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Visualizing set relationships: EVenn's comprehensive approach to Venn diagrams
2024
Venn diagrams serve as invaluable tools for visualizing set relationships due to their ease of interpretation. Widely applied across diverse disciplines such as metabolomics, genomics, transcriptomics, and proteomics, their utility is undeniable. However, the operational complexity has been compounded by the absence of standardized data formats and the need to switch between various platforms for generating different Venn diagrams. To address these challenges, we introduce the EVenn platform, a versatile tool offering a unified interface for efficient data exploration and visualization of diverse Venn diagrams. EVenn (http://www.ehbio.com/test/venn) streamlines the data upload process with a standardized format, enhancing the capabilities for multimodule analysis. This comprehensive protocol outlines various applications of EVenn, featuring representative results of multiple Venn diagrams, data uploads in the centralized data center, and step‐by‐step case demonstrations. Through these functionalities, EVenn emerges as a valuable and user‐friendly tool for the in‐depth exploration of multiomics data.
The use of Venn diagrams greatly aids in illustrating and visualizing set relationships within metabolomics, genomics, transcriptomics, and proteomics. Here, we introduce EVenn, an all‐encompassing platform that provides a unified interface for a wide range of Venn diagram functionalities. This protocol delineates the features of EVenn, encompassing interactive Venn diagrams, interactive Edwards diagrams, Euler diagrams, UpSet plots, flower plots, and Venn network diagrams, solidifying its role as an invaluable tool for the analysis of multiomics data.
Highlights
Comprehensive Venn functionality: EVenn introduces a unified platform with diverse Venn diagram tools, from interactive diagrams to network representations, catering to the intricate needs of multiomics data analysis across metabolomics, genomics, transcriptomics, and proteomics.
Efficient data exploration: EVenn's data center streamlines exploration by supporting a standardized data format, allowing researchers to effortlessly upload and analyze data. The manuscript demonstrates its practical utility through representative results and detailed case demonstrations.
User‐friendly interface: With a user‐friendly interface, EVenn simplifies the generation of various Venn diagrams, Euler diagrams, UpSet plots, and more. This protocol establishes EVenn as a valuable resource for researchers seeking a cohesive and accessible tool for multiomics data interpretation.
Journal Article
InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams
by
da Silva, Felipe R
,
Heberle, Henry
,
Meirelles, Gabriela Vaz
in
Algorithms
,
Bioinformatics
,
Biomarkers, Tumor - analysis
2015
Background
Set comparisons permeate a large number of data analysis workflows, in particular workflows in biological sciences. Venn diagrams are frequently employed for such analysis but current tools are limited.
Results
We have developed InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.
Conclusions
InteractiVenn allows set unions in Venn diagrams to be explored thoroughly, by consequence extending the ability to analyze combinations of sets with additional observations, yielded by novel interactions between joined sets. InteractiVenn is freely available online at: www.interactivenn.net.
Journal Article
The Cambridge Photographic Star Atlas
by
Mellinger, Axel
,
Stoyan, Ronald
in
Astronomy
,
Astronomy -- Charts, diagrams, etc
,
Northern Hemisphere
2011
Using the latest methods in digital photography and image processing, The Cambridge Photographic Star Atlas presents the whole sky through large-scale photographic images with corresponding charts. Each double-page spread shows a section of the night sky and is accompanied by an inverted chart highlighting and naming double stars, variable stars, open clusters, galactic and planetary nebulae, globular clusters and galaxies. The 82 large-scale charts, with a scale of 1° per cm, identify over 1500 deep-sky objects and 2500 stars. Providing a giant mosaic of the entire sky, this unique atlas is unparalleled in detail and completeness, making it indispensable for visual observers and astrophotographers.
