Updated Examples

Updated LCDM Lite YAML to use correct priors, LCDM Lite example to use new YAML file and updated example notebook to include warmstart points

Author: nathyglobal

examples/Example Notebook.ipynb

@@ -661,6 +661,33 @@
     "   )"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "id": "c82252ba-8982-476f-91ec-c53ae21d1a8b",
+   "metadata": {},
+   "source": [
+    "One can alternatively provide initialisation or 'warmstart' points to BOBE instead of using Cobaya initialisation samples. This is particularly useful for cases such as nested cosmological models but one must be careful to ensure the init_train_y are valid for the new likelihood"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "c01795ae-c26a-4b9b-804c-5217f867357a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "sampler = BOBE(\n",
+    "       loglikelihood='path/to/cobaya_input.yaml',\n",
+    "       likelihood_name='CobayaLikelihood',\n",
+    "       n_sobol_init=4,\n",
+    "       init_train_x=init_train_x,\n",
+    "       init_train_y=init_train_y,\n",
+    "       likelihood_name='quickstart_cobaya_example', # name for output files\n",
+    "       save_dir='./results',\n",
+    "       use_clf=True # recommended to enable classifiers for cosmological examples where likelihood can sometimes return -inf values\n",
+    "   )"
+   ]
+  },
   {
    "cell_type": "markdown",
    "id": "81c3be5d-24be-49dc-850e-f7c035c8741f",

examples/Planck_lite_LCDM.py

@@ -33,7 +33,6 @@ def main():
         n_sobol_init=8,
         use_clf=True,
         clf_type='svm',
-        #clf_nsigma_threshold=15,
         minus_inf=-1e5,
         seed=10,
     )

examples/cosmo_input/LCDM_lite.yaml

@@ -9,98 +9,87 @@ theory:
       nnu: 3.044
       dark_energy_model: 'fluid'
 likelihood:
-  # one:
   planck_2018_lowl.TT: null
   planck_2018_lowl.EE: null
   planck_2018_highl_plik.TTTEEE_lite_native: null
   planck_2018_lensing.native: null
 params:
-  w: -1.
-  omk:
-    value: 0
-    renames:
-    - omegak
   omch2:
-    latex: \Omega_\mathrm{c} h^2
-    prior:
-      min: 0.1
-      max: 0.14
-    ref:
-      dist: norm
-      loc: 0.12
-      scale: 0.001
-    proposal: 0.0005
-    renames:
-    - omegach2
-  ombh2:
-    prior:
-      min: 0.015
-      max: 0.028
-    ref:
-      dist: norm
-      loc: 0.0224
-      scale: 0.0001
-    proposal: 0.0001
-    latex: \Omega_\mathrm{b} h^2
-    renames:
-    - omegabh2
+   latex: \Omega_\mathrm{c} h^2
+   prior:
+     min: 0.11
+     max: 0.13
+   ref:
+     dist: norm
+     loc: 1.186384753e-01
+     scale: 0.0005
+   proposal: 0.0005
   logA:
     prior:
-      min: 2.9
-      max: 3.2
+      min: 2.98
+      max: 3.10
     ref:
       dist: norm
-      loc: 3.05
+      loc: 3.040776555e+00
       scale: 0.001
     proposal: 0.001
     latex: \log(10^{10} A_\mathrm{s})
+    # drop: true
   As:
-    value: 'lambda logA: 1e-10*np.exp(logA)'
-    latex: A_\mathrm{s}
-    derived: true
+      value: 'lambda logA: 1e-10*np.exp(logA)'
+      latex: A_\mathrm{s}
   ns:
     prior:
-      min: 0.92
-      max: 1.0
+      min: 0.94 
+      max: 0.99
     ref:
       dist: norm
-      loc: 0.965
-      scale: 0.004
+      loc: 9.652909209e-01  
+      scale: 0.002
     proposal: 0.002
     latex: n_\mathrm{s}
-  H0:
+  H0: 
     latex: H_0
     prior:
-      min: 62
+      min: 64
       max: 72
     ref:
       dist: norm
-      loc: 67.2
-      scale: 0.1
-    proposal: 0.05
+      loc: 6.771234910e+01
+      scale: 0.05
+    proposal: 0.05 
+  ombh2:
+    prior:
+      min: 0.021
+      max: 0.023
+    ref:
+      dist: norm
+      loc: 2.224954976e-02
+      scale: 0.0001
+    proposal: 0.0001
+    latex: \Omega_\mathrm{b} h^2
   tau:
     latex: \tau_\mathrm{reio}
     prior:
       min: 0.03
       max: 0.08
     ref:
       dist: norm
-      loc: 0.055
-      scale: 0.006
+      loc: 5.546101493e-02
+      scale: 0.003
     proposal: 0.003
   A_planck:
-    latex: y_\mathrm{cal}
-    renames: calPlanck
     value: 1.0
+
 sampler:
-  # polychord:
-  #   nlive: 10d
-  #   precision_criterion: 0.01
-  mcmc:
-    drag: False
-    oversample_power: 0.4
-    proposal_scale: 1.9
-    covmat: auto
-    Rminus1_stop: 0.01
-    Rminus1_cl_stop: 0.2   
-output: chains/Planck_lite_mcmc
+  polychord:
+    nlive: 30d
+    precision_criterion: 0.01
+  # mcmc:
+  #   drag: False
+  #   oversample_power: 0.4
+  #   proposal_scale: 1.9
+  #   covmat: auto
+  #   Rminus1_stop: 0.01
+  #   Rminus1_cl_stop: 0.2   
+output: chains/Planck_lite_pchord