run: same as ed11b3e, but 64 TI steps, not 16

rmnldwg · Dec 6, 2022 · b633311 · b633311
1 parent 9a39b94
commit b633311
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Showing 3 changed files with 205 additions and 63 deletions.
diff --git a/dvc.lock b/dvc.lock
@@ -34,16 +34,16 @@ stages:
       size: 1092093
       nfiles: 8
     - path: ./models
-      md5: 55d558452b577fe937eaa6f9997c6808.dir
-      size: 38190520
+      md5: bd837dffb9ea845fabb2cc356020458a.dir
+      size: 146406528
       nfiles: 1
     - path: ./plots
-      md5: 75d3337f0ed1d7862dc94a9d6a37e81f.dir
-      size: 4338558
+      md5: b14919f761caa35ded92956741badc76.dir
+      size: 4223722
       nfiles: 5
     - path: metrics.json
-      md5: ae7394fe35c6b2b7669081cbde141485
-      size: 159
+      md5: 28d9022c6ba16a3c63188b4ef84d8edf
+      size: 160
   mermaid-readme:
     cmd: cat dag.md | sed 's/^/3i/' | sed -f- README.template > README.md
     deps:

diff --git a/params.yaml b/params.yaml
@@ -10,9 +10,7 @@ general:
 
 ########################################################################################
 # This dictionary defines which LNLs are present in the
-# graph and how they are connected. In this case, the
-# primary tumors spreads to the LNLs II, III and IV.
-# Subsequently, level II spreads to III and III to IV.
+# graph and how they are connected.
 graph:
   tumor:
     primary: [I, II, III, IV, V, VII]
@@ -98,20 +96,68 @@ sampling:
   thin_by: 10                   # draw this many samples for one step in `nsteps`
   temp_schedule:                # use this as the inverse temp schedule for TI
   - 0.0
-  - 1.316872427983539e-06
-  - 4.2139917695473246e-05
-  - 0.0003200000000000001
-  - 0.0013484773662551439
+  - 1.0076210988534706e-09
+  - 3.224387516331106e-08
+  - 2.448519270213934e-07
+  - 1.031804005225954e-06
+  - 3.148815933917096e-06
+  - 7.835261664684588e-06
+  - 1.6935087808430282e-05
+  - 3.3017728167230525e-05
+  - 5.949901826619859e-05
+  - 0.00010076210988534707
+  - 0.0001622783855914503
+  - 0.0002507283732699068
+  - 0.0003741226606566017
+  - 0.000541922809869769
+  - 0.0007651622719418543
+  - 0.0010565673013513768
+  - 0.0014306778705547923
+  - 0.001903968584518355
+  - 0.00249496959524998
+  - 0.0032243875163311063
   - 0.004115226337448558
-  - 0.010240000000000003
-  - 0.022132674897119342
-  - 0.043151275720164604
-  - 0.07775999999999998
+  - 0.00519290833892641
+  - 0.006485395006257844
+  - 0.008023307944637018
+  - 0.009840049793490924
+  - 0.011971925141011254
+  - 0.014458261438686257
+  - 0.01734152991583261
+  - 0.020667466494127266
+  - 0.02448519270213934
+  - 0.02884733658986194
+  - 0.03381015364324406
+  - 0.0394336476987224
+  - 0.045781691857753354
+  - 0.05292214940134466
+  - 0.06092699470458736
+  - 0.06987243415118778
+  - 0.07983902704799936
+  - 0.09091180653955425
+  - 0.1031804005225954
+  - 0.11673915256060852
   - 0.13168724279835387
-  - 0.21208362139917689
-  - 0.3276800000000001
-  - 0.48894551440329226
-  - 0.708245596707819
+  - 0.14812880887639787
+  - 0.16617306684564512
+  - 0.18593443208187052
+  - 0.207532640200251
+  - 0.231092867969897
+  - 0.2567458542283846
+  - 0.28462802079628763
+  - 0.31488159339170957
+  - 0.34765472254481466
+  - 0.38310160451236014
+  - 0.4213826021922288
+  - 0.46266436603796024
+  - 0.5071199549732823
+  - 0.5549289573066435
+  - 0.6062776116457449
+  - 0.6613589278120725
+  - 0.7203728077554274
+  - 0.7835261664684589
+  - 0.8510330529011965
+  - 0.923114770875582
   - 1.0
   # only used when sampling until convergence
   kwargs:

diff --git a/pipeline/dvc.lock b/pipeline/dvc.lock
@@ -135,20 +135,68 @@ stages:
           thin_by: 10
