WIP Jameshennessy/unittests #3
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…ions for the DHS Index data
…ions for the DHS Index data
Fixes formatting in the 'Tasks and Potential Roadmap' section
-add new scatter plot on the kl divergence data - The new metrics is working now (The sampled final sequences were mixed with noised versions previously )
Resolve contributor list in an independant file
Linked the gdoc sheet to keep this list updated based on what we discussed at the last meeting.
Minor formatting
Add discord link for people interested in joining
Sahu, B., Hartonen, T., Pihlajamaa, P. et al. Sequence determinants of human gene regulatory elements. Nat Genet 54, 283–294 (2022). https://doi.org/10.1038/s41588-021-01009-4
…fusion into dna-diffusion
https://huggingface.co/blog/annotated-diffusion) - MILESTONE -> Conditioning is tested and working (check diagonal plot after training to see the results) (Thanks Zach ) - Training using 1000 sequences is enought to see the results after ~1000 epochs (kl divergence going down to train and test sequences and increascing to shuffled sequences) - Added EMA to smooth the training. - Added a function to deal with dataload, motifs generation and training creation - New metrics added KL divergence tested agains (test, train, train shuffled) sequences and per component heatmap plot. - Added a simple loss visualization using livelossplot. - Refactored several functions to plot motif metrix ( others are inside the dataloader new class) Contributions Lucas Ferreira da Silva Luca Pinello Zach Nussbaum
Adding the modified NB
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