Magnetostriction of helimagnets in the skyrmion crystal phase
by
Tian, Mingliang
,
Du, Haifeng
,
Wang, Shasha
in
Hypothetical particles
,
Magnetostriction
,
Mathematical analysis
2019
We solve the magnetostriction strains for B20 helimagnets in the skyrmion crystal phase. By taking MnSi as an example, we reproduce its temperature-magnetic field (T-B) phase diagrams within a thermodynamic potential incorporating magnetoelastic interactions. The calculation shows that the normal strain 33 undergoes a sudden jump through a conical-skyrmion phase transition at any temperature. The corresponding experimental measurements for MnSi agree quantitatively well with the calculation.
Journal Article
A combinatorial model for computing volumes of flow polytopes
2019
We introduce new families of combinatorial objects whose enumeration computes volumes of flow polytopes. These objects provide an interpretation, based on parking functions, of Baldoni and Vergne’s generalization of a volume formula originally due to Lidskii. We recover known flow polytope volume formulas and prove new volume formulas for flow polytopes. A highlight of our model is an elegant formula for the flow polytope of a graph we call the caracol graph. As by-products of our work, we uncover a new triangle of numbers that interpolates between Catalan numbers and the number of parking functions, we prove the log-concavity of rows of this triangle along with other sequences derived from volume computations, and we introduce a new Ehrhart-like polynomial for flow polytope volume and conjecture product formulas for the polytopes we consider.
Journal Article
Petri net models of discrete logics used in control algorithms developed in ladder diagram language
by
Baños, Esperanza
,
Quezada, Víctor
,
Quezada, José Carlos
in
Algorithms
,
Block diagrams
,
Control algorithms
2023
Control algorithms for programmable logic controllers are still developed based on the experience of those responsible for control in the industry. The IEC-61131-3 standard considers five programming languages: Ladder Diagram, Structured Text, Function Block Diagram, Instruction List, and Sequential Function Diagram, which use different function blocks to develop control algorithms. Within the control algorithms for discrete event systems, there are two types of blocks: those with discrete inputs and outputs, and those with discrete and analog inputs and discrete output. Of the latter, the present research shows the analysis and formal model of the blocks including the problems of accumulation of tokens and the restoration of the coils. This proposal includes logical blocks of timers, counters, positive and negative transition detectors and bistable elements, which, together with the AND, OR, AND-OR, contact lock, auto-loop and Set-Reset logics, can be modeled and analyzed control algorithms with a greater degree of complexity. This guarantees the safety of workers as well as machines.
Journal Article
Qualitative Analysis of Household Energy Awareness in Poland
by
Rosak-Szyrocka, Joanna
,
Żywiołek, Justyna
in
Alternative energy sources
,
customer awareness
,
energy
2022
Because of disruptive changes in energy businesses and services, as well as changes in people’s lifestyles around the world, energy demand and consumption have risen quickly in recent decades. A household energy awareness literature review was conducted. The survey was conducted in Poland with over 1097 respondents. Additionally, it was given a qualitative analysis. At the same time, in order to consider why energy consumption in households is increasing, a traditional quality management tool was used—the Ishikawa diagram. The Pareto–Lorenz diagram was used to analyze the causes of the increase in energy consumption in households. A model of the causes of increasing energy consumption in households has been built. The researchers calculated the chi-square test, which allows them to determine Pearson’s C coefficient. The C-Pearson coefficient can be calculated using the Chi square value. The results of the study clearly show that the respondents have knowledge of energy and the factors that influence the increase in its consumption but are not aware of why energy should be saved and what it means for the environment. The authors propose ways to build the awareness of household users through a modern quality management tool called the interrelationship diagram.