           temp_schedule:
           - 0.0
-          - 1.316872427983538e-06
-          - 4.2139917695473246e-05
-          - 0.0003200000000000001
-          - 0.0013484773662551439
+          - 1.0076210988534706e-09
+          - 3.224387516331105e-08
+          - 2.448519270213932e-07
+          - 1.031804005225953e-06
+          - 3.148815933917096e-06
+          - 7.835261664684588e-06
+          - 1.6935087808430282e-05
+          - 3.3017728167230525e-05
+          - 5.949901826619859e-05
+          - 0.00010076210988534707
+          - 0.0001622783855914503
+          - 0.0002507283732699068
+          - 0.0003741226606566017
+          - 0.000541922809869769
+          - 0.0007651622719418543
+          - 0.0010565673013513768
+          - 0.0014306778705547923
+          - 0.001903968584518355
+          - 0.00249496959524998
+          - 0.0032243875163311063
           - 0.004115226337448558
-          - 0.010240000000000003
-          - 0.022132674897119342
-          - 0.043151275720164604
-          - 0.07775999999999998
+          - 0.00519290833892641
+          - 0.006485395006257844
+          - 0.008023307944637018
+          - 0.009840049793490924
+          - 0.011971925141011254
+          - 0.014458261438686257
+          - 0.01734152991583261
+          - 0.020667466494127266
+          - 0.02448519270213934
+          - 0.02884733658986194
+          - 0.03381015364324406
+          - 0.0394336476987224
+          - 0.045781691857753354
+          - 0.05292214940134466
+          - 0.06092699470458736
+          - 0.06987243415118778
+          - 0.07983902704799936
+          - 0.09091180653955425
+          - 0.1031804005225954
+          - 0.11673915256060852
           - 0.13168724279835387
-          - 0.21208362139917689
-          - 0.3276800000000001
-          - 0.48894551440329226
-          - 0.708245596707819
+          - 0.14812880887639787
+          - 0.16617306684564512
+          - 0.18593443208187052
+          - 0.207532640200251
+          - 0.231092867969897
+          - 0.2567458542283846
+          - 0.28462802079628763
+          - 0.31488159339170957
+          - 0.34765472254481466
+          - 0.38310160451236014
+          - 0.4213826021922288
+          - 0.46266436603796024
+          - 0.5071199549732823
+          - 0.5549289573066435
+          - 0.6062776116457449
+          - 0.6613589278120725
+          - 0.7203728077554274
+          - 0.7835261664684589
+          - 0.8510330529011965
+          - 0.923114770875582
           - 1.0
           kwargs:
             max_steps: 20000
@@ -157,14 +205,14 @@ stages:
             rel_acor_threshold: 0.075
     outs:
     - path: models/samples.hdf5
-      md5: b314e1668e0650671f4b65b931871211
-      size: 38190520
+      md5: a450ea18766cd65808fc2d5aeebaa5fa
+      size: 146406528
     - path: plots/sampling/accept_rates.csv
-      md5: 3392ab60b85ae61836adb34ff409bcbc
-      size: 611
+      md5: b59131b140a0c2d80bf55fad09d3638e
+      size: 2444
     - path: plots/sampling/acor_times.csv
-      md5: 0ef014f1199e153daaada68b7eb65e1f
-      size: 605
+      md5: aa568105e0936df7071ad943caebc7b4
+      size: 2449
   predict-risks:
     cmd: "lyscripts predict risks models/samples.hdf5 models/risks.hdf5\n"
     deps:
@@ -290,8 +338,8 @@ stages:
       md5: 5c2b261b840a237ad630c450ec0d9ae4
       size: 155737
     - path: models/samples.hdf5
-      md5: b314e1668e0650671f4b65b931871211
-      size: 38190520
+      md5: a450ea18766cd65808fc2d5aeebaa5fa
+      size: 146406528
     params:
       params.yaml:
         graph:
@@ -355,20 +403,68 @@ stages:
           thin_by: 10
           temp_schedule:
           - 0.0
