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clade_prediction's Introduction

SARS-COV2 sequence generation

SARS-COV2 sequence generation by applying deep learning techniques on amino acid sequences (sequence to sequence encoder-decoder, GAN)

Spike protein reference

NCBI Reference Sequence: YP_009724390.1

https://www.ncbi.nlm.nih.gov/protein/YP_009724390.1

Resources

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8056063/ https://www.mdpi.com/1420-3049/26/9/2622/pdf https://www.nature.com/articles/s42003-021-01754-6 https://www.nature.com/articles/s41401-020-0485-4 https://www.nature.com/articles/s41586-020-2895-3 https://www.sciencedirect.com/science/article/pii/S2405844021006757 https://www.tensorflow.org/addons/tutorials/networks_seq2seq_nmt https://arxiv.org/pdf/2008.11790.pdf https://www.nature.com/articles/s41579-021-00573-0#Sec3 https://pubmed.ncbi.nlm.nih.gov/33423311/

https://www.mdpi.com/2076-2607/9/5/1035/pdf https://virological.org/t/recent-evolution-and-international-transmission-of-sars-cov-2-clade-19b-pango-a-lineages/711 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7709189/ https://www.ecdc.europa.eu/sites/default/files/documents/SARS-CoV-2-variant-multiple-spike-protein-mutations-United-Kingdom.pdf https://www.cell.com/cell/pdf/S0092-8674(20)30820-5.pdf https://covariants.org/variants https://www.nature.com/articles/s41598-021-96950-z https://www.nature.com/articles/s41467-020-19843-1 https://journals.asm.org/doi/10.1128/mBio.01188-21 http://www.cryst.bbk.ac.uk/education/AminoAcid/the_twenty.html

Structured noise injection

https://openaccess.thecvf.com/content_CVPR_2020/papers/Alharbi_Disentangled_Image_Generation_Through_Structured_Noise_Injection_CVPR_2020_paper.pdf

F5L, F12S, D614G

https://www.frontiersin.org/articles/10.3389/fimmu.2021.725240/full

Unrolled GAN

https://github.com/MarisaKirisame/unroll_gan/blob/master/main.py https://github.com/andrewliao11/unrolled-gans/blob/master/unrolled_gan.ipynb

  1. conda create --name clade_pred python=3.9
  2. conda activate clade_pred
  3. pip install tensorflow-gpu pandas matplotlib bio h5py scikit-learn nltk python-Levenshtein

Cross batch statefullness

https://www.tensorflow.org/guide/keras/rnn

Teacher forcing

https://aclanthology.org/2020.lrec-1.576.pdf https://dafx2020.mdw.ac.at/proceedings/papers/DAFx20in21_paper_12.pdf https://en.wikipedia.org/wiki/Gibbs_sampling http://people.csail.mit.edu/andyyuan/docs/interspeech-16.audio2vec.paper.pdf https://arxiv.org/pdf/2108.11992.pdf

Clade emergence date

https://github.com/nextstrain/ncov/blob/master/defaults/clade_emergence_dates.tsv

Clade assignment

https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/index.html

Acknowledgements

Data from this analysis have been downloaded from GISAID (https://www.gisaid.org/help/publish-with-data-from-gisaid/)

  • Khare, S., et al (2021) GISAID’s Role in Pandemic Response. China CDC Weekly, 3(49): 1049-1051. doi: 10.46234/ccdcw2021.255 PMCID: 8668406
  • Elbe, S. and Buckland-Merrett, G. (2017) Data, disease and diplomacy: GISAID’s innovative contribution to global health. Global Challenges, 1:33-46. doi:10.1002/gch2.1018 PMCID: 31565258
  • Shu, Y. and McCauley, J. (2017) GISAID: from vision to reality. EuroSurveillance, 22(13) doi:10.2807/1560-7917.ES.2017.22.13.30494 PMCID: PMC5388101

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clade_prediction's Issues

Missing data

Hi Anup,
We found this work and we are willing to use it for our research in Data Science course in the Hebrew University of Jerusalem.
We want to generate sequences from several types of SARS-COV-2.
Unfortunately, when we trying to run the model (from the pretrained models), it seems that we are missing some files.
We tried to gather some files from different directories in "test results", but still we are missing files and we are not sure that the fact we use files from different runs is ok.

Can you help us in running the model? maybe upload updated data and test results folder?
Thanks,
Sean

input files

could you please explain what are the input files that are missing so we can reproduce results using our own data, I understand that you are using next clade tool and that you're not allowed to share data but it would be extremely helpful if you let us know what are the names, directories and content of missing files.

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