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b/_images/84d827c4b953344e32ac2f584488eef8a32126d47272d67c80ca21b298c9ebef.svg @@ -9,22 +9,22 @@ %3 - - -tonic_volatility_1 - -tonic_volatility_1 -~ -Uniform - - + hgf_loglike hgf_loglike ~ Potential + + +tonic_volatility_1 + +tonic_volatility_1 +~ +Uniform + tonic_volatility_1->hgf_loglike diff --git a/_images/84f22506a5fa9694a204cfbbfac4c8b359574b48970a401d97e9951259c274b6.png b/_images/84f22506a5fa9694a204cfbbfac4c8b359574b48970a401d97e9951259c274b6.png new file mode 100644 index 000000000..5c836a198 Binary files /dev/null and b/_images/84f22506a5fa9694a204cfbbfac4c8b359574b48970a401d97e9951259c274b6.png differ diff --git a/_images/90d8f4318d65b623884932bd7275e93b57903c65e79612140e1db15d1239e66f.png b/_images/90d8f4318d65b623884932bd7275e93b57903c65e79612140e1db15d1239e66f.png new file mode 100644 index 000000000..9f29fd02d Binary files /dev/null and b/_images/90d8f4318d65b623884932bd7275e93b57903c65e79612140e1db15d1239e66f.png differ diff --git a/_images/92e7aaa45b43d4dfe5c4a2b4b175c521a401908a0b07a161a64dca2e383de0f8.svg b/_images/92e7aaa45b43d4dfe5c4a2b4b175c521a401908a0b07a161a64dca2e383de0f8.svg new file mode 100644 index 000000000..5645dc81f --- /dev/null +++ b/_images/92e7aaa45b43d4dfe5c4a2b4b175c521a401908a0b07a161a64dca2e383de0f8.svg @@ -0,0 +1,82 @@ + + + + + + +%3 + + +cluster8 + +8 + + + +hgf_loglike + +hgf_loglike +~ +Potential + + + +mu_omega_1 + +mu_omega_1 +~ +Normal + + + +tonic_volatility_1 + +tonic_volatility_1 +~ +Deterministic + + + +mu_omega_1->tonic_volatility_1 + + + + + +sigma_omega_1 + +sigma_omega_1 +~ +HalfCauchy + + + +sigma_omega_1->tonic_volatility_1 + + + + + +offset + +offset +~ +Normal + + + +offset->tonic_volatility_1 + + + + + +tonic_volatility_1->hgf_loglike + + + + + \ No newline at end of file diff --git a/_images/94a332ebeeb2f2432f930318383d56656f284b6427f989281ee398e1b5e750d2.png b/_images/94a332ebeeb2f2432f930318383d56656f284b6427f989281ee398e1b5e750d2.png new file mode 100644 index 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index c06f690b4..000000000 Binary files a/_images/a041d03e217f1accf199119a0f823858acae52300789d4f4021430c91cc96c90.png and /dev/null differ diff --git a/_images/a128e5fa7e2f81bdbc21ffb001e7bc370b649bde5991126f17e98fd2b8461fee.svg b/_images/a128e5fa7e2f81bdbc21ffb001e7bc370b649bde5991126f17e98fd2b8461fee.svg deleted file mode 100644 index d1df0e623..000000000 --- a/_images/a128e5fa7e2f81bdbc21ffb001e7bc370b649bde5991126f17e98fd2b8461fee.svg +++ /dev/null @@ -1,82 +0,0 @@ - - - - - - -%3 - - -cluster5 - -5 - - - -sigma_omega_1 - -sigma_omega_1 -~ -HalfCauchy - - - -tonic_volatility_2 - -tonic_volatility_2 -~ -Deterministic - - - -sigma_omega_1->tonic_volatility_2 - - - - - -hgf_loglike - -hgf_loglike -~ -Potential - - - -mu_omega_1 - -mu_omega_1 -~ -Uniform - - - -mu_omega_1->tonic_volatility_2 - - - - - -offset - -offset -~ -Normal - - - -offset->tonic_volatility_2 - - - - - -tonic_volatility_2->hgf_loglike - - - - - \ No newline at end of file diff --git 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a/_images/f6a5cfa521a4fb6e1ba07777384828dbae363ba136633b4ab68e9c11a20618fd.png b/_images/f6a5cfa521a4fb6e1ba07777384828dbae363ba136633b4ab68e9c11a20618fd.png deleted file mode 100644 index 525ad0004..000000000 Binary files a/_images/f6a5cfa521a4fb6e1ba07777384828dbae363ba136633b4ab68e9c11a20618fd.png and /dev/null differ diff --git a/_images/f8c13db9a7c0e58da99334052c4b405cb3b8e8dafdb550220e812071d05a4af0.png b/_images/f8c13db9a7c0e58da99334052c4b405cb3b8e8dafdb550220e812071d05a4af0.png deleted file mode 100644 index 8c9ddf32f..000000000 Binary files a/_images/f8c13db9a7c0e58da99334052c4b405cb3b8e8dafdb550220e812071d05a4af0.png and /dev/null differ diff --git a/notebooks/0-Creating_networks.html b/notebooks/0-Creating_networks.html index 28a24b001..d05ab023f 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 00:00:1702372777.100098    2406 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373656.784113    2375 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/62acf1904d76e2e2e7b9e870ff4c697c4a337990986fb7cae63c82680d303139.png +../_images/0f69fb3b24b9a33ca55334cd4dd7fb2f62434a8aa3ec94c62ecdcde5171448fb.png
@@ -867,7 +867,7 @@
Coupling with binary nodes
Adding 1000 new observations.
-
<pyhgf.model.HGF at 0x7f83d8543ac0>
+
<pyhgf.model.HGF at 0x7ffaac321d80>
diff --git a/notebooks/0-Theory.html b/notebooks/0-Theory.html index cceb01b7d..30622c116 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 b34bed51f..abf53729d 100644 --- a/notebooks/1.1-Binary_HGF.html +++ b/notebooks/1.1-Binary_HGF.html @@ -539,7 +539,7 @@

