25 papers · ranked by Valyu relevance
Dominik Seidel
The three-dimensional forest structure affects many ecosystem functions and services provided by forests. As forests are made of trees it seems reasonable to approach their structure by investigating individual tree structure. Based on three-dimensional point clouds from laser scanning, a newly developed holistic…
Katharina Jahn, Niko Beerenwinkel, Louxin Zhang
Mutation trees are rooted trees of arbitrary node degree in which each node is labeled with a mutation set. These trees, also referred to as clonal trees, are used in computational oncology to represent the mutational history of tumours. Classical tree metrics such as the popular Robinson–Foulds distance are of limited…
Yi Lin, Miao Jiang, Petri Pellikka, Janne Heiskanen
Mensuration of tree growth habits is of considerable importance for understanding forest ecosystem processes and forest biophysical responses to climate changes. However, the complexity of tree crown morphology that is typically formed after many years of growth tends to render it a non-trivial task, even for the…
Jacques Chabin, Mírian Halfeld Ferrari, Nicolas Hiot
We present a general methodology for structuring textual data, represented as syntax trees enriched with semantic information, guided by a meta-model G defined as an attribute grammar. The method involves an evolution process where both the instance and its grammar evolve, with instance transformations guided by…
Pierre Dutilleul, Nishan Mudalige, Louis-Paul Rivest, Esmaiel Jabbari
'Esmaiel Jabbari'] The increasingly large size of the graphical and numerical data sets collected with modern technologies requires constant update and upgrade of the statistical models, methods and procedures to be used for their analysis in order to optimize learning and maximize knowledge and understanding. This is…
Wei Wei, David Koslicki
Distance-guided tree construction with unknown tree topology and branch lengths has been a long studied problem. In contrast, distance-guided branch lengths assignment with fixed tree topology has not yet been systematically investigated, despite having significant applications. In this paper, we provide a formal…
Pengyu Liu, Matthew Gould, Caroline Colijn
Phylogenetic trees are a central tool in evolutionary biology. They demonstrate evolutionary patterns among species, genes, and with modern sequencing technologies, patterns of ancestry among sets of individuals. Phylogenetic trees usually consist of tree shapes, branch lengths and partial labels. Comparing tree shapes…
David Carral, Pascal Hitzler, Hilmar Lapp, Sebastian Rudolph
Trees – i.e., the type of data structure known under this name – are central to many aspects of knowledge organization. We investigate some central design choices concerning the ontological modeling of such trees. In particular, we consider the limits of what is expressible in the Web Ontology Language, and provide a…
Yang Zhao, Morihiro Hayashida, Yue Cao, Jaewook Hwang + 1 more
'Tatsuya Akutsu'] Background Many tree structures are found in nature and organisms. Such trees are believed to be constructed on the basis of certain rules. We have previously developed grammar-based compression methods for ordered and unordered single trees, based on bisection-type tree grammars. Here, these methods…
Petr Novotný, Jan Wild
The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures…
Daniel Neider, Leif Sabellek, Johannes Schmidt, Fabian Vehlken + 1 more
'Thomas Zeume'] Explaining why and how a tree t structurally differs from another tree t ⋆ is a question that is encountered throughout computer science, including in understanding tree-structured data such as XML or JSON data. In this article, we explore how to learn explanations for structural differences between…
Hadi Poormohammadi, Mohsen Sardari Zarchi
Phylogenetic networks construction is one the most important challenge in phylogenetics. These networks can present complex non-treelike events such as gene flow, horizontal gene transfers, recombination or hybridizations. Among phylogenetic networks, rooted structures are commonly used to represent the evolutionary…
Pengyu Liu, Jacob Lusk, Nataša Jonoska, Mariel Vázquez
R-loops are a class of non-canonical nucleic acid structures that typically form during transcription when the nascent RNA hybridizes the DNA template strand, leaving the DNA coding strand unpaired. Co-transcriptional R-loops are abundant in nature and biologically relevant. Recent research shows that DNA sequence and…
