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View Code? Open in Web Editor NEWDeep Rapid Annotation using Submodels Training in Cells
Deep Rapid Annotation using Submodels Training in Cells
First model to consider for the first milestone.
Reference: Stephen Merity, Nitish Shirish Keskar, Richard Socher (2017). Regularizing and Optimizing LSTM Language Models.
We should account sometime to prepare the poster and coordinate the presentation.
notes while we work and develop models
first draft in latex
review 1
Having defined all of the pre-processing functions (embeddings not included), we need to define some API for the user to transform the raw data into a suitable format:
/bin
to go from paths to files (FASTA and feature table) to the pre-processed dataframe (maybe a CSV).Which license should we use for the repository? I guess it's fine with a MIT or GNU license.
The preprocessing task involves sampling from the genomes on varying length chunks.
minimum_size
of the chunks (maximum length of a gene)Now that we have something working, we should prepare the notebooks and organize the different models:
.py
ready to be imported.src/data/
, ready to be imported.The README should have the models and features we are going to accomplish.
Christmas is coming and the deadline is looming! Please tell others if you are working on one of the tasks and edit this issue as you please.
pd.DataFrame
about theGiven that we have defined the functions for extracting labeled ranges from the data (#3), all that is left is to build a dataframe (I suppose in pandas) using these ranges and the genome sequence.
My first guess is that the dataset would contain two columns, one for the sequence and other for the label.
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