Create the model 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372799.168550    2643 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373678.570114    2594 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.)
@@ -816,7 +816,7 @@

Sampling
-../_images/6fb6bc8c77c05f674b19a6827f19c922cf27062a575304ed76674dd7e7dbfdca.png +../_images/d15732e5d4bb6bda7b6082f3f2ac003d5a8ca52b1e7167d2e24b2139603a45ff.png
@@ -865,7 +865,7 @@

Using the learned parameters -../_images/9582eff415e19b3f09c537a9349d1e6d6ff650098c4cc2a70af6c9adc807473a.png +../_images/84f22506a5fa9694a204cfbbfac4c8b359574b48970a401d97e9951259c274b6.png
@@ -875,7 +875,7 @@

Using the learned parameters -
Array(202.53, dtype=float32)
+
Array(202.52956, dtype=float32)
@@ -927,7 +927,7 @@

Visualizing the model -../_images/e3093df40c606a365fce51328bb90c832e9b204e89fed0d0688e3e2fdb1677dd.svg

+../_images/2ec19856911096fbe9c3234ef83ab3600af54719c813af4a3f819412cb3c0342.svg

@@ -989,7 +989,7 @@

Sampling#
-../_images/e2f7c090768f22b63393ef29d1fcf446175f84024f418b9c3e4392627e5b2c6d.png +../_images/05df6e2dd62ba1aedd4f0addb34bdba57d3dca76a7b1fbc119072441ec6e421a.png

@@ -1039,7 +1039,7 @@

Using the learned parameters -../_images/a041d03e217f1accf199119a0f823858acae52300789d4f4021430c91cc96c90.png +../_images/6a8f6ce1df052fd40fe028cee2c4fea53a2de5465bc791bb016b68fa5d3dfeca.png
@@ -1049,7 +1049,7 @@

Using the learned parameters -
Array(203.0021, dtype=float32)
+
Array(203.01422, dtype=float32)
@@ -1077,12 +1077,12 @@

System configuration

diff --git a/notebooks/1.2-Categorical_HGF.html b/notebooks/1.2-Categorical_HGF.html index f3e1d087f..7daf71550 100644 --- a/notebooks/1.2-Categorical_HGF.html +++ b/notebooks/1.2-Categorical_HGF.html @@ -534,7 +534,7 @@

Simulating a dataset

-../_images/372721b18d1682d7d6e1effc153be6fe94cb15a2d7f75d89ea494aa8d43b4acf.png +../_images/e72924449dedf654628cbe082a06ecbbd67b55d49a78f872ddb50de6f5e8ca9d.png
@@ -575,7 +575,7 @@

Creating the probabilistic network 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372846.968562    3016 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373726.056087    2984 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.)
@@ -658,7 +658,7 @@

