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We consider construction of the suffix tree and the directed acyclic word graph (DAWG) indexing data structures for a collection $\mathcal{T}$ of texts, where a new symbol may be appended to any text in $\mathcal{T} = \{T_1, \ldots, T_K\}$,…
There are numerous emerging applications for digitizing trees using terrestrial and aerial laser scanning, particularly in the fields of agriculture and forestry. Interpretation of LiDAR point clouds is increasingly relying on data-driven…
This work addresses the intrinsic relationship between trees and networks (i.e. graphs). A complete (invertible) mapping is presented which allows trees to be mapped into weighted graphs and then backmapped into the original tree without…
Efficiently navigating and understanding academic papers is crucial for scientific progress. Traditional linear formats like PDF and HTML can cause cognitive overload and obscure a paper's hierarchical structure, making it difficult to…
Patent documents in the patent database (PatDB) are crucial for research, development, and innovation as they contain valuable technical information. However, PatDB presents a multifaceted challenge compared to publicly available…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
This system paper presents the Topology ToolKit (TTK), a software platform designed for topological data analysis in scientific visualization. TTK provides a unified, generic, efficient, and robust implementation of key algorithms for the…
Vision-Language models (VLMs) have proven to be effective at aligning image and text representations, producing superior zero-shot results when transferred to many downstream tasks. However, these representations suffer from some key…
We propose a novel tree-like curvilinear structure reconstruction algorithm based on supervised learning and graph theory. In this work we analyze image patches to obtain the local major orientations and the rankings that correspond to the…
Random forests are widely used in regression. However, the decision trees used as base learners are poor approximators of linear relationships. To address this limitation we propose RaFFLE (Random Forest Featuring Linear Extensions), a…
Attack Trees are a graphical model of security used to study threat scenarios. While visually appealing and supported by solid theories and effective tools, one of their main drawbacks remains the amount of effort required by security…
Treemaps have been widely applied to the visualization of hierarchical data. A treemap takes a weighted tree and visualizes its leaves in a nested planar geometric shape, with sub-regions partitioned such that each sub-region has an area…
Interpretability is crucial for doctors, hospitals, pharmaceutical companies and biotechnology corporations to analyze and make decisions for high stakes problems that involve human health. Tree-based methods have been widely adopted for…
Reconstruction of evolutionary relationships between species is an important topic in the field of computational biology. Pairwise compatibility graphs (PCGs) are used to model such relationships. A graph is a PCG if its edges can be…
A merge tree is a topological descriptor of a real-valued function. Merge trees are used in visualization and topological data analysis, either directly or as a means to another end: computing a 0-dimensional persistence diagram,…
In recent years, graph representation learning has gained significant popularity, which aims to generate node embeddings that capture features of graphs. One of the methods to achieve this is employing a technique called random walks that…
Topic modelling is a popular unsupervised method for identifying the underlying themes in document collections that has many applications in information retrieval. A topic is usually represented by a list of terms ranked by their…
In this paper, we introduce a new problem called Tree-Residue Vertex-Breaking (TRVB): given a multigraph $G$ some of whose vertices are marked "breakable," is it possible to convert $G$ into a tree via a sequence of "vertex-breaking"…
Neuronal morphology is essential for studying brain functioning and understanding neurodegenerative disorders. As acquiring real-world morphology data is expensive, computational approaches for morphology generation have been studied.…
Routing tables in ad hoc and wireless routing protocols can be represented using rooted trees. The constant need for communication and storage of these trees in routing protocols demands an efficient rooted tree coding algorithm. This…