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_images/ac350ab8cec2148a69e6fe292cbe1aba7d9d0cc399376204bf2e62ccf2760942.svg index 18283e859..86b3d9d6b 100644 --- a/_images/94d106cf43028aa4c682dab5986e909be971fc4ab7a8cf31a05de096b3a82b39.svg +++ b/_images/ac350ab8cec2148a69e6fe292cbe1aba7d9d0cc399376204bf2e62ccf2760942.svg @@ -39,7 +39,7 @@ Deterministic - + sigma_omega_1->tonic_volatility_1 @@ -67,7 +67,7 @@ Normal - + offset->tonic_volatility_1 diff --git a/_images/b0e1fd0599c4b98b60cde75c3b82c8ab135cfbe721eee2138f87cc883079ba24.png b/_images/b0e1fd0599c4b98b60cde75c3b82c8ab135cfbe721eee2138f87cc883079ba24.png new file mode 100644 index 000000000..07a1b669d Binary files /dev/null and b/_images/b0e1fd0599c4b98b60cde75c3b82c8ab135cfbe721eee2138f87cc883079ba24.png differ diff --git a/_images/b3b9502f80745faed01b51bef10aa8bd5288e59cb521eca58677450d2647a177.png b/_images/b3b9502f80745faed01b51bef10aa8bd5288e59cb521eca58677450d2647a177.png deleted file mode 100644 index eaaae1a99..000000000 Binary files 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a/_images/dcf085bed0d59b03e8fef7d1d788fdbcd892ca4519b4bacd1b2249761f3fedf2.png and /dev/null differ diff --git a/_images/06729f219d3f33ccbc8b2dd4e49a048c09bdf5685aa8a1a16f34809168939c04.svg b/_images/df35072d69fc3bd493aa02bf23ff71d25154b293fa99ddeb73067febd690270e.svg similarity index 100% rename from _images/06729f219d3f33ccbc8b2dd4e49a048c09bdf5685aa8a1a16f34809168939c04.svg rename to _images/df35072d69fc3bd493aa02bf23ff71d25154b293fa99ddeb73067febd690270e.svg index 724fe4fab..9abe2afd0 100644 --- a/_images/06729f219d3f33ccbc8b2dd4e49a048c09bdf5685aa8a1a16f34809168939c04.svg +++ b/_images/df35072d69fc3bd493aa02bf23ff71d25154b293fa99ddeb73067febd690270e.svg @@ -31,7 +31,7 @@ HalfCauchy - + tonic_volatility_2 tonic_volatility_2 @@ -39,7 +39,7 @@ Deterministic - + sigma_omega_1->tonic_volatility_2 @@ -58,8 +58,14 @@ + + +tonic_volatility_2->hgf_loglike + + + - + offset offset @@ -67,16 +73,10 @@ Normal - + offset->tonic_volatility_2 - - -tonic_volatility_2->hgf_loglike - - - \ No newline at end of file diff --git a/_images/e223b6bf3430df37657e7febee959fdb0e801fbe47164c3f02c41779f87781ad.png b/_images/e223b6bf3430df37657e7febee959fdb0e801fbe47164c3f02c41779f87781ad.png deleted file mode 100644 index 41a780322..000000000 Binary files a/_images/e223b6bf3430df37657e7febee959fdb0e801fbe47164c3f02c41779f87781ad.png and /dev/null differ diff --git a/_images/e42eea0f4c2e5b77363ebdd3b45d209b62ba670a547992f6679ec567d1d13b75.png b/_images/e42eea0f4c2e5b77363ebdd3b45d209b62ba670a547992f6679ec567d1d13b75.png new file mode 100644 index 000000000..a26201441 Binary files /dev/null and b/_images/e42eea0f4c2e5b77363ebdd3b45d209b62ba670a547992f6679ec567d1d13b75.png differ diff --git a/_images/e877cc55de333c0e47af8a2b861ad7d232a8dcd89195b40b7b0409dac3137170.png b/_images/e877cc55de333c0e47af8a2b861ad7d232a8dcd89195b40b7b0409dac3137170.png new file mode 100644 index 000000000..0bcbfe7b9 Binary files /dev/null and b/_images/e877cc55de333c0e47af8a2b861ad7d232a8dcd89195b40b7b0409dac3137170.png differ diff --git a/_images/f2b6ffa660aabfdcb6d4550c222828461858612755f7ed670decae347978fbd1.png b/_images/f2b6ffa660aabfdcb6d4550c222828461858612755f7ed670decae347978fbd1.png deleted file mode 100644 index b178be392..000000000 Binary files a/_images/f2b6ffa660aabfdcb6d4550c222828461858612755f7ed670decae347978fbd1.png and /dev/null differ diff --git a/_images/fe28083e61fb97dea33fbf410b739726e49505adc726ed51b1963eb845d30aca.png b/_images/fe28083e61fb97dea33fbf410b739726e49505adc726ed51b1963eb845d30aca.png deleted file mode 100644 index 978d94555..000000000 Binary files a/_images/fe28083e61fb97dea33fbf410b739726e49505adc726ed51b1963eb845d30aca.png and /dev/null differ diff --git a/notebooks/0-Creating_networks.html b/notebooks/0-Creating_networks.html index e493f1c38..ff9eb18f5 100644 --- a/notebooks/0-Creating_networks.html +++ b/notebooks/0-Creating_networks.html @@ -537,7 +537,7 @@