Fitting the model forwards -../_images/9f44aa77ea85db942ef6d0585ee813adf588c2b744f0bf56e587c14d1ec523c1.png +../_images/e03998e684cce8e8bddf1b2465300b7ac5588e2af284543b949d492e8c4b9ced.png

@@ -672,15 +672,15 @@

Fitting the model forwards

diff --git a/notebooks/1.3-Continuous_HGF.html b/notebooks/1.3-Continuous_HGF.html index a7dcc9719..81c41132e 100644 --- a/notebooks/1.3-Continuous_HGF.html +++ b/notebooks/1.3-Continuous_HGF.html @@ -534,7 +534,7 @@

Create the model 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372892.600170    3142 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373771.132141    3099 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.)
@@ -819,7 +819,7 @@

Visualizing the model
-../_images/276f245ebd9fd4bcae5e926f51a69ac0c4a8b7994776641b7ca80207aba0e073.svg
+../_images/0747ca4d2db1d73075db0036fa2d7adb40e86a06d3c587c73103c1d2a5698bb6.svg
@@ -881,7 +881,7 @@

Sampling
-../_images/09f86eebf56b3d0843556d65b959fe24aacc19df1884c10a9a5ccd284dd32eab.png +../_images/a82780ee89144bf9b72436be7a384d1b8f3e027699b8d1aff7a26ad4d65b38fc.png

@@ -927,7 +927,7 @@

Using the learned parameters -../_images/663667d281f728b062158358faacefa26546bc5a79e3a720bb5c6c6bd5e7e6ad.png +../_images/c832370833ecdd49d6b3f27f0e6febf08a5768ac10849e1213b1cd4d7f88a602.png
@@ -937,7 +937,7 @@

Using the learned parameters -
Array(-1106.0919, dtype=float32)
+
Array(-1106.0508, dtype=float32)
@@ -987,7 +987,7 @@

Visualizing the model -../_images/276f245ebd9fd4bcae5e926f51a69ac0c4a8b7994776641b7ca80207aba0e073.svg

+../_images/0747ca4d2db1d73075db0036fa2d7adb40e86a06d3c587c73103c1d2a5698bb6.svg

@@ -1031,9 +1031,9 @@

Sampling#
- 100.00% [4000/4000 00:09<00:00 Sampling 2 chains, 1 divergences] + 100.00% [4000/4000 00:09<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 10 seconds.
+    
Sampling 2 chains for 1_000 tune and 1_000 draw iterations (2_000 + 2_000 draws total) took 9 seconds.
 
We recommend running at least 4 chains for robust computation of convergence diagnostics
@@ -1049,7 +1049,7 @@ 
Sampling#
-../_images/01815cbec2b86d6b77a4fa3c8b3fe3bf11fd50f3d397255060542a80c34f863a.png +../_images/90d8f4318d65b623884932bd7275e93b57903c65e79612140e1db15d1239e66f.png

@@ -1094,7 +1094,7 @@

Using the learned parameters -../_images/2e69d0f686fc8636c0294befded5f765bb90f68de93e6419c646ceb19630da80.png +../_images/736602f2fe8922750c73be3bf6b2eb9bed942ba8f8d4af7ab181c4d47d8bd905.png
@@ -1104,7 +1104,7 @@

Using the learned parameters -
Array(-1117.966, dtype=float32)
+
Array(-1118.021, dtype=float32)
@@ -1132,12 +1132,12 @@

System configuration

diff --git a/notebooks/2-Using_custom_response_functions.html b/notebooks/2-Using_custom_response_functions.html index e613b0941..f370008f6 100644 --- a/notebooks/2-Using_custom_response_functions.html +++ b/notebooks/2-Using_custom_response_functions.html @@ -527,7 +527,7 @@

Creating a new response function: the binary surprise 
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372772.525524    2302 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373651.934209    2262 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.)
@@ -920,19 +920,19 @@

Recovering HGF parameters from the observed behaviors tonic_volatility_2 - -3.952 - 0.495 - -4.876 - -3.007 - 0.012 + -3.96 + 0.499 + -4.929 + -3.075 + 0.013 0.009 - 1691.0 - 2450.0 + 1589.0 + 2094.0 1.0 -

../_images/f6a5cfa521a4fb6e1ba07777384828dbae363ba136633b4ab68e9c11a20618fd.png +../_images/2c89b73cc43e4a4e28a2ec29355a9894a5e161035ffa0776052e62d7cd5571ca.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.

