language to describe molecules, proteins, reactions, and industrial processes. They capture interactions and structures that underpin materials, biology, and medicine. This…
Graph transformation formalisms have proven to be suitable tools for the modelling of chemical reactions. They are well established in theoretical studies and increasingly also in practical applications in chemistry. The latter is made…
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…
Modern communication networks are inherently complex in nature. First of all, they have a large number of heterogeneous components. Secondly, their connectivity is extremely dynamic. Nodes can come and go, links can be removed and added…
Variety of machine learning problems can be formulated as an optimization task for some (surrogate) loss function. Calculation of loss function can be viewed in terms of stochastic computation graphs (SCG). We use this formalism to analyze…
Systems now exist which are able to compile unification grammars into language models that can be included in a speech recognizer, but it is so far unclear whether non-trivial linguistically principled grammars can be used for this purpose.…