Visualizing probabilistic networks 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264009.057993    2370 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265219.042307    2576 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -707,7 +707,7 @@
Continuous value coupling
Adding 1000 new observations.
-../_images/ce99d6c0c9c8e9e4a1eef221f92fecbe42e7e4e0148399cf3bc134064429750c.png +../_images/094386cffe2218c8214ada7a9e75544064c17ed88afca13a4844cfc2d015544a.png
@@ -867,7 +867,7 @@
Coupling with binary nodes
Adding 1000 new observations.
-
<pyhgf.model.HGF at 0x7f5c4c9fa470>
+
<pyhgf.model.HGF at 0x7f280cff0be0>
@@ -987,10 +987,10 @@

System configuration

diff --git a/notebooks/0-Theory.html b/notebooks/0-Theory.html index b4483d0a6..2bffdf0fe 100644 --- a/notebooks/0-Theory.html +++ b/notebooks/0-Theory.html @@ -849,9 +849,9 @@

System configuration diff --git a/notebooks/1.1-Binary_HGF.html b/notebooks/1.1-Binary_HGF.html index b39a1261d..c94ee6b40 100644 --- a/notebooks/1.1-Binary_HGF.html +++ b/notebooks/1.1-Binary_HGF.html @@ -533,7 +533,7 @@

Create the model 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264026.802958    2511 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265237.561342    2718 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -810,7 +810,7 @@

Sampling
-../_images/5f0759e2451c9b006ce39fe17490ac1866c479dd4f7178123fe2529423a92337.png +../_images/a69fd1280f11909a39413d1e8c792559c044bd96c39ce669d4183afbcdbd57ef.png
@@ -844,9 +844,7 @@

Using the learned parameters
Creating a binary Hierarchical Gaussian Filter with 2 levels.
 ... Create the update sequence from the network structure.
 ... Create the belief propagation function.
-
- -
... Cache the belief propagation function.
+... Cache the belief propagation function.
 Adding 320 new observations.
@@ -859,7 +857,7 @@

Using the learned parameters -../_images/c012dc6d95b985a042735a6e81a2b0f913e2729d1fc0c3cee1d1bbb3c22fbc64.png +../_images/75e4ff6b6e9240e9bc825ac11372fde3c73c8ff58ee9cc1da51eb9d8306d2a57.png
@@ -869,7 +867,7 @@

Using the learned parameters -
Array(202.53232, dtype=float32)
+
Array(202.52957, dtype=float32)
@@ -921,7 +919,7 @@

Visualizing the model -../_images/906f003ac3c62510821da40b51513f921c716a616f423184ce543353e719929c.svg

+../_images/69539e2739458d7218e514133841304a4e4b0eb711fc8054497123f2e226d095.svg

@@ -967,7 +965,7 @@

Sampling# 100.00% [4000/4000 00:07<00:00 Sampling 2 chains, 0 divergences] - 
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 7 seconds.
+    
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 8 seconds.
 
We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -983,7 +981,7 @@ 
Sampling#
-../_images/2f7d40fbcdf66311f0ed282504eade02f34a37d319fc30cc14ef3da776a1f5f9.png +../_images/40561baa083b9ed00cba27e0c3f44db086f7fb9091463ed17a1cb3ee612e9e5d.png

@@ -1033,7 +1031,7 @@

Using the learned parameters -../_images/524e3ff76e4520cebbd0b25fc39c7025427dad28ba0b35a4f360d06dde07aa62.png +../_images/be2b1a2bd2e29ca834887c4a37ca696c365c24180cfb5540bfc7d10829b6166d.png
@@ -1043,7 +1041,7 @@

Using the learned parameters -
Array(203.0082, dtype=float32)
+
Array(203.01764, dtype=float32)
@@ -1071,12 +1069,12 @@

System configuration

diff --git a/notebooks/1.2-Categorical_HGF.html b/notebooks/1.2-Categorical_HGF.html index e2a20ba09..4a9c0e6d3 100644 --- a/notebooks/1.2-Categorical_HGF.html +++ b/notebooks/1.2-Categorical_HGF.html @@ -528,7 +528,7 @@