@@ -970,11 +970,11 @@

System configurationModel#<
-../_images/68efddc43e8be74f1b9b201228cd9b19c20f76981ca6f52caf464565a9a0f845.svg
+../_images/92e7aaa45b43d4dfe5c4a2b4b175c521a401908a0b07a161a64dca2e383de0f8.svg
@@ -643,7 +643,7 @@

Model#< 

WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372818.288411    2622 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373695.736238    2588 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.)
@@ -672,7 +672,7 @@

Model#<
- 100.00% [2000/2000 01:04<00:00 Sampling chain 0, 1 divergences] + 100.00% [2000/2000 01:04<00:00 Sampling chain 0, 0 divergences] 
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 65 seconds.
@@ -690,7 +690,7 @@

Model#<

-../_images/0b90438ddf455efef0e0057476cce1a02daa5230779e2f4bf8a6930a1f40f5c1.png +../_images/771c35c39d3f1fac01c44b466b61f38cb670abdff55f52bae31b4c29736b3be1.png

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

@@ -771,7 +771,7 @@

Visualizing the model
-../_images/a128e5fa7e2f81bdbc21ffb001e7bc370b649bde5991126f17e98fd2b8461fee.svg
+../_images/24e7d24fbeec070c32b902d8c0381d6926a8b2fc93b068277c73a8f2e20739a1.svg
@@ -815,9 +815,9 @@

Sampling
- 100.00% [2000/2000 00:19<00:00 Sampling chain 0, 41 divergences] + 100.00% [2000/2000 00:21<00:00 Sampling chain 0, 14 divergences]
- 
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 19 seconds.
+    
Sampling 1 chain for 1_000 tune and 1_000 draw iterations (1_000 + 1_000 draws total) took 21 seconds.
 
Only one chain was sampled, this makes it impossible to run some convergence checks
@@ -833,7 +833,7 @@ 
Sampling
-../_images/38661f681e1cf07f82a2b9d83c61297b789eb885eb6596cecdb87fe63d7ae613.png +../_images/441d64d04a6fcdf774641e90fa2897decb805a70d3c7e056bd977ac367761e62.png

@@ -860,12 +860,12 @@

System configuration diff --git a/notebooks/4-Parameter_recovery.html b/notebooks/4-Parameter_recovery.html index 9dc918a32..74e99cb8d 100644 --- a/notebooks/4-Parameter_recovery.html +++ b/notebooks/4-Parameter_recovery.html @@ -600,7 +600,7 @@

Embedding a serie of HGFs in a graphical model
WARNING: All log messages before absl::InitializeLog() is called are written to STDERR
-I0000 00:00:1702372924.774474    3460 tfrt_cpu_pjrt_client.cc:349] TfrtCpuClient created.
+I0000 00:00:1702373803.591759    3279 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.)
@@ -629,7 +629,7 @@

Embedding a serie of HGFs in a graphical model
- 100.00% [4000/4000 00:26<00:00 Sampling 2 chains, 0 divergences] + 100.00% [4000/4000 00:25<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 26 seconds.
@@ -647,7 +647,7 @@

Embedding a serie of HGFs in a graphical model -../_images/b9cfecfc8a1488bb8f3ba0d0d83db90f4c397fbe626b22460f4410cf06ea8dec.png +../_images/56ed73af8c0f75a69f00827601fb0f632bf9daafb1a183199c92942604343c8b.png

@@ -689,74 +689,74 @@

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 1e8cefa45..eed459f59 100644 --- a/notebooks/Example_1_Heart_rate_variability.html +++ b/notebooks/Example_1_Heart_rate_variability.html @@ -821,16 +821,16 @@

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,  1.46it/s]
+
Downloading ECG channel:  50%|█████     | 1/2 [00:00<00:00,  2.73it/s]
 

 

-
Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  1.46it/s]
+
Downloading Respiration channel:  50%|█████     | 1/2 [00:00<00:00,  2.73it/s]
 

 

-
Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.36it/s]
+
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  3.15it/s]
 

 

-
Downloading Respiration channel: 100%|██████████| 2/2 [00:01<00:00,  1.37it/s]
+
Downloading Respiration channel: 100%|██████████| 2/2 [00:00<00:00,  3.07it/s]
 

 

 

@@ -855,12 +855,12 @@ 
Plot the signal with instantaneous heart rate derivations

+