26 papers · ranked by Valyu relevance
Yuchen Zhou, Hongtao Huo, Zhiwen Hou, Fanliang Bu + 1 more
Graph Convolutional Networks (GCNs) are powerful deep learning methods for non-Euclidean structure data and achieve impressive performance in many fields. But most of the state-of-the-art GCN models are shallow structures with depths of no more than 3 to 4 layers, which greatly limits the ability of GCN models to…
Saiful Islam, Md. Nahid Hasan, Pitambar Khanra
Classification Authors: ['Saiful Islam' 'Md. Nahid Hasan' 'Pitambar Khanra'] The increasing prevalence of graph-structured data across various domains has intensified greater interest in graph classification tasks. While numerous sophisticated graph learning methods have emerged, their complexity often hinders…
Jinyin Chen, Haiyang Xiong, Haibin Zheng, Dunjie Zhang + 3 more
'Mingwei Jia' 'Yi Liu'] Graph classification is crucial in network analyses. Networks face potential security threats, such as adversarial attacks. Some defense methods may trade off the algorithm complexity for robustness, such as adversarial training, whereas others may trade off clean example performance, such as…
Masoud Kargar, Nasim Jelodari, Alireza Assadzadeh
graphs and graph convolutional networks for high-level feature extraction Authors: ['Masoud Kargar' 'Nasim Jelodari' 'Alireza Assadzadeh'] Graphs, comprising nodes and edges, visually depict relationships and structures, posing challenges in extracting high-level features due to their intricate connections Multiple…
Ilya Makarov, Dmitrii Kiselev, Nikita Nikitinsky, Lovro Subelj + 1 more
Dealing with relational data always required significant computational resources, domain expertise and task-dependent feature engineering to incorporate structural information into a predictive model. Nowadays, a family of automated graph feature engineering techniques has been proposed in different streams of…
Ali Deeb, Abdalrahman Ibrahim, Mohamed Salem, Joachim Pichler + 6 more
'Sergii Tkachov' 'Anjeza Karaj' 'Fadi Al Machot' 'Kyamakya Kyandoghere' 'Marco Lanuzza' 'Lionel Trojman'] Analog mixed-signal (AMS) verification is one of the essential tasks in the development process of modern systems-on-chip (SoC). Most parts of the AMS verification flow are already automated, except for stimuli…
James P. Canning, Emma E. Ingram, Sammantha Nowak-Wolff, Adriana M. Ortiz + 4 more
Networks are often categorized according to the underlying phenomena that they represent, such as re-tweets, protein interactions, or web page links. It is generally believed that networks from different categories have inherently unique network characteristics. In this work, we find strong evidence supporting this…
Lida Kanari, Stanislav Schmidt, Francesco Casalegno, Emilie Delattre + 7 more
The shape of neuronal morphologies plays a critical role in determining their dynamical properties and the functionality of the brain. With an abundance of neuronal morphology reconstructions, a robust definition of cell types is important to understand their role in brain functionality. However, an objective…
Jose Lugo-Martinez, Predrag Radivojac
Biological and cellular systems are often modeled as graphs in which vertices represent objects of interest (genes, proteins, drugs) and edges represent relational ties among these objects (binds-to, interacts-with, regulates). This approach has been highly successful owing to the theory, methodology and software that…
Ping Yang, E. Adrian Henle, Cory M. Simon, Xiaoli Fern
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are valuable as pollinators. Thus, candidate pesticides in development pipelines must be assessed for toxicity to bees. Leveraging a data set of 382 molecules with toxicity labels from…
Ping Yang, E. Adrian Henle, Xiaoli Fern, Cory M. Simon
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are agriculturally and ecologically vital as pollinators. The development of new pesticides---driven by pest resistance to and demands to reduce negative environmental impacts of…
Manfred Jaeger
Reasoning about graphs, and learning from graph data is a field of artificial intelligence that has recently received much attention in the machine learning areas of graph representation learning and graph neural networks. Graphs are also the underlying structures of interest in a wide range of more traditional fields…
Vincent Guillemot, Arthur Tenenhaus, Laurent Le Brusquet, Vincent Frouin + 1 more
'Vincent Frouin' 'Arkady B. Khodursky'] Integrating gene regulatory networks (GRNs) into the classification process of DNA microarrays is an important issue in bioinformatics, both because this information has a true biological interest and because it helps in the interpretation of the final classifier. We present a…