Daiji Fukagawa, Takeyuki Tamura, Atsuhiro Takasu, Etsuji Tomita + 1 more
'Tatsuya Akutsu'] Background Measuring similarities between tree structured data is important for analysis of RNA secondary structures, phylogenetic trees, glycan structures, and vascular trees. The edit distance is one of the most widely used measures for comparison of tree structured data. However, it is known that…
Richard Apodaca
Despite its widespread use, Simplified Molecular Input Line Entry System (SMILES) remains underspecified. The lack of a detailed specification encourages improvisation by software developers, complicates data standardization efforts, and undermines extension development. Balsa, a reformulation of SMILES, addresses…
Juan Zhang, Wei Xu, Zhiqiang Dou, Liuyi Pan + 5 more
'Zhifang Yang' 'Yuliang Cai' 'Ali Akbar Ghasemi-Soloklui'] Different tree shapes (TSs) directly influence canopy structure, light interception, and photosynthetic activity, impacting fruit quality and yield. This study investigated the effects of light interception efficiency (LIE) on the quality and yield of “Jimei”…
Yinhui Yang, Rui Wang, Yuchi Huo
In some entertainment and virtual reality applications, it is necessary to model and draw the real world realistically, so as to improve the fidelity of natural scenes and make users have a better sense of immersion. However, due to the morphological structure of trees The complexity and variety present many challenges…
Rasa Meskauskiene, Oliver Laule, Nikolai V Ivanov, Florian Martin + 3 more
'Markus Wyss' 'Wilhelm Gruissem' 'Philip Zimmermann'] Background It is generally accepted that controlled vocabularies are necessary to systematically integrate data from various sources. During the last decade, several plant ontologies have been developed, some of which are community specific or were developed for a…
Jonas Schaub, Julian Zander, Achim Zielesny, Christoph Steinbeck
The concept of molecular scaffolds as defining core structures of organic molecules is utilised in many areas of chemistry and cheminformatics, e.g. drug design, chemical classification, or the analysis of high-throughput screening data. Here, we present Scaffold Generator, a comprehensive open library for the…
Authors not listed
We present a simple yet efficient random (brute-force) algorithm for constructing solvated molecular systems. By placing solvent molecules at random positions and orientations within a simulation box, we circumvent the complexities typically associated with more sophisticated packing algorithms. The main computational…
Jacob Gilbert, Chih Hao Wu, Marina Knittel, Alejandro A. Schäffer + 2 more
Understanding and comparing tumor evolutionary histories is fundamental to cancer genomics. Clonal trees, used to model tumor progression, are rooted, unordered trees in which each node represents a subclone labeled by a set of distinct mutations. To compare two clonal trees, we introduce omlta, the optimal multi-label…
Dominique Sydow, Eva Aßmann, Albert J. Kooistra, Friedrich Rippmann + 1 more
Protein kinases are among the most important drug targets because their dysregulation can cause cancer, inflammatory, and degenerative diseases. Developing selective inhibitors is challenging due to the highly conserved binding sites across the roughly 500 human kinases. Thus, detecting subtle similarities on a…
Kieran Greer
– Concept Trees are a type of database that can organise arbitrary textual information using a very simple rule. Each tree ideally represents a single cohesive concept and the trees can link with each other for navigation and semantic purposes. The trees are therefore a type of semantic network and would benefit from…
Authors not listed
RNA molecules fold into complex three-dimensional structures that determine their function. A wide range of mathematical frameworks, such as chord diagrams, fatgraphs, and context-free grammars, have been used to represent these structures; however, these models have largely been developed from mathematical motivations…
Vladimir Kondratyev, Marian Dryzhakov, Timur Gimadiev, Dmitriy Slutskiy
In this work, we provide further development of the junction tree variational autoencoder (JT VAE) architecture in terms of implementation and application of the internal feature space of the model. Pretraining of JT VAE on a large dataset and further optimization with a regression model led to a latent space that can…