Related papers: Enumerating consistent subgraphs of directed acycl…
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…
Counting non-isomorphic tree-like multigraphs that include self-loops and multiple edges is an important problem in combinatorial enumeration, with applications in chemical graph theory, polymer science, and network modeling. Traditional…
Datasets from several domains, such as life-sciences, semantic web, machine learning, natural language processing, etc. are naturally structured as acyclic graphs. These datasets, particularly those in bio-informatics and computational…
We define persistent homology groups over any set of spaces which have inclusions defined so that the corresponding directed graph between the spaces is acyclic, as well as along any subgraph of this directed graph. This method…
We present a new unified graph-based representation of medical data, combining genetic information and medical records of patients with medical knowledge via a unique knowledge graph. This approach allows us to infer meaningful information…
Acyclic and cyclic orientations of an undirected graph have been widely studied for their importance: an orientation is acyclic if it assigns a direction to each edge so as to obtain a directed acyclic graph (DAG) with the same vertex set;…
Ontology-based approaches for predicting gene-disease associations include the more classical semantic similarity methods and more recently knowledge graph embeddings. While semantic similarity is typically restricted to hierarchical…
While coreference resolution is traditionally used as a component in individual document understanding, in this work we take a more global view and explore what can we learn about a domain from the set of all document-level coreference…
Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community.…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
The enumeration of chemical graphs is an important topic in cheminformatics and bioinformatics, particularly in the discovery of novel drugs. These graphs are typically either tree-like multigraphs or composed of tree-like multigraphs…
Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1,000 scientific papers into an ontological knowledge graph. Through an in-depth structural analysis, we have calculated node degrees, identified…
We associate all small subgraph counting problems with a systematic graph encoding/representation system which makes a coherent use of graphlet structures. The system can serve as a unified foundation for studying and connecting many…
In many situations, it would be useful to know not just the best phylogenetic tree for a given data set, but the collection of high-quality trees. This goal is typically addressed using Bayesian techniques, however, current Bayesian methods…
Subgraph enumeration problems ask to output all subgraphs of an input graph that belongs to the specified graph class or satisfy the given constraint. These problems have been widely studied in theoretical computer science. As far, many…
It is known that annotating named entities in unstructured and semi-structured data sets by their concepts improves the effectiveness of answering queries over these data sets. As every enterprise has a limited budget of time or…
In this work we give a community detection algorithm in which the communities both respects the intrinsic order of a directed acyclic graph and also finds similar nodes. We take inspiration from classic similarity measures of bibliometrics,…
We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field.…
Euclidean geometry has historically played a central role in cultivating logical reasoning and abstract thinking within mathematics education, but has experienced waning emphasis in recent curricula. The resurgence of interest, driven by…
In recent work we have presented a formal framework for linguistic annotation based on labeled acyclic digraphs. These `annotation graphs' offer a simple yet powerful method for representing complex annotation structures incorporating…