Journal Article
On the order of the QCD chiral phase transition for different numbers of quark flavours
by
Philipsen, Owe
,
Sciarra, Alessandro
,
Cuteri, Francesca
in
Classical and Quantum Gravitation
,
Elementary Particles
,
Fermions
2021
A
bstract
The nature of the QCD chiral phase transition in the limit of vanishing quark masses has remained elusive for a long time, since it cannot be simulated directly on the lattice and is strongly cutoff-dependent. We report on a comprehensive ongoing study using unimproved staggered fermions with
N
f
∈ [2, 8] mass-degenerate flavours on
N
τ
∈ {4
,
6
,
8} lattices, in which we locate the chiral critical surface separating regions with first-order transitions from crossover regions in the bare parameter space of the lattice theory. Employing the fact that it terminates in a tricritical line, this surface can be extrapolated to the chiral limit using tricritical scaling with known exponents. Knowing the order of the transitions in the lattice parameter space, conclusions for approaching the continuum chiral limit in the proper order can be drawn. While a narrow first-order region cannot be ruled out, we find initial evidence consistent with a second-order chiral transition in all massless theories with
N
f
≤ 6, and possibly up to the onset of the conformal window at 9 ≲
N
f
∗
≲ 12. A reanalysis of already published
O
(
a
)-improved
N
f
= 3 Wilson data on
N
τ
∈ [4
,
12] is also consistent with tricritical scaling, and the associated change from first to second-order on the way to the continuum chiral limit. We discuss a modified Columbia plot and a phase diagram for many-flavour QCD that reflect these possible features.
Journal Article
A review of deep learning methods for digitisation of complex documents and engineering diagrams
by
Francisco Moreno-García, Carlos
,
Jamieson, Laura
,
Elyan, Eyad
in
Acknowledgment
,
Annotations
,
Artificial Intelligence
2024
This paper presents a review of deep learning on engineering drawings and diagrams. These are typically complex diagrams, that contain a large number of different shapes, such as text annotations, symbols, and connectivity information (largely lines). Digitising these diagrams essentially means the automatic recognition of all these shapes. Initial digitisation methods were based on traditional approaches, which proved to be challenging as these methods rely heavily on hand-crafted features and heuristics. In the past five years, however, there has been a significant increase in the number of deep learning-based methods proposed for engineering diagram digitalisation. We present a comprehensive and critical evaluation of existing literature that has used deep learning-based methods to automatically process and analyse engineering drawings. Key aspects of the digitisation process such as symbol recognition, text extraction, and connectivity information detection, are presented and thoroughly discussed. The review is presented in the context of a wide range of applications across different industry sectors, such as Oil and Gas, Architectural, Mechanical sectors, amongst others. The paper also outlines several key challenges, namely the lack of datasets, data annotation, evaluation and class imbalance. Finally, the latest development in digitalising engineering drawings are summarised, conclusions are drawn, and future interesting research directions to accelerate research and development in this area are outlined.
Journal Article
Entanglement Phase Transitions in Measurement-Only Dynamics
by
Gopalakrishnan, Sarang
,
Huse, David A.
,
Khemani, Vedika
in
Chaos theory
,
Circuit diagrams
,
Competition
2021
Unitary circuits subject to repeated projective measurements can undergo an entanglement phase transition (EPT) as a function of the measurement rate. This transition is generally understood in terms of a competition between the scrambling effects of unitary dynamics and the disentangling effects of measurements. We find that, surprisingly, EPTs are possible even in the absence of scrambling unitary dynamics, where they are best understood as arising from measurements alone. This finding motivates us to introduce measurement-only models, in which the “scrambling” and “unscrambling” effects driving the EPT are fundamentally intertwined and cannot be attributed to physically distinct processes. These models represent a novel form of an EPT, conceptually distinct from that in hybrid unitary-projective circuits. We explore the entanglement phase diagrams, critical points, and quantum code properties of some of these measurement-only models. We find that the principle driving the EPTs in these models is frustration, or mutual incompatibility, of the measurements. Surprisingly, an entangling (volume-law) phase is the generic outcome when measuring sufficiently long but still local (≳3-body) operators. We identify a class of exceptions to this behavior (“bipartite ensembles”) which cannot sustain an entangling phase but display dual area-law phases, possibly with different kinds of quantum order, separated by self-dual critical points. Finally, we introduce a measure of information spreading in dynamics with measurements and use it to demonstrate the emergence of a statistical light cone, despite the nonlocality inherent to quantum measurements.
Journal Article