-          - 1.316872427983538e-06
-          - 4.2139917695473246e-05
-          - 0.0003200000000000001
-          - 0.0013484773662551439
+          - 1.0076210988534706e-09
+          - 3.224387516331105e-08
+          - 2.448519270213933e-07
+          - 1.031804005225953e-06
+          - 3.148815933917096e-06
+          - 7.835261664684588e-06
+          - 1.6935087808430282e-05
+          - 3.3017728167230525e-05
+          - 5.949901826619859e-05
+          - 0.00010076210988534707
+          - 0.0001622783855914503
+          - 0.0002507283732699068
+          - 0.0003741226606566017
+          - 0.000541922809869769
+          - 0.0007651622719418543
+          - 0.0010565673013513768
+          - 0.0014306778705547923
+          - 0.001903968584518355
+          - 0.00249496959524998
+          - 0.0032243875163311063
           - 0.004115226337448558
-          - 0.010240000000000003
-          - 0.022132674897119342
-          - 0.043151275720164604
-          - 0.07775999999999998
+          - 0.00519290833892641
+          - 0.006485395006257844
+          - 0.008023307944637018
+          - 0.009840049793490924
+          - 0.011971925141011254
+          - 0.014458261438686257
+          - 0.01734152991583261
+          - 0.020667466494127266
+          - 0.02448519270213934
+          - 0.02884733658986194
+          - 0.03381015364324406
+          - 0.0394336476987224
+          - 0.045781691857753354
+          - 0.05292214940134466
+          - 0.06092699470458736
+          - 0.06987243415118778
+          - 0.07983902704799936
+          - 0.09091180653955425
+          - 0.1031804005225954
+          - 0.11673915256060852
           - 0.13168724279835387
-          - 0.21208362139917689
-          - 0.3276800000000001
-          - 0.48894551440329226
-          - 0.708245596707819
+          - 0.14812880887639787
+          - 0.16617306684564512
+          - 0.18593443208187052
+          - 0.207532640200251
+          - 0.231092867969897
+          - 0.2567458542283846
+          - 0.28462802079628763
+          - 0.31488159339170957
+          - 0.34765472254481466
+          - 0.38310160451236014
+          - 0.4213826021922288
+          - 0.46266436603796024
+          - 0.5071199549732823
+          - 0.5549289573066435
+          - 0.6062776116457449
+          - 0.6613589278120725
+          - 0.7203728077554274
+          - 0.7835261664684589
+          - 0.8510330529011965
+          - 0.923114770875582
           - 1.0
           kwargs:
             max_steps: 20000
@@ -377,11 +473,11 @@ stages:
             rel_acor_threshold: 0.075
     outs:
     - path: metrics.json
-      md5: ae7394fe35c6b2b7669081cbde141485
-      size: 159
+      md5: 28d9022c6ba16a3c63188b4ef84d8edf
+      size: 160
     - path: plots/ti/accuracies.csv
-      md5: 92a3de2abe595e59338e3e9070b4cf19
-      size: 922
+      md5: ff887747457397d39b6bb616f5b00646
+      size: 3721
   predict-prevalences:
     cmd: "lyscripts predict prevalences models/samples.hdf5 data/cleaned.csv models/prevalences.hdf5\n"
     deps:
@@ -474,12 +570,12 @@ stages:
     cmd: "lyscripts plot corner models/samples.hdf5 plots/corner.png\n"
     deps:
     - path: models/samples.hdf5
-      md5: b314e1668e0650671f4b65b931871211
-      size: 38190520
+      md5: a450ea18766cd65808fc2d5aeebaa5fa
+      size: 146406528
     outs:
     - path: plots/corner.png
-      md5: 635ef3e2ec9d93fb04c91f4d28313b3a
-      size: 816117
+      md5: 0b6334c292e6d37e15aa4fa2918a8ee4
+      size: 767204
     - path: plots/corner.svg
-      md5: 726b61c695d3b664c32cb1be91e26b4c
-      size: 3520303
+      md5: d7ad54a3fb73adfbfdc8c50d7e76dc43
+      size: 3447904