neuralee 0.1.3

Installation

1. Install Python 3.7.

2. Install PyTorch. If you have an NVIDIA GPU, be sure to install a version of PyTorch that supports it. NeuralEE runs much faster with a discrete GPU.

3. Install NeuralEE through pip or from GitHub:

pip install neuralee

git clone git://github.com/HiBearME/NeuralEE.git
cd NeuralEE
python setup.py install --user

How to use NeuralEE

from neuralee.dataset import CortexDataset
from neuralee.embedding import NeuralEE

import torch
device = torch.device('cuda' if torch.cuda.is_available() else 'cpu')

# preprocess dataset
cortex_dataset = CortexDataset(save_path='../data/')
cortex_dataset.log_shift()
cortex_dataset.subsample_genes(558)
cortex_dataset.standardscale()

cortex_dataset.affinity()
NEE = NeuralEE(cortex_dataset, device=device)

results = NEE.EE()  # Elastic embedding results.
results_Neural = NEE.fine_tune()  # NeuralEE results.

# with 'mini-batch' trick
cortex_dataset.affinity_split(N_small=0.25)
NEE = NeuralEE(cortex_dataset, device=device)
results_Neural_with4batches = NEE.fine_tune()

Reproduction. Reference from notebook files.

Examples

HEMATO

BRAIN LARGE