Comments (7)
Quoting from the manuscript:
Overall, 709 of the 1,206 metapaths exhibited a statistically significant Δ AUROC at a false discovery rate cutoff of 5%. These 709 metapaths included all 24 metaedges, suggesting that each type of relationship we integrated provided at least some therapeutic utility.
I was unable to locate these 709 metapaths.
We have an interactive table of the metapaths here, but it doesn't look like it has the fdr adjusted p-values.
I think the dataset you want is all-features/data/feature-performance/auroc.tsv
. We then computed the FDR using the following R command in 6-rvisualize.ipynb:
fdr_delta_auroc = p.adjust(p = pval_delta_auroc, method = 'fdr')
I think we also saved the FDR adjusted p-values in 5-primary-aucs.ipynb
to data/feature-performance/primary-aurocs.tsv
. If you filter this dataset to feature_type == "dwpc"
and fdr_pval_auroc < 0.5
, I hope you get 709 rows 😃
from hetionet.
Thank you very much for your prompt reply.
I have successfully identified 1069 metapaths that meet the above criteria. My next objective is to find the instance paths for these metapaths. From my understanding, and based on the information you've provided, it seems you have generated query statements for each metapath to measure their effectiveness as features. Do you have the instance paths generated during the query process for metapaths?
If these data are not available, would I need to execute the queries individually on Neo4j to retrieve the information for all metapaths? Given that Neo4j in https://neo4j.het.io/ often experiences timeouts, this approach seems somewhat impractical.
Could you advise on the best course of action to obtain these data? Any suggestions or alternative methods you could provide would be immensely helpful.
from hetionet.
Do you have the instance paths generated during the query process for metapaths?
We do not store actual paths corresponding to source node, target node, metapath combinations. Instead we generate them on the fly via Cypher queries to Neo4j.
When the path count is large, i.e. over 10,000, then I don't suggest trying to generate all paths. I don't see a valid use case for generating such a large number of paths though. When the path count is that large, any individual path tends to be pretty meaningless.
Also noting our recent publication Hetnet connectivity search provides rapid insights into how two biomedical entities are related.
from hetionet.
Thanks a lot! I also have a question about the undirected metaedges in the paper. You mentioned it in the last sentence of the first paragraph on page 7: "Note that all metaedges besides Gene->regulates->Gene are undirected." Take Anatomy–upregulates–Gene as an example, we can not say Gene–>upregulates–>Anatomy but Anatomy-> was upregulated->Gene. Isn't this just a directed edge?
from hetionet.
question about the undirected metaedges in the paper
See related issue #23.
Whether a metaedge/edge is directional or symmetric is a distinction that is most relevant when the source and target metanode are the same. When there are different source and target metanodes, we encoded "directionality" as different metaedges like:
- Anatomy–upregulates–Gene
- Anatomy–downregulates–Gene
from hetionet.
You mean you use different edges between the same node pair to express the directionality. However, the entity pair, Compound and Disease, do not have different edges to represent the direction, but the same edge is used to represent the reverse direction in the metapath, e.g., Compound–palliates–Disease–palliates–Compound-treat-Disease. So I'm confused about how to distinguish the direction, or whether all edges in the meta-knowledge graph are bidirectional, even for Anatomy–upregulates–Gene and Anatomy–downregulates–Gene.
from hetionet.
Compound–palliates–Disease and Disease–palliates–Compound are the same edge type, just with different orientations. There is no difference in the semantic meaning between the two, which is why we consider the bipartite edges in Hetionet as bidirectional.
from hetionet.
Related Issues (20)
- Local files HOT 2
- Multiple Match Queries Not Working HOT 2
- Question About Hetionet's Dictionary HOT 3
- How to add new disease and anatomy nodes HOT 2
- Providing a dump version of Hetionet HOT 11
- http://neo4j.het.io/browser/ time out HOT 4
- Neo4J instance down (?) HOT 7
- Updated TSV version HOT 6
- graph.db database offline in neo4j HOT 3
- neo4j website down HOT 6
- Hetionet Browser is down HOT 4
- Mapping to original databases HOT 2
- Cannot map non-existing file HOT 5
- Do any relations imply another relation? HOT 1
- Connectivity Search Automated Query Question HOT 8
- Docker compatibility question HOT 4
- Question on metrics HOT 1
- What does it mean if something up regulates a disease in this context? HOT 3
- Speeding up data import to Neo4j v5 and CSV format data HOT 2
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from hetionet.