22 papers · ranked by Valyu relevance
Gómez-Rodríguez, Carlos, Alemany-Puig, Lluís
Dependency syntax represents the structure of a sentence as a tree composed of dependencies, i.e., directed relations between lexical units. While in its more general form any such tree is allowed, in practice many are not plausible or are very infrequent in attested language. This has motivated a search for…
Miloš Stanojević
Most computational models of dependency syntax consist of distributions over spanning trees. However, the majority of dependency treebanks require that every valid dependency tree has a single edge coming out of the ROOT node, a constraint that is not part of the definition of spanning trees. For this reason all…
Ran Zmigrod, Tim Vieira, Ryan Cotterell
The connection between dependency trees and spanning trees is exploited by the NLP community to train and to decode graph-based dependency parsers. However, the NLP literature has missed an important difference between the two structures: only one edge may emanate from the root in a dependency tree. We analyzed the…
Seongsik Park, Harksoo Kim, Željko Stević
The syntactic information of a dependency tree is an essential feature in relation extraction studies. Traditional dependency-based relation extraction methods can be categorized into hard pruning methods, which aim to remove unnecessary information, and soft pruning methods, which aim to utilize all lexical…
Katherine E. Isaacs, Todd Gamblin
— Package managers provide ease of access to applications by removing the time-consuming and sometimes completely prohibitive barrier of successfully building, installing, and maintaining the software for a system. A package dependency contains dependencies between all packages required to build and run the target…
Valentin Rineau, René Zaragüeta, Jérémie Bardin
The three-taxon statement (also called triplet) is the fundamental unit of rooted trees in phylogenetic systematics. Various supertree and phylogenetic methods use three-taxon statements that are minimal rooted statements of degree of kinship relationships. Because of their fundamental role in phylogenetics…
Kaeser M. Sabrin, Constantine Dovrolis
Many hierarchically modular systems are structured in a way that resembles an hourglass. This "hourglass effect" means that the system generates many outputs from many inputs through a relatively small number of intermediate modules that are critical for the operation of the entire system, referred to as the waist of…
Zuguang Gu, Daniel Hübschmann
Numerous R packages have been developed for bioinformatics analysis in the last decade and dependencies among packages have become critical issues to consider. In this work, we proposed a new metric named dependency heaviness that measures the number of unique dependencies that a parent brings to a package, and we…
Rui Li, Shili Shu, Shunli Wang, Yang Liu + 3 more
'Stanisław Drożdż'] The rapid development of information technology has made the amount of information in massive texts far exceed human intuitive cognition, and dependency parsing can effectively deal with information overload. In the background of domain specialization, the migration and application of syntactic…
Luca Arnaboldi, David Aspinall
We present a way to combine security and safety assessments using Bowtie Diagrams. Bowties model both the causes leading up to a central failure event and consequences which arise from that event, as well as barriers which impede events. Bowties have previously been used separately for security and safety assessments…
Himanshu Yadav, Shubham Mittal, Samar Husain
Dependency length minimization is widely regarded as a cross-linguistic universal reflecting syntactic complexity in natural languages. A typical way to operationalize dependency length in corpus-based studies has been to count the number of words between syntactically related words. However, such a formulation ignores…
Shuvendu K. Lahiri, Chao Wang, Sriram Sankaranarayanan
In this paper, we study efficient approaches to reachability analysis for discrete-time nonlinear dynamical systems when the dependencies among the variables of the system have low treewidth. Reachability analysis over nonlinear dynamical systems asks if a given set of target states can be reached, starting from an…
Aida Akbarzadeh, Sokratis Katsikas, Panagiotis Sarigiannidis
Contemporary Critical Infrastructures (CIs), such as the power grid, comprise cyber physical systems that are tightly coupled, to form a complex system of interconnected components with interacting dependencies. Modelling methodologies have been suggested as proper tools to provide better insight into the dependencies…
Miguel Pignatelli
Summary: There is an increasing need for rich and dynamic biological data visualizations in bioinformatic web applications. New standards in web technologies, like SVG or Canvas, are now supported by most modern web browsers allowing the blossoming of powerful visualizations in biological data analysis. The exploration…
Grigoriy Gogoshin, Sergio Branciamore, Andrei S. Rodin
Bayesian Network (BN) modeling is a prominent and increasingly popular computational systems biology method. It aims to construct probabilistic networks from the large heterogeneous biological datasets that reflect the underlying networks of biological relationships. Currently, a variety of strategies exist for…
Remco R. Bouckaert, Joseph Heled
Phylogenetic analysis like Bayesian MCMC or bootstrapping result in a collection of trees. Trees are discrete objects and it is generally difficult to get a mental grip on a distributions over trees. Visualisation tools like DensiTree can give good intuition on tree distributions. It works by drawing all trees in the…
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…
Sergio Pablo-García, Raúl Pérez-Soto, Albert Sabadell-Rendón, Diego Garay-Ruiz + 2 more
In the study of chemical reactions, visualizing reaction networks is pivotal for identifying crucial compounds and reactions. Traditional methods, such as network schematics and reaction path linear plots, often struggle to effectively represent complex reaction networks due to their size and intricate connectivity.…
Grzegorz Skoraczyński, Mateusz Kitlas, Błażej Miasojedow, Anna Gambin
Modern computer-assisted synthesis planning tools provide strong support for this problem. However, they are still limited by computational complexity. This limitation may be overcome by scoring the synthetic accessibility as a pre-retrosynthesis heuristic. A wide range of machine learning scoring approaches is…
Valentin Rineau, Stéphane Prin
Three-item statements, as minimal informative rooted binary phylogenetic trees on three items, are the minimal units of cladistic information. Their importance for phylogenetic reconstruction, consensus and supertree methods relies on both (i) the fact that any cladistic tree can always be decomposed into a set of…
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…
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…