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Implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTorch (NeurIPS 2021)

Home Page: https://arxiv.org/abs/2109.09740

License: MIT License

Python 83.87% Jupyter Notebook 13.82% Cython 2.31%
machine-learning bioinformatics biological-sequences pytorch hierarchical-clustering multiple-sequence-alignment neurips-2021

neuroseed's People

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gcorso avatar pchlenski avatar

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biochunan thisislim xuanheiiis pchlenski mbiemans xinformatics nongiga cryptowealth-technology proudc arunadevikaruppasamy rnaimehaom somous-jhzhao barneyhill idohasson piyumalanthony antecede

neuroseed's Issues

Greengenes dataset link is broken

Hi all,
It seems that the download link for the Greengenes dataset is no longer present in the google drive folder. It's not a huge deal since I can just try to get it directly from the source, but I thought I'd let you know. On that note, is there any sort of preprocessing/QC done on the sequences in the dataset that I should be aware of? I'm interested in using this data to reproduce some results.

Data preprocessing

Could you please provide details about how the sequences were preprocessed into tensors in the PKL files?

Dataset access & Google Drive links

Could you please make the google drive links & gdown commands accessible to "anyone with the link"? I cannot download them because of permissions.

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