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1000-genomes-project-analysis's Introduction

1000 Genomes Project Analysis

In this repository, we analyze the 1000 genomes project data.

To download the data, run download.sh. To run our model, cd into the mlp folder. Run python main.py -h to see all available options.

usage: main.py [-h] [--lr N] [--lr_decay_factor N] [--lr_decay_patience N]
               [--lr_decay_cooldown N] [--b N] [--wd N] [--dp N] [--arch ARCH]
               [--seed N] [--data DIR] [--label DIR] [--model DIR]
               [--epochs N] [--verbose] [--features N] [--savepath DIR]
               [--print_freq N] [--val_fraction float] [--pca_components N]
               [--cross_val_splits N] [-e] [-t]

optional arguments:
  -h, --help            show this help message and exit
  --lr N                learning rate, default=5e-3
  --lr_decay_factor N   lr decay, default=0.99 (no decay)
  --lr_decay_patience N lr decay patience, default=10
  --lr_decay_cooldown N lr decay cooldown, default=5
  --b N                 batch size, default=128
  --wd N                weight decay, default=0
  --dp N                dropout probability, default=0.50
  --arch ARCH           which model to use: MLP|Exp|LogReg, default=MLP
  --seed N              random seed for train/test split, default=-1 (random)
  --data DIR            path to raw (np array) data
  --label DIR           path to raw (np array) labels
  --model DIR           path to model, default=None
  --epochs N            number of epochs, default=600
  --verbose             print more frequently
  --features N          number of features to use, default=-1 (all)
  --savepath DIR        directory to save model and logs
  --print_freq N        printing/logging frequency, default=100
  --val_fraction float  fraction of train to use as val, default=0.2
  --pca_components N    number of components for PCA, default=200
  --cross_val_splits N  number of times to cross-validate, default=5
  -e, --eval            evaluate and do not train, default: False
  -t, --test            evaluate on the test set after training, default: False

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