Simulating a dataset

-../_images/b3b9502f80745faed01b51bef10aa8bd5288e59cb521eca58677450d2647a177.png +../_images/8f1c2ff9f9eb29dd3987a1dc5e572fd1fcd4d65147161caa3be3bfbe9b78b6cf.png
@@ -569,7 +569,7 @@

Creating the probabilistic network 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264005.413104    2285 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265215.594381    2490 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -652,7 +652,7 @@

Fitting the model forwards -../_images/02284604406188eb3ab5adebfeeda92d8c48d6635ba2d08602259da3f85f3869.png +../_images/16e0b24278efea6cc2f3debb5a145d3c853ff999e6d2861c9810bf0d14290e23.png

@@ -806,14 +806,14 @@

System configuration diff --git a/notebooks/1.3-Continuous_HGF.html b/notebooks/1.3-Continuous_HGF.html index 0a8e83758..04caaf3ad 100644 --- a/notebooks/1.3-Continuous_HGF.html +++ b/notebooks/1.3-Continuous_HGF.html @@ -528,7 +528,7 @@

Create the model 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264043.461034    2676 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265254.622774    2894 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -857,9 +857,9 @@

Sampling
- 100.00% [4000/4000 00:05<00:00 Sampling 2 chains, 0 divergences] + 100.00% [4000/4000 00:06<00:00 Sampling 2 chains, 0 divergences]
- 
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 6 seconds.
+    
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 7 seconds.
 
We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -875,7 +875,7 @@ 
Sampling
-../_images/8527681dc9855435657d55e7d246a4454505171fe47f19796828efffdf336701.png +../_images/d872334795e2a94d68553933385e0b4e47e32aaa95a32bdceaf67ba77ed5cc60.png
@@ -921,7 +921,7 @@

Using the learned parameters -../_images/154b1bd785db9c306be142e3301731fb1346f37d49398afb8e614d5cc90cc43a.png +../_images/3b55fc7355a470b3bd8689f96b25d7208bd92d6fe1ce2170bf7cab52a8b03d3a.png
@@ -931,7 +931,7 @@

Using the learned parameters -
Array(-1106.0878, dtype=float32)
+
Array(-1106.104, dtype=float32)
@@ -1027,7 +1027,7 @@

Sampling# 100.00% [4000/4000 00:07<00:00 Sampling 2 chains, 0 divergences]

- 

Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 8 seconds.
+    
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 7 seconds.
 
We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -1043,7 +1043,7 @@ 
Sampling#
-../_images/01867fda7b3f26749465f9993a7de7b480108ef31d6d9abeccc7a2bb67f66d5f.png +../_images/43b29dcf08f656264b7c90b6975a1aaa39c8d202c6c8eddd382125f61e53ba0e.png
@@ -1088,7 +1088,7 @@

Using the learned parameters -../_images/55a73da7851caa2796c317b4a010bfcc93eb8b49eff87912435658e042338733.png +../_images/01d2c3719383c671bad900328a81868d7e43328d91e089c0da7faa8ec67d53f1.png
@@ -1098,7 +1098,7 @@

Using the learned parameters -
Array(-1118.0107, dtype=float32)
+
Array(-1118.0353, dtype=float32)
@@ -1126,12 +1126,12 @@

System configuration

diff --git a/notebooks/2-Using_custom_response_functions.html b/notebooks/2-Using_custom_response_functions.html index 9c11448a6..b89ae4e75 100644 --- a/notebooks/2-Using_custom_response_functions.html +++ b/notebooks/2-Using_custom_response_functions.html @@ -521,7 +521,7 @@

Creating a new response function: the binary surprise 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264081.947060    2959 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265294.043813    3178 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -914,19 +914,19 @@

Recovering HGF parameters from the observed behaviors tonic_volatility_2 - -3.969 - 0.503 - -4.858 - -2.994 - 0.013 + -3.948 + 0.506 + -4.902 + -2.992 + 0.012 0.009 - 1604.0 - 2514.0 + 1775.0 + 2261.0 1.0 -

../_images/f2b6ffa660aabfdcb6d4550c222828461858612755f7ed670decae347978fbd1.png +../_images/6dfb6db5a6d5c58ae336e302a0953ff46f0e2aba5503cad429de64df252638b4.png

The results above indicate that given the responses provided by the participant, the most likely values for the parameter \(\omega_2\) are between -4.9 and -3.1, with a mean at -3.9 (you can find slightly different values if you sample different actions from the decisions function). We can consider this as an excellent estimate given the sparsity of the data, and the complexity of the model.

