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Update decoding probability threshold #69

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merged 2 commits into from
Jul 21, 2023
Merged

Update decoding probability threshold #69

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411c657
Update decoding prob threshold
elaubsch Jul 20, 2023
ce7d916
Loosen simple test threshold
elaubsch Jul 21, 2023
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6 changes: 3 additions & 3 deletions deepcell_spots/applications/spot_decoding.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,7 +220,7 @@ def _decoding_output_to_dict(self, out):
'prediction', len(decoded_dict['probability'])).astype('U25')
return decoded_dict

def _threshold_unknown_by_prob(self, decoded_dict, unknown_index, pred_prob_thresh=0.5):
def _threshold_unknown_by_prob(self, decoded_dict, unknown_index, pred_prob_thresh=0.95):
"""Threshold the decoded spots to identify unknown. If the highest probability
if below a certain threshold, the spot will be classfied as Unknown.

Expand Down Expand Up @@ -451,7 +451,7 @@ def predict(self,
spots_intensities_vec,
num_iter=500,
batch_size=1000,
pred_prob_thresh=0.5,
pred_prob_thresh=0.95,
rescue_errors=True,
rescue_mixed=False):
"""Predict the gene assignment of each spot.
Expand All @@ -461,7 +461,7 @@ def predict(self,
`[num_spots, (rounds * channels)]`.
num_iter (int): Number of iterations for training. Defaults to 500.
batch_size (int): Size of batches for training. Defaults to 1000.
pred_prob_thresh (float): The threshold of unknown category, within [0,1]. Defaults to 0.5.
pred_prob_thresh (float): The threshold of unknown category, within [0,1]. Defaults to 0.95.
rescue_errors (bool): Whether to check if `'Background'`- and `'Unknown'`-assigned
spots have a Hamming distance of 1 to other barcodes.
rescue_mixed (bool): Whether to check if low probability predictions are the result of
Expand Down
6 changes: 4 additions & 2 deletions deepcell_spots/applications/spot_decoding_test.py
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Original file line number Diff line number Diff line change
Expand Up @@ -76,7 +76,8 @@ def test_spot_decoding_app(self):

spots_intensities_vec21 = np.ones((100, 6))
decoding_dict_trunc21 = app2.predict(
spots_intensities_vec=spots_intensities_vec21, num_iter=20, batch_size=100
spots_intensities_vec=spots_intensities_vec21, num_iter=20, batch_size=100,
pred_prob_thresh=0.5
)
self.assertListEqual(
decoding_dict_trunc21["predicted_id"].tolist(), (2 * np.ones((100,))).tolist()
Expand All @@ -85,7 +86,8 @@ def test_spot_decoding_app(self):

spots_intensities_vec22 = np.zeros((100, 6))
decoding_dict_trunc22 = app2.predict(
spots_intensities_vec=spots_intensities_vec22, num_iter=20, batch_size=100
spots_intensities_vec=spots_intensities_vec22, num_iter=20, batch_size=100,
pred_prob_thresh=0.5
)
self.assertListEqual(
decoding_dict_trunc22["predicted_id"].tolist(), np.ones((100,)).tolist()
Expand Down