Ping Yang, E. Adrian Henle, Xiaoli Fern, Cory M. Simon
Pesticides benefit agriculture by increasing crop yield, quality, and security. However, pesticides may inadvertently harm bees, which are agriculturally and ecologically vital as pollinators. The development of new pesticides---driven by pest resistance to and demands to reduce negative environmental impacts of…
Serkan Ucer, Tansel Ozyer, Reda Alhajj
We propose a new type of supervised visual machine learning classifier, GSNAc, based on graph theory and social network analysis techniques. In a previous study, we employed social network analysis techniques and introduced a novel classification model (called Social Network Analysis-based Classifier-SNAc) which…
Jiate Li, Binghui Wang
Perturbations with Deterministic Certification Authors: ['Jiate Li' 'Binghui Wang'] Graph neural networks (GNNs) achieve the state-of-the-art on graph-relevant tasks such as node and graph classification. However, recent works show GNNs are vulnerable to adversarial perturbations include the perturbation on edges…
Daniel M. Gonçalves, André Patrício, Rafael S. Costa, Rui Henriques
The growing availability and complexity of omics data have driven the development of specialized algorithms for modeling molecular systems. Although graph-based learning methods effectively represent biological interactions, they often neglect the statistical information embedded in node and edge annotations. To…
Tom C. Freeman, Sebastian Horsewell, Anirudh Patir, Josh Harling-Lee + 5 more
Quantitative and qualitative data derived from the analysis of genomes, genes, proteins or metabolites from tissue or cells are currently generated in huge volumes during biomedical research. Graphia is an open-source platform created for the graph-based analysis of such complex data, e.g. transcriptomics, proteomics…
Miguel E. Coimbra, Alexandre P. Francisco, Luís Veiga
The value of graph-based big data can be unlocked by exploring the topology and metrics of the networks they represent, and the computational approaches to this exploration take on many forms. For the use-case of performing global computations over a graph, it is first ingested into a graph processing system from one…
Benedict Paten, Adam M Novak, Erik Garrison, Glenn Hickey
A superbubble is a type of directed acyclic subgraph with single distinct source and sink vertices. In genome assembly and genetics, the possible paths through a superbubble can be considered to represent the set of possible sequences at a location in a genome. Bidirected and biedged graphs are a generalization of…
Renming Liu, Christopher A Mancuso, Anna Yannakopoulos, Kayla A Johnson + 1 more
Assigning every human gene to specific functions, diseases, and traits is a grand challenge in modern genetics. Key to addressing this challenge are computational methods such as supervised-learning and label-propagation that can leverage molecular interaction networks to predict gene attributes. In spite of being a…
Srijani Bagchi, Anasua Sarkar, Ujjwal Maulik
In times like this, it is imperative to be cautious about the effects of drugs or vaccination doses on patients who are already suffering from other serious diseases. It’s not only the virus which can affect the body metabolisms, drugs to encounter the virus may also end up having unwanted negative effects. Therapeutic…
Authors not listed
Computational methods for predictive modeling have been increasingly utilized in the early stages of drug discovery to supplement high-throughput screening. The advent of highly efficient and complex machine learning architectures necessitates new methods of collating the plethora of topological, geometrical, and…
Alexander Smith, Spencer Runde, Alex Chew, Atharva Kelkar + 3 more
Molecular dynamics (MD) simulations are used in diverse scientific and engineering fields such as drug discovery, materials design, separations, biological systems, and reaction engineering. These simulations generate highly complex datasets that capture the 3D spatial positions, dynamics, and interactions of thousands…
Steven B. Gillispie, Michael D. Perlman
Graphical Markov models determined by acyclic digraphs (ADGs), also called directed acyclic graphs (DAOs), are widely studied in statistics, computer science (as Bayesian networks), operations research (as influence diagrams), and many related fields. Because different ADOs may determine the same Markov equivalence…
Paul Kruse, Caroline Ring
This paper presents the treecompareR package for R, which provides tools for reproducible visualizations of data through the use of taxonomies. The package builds on developments from ggplot2 and ggtree to provide visualizations tailored for use with taxonomic classification data. Additionally, it provides tools that…