@@ -964,12 +964,12 @@

System configuration diff --git a/notebooks/3-Multilevel_HGF.html b/notebooks/3-Multilevel_HGF.html index e3a18653f..8f52bfa7a 100644 --- a/notebooks/3-Multilevel_HGF.html +++ b/notebooks/3-Multilevel_HGF.html @@ -620,7 +620,7 @@

Model#<
-../_images/94d106cf43028aa4c682dab5986e909be971fc4ab7a8cf31a05de096b3a82b39.svg
+../_images/ac350ab8cec2148a69e6fe292cbe1aba7d9d0cc399376204bf2e62ccf2760942.svg
@@ -637,7 +637,7 @@

Model#< 

WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264109.249919    3083 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265321.686167    3301 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -666,9 +666,9 @@

Model#<
- 100.00% [2000/2000 00:47<00:00 Sampling chain 0, 1 divergences] + 100.00% [2000/2000 00:49<00:00 Sampling chain 0, 10 divergences]
- 
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 48 seconds.
+    
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 49 seconds.
 
Only one chain was sampled, this makes it impossible to run some convergence checks
@@ -684,7 +684,7 @@ 
Model#<
-../_images/fe28083e61fb97dea33fbf410b739726e49505adc726ed51b1963eb845d30aca.png +../_images/7c8ad6cbee1038bd7df9c37e52cb222cdb9df67fb0fec03e93f03ba179e47860.png

As expected, the highest density aroud the group-level mean estimate inlcude 10.0, the real value.

@@ -765,7 +765,7 @@

Visualizing the model
-../_images/06729f219d3f33ccbc8b2dd4e49a048c09bdf5685aa8a1a16f34809168939c04.svg
+../_images/df35072d69fc3bd493aa02bf23ff71d25154b293fa99ddeb73067febd690270e.svg
@@ -809,9 +809,9 @@

Sampling
- 100.00% [2000/2000 00:15<00:00 Sampling chain 0, 79 divergences] + 100.00% [2000/2000 00:18<00:00 Sampling chain 0, 35 divergences]
- 
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 16 seconds.
+    
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 19 seconds.
 
Only one chain was sampled, this makes it impossible to run some convergence checks
@@ -827,7 +827,7 @@ 
Sampling
-../_images/6d34abc6f3a5e978f43757238380ae98bf6d217c5ba22be6a18dafbaecdd4454.png +../_images/b0e1fd0599c4b98b60cde75c3b82c8ab135cfbe721eee2138f87cc883079ba24.png

@@ -854,12 +854,12 @@

System configuration diff --git a/notebooks/4-Parameter_recovery.html b/notebooks/4-Parameter_recovery.html index b8bf6a07b..b68d469b2 100644 --- a/notebooks/4-Parameter_recovery.html +++ b/notebooks/4-Parameter_recovery.html @@ -594,7 +594,7 @@

Embedding a serie of HGFs in a graphical model
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1701264191.916028    3327 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1701265409.360767    3536 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
 No GPU/TPU found, falling back to CPU. (Set TF_CPP_MIN_LOG_LEVEL=0 and rerun for more info.)
@@ -641,7 +641,7 @@

Embedding a serie of HGFs in a graphical model -../_images/03c16dc372238ea8a364eeb232c084291178136b760ec6de892a461bc13f9f3f.png +../_images/e877cc55de333c0e47af8a2b861ad7d232a8dcd89195b40b7b0409dac3137170.png
@@ -683,74 +683,74 @@

Embedding a serie of HGFs in a graphical model

diff --git a/notebooks/Example_1_Heart_rate_variability.html b/notebooks/Example_1_Heart_rate_variability.html index 3d1b5fce1..c89688f0b 100644 --- a/notebooks/Example_1_Heart_rate_variability.html +++ b/notebooks/Example_1_Heart_rate_variability.html @@ -815,16 +815,16 @@

Loading and preprocessing physiological recording
Downloading ECG channel:   0%|          | 0/2 [00:00<?, ?it/s]
-
Downloading ECG channel:  50%|█████     | 1/2 [00:00<00:00,  2.00it/s]
+
Downloading ECG channel:  50%|█████     | 1/2 [00:01<00:01,  1.33s/it]
 

 

-
Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  2.00it/s]
+
Downloading Respiration channel:  50%|█████     | 1/2 [00:01<00:01,  1.33s/it]
 

 

-
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  2.07it/s]
+
Downloading Respiration channel: 100%|██████████| 2/2 [00:02<00:00,  1.46s/it]
 

 

-
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  2.06it/s]
+
Downloading Respiration channel: 100%|██████████| 2/2 [00:02<00:00,  1.44s/it]
 

 

 

@@ -849,12 +849,12 @@ 
Plot the signal with instantaneous heart rate derivations

+