eXamine: a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput "omics" data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

eXamine: Visualizing annotated networks in Cytoscape [version 1; referees: 1 approved, 2 approved with reservations]

eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,200 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs

Where innovation starts Dynamic Visualization of Metabolic Pathways Combining Mental Maps and Static Metabolic Pathway Rendering Techniques Dynamic Visualization of Metabolic Pathways

MASTER Dynamic visualization of metabolic pathways combining mental maps and static metabolic pathway rendering techniques Direks, G.L.F. Award date: 2014 Link to publication Disclaimer This document contains a student thesis (bachelor's or master's), as authored by a student at Eindhoven University of Technology. Student theses are made available in the TU/e repository upon obtaining the required degree. The grade received is not published on the document as presented in the repository. The required complexity or quality of research of student theses may vary by program, and the required minimum study period may vary in duration. General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain Where innovation starts Dynamic Visualization of Metabolic Pathways Combining Mental Maps and Static Metabolic Pathway Rendering Techniques Abstract In this thesis, we identify the requirements of creating static metabolic pathway layouts and maintaining the mental map when adding additional pathways to an existing visualization in an interactive setting. We describe methods which accomplish a good static layout, as well as methods which maintain the mental map. We combine a static layout algorithm by Karp and Paley with a mental map preserving algorithm by Misue et al. with good results. We also detail how to combine other algorithms to achieve a similar effect. We take special care when trying to find a good balance between maintaining the mental map and creating a clear layout. This results in an algorithm which is good at maintaining the mental map when combining multiple metabolic pathways. The prototype application which implements this algorithm generates these layouts quickly, without any noticeable delay. While the prototype is algorithmically complete, it can use some aesthetic improvements

elbow benders

elbow benderThe Newfoundland Board of Liquor Control had good news on Thusday for elbow benders. Slow-selling stocks of local beer and one Nova Scotia brew has been reduced from 32 to 30 cents a pint. Some slow-selling whiskey have also been reduced.PRINTED ITEMG.M.Story Sept, 1957SlangNot usedNot usedWithdrawnChecked by Rebecca Nolan on Thu 12 Mar 201

eXamine: Visualizing annotated networks in Cytoscape [version 2; referees: 2 approved, 2 approved with reservations]

eXamine is a Cytoscape app that displays set membership as contours on top of a node-link layout of a small graph. In addition to facilitating interpretation of enriched gene sets of small biological networks, eXamine can be used in other domains such as the visualization of communities in small social networks. eXamine was made available on the Cytoscape App Store in March 2014, has since registered more than 7,700 downloads, and has been highly rated by more than 25 users. In this paper, we present eXamine's new automation features that enable researchers to compose reproducible analysis workflows to generate visualizations of small, set-annotated graphs

Kelp diagrams : Point set membership visualization

We present Kelp Diagrams, a novel method to depict set relations over points, i.e., elements with predefined positions. Our method creates schematic drawings and has been designed to take aesthetic quality, efficiency, and effectiveness into account. This is achieved by a routing algorithm, which links elements that are part of the same set by constructing minimum cost paths over a tangent visibility graph. There are two styles of Kelp Diagrams to depict overlapping sets, a nested and a striped style, each with its own strengths and weaknesses. We compare Kelp Diagrams with two existing methods and show that our approach provides a more consistent and clear depiction of both element locations and their set relations

eXamine : a Cytoscape app for exploring annotated modules in networks

Background. Biological networks have growing importance for the interpretation of high-throughput omics data. Statistical and combinatorial methods allow to obtain mechanistic insights through the extraction of smaller subnetwork modules. Further enrichment analyses provide set-based annotations of these modules. Results. We present eXamine, a set-oriented visual analysis approach for annotated modules that displays set membership as contours on top of a node-link layout. Our approach extends upon Self Organizing Maps to simultaneously lay out nodes, links, and set contours. Conclusions. We implemented eXamine as a freely available Cytoscape app. Using eXamine we study a module that is activated by the virally-encoded G-protein coupled receptor US28 and formulate a novel hypothesis about its functioning

Robust PDF Document Conversion Using Recurrent Neural Networks

The number of published PDF documents has increased exponentially in recent decades. There is a growing need to make their rich content discoverable to information retrieval tools. In this paper, we present a novel approach to document structure recovery in PDF using recurrent neural networks to process the low-level PDF data representation directly, instead of relying on a visual re-interpretation of the rendered PDF page, as has been proposed in previous literature. We demonstrate how a sequence of PDF printing commands can be used as input into a neural network and how the network can learn to classify each printing command according to its structural function in the page. This approach has three advantages: First, it can distinguish among more fine-grained labels (typically 10-20 labels as opposed to 1-5 with visual methods), which results in a more accurate and detailed document structure resolution. Second, it can take into account the text flow across pages more naturally compared to visual methods because it can concatenate the printing commands of sequential pages. Last, our proposed method needs less memory and it is computationally less expensive than visual methods. This allows us to deploy such models in production environments at a much lower cost. Through extensive architectural search in combination with advanced feature engineering, we were able to implement a model that yields a weighted average F1 score of 97% across 17 distinct structural labels. The best model we achieved is currently served in production environments on our Corpus Conversion Service (CCS), which was presented at KDD18 (arXiv:1806.02284). This model enhances the capabilities of CCS significantly, as it eliminates the need for human annotated label ground-truth for every unseen document layout. This proved particularly useful when applied to a huge corpus of PDF articles related to COVID-19.Comment: 9 pages, 2 tables, 4 figures, uses aaai21.sty. Accepted at the "Thirty-Third Annual Conference on Innovative Applications of Artificial Intelligence (IAAI-21)". Received the "IAAI-21 Innovative Application Award