DREAM Single Cell Transcriptomics Challenge


Created By Thomas Yu thomas.yu

Post your final scores and write up here
Coming to the DREAM conference?
Not receiving the scores
Change we change the wrong results in challenge 1?
How can we know our rank after getting the score?
Gene CSV submission is dued?
current leaderboard
Writeup deadline extension
Source Code submission confirmation
confirmation for submission
write up submission
Cell ids or indeces?
randomly select
leaderboard and final submission
Final CSV submission
Why the email dose not contain score after submission?
Clarification of genes for sub challenges
Final submission on 21/11
Questions about the final write-up
Usage of "dge_binarized_distMap.csv" file
Workflow question
What are some typical approaches?
After success submission, I cannot get my score via email (neither my team leader)
Selecting 60, 40 and 20 genes
Could not submit results
Webinar Question: Approach
When exactly will the mid-way submission be closed?
are higher scores better?
Can we submit fewer genes?
Scoring Metrics
Question about pre-selecting 20/40/60 genes
Instruction for submissions to the leaderboard
About Overfitting
Gene Name of Submission
more questions
Cell barcode naming
Question about submission
When is exact deadline for the mid-way submission?
regulatory info about insitu genes
question regarding evaluation and ground truth
still confused
Training and testing of predictive model
Is it possible to get the original data?
Webinar Question: Usage of actual position labels computed by DistMap
What is the rationale for gene weights during evaluation?
Webinar Question: Unique mapping further processes.
Question about using "True" cell locations from 84 in situ matrix
Can we use the 84 genes in situ matrix when mapping?
Supervised learning or Unsupervised learning ?
Why sub challenges limited to a subset of 84 genes?
Webinar Question: Using 84 genes
Webinar Question: Usage of genes.
sub-challenges 3 : feature genes
Webinar Question: Do we have to choose randomly the 20,40,60 genes or do you provide them for us
Selecting 20/40/60 genes
Please Re-register for the challenge
Regulatory relationship data
Webinar Question: Do we know the real locations (experimentally validated) of the cells?
Webinar Question: Is it allowed to use existing softwares? or original softwares have to be developed?
Webinar Question: In associating xyz coordinates to numbered positions, should we use row indices in the geometry file?
Webinar Question: If we build models in TensorFlow and feed coefficients into R, what should we submit?
Webinar Question: Final performance score
Webinar Question: Which genes to use?
Webinar Question: What?s the incentive for this challenge?
Webinar Question: Are we supposed to remove the positions with negative Y values from our prediction considering bilateral symmetry on Y?
Webinar Question: Is it appropriate to use MCC as the gold standard for evaluation instead of actual measured method?
Webinar Question: Can we use the raw read dropseq files to measure the gene expression ourselves, or it has to be the matrix given to us?
Webinar Question: Can we open a slack channel for discussing the topic?
Webinar Question: Where are the instruction slides?
Webinar Question: Evaluation of how the 20/40/60 genes selected
Webinar Question: Submission Evaluation
Webinar Question: Train with the actual positions of 1294 cells using 60/40/20 and predict the position of the 1294 cells?
Webinar Question: Unique mapping by max MCC
Webinar Question: Will you reveal the secret third evaluation method?
Webinar Question: Can I use DistMAp to find the exact location of all 1300 cells?
Webinar Question: Is there a gold standard set of 20/40/60 genes that should be used to make all positions correct?"
Webinar Question: Is it allowed to use prior(biological) informations regarding 8840 genes? (except for in situ genes)
About the ground truth
Challenge scoring: adequate prediction of gene patterns
Blank data?
An error in the example code and the solution
y-coordinate question in geometry.txt
Accessing the data?
20/40/60 genes file
When will the data be out ?

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