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curation_machine_learning_models

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1

Remove `analyzer_0` from json

#1
by chrishalcrow - opened
base: refs/heads/main
←
from: refs/pr/1
Discussion Files changed
+169
-171
Files changed (1) hide show
  1. model_info.json +169 -171
model_info.json CHANGED
@@ -1,172 +1,170 @@
1
- {
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- "metric_params": {
3
- "analyzer_0": {
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- "quality_metric_params": {
5
- "metric_names": [
6
- "amplitude_cutoff",
7
- "amplitude_cv",
8
- "amplitude_median",
9
- "d_prime",
10
- "drift",
11
- "firing_range",
12
- "firing_rate",
13
- "isi_violation",
14
- "isolation_distance",
15
- "l_ratio",
16
- "nearest_neighbor",
17
- "num_spikes",
18
- "presence_ratio",
19
- "rp_violation",
20
- "sd_ratio",
21
- "silhouette",
22
- "sliding_rp_violation",
23
- "snr",
24
- "synchrony"
25
- ],
26
- "peak_sign": null,
27
- "seed": null,
28
- "qm_params": {
29
- "presence_ratio": {
30
- "bin_duration_s": 60,
31
- "mean_fr_ratio_thresh": 0.0
32
- },
33
- "snr": {
34
- "peak_sign": "neg",
35
- "peak_mode": "extremum"
36
- },
37
- "isi_violation": {
38
- "isi_threshold_ms": 1.5,
39
- "min_isi_ms": 0
40
- },
41
- "rp_violation": {
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- "refractory_period_ms": 1.0,
43
- "censored_period_ms": 0.0
44
- },
45
- "sliding_rp_violation": {
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- "min_spikes": 0,
47
- "bin_size_ms": 0.25,
48
- "window_size_s": 1,
49
- "exclude_ref_period_below_ms": 0.5,
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- "max_ref_period_ms": 10,
51
- "contamination_values": null
52
- },
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- "synchrony": {
54
- "synchrony_sizes": [
55
- 2,
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- 4,
57
- 8
58
- ]
59
- },
60
- "firing_range": {
61
- "bin_size_s": 5,
62
- "percentiles": [
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- 5,
64
- 95
65
- ]
66
- },
67
- "amplitude_cv": {
68
- "average_num_spikes_per_bin": 50,
69
- "percentiles": [
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- 5,
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- 95
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- ],
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- "min_num_bins": 10,
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- "amplitude_extension": "spike_amplitudes"
75
- },
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- "amplitude_cutoff": {
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- "peak_sign": "neg",
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- "num_histogram_bins": 100,
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- "histogram_smoothing_value": 3,
80
- "amplitudes_bins_min_ratio": 5
81
- },
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- "amplitude_median": {
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- "peak_sign": "neg"
84
- },
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- "drift": {
86
- "interval_s": 60,
87
- "min_spikes_per_interval": 100,
88
- "direction": "y",
89
- "min_num_bins": 2
90
- },
91
- "nearest_neighbor": {
92
- "max_spikes": 10000,
93
- "n_neighbors": 5
94
- },
95
- "nn_isolation": {
96
- "max_spikes": 10000,
97
- "min_spikes": 10,
98
- "min_fr": 0.0,
99
- "n_neighbors": 4,
100
- "n_components": 10,
101
- "radius_um": 100,
102
- "peak_sign": "neg"
103
- },
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- "nn_noise_overlap": {
105
- "max_spikes": 10000,
106
- "min_spikes": 10,
107
- "min_fr": 0.0,
108
- "n_neighbors": 4,
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- "n_components": 10,
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- "radius_um": 100,
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- "peak_sign": "neg"
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- },
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- "silhouette": {
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- "method": [
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- "simplified"
116
- ]
117
- }
118
- },
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- "skip_pc_metrics": false
120
- },
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- "template_metric_params": {
122
- "metric_names": [
123
- "half_width",
124
- "num_negative_peaks",
125
- "num_positive_peaks",
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- "peak_to_valley",
127
- "peak_trough_ratio",
128
- "recovery_slope",
129
- "repolarization_slope"
130
- ],
131
- "sparsity": null,
132
- "peak_sign": "neg",
133
- "upsampling_factor": 10,
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- "metrics_kwargs": {
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- "recovery_window_ms": 0.7,
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- "peak_relative_threshold": 0.2,
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- "peak_width_ms": 0.1,
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- "depth_direction": "y",
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- "min_channels_for_velocity": 5,
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- "min_r2_velocity": 0.5,
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- "exp_peak_function": "ptp",
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- "min_r2_exp_decay": 0.5,
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- "spread_threshold": 0.2,
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- "spread_smooth_um": 20,
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- "column_range": null
146
- }
147
- }
148
- }
149
- },
150
- "requirements": {
151
- "spikeinterface": "0.100.1",
152
- "scikit-learn": "1.3.2"
153
- },
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- "label_conversion": {
155
- "1": "noise",
156
- "2": "mua",
157
- "3": "sua"
158
- },
159
- "additional_required_files": {
160
- "filename": "cascaded_classifier.py"
161
- },
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- "untrusted_types_imports": {
163
- "untrusted_types": [
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- "numpy.dtype",
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- "sklearn.metrics._classification.balanced_accuracy_score",
166
- "sklearn.metrics._scorer._PredictScorer",
167
- "sklearn.model_selection._search_successive_halving.HalvingGridSearchCV",
168
- "sklearn.model_selection._split.StratifiedKFold",
169
- "__main__.CascadedClassifier"
170
- ]
171
- }
172
  }
 
