13 research outputs found
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
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
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
HiGlass: web-based visual exploration and analysis of genome interaction maps
We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at
http://higlass.io
and is also available as a containerized application that can be run on any platform.National Institutes of Health (U.S.) (U01 CA200059)National Institutes of Health (U.S.) (R00 HG007583)National Institutes of Health (U.S.) (U54 HG007963