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Record W2122306708 · doi:10.1109/iv.2002.1028774

Visualizing metabolic networks in VRML

2003· article· en· W2122306708 on OpenAlex

Why this work is in the frame

A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.

affAt least one author lists a Canadian institution in the pinned OpenAlex snapshot.

Bibliographic record

VenueProceedings Sixth International Conference on Information Visualisation · 2003
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicBioinformatics and Genomic Networks
Canadian institutionsWestern University
Fundersnot available
KeywordsComputer scienceVRMLGlyph (data visualization)Scripting languageVisualizationHuman–computer interactionSoftwareAvatarData visualizationThe InternetVirtual realityMultimediaWorld Wide WebProgramming languageArtificial intelligence

Abstract

fetched live from OpenAlex

A successful data collection visualization should satisfy conflicting requirements: unification of diverse data formats, support for serendipity research, support of hierarchical structures, algorithmizability, vast information density, Internet-readiness, etc. The traditional 2D representations of metabolic pathways lack compactness and information density. Virtual reality (VR) has made significant progress in engineering, architectural design, entertainment and communication. Evident advantages of using VR for scientific visualization are subconscious orientation, compromise between overview and detail, memorizing search results, and customization. We experiment with the possibility of using immersive abstract 3D visualizations of metabolic networks. We present the trial Metabolic Network Visualizer (MNV) software, which produces graphical representation of a metabolic network as a VRML (Virtual Reality Modeling Language) world. The entities in the metabolic network are identified as "compartment", "species", "reaction" and "transporter". The properties of the above objects are described using a simple scripting language. The demonstration of the MNV software is available at http://130.239.139.41/sciencevr/mnv/indexview.html.

Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.

Full frame distilled prediction

Teacher imitation

Not calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.

metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.000
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Theoretical or conceptual · Consensus signal: none
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.964
Threshold uncertainty score0.791

Codex and Gemma teacher scores by category

CategoryCodexGemma
Metaresearch0.0010.000
Meta-epidemiology (narrow)0.0000.000
Meta-epidemiology (broad)0.0000.000
Bibliometrics0.0000.000
Science and technology studies0.0000.000
Scholarly communication0.0000.000
Open science0.0000.000
Research integrity0.0000.000
Insufficient payload (model declined to judge)0.0000.000

Machine scores (provisional)

The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.

Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.

Opus teacher head0.025
GPT teacher head0.293
Teacher spread0.268 · how far apart the two teachers sit on this one work
Validation statusscore_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from it