1
+ {
2
+ "metric_params": {
3
+ "quality_metric_params": {
4
+ "metric_names": [
5
+ "amplitude_cutoff",
6
+ "amplitude_cv",
7
+ "amplitude_median",
8
+ "d_prime",
9
+ "drift",
10
+ "firing_range",
11
+ "firing_rate",
12
+ "isi_violation",
13
+ "isolation_distance",
14
+ "l_ratio",
15
+ "nearest_neighbor",
16
+ "num_spikes",
17
+ "presence_ratio",
18
+ "rp_violation",
19
+ "sd_ratio",
20
+ "silhouette",
21
+ "sliding_rp_violation",
22
+ "snr",
23
+ "synchrony"
24
+ ],
25
+ "peak_sign": null,
26
+ "seed": null,
27
+ "qm_params": {
28
+ "presence_ratio": {
29
+ "bin_duration_s": 60,
30
+ "mean_fr_ratio_thresh": 0.0
31
+ },
32
+ "snr": {
33
+ "peak_sign": "neg",
34
+ "peak_mode": "extremum"
35
+ },
36
+ "isi_violation": {
37
+ "isi_threshold_ms": 1.5,
38
+ "min_isi_ms": 0
39
+ },
40
+ "rp_violation": {
41
+ "refractory_period_ms": 1.0,
42
+ "censored_period_ms": 0.0
43
+ },
44
+ "sliding_rp_violation": {
45
+ "min_spikes": 0,
46
+ "bin_size_ms": 0.25,
47
+ "window_size_s": 1,
48
+ "exclude_ref_period_below_ms": 0.5,
49
+ "max_ref_period_ms": 10,
50
+ "contamination_values": null
51
+ },
52
+ "synchrony": {
53
+ "synchrony_sizes": [
54
+ 2,
55
+ 4,
56
+ 8
57
+ ]
58
+ },
59
+ "firing_range": {
60
+ "bin_size_s": 5,
61
+ "percentiles": [
62
+ 5,
63
+ 95
64
+ ]
65
+ },
66
+ "amplitude_cv": {
67
+ "average_num_spikes_per_bin": 50,
68
+ "percentiles": [
69
+ 5,
70
+ 95
71
+ ],
72
+ "min_num_bins": 10,
73
+ "amplitude_extension": "spike_amplitudes"
74
+ },
75
+ "amplitude_cutoff": {
76
+ "peak_sign": "neg",
77
+ "num_histogram_bins": 100,
78
+ "histogram_smoothing_value": 3,
79
+ "amplitudes_bins_min_ratio": 5
80
+ },
81
+ "amplitude_median": {
82
+ "peak_sign": "neg"
83
+ },
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+ "drift": {
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+ "interval_s": 60,
86
+ "min_spikes_per_interval": 100,
87
+ "direction": "y",
88
+ "min_num_bins": 2
89
+ },
90
+ "nearest_neighbor": {
91
+ "max_spikes": 10000,
92
+ "n_neighbors": 5
93
+ },
94
+ "nn_isolation": {
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+ "max_spikes": 10000,
96
+ "min_spikes": 10,
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+ "min_fr": 0.0,
98
+ "n_neighbors": 4,
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+ "n_components": 10,
100
+ "radius_um": 100,
101
+ "peak_sign": "neg"
102
+ },
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+ "nn_noise_overlap": {
104
+ "max_spikes": 10000,
105
+ "min_spikes": 10,
106
+ "min_fr": 0.0,
107
+ "n_neighbors": 4,
108
+ "n_components": 10,
109
+ "radius_um": 100,
110
+ "peak_sign": "neg"
111
+ },
112
+ "silhouette": {
113
+ "method": [
114
+ "simplified"
115
+ ]
116
+ }
117
+ },
118
+ "skip_pc_metrics": false
119
+ },
120
+ "template_metric_params": {
121
+ "metric_names": [
122
+ "half_width",
123
+ "num_negative_peaks",
124
+ "num_positive_peaks",
125
+ "peak_to_valley",
126
+ "peak_trough_ratio",
127
+ "recovery_slope",
128
+ "repolarization_slope"
129
+ ],
130
+ "sparsity": null,
131
+ "peak_sign": "neg",
132
+ "upsampling_factor": 10,
133
+ "metrics_kwargs": {
134
+ "recovery_window_ms": 0.7,
135
+ "peak_relative_threshold": 0.2,
136
+ "peak_width_ms": 0.1,
137
+ "depth_direction": "y",
138
+ "min_channels_for_velocity": 5,
139
+ "min_r2_velocity": 0.5,
140
+ "exp_peak_function": "ptp",
141
+ "min_r2_exp_decay": 0.5,
142
+ "spread_threshold": 0.2,
143
+ "spread_smooth_um": 20,
144
+ "column_range": null
145
+ }
146
+ }
147
+ },
148
+ "requirements": {
149
+ "spikeinterface": "0.100.1",
150
+ "scikit-learn": "1.3.2"
151
+ },
152
+ "label_conversion": {
153
+ "1": "noise",
154
+ "2": "mua",
155
+ "3": "sua"
156
+ },
157
+ "additional_required_files": {
158
+ "filename": "cascaded_classifier.py"
159
+ },
160
+ "untrusted_types_imports": {
161
+ "untrusted_types": [
162
+ "numpy.dtype",
163
+ "sklearn.metrics._classification.balanced_accuracy_score",
164
+ "sklearn.metrics._scorer._PredictScorer",
165
+ "sklearn.model_selection._search_successive_halving.HalvingGridSearchCV",
166
+ "sklearn.model_selection._split.StratifiedKFold",
167
+ "__main__.CascadedClassifier"
168
+ ]
169
+ }
 
 
170
  }