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Aditya - Reproduction Info Updated #145

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Jan 20, 2023
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Aditya - Reproduction Info Updated #145

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8 changes: 4 additions & 4 deletions examples/single_modality/clustering/graphsc.py
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Expand Up @@ -76,14 +76,14 @@ def pipeline(**args):
pipeline(**vars(args))
""" Reproduction information
10X PBMC:
python graphsc.py --dataset='10X_PBMC'
python graphsc.py --dataset 10X_PBMC

Mouse ES:
python graphsc.py --dataset='mouse_ES_cell'
python graphsc.py --dataset mouse_ES_cell

Worm Neuron:
python graphsc.py --dataset='worm_neuron_cell'
python graphsc.py --dataset worm_neuron_cell

Mouse Bladder:
python graphsc.py --dataset='mouse_bladder_cell'
python graphsc.py --dataset mouse_bladder_cell
"""
8 changes: 4 additions & 4 deletions examples/single_modality/clustering/scdcc.py
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Expand Up @@ -115,14 +115,14 @@
np.savetxt(args.label_cells_files, label_cell_indx, fmt="%i")
""" Reproduction information
10X PBMC:
python scdcc.py --data_file='10X_PBMC' --label_cells_files='label_10X_PBMC.txt' --gamma=1.5
python scdcc.py --data_file 10X_PBMC --label_cells_files label_10X_PBMC.txt --gamma=1.5

Mouse ES:
python scdcc.py --data_file='mouse_ES_cell' --label_cells_files='label_mouse_ES_cell.txt' --gamma=1 --ml_weight=0.8 --cl_weight=0.8
python scdcc.py --data_file mouse_ES_cell --label_cells_files label_mouse_ES_cell.txt --gamma 1 --ml_weight 0.8 --cl_weight 0.8

Worm Neuron:
python scdcc.py --data_file='worm_neuron_cell' --label_cells_files='label_worm_neuron_cell.txt' --gamma=1 --pretrain_epochs=300
python scdcc.py --data_file worm_neuron_cell --label_cells_files label_worm_neuron_cell.txt --gamma 1 --pretrain_epochs 300

Mouse Bladder:
python scdcc.py --data_file='mouse_bladder_cell' --label_cells_files='label_mouse_bladder_cell.txt' --gamma=1.5 --pretrain_epochs=100 --sigma=3
python scdcc.py --data_file mouse_bladder_cell --label_cells_files label_mouse_bladder_cell.txt --gamma 1.5 --pretrain_epochs 100 --sigma 3
"""
8 changes: 4 additions & 4 deletions examples/single_modality/clustering/scdeepcluster.py
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Expand Up @@ -96,14 +96,14 @@
print("ACC: {:.4f}, NMI: {:.4f}, ARI: {:.4f}".format(acc, nmi, ari))
""" Reproduction information
10X PBMC:
python scdeepcluster.py --data_file='10X_PBMC'
python scdeepcluster.py --data_file 10X_PBMC

Mouse ES:
python scdeepcluster.py --data_file='mouse_ES_cell'
python scdeepcluster.py --data_file mouse_ES_cell

Worm Neuron:
python scdeepcluster.py --data_file='worm_neuron_cell' --pretrain_epochs 300
python scdeepcluster.py --data_file worm_neuron_cell --pretrain_epochs 300

Mouse Bladder:
python scdeepcluster.py --data_file='mouse_bladder_cell' --pretrain_epochs 300 --sigma=2.75
python scdeepcluster.py --data_file mouse_bladder_cell --pretrain_epochs 300 --sigma 2.75
"""
8 changes: 4 additions & 4 deletions examples/single_modality/clustering/scdsc.py
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Expand Up @@ -108,14 +108,14 @@
print("ACC: {:.4f}, NMI: {:.4f}, ARI: {:.4f}".format(acc, nmi, ari))
"""Reproduction information
10X PBMC:
python scdsc.py --name='10X_PBMC' --method='cos' --topk=30 --v=7 --binary_crossentropy_loss=0.75 --ce_loss=0.5 --re_loss=0.1 --zinb_loss=2.5 --sigma=0.4
python scdsc.py --name 10X_PBMC --method cos --topk 30 --v 7 --binary_crossentropy_loss 0.75 --ce_loss 0.5 --re_loss 0.1 --zinb_loss 2.5 --sigma 0.4

Mouse Bladder:
python scdsc.py --name='mouse_bladder_cell' --method='p' --topk=50 --v=7 --binary_crossentropy_loss=2.5 --ce_loss=0.1 --re_loss=0.5 --zinb_loss=1.5 --sigma=0.6
python scdsc.py --name mouse_bladder_cell --method p --topk 50 --v 7 --binary_crossentropy_loss 2.5 --ce_loss 0.1 --re_loss 0.5 --zinb_loss 1.5 --sigma 0.6

Mouse ES:
python scdsc.py --name='mouse_ES_cell' --method='heat' --topk=50 --v=7 --binary_crossentropy_loss=0.1 --ce_loss=0.01 --re_loss=1.5 --zinb_loss=0.5 --sigma=0.1
python scdsc.py --name mouse_ES_cell --method heat --topk 50 --v 7 --binary_crossentropy_loss 0.1 --ce_loss 0.01 --re_loss 1.5 --zinb_loss 0.5 --sigma 0.1

Worm Neuron:
python scdsc.py --name='worm_neuron_cell' --method='p' --topk=20 --v=7 --binary_crossentropy_loss=2 --ce_loss=2 --re_loss=3 --zinb_loss=0.1 --sigma=0.4
python scdsc.py --name worm_neuron_cell --method p --topk 20 --v 7 --binary_crossentropy_loss 2 --ce_loss 2 --re_loss 3 --zinb_loss 0.1 --sigma 0.4
"""
8 changes: 4 additions & 4 deletions examples/single_modality/clustering/sctag.py
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Expand Up @@ -91,14 +91,14 @@
print(args)
"""Reproduction information
10X PBMC:
python sctag.py --pretrain_epochs 100 --data_file='10X_PBMC' --W_a=0.01 --W_x=3 --W_c=0.1 --dropout=0.5
python sctag.py --pretrain_epochs 100 --data_file 10X_PBMC --W_a 0.01 --W_x 3 --W_c 0.1 --dropout 0.5

Mouse ES:
python sctag.py --pretrain_epochs 100 --data_file='mouse_ES_cell' --W_a=0.01 --W_x=0.75 --W_c=1
python sctag.py --pretrain_epochs 100 --data_file mouse_ES_cell --W_a 0.01 --W_x 0.75 --W_c 1

Worm Neuron:
python sctag.py --data_file='worm_neuron_cell' --W_a=0.01 --W_x=2 --W_c=0.25 --k=1
python sctag.py --data_file worm_neuron_cell --W_a 0.01 --W_x 2 --W_c 0.25 --k 1

Mouse Bladder:
python sctag.py --pretrain_epochs 100 --data_file='mouse_bladder_cell' --W_a=0.1 --W_x=2.5 --W_c=3
python sctag.py --pretrain_epochs 100 --data_file mouse_bladder_cell --W_a 0.1 --W_x 2.5 